Intro to HPC
High performance computing is a way to process data much faster than a single computer possibly could. This is achieved by parallelizing code across a cluster of computer and nodes.
Logging in
Setting up VPN (if not on university premises)
If you are not on university premises you will have to set up the University VPN. Setting up a connection on Linux can be done as follows:
- Go to https://uobnet2.bristol.ac.uk and sign in.
- If this is the first time you do this on your computer then you need to install F5 Network Acess. There will be a link to download it on the website.
- If you have already done step 2 before you will be shown a prompt to launch the application.
Once you are connected you should see this window
Log in using ssh
Now you are ready to log into the cluster using ssh
. On Linux you simply use the terminal and type the following (and enter your password if needed).
ssh -X<EMAIL_ADDRESS>Note: the -X
flag allows us to run graphical applications remotely but for them to be displayed locally.
Copy files to and from cluster
At some point you will most definitely need to transfer data or source code from your computer to the cluster. Note that the cluster is not intended for long-term file storage, so anything that you leave there has no guarantee that it will remain there. For that reason make sure you always transfer your results back to your local machine. To check you file storage quota you can use: pan_quota
and it shows the result in bytes.
We use scp
, which stands for secure copy protocol
, and we always do this from our local machine.
copy from local to remote home directory:
scp data.r ky19161@bluecrystalp3.acrc.bris.ac.uk:~
copy from remote to local current directory:
scp ky19161@bluecrystalp3.acrc.bris.ac.uk:data.r .
Advice for file usage: using a few larger files helps the job run faster than many small ones. This is because locating files on the cluster takes quite a bit of time.
Environment Modules
BlueCrystal has an environment modules package which enables one to customize their environment. What is perhaps the most important is that you must always make sure that the required modules are loaded. The main commands to do this are:
module avail
: list available modulesmodule list
: list loaded modulesmodule add module_name
: load modulemodule del
: remove modulemodule whatis
: details about the module
It is recommended that you include the required modules in your shell startup file .bashrc
. However, make sure you know what you are doing beforehand and don’t modify anything else just yet.
For example, if you want to use R
and Python
your .bashrc
should inclue
module add languages/R-3.0.2
module add languages/python-3.3.2
How to run a job
- Include the required modules in your
.bashrc
. - Compile code if needed.
- Copy scripts or data to the cluster.
- Create job submission script.
- Submit job script to queuing system.
Queuing system
qstat -q
: see all the queuesqstat job_number
: check status of jobwatch qstat job_id
: watch status of your jobqstat username
: see all jobs from a user
Submission script
Single-thread job: runs a program using a single processor
#!/bin/bash
# resources
#PBS -l nodes=1:ppn=1
#PBS -l walltime=02:00:00
# on compute node, change directory to 'submission directory':
cd $PBS_O_WORKDIR
# time the program:
time ./my-serial-program
#!/bin/bash
is called a shebang and it is used to say that the script is a shell scriptPBS -l nodes=1:ppn=1
: tells the computer to use a single node for the job. Note that all#PBS
commands are for the queuing system.#PBS -l walltime=02:00:00
: how long we estimate the job to take (2 hours in this case). It is always better to overestimate, rather than underestimate.cd $PBS_O_WORKDIR
: ensures that the job is run from the submission directorytime ./my-serial-program
: times how long the job took to run
To submit the job, simply type:
qsub submission_script
.
Note: if a permission error occurs you might have to run `chmod u+x filename’ to make the file executable for your user.
Example
We have the following script that we want to run. This is a similar script to the one in the Linux portfolio. It takes the specified text files and returns the top most common words in different files, except for the specified stop words (for, at, a etc).
#!/bin/bash
for text_file in Alices_Adventures_in_Wonderland.txt Metamorphosis.txt The_Impo\
rtance_of_Being_Earnest.txt The_Picture_of_Dorian_Gray.txt
do
echo $text_file
file_name="${text_file%.*}_count.txt"
echo $file_name
cat $text_file |tr -d '[:punct:]'|tr " " "\n" | tr '[:upper:]' '[:lower:]'| sort |
uniq -c|sort -n | fgrep -vwf stop_words.txt | tail -n 15 >> $file_name
done
To run this, we need to upload it to the remote directory together with the stop words file and the text files.
Next we log into the server using ssh and note that all the required files are now in the book directory.
Moreover, we have created a submission script. As we see, the job is set to run the script on a single node, and sets the estimated run time to 10 minutes. Moreover, we set the working directory to books
and we use that to obtain and create our files.
#!/bin/bash
#PBS -l nodes=1:ppn=1,walltime=00:10:00
# Define working directory
export WORK_DIR=$HOME/books
# Define executable
export EXE=/bin/hostname
# Change into working directory
cd $WORK_DIR
# Print job id and working directory
echo JOB ID: $PBS_JOBID
echo Working Directory: `pwd`
# Execute code
$EXE
time most_used_words.sh
We submit the job, and check its status. The status can be seen under the S
column as Q
for Queued, R
for Running and C
for Completed. Once the job finishes we obtain the new files that contain the top word counts and two additional files.
The .e
file contains the running time in this case. But it can contain errors.
The .o
file has the outputs that we have printed as part of our submission script (workind directory and node) and the actual code (input and output file names).
While we have only examined how to submit a serial job, the HPC facilities are perhaps even more usefull for parallel jobs.


There are multiple ways to access blackboard. The easiest way is to go to myUoN and login using your student number and password.
MyUoN is your dashboard which you can navigate to find numerous resources that you will need throughout your University degree. The red circle in the image shows where the blackboard link is located. Clicking this card will take you to blackboard.
Welcome to Blackboard! This welcome page gives you a preview of student and study essentials. It also provides IT support where you can learn about the University Wi-Fi and how students can use Microsoft Office during their study. Clicking the link in the red circle will take you to your course sites.
This webpage contains links to all your courses and course information for this semester and previous semesters. The most important sections of this page are:
This section lists the courses you are taking this semester. Clicking one of these courses will take you to the main hub for your courses. To see how to naviagate through your course page, keep scrolling below.
Some of these sites listed are very important as you will be required to compelete some of these tasks before your first week of University. Below is a small description of some of these hubs which will be very important for students:
– Academic Learning Support
This will take you to the Academic Learning Support hub where you can receive help with the fundamentals of your courses and learn about the standard the University holds in regard to assignments and different assignment types.
– Consent Matters
The consent matters module needs to be completed by all students who are undertaking University at Newcastle Uni to ensure the understanding and importance of consent.
– MATH1110 Maths Placement Test
Some programs will require students to do MATH1110 (mostly Engineering and Science degrees) which will require some students to complete a placement test in order to be allowed to take this course. This test can only be taken once so make sure you practice before taking the exam.
– University Academic Inegrity Module
Before completing your first semester, the academic integrity module MUST be completed in order to receive your Semester 1 results. This is to ensure you have understanding of plagiarism.
The pages for your courses will be your go-to domain for all your course learning and information. You can view the announcements from your course demonstrators, view lecture slides, access assignment information, check your grades, and review any previous recorded lectures. Click on any of the menu items on the left hand side to view their corresponding page.


---
layout: site
permalink: perth
location: Perth
dates: February 1-3, 2016
splashImage: https://farm1.staticflickr.com/681/22032155473_bca28567d4_z.jpg
map: sites/perth.geojson
menu: The Research Bazaar is a 3-day intensive conference where researchers come together to up-skill in 'next generation digital research tools and skills'. For more info see our FAQ.
Below are the tools on offer at Perth ResBaz 2016. Registration has now closed.
The registration fee includes morning tea, lunch, and afternoon tea, along with refreshments and drinks at the end of the first day, as well as dinner and drinks on the second day.
You can find a more detailed syllabus along with preparation instructions at the Software Carpentry Perth page.
classes:
- class: Main Streams
tools:
- name: Using the Unix shell
id: unix
blurb: Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively.
- name: Programming with R
id: r1
blurb: R is widely used across a range of disciplines for statistical computing and generating publication-quality figures. In this Software Carpentry workshop, you’ll learn the fundamentals of R for data science, Unix Shell for interacting with other programs, as well as version control and useful concepts for scientific computing such as breaking down problems into modular units, reproducibility, tracking changes to code, collaborating with others, and working with structured data.
- name: Programming with Python
id: python
blurb: Python is a powerful, general purpose programming language that has several popular scientific libraries that make it ideal for research. This workshop will equip you with the essential skills you need to use the Python programming language. It covers fundamentals as well as creating reusable functions, graphing with matplotlib and what to do to find and fix errors in your code.
- name: Version Control with Git
id: git
blurb: Version control is the lab notebook of the digital world - it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Keeping a record of what was changed, when, and why is extremely useful for all researchers if they ever need to come back to the project later on.
- class: Minor Electives
tools:
- name: Document editing with LaTeX
id: latex
blurb: Learn how to make your technical or scientific documents look brilliant with LaTeX typesetting.
- name: Visualizing your data on the web using D3
id: d3_js
blurb: D3 is a JavaScript library for working with data and displaying it online. D3 helps you bring data to life using HTML, SVG, and CSS. This workshop will introduce you to the basics of using D3 to create beautiful, animated and interactive graphics out of your data.
- name: Analysing qualitative data with Nvivo
id: nvivo
blurb:
schedule: Each day at ResBaz will be split into daytime and evening events. The day will be dedicated to classroom teaching time where we will fill your brains with the latest digital research skills. The evening will be about networking with your fellow cross-disciplinary researchers and having fun.
days:
- day: Monday February 1
sessions:
- title: 9:30 - 10:30 | The Unix Shell 1
- title: 10:30 - 11:00 | Morning tea
- title: 11:00 - 13:00 | The Unix Shell 2
- title: 13:00 - 14:00 | Lunch
- title: 14:00 - 15:30 | Social Media in Research
- title: 15:30 - 16:00 | Afternoon tea
- title: 16:00 - 16:15 | AWARE presentation
- title: 16:15 - 17:30 | CV advice
- title: 17:30 - late | Digital Toolbox Poster Session
- day: Tuesday February 2
sessions:
- title: 9:30 - 17:30 | Programming with Python
- title: 9:30 - 17:30 | Programming with R
- title: 10:30 - 11:00 | Morning tea
- title: 13:00 - 14:00 | Lunch
- title: 15:30 - 16:00 | Afternoon tea
- title: Social dinner or BBQ, Telescope experience
- day: Wednesday February 3
sessions:
- title: 9:30 - 10:30 | Version Control with Git 1
- title: 10:30 - 11:00 | Morning tea
- title: 11:00 - 13:00 | Version Control with Git 2
- title: 13:00 - 14:00 | Lunch
- title: 14:00 - 17:00 | Document editing with LaTeX
- title: 14:00 - 17:00 | Visualizing data on the web with D3
- title: 14:00 - 17:00 | Analyzing qualitative data with NVivo
- title: 15:30 - 16:00 | Afternoon tea
speakers:
- name: Andrew Rohl
img: img/rohl.png
blurb: Andrew is a leading expert in the application of supercomputing and computer simulation technologies.
- name: Tama Leaver
img: img/leaver.png
blurb: Tama teaches and researches a range of issues in the broad area of internet communications.
- name: Philipp Bayer
img: img/bayer.jpg
blurb: Philipp is a new Postdoc at UWA, where he works on the intricacies of complex plant genomes.
- name: Raffaella Demichelis
img: img/demichelis.png
blurb: Raffaella is research academic at Curtin University, working in the field of computational materials science.
- name: Lukas Weber
img: img/Lukas_Weber.jpg
blurb: Lukas is a PhD student in biostatistics at the University of Zurich in Switzerland, working on statistical methods for bioinformatics data.
- name: Matthias Liffers
img: img/matthias_liffers.jpg
blurb: Matthias helps researchers feed and care for their data.
- name: Amma Buckley
img: img/amma_buckley.png
blurb: As a research academic, Amma is regularly engaged in research projects, mostly of a qualitative nature, that necessitate the use of data management approaches and tools.
- name: Gill Neville
img: img/placehold.jpg
blurb:
sponsors:
- name: 'Sponsor Number One'
img: fake-sponsor.png
- name: 'Sponsor Number Two'
img: fake-sponsor.png
- name: 'Sponsor Number Three'
img: fake-sponsor.png
---
{{page.dates}}
{{page.schedule}}
Registrations for the {{page.location}} Research Bazaar are now closed. However, there will be some additional places available so feel free to contact Andrew Rohl at<EMAIL_ADDRESS>{{ speaker.blurb }}


My name is Joe Sirianni and I am a Senior at Grand Valley. I am an Engineering Operations Intern at Blue Medora, a software company in Grand Rapids.
I play on a semi-profesional Xball team (a style of Tournement Paintball). We travel around the country, and sometimes outside of the country, to compete against other teams in several regional and international leagues
Outside of school, work, and paintball I enjoy working on my homelab, working out, riding my bike, camping, kyaking, and playing Arma 3
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"From what comes before" "From here on" "Action not words" |


--- layout: default title: Lukas Himsel --- Lukas Himsel Digitale Produkte lukas (at) himsel.me +49 173 – 560 9184


Version History
0.3.3 (2021-02-20)
- Rebuilt with Ant 1.10.9.
- Various small fixes.
0.3.2 (2016-10-22)
- Increased timeout when calling fasm executable.
- Assembling zip file with Maven assembly plugin.
0.3.1 (2016-07-13)
- Only source files ending in .asm included by default.
0.3.0 (2016-07-09)
- Added command line parameters memory and passes.
- Added nested element compiler args.
- Destination file extension from format directive.
- Added unit tests and assembly test files.
- Building with Maven.
0.2.0 (2015-12-30)
- Fixed problem with source file path.
- Added support for includes and excludes configuration.
- Made destination file extension configurable.
0.1.0 (2015-12-23)


LITTLE VOICE (Miramax) Starring: Brenda Blethyn, Michael Caine, Jane Horrocks, Jim Broadbent, Ewan McGregor. Screenplay: Mark Herman, based on the play by Jim Cartwright. Producer: Elizabeth Karlsen. Director: Mark Herman. MPAA Rating: R (profanity, adult themes, brief nudity) Running Time: 96 minutes. Reviewed by Scott Renshaw.
Jane Horrocks delivers a show-stopping stage performance in LITTLE VOICE, the kind worthy of the divas she honors. In this adaptation of Jim Cartwright's play "The Rise and Fall of Little Voice," Horrocks reprises her stage role as L. V. (for Little Voice) Hoff, a timid young woman living in a small seaside town in the north of England. Still living with her brash, bawdy mother Mari (Brenda Blethyn), L. V. rarely speaks a word and even more rarely leaves the house. But when she sings, tearing into the classic Judy Garland, Shirley Bassey and Edith Piaf tunes beloved by her late father, she is transformed, taking on the pipes and the personality of whichever chanteuse she happens to be channeling at the moment.
The most astonishing element of Horrocks' performance is that she gets no assistance from the original vocalists. The actress truly can do frighteningly dead-on recreations of Garland, Dietrich, Holliday, Monroe and half a dozen others, and its a wonder to behold. The showcase for both Horrocks and her character is a performance at a run-down cabaret, set up by Mari's current flame, small-time talent scout Ray Say (Michael Caine). Recognizing L. V. as his ticket to the Big Time, Ray sinks everything he has into a one-night performance he finally coaxes out of the reluctant girl. And once she spots the visage of her dad in the crowd, encouraging her, away she goes.
In a live theater setting, you can imagine Horrocks' musical numbers being positively electrifying. Even on-screen her transformation from Minnie Mouse to mighty mouth is grand theater at its finest, and the renditions of standards like "Get Happy" and "I Wanna Be Loved By You" are extremely appealing. It doesn't take long, however, to realize that LITTLE VOICE is built entirely around Horrocks' admittedly impressive party trick. Once her centerpiece performance ends, the film starts working desperately to tie up loose ends -- L. V.'s infatuation with her father's memory, her relationships with her mother and an equally shy telephone technician (Ewan McGregor), the frustrations of Ray as his one shot at success seems about to pass him by. As flawed as Ray and Mari are, they deserve better than to vanish after receiving a comeuppance. It's frustrating watching them reduced to impediments to L. V.'s ability finally to spread her wings (and it's not as though the bird metaphor isn't beaten to an ugly death).
It's all the more disappointing because, for most of its running time, LITTLE VOICE doesn't seem headed that way at all. Its eccentric characters, while stagey, all have their goofy appeal, particularly Jim Broadbent as the nightclub's cheesy owner/emcee. Director Mark Herman develops his small-town atmosphere nicely, and his adapted screenplay keeps the humor fairly consistent. It's actually nearly half an hour into the film before L. V. breaks into song for the first time, allowing ample time to build the significance of the characters and their relationships. Then comes L. V.'s big debut, and it starts to seem that everyone else was just part of the warm-up act. L. V. emerges from her shell, she sings and she changes, and about as abruptly as you can imagine, the credits begin to roll. LITTLE VOICE is largely diverting in its way, and Horrocks is truly wonderful, but eventually it's somewhat disappointing. I didn't expect to leave the theater feeling that an ensemble story had been turned into a one-woman show of Judymania.
On the Renshaw scale of 0 to 10 Christmas Garlands: 6.
Visit Scott Renshaw's MoviePage http://www.inconnect.com/~renshaw/ *** Subscribe to receive new reviews directly by email! See the MoviePage for details, or reply to this message with subject line "Subscribe".
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
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Related links: index of all rec.arts.movies.reviews reviews


Tutoring Sessions
| Student Name | Subject Matter | Date | Session Type | Feedback |
|---|---|---|---|---|
| Ernst Handel | Chemistry | 10/03/2019 | Review | Completed |
| Alfreds Futterkiste | Math | 11/14/2019 | Private | Not completed |
| Jessica Valentine | English | 12/11/2019 | Private | Not completed |
We care for your success.
I have a B.Eng in Chemical Engineering. I was a TA at Waterloo University for 3 years for CHEM204 and CHEM551. I graduated with a 3.9 CGPA. I am now doing my master's in Stem Cell Bioprocessing at McGill University.
Email<EMAIL_ADDRESS>| Subject Matter | Hoourly Rate ($) |
|---|---|
| Math | 20 |
| Chemistry | 20 |
| English | 15 |
| Student Name | Subject Matter | Date | Session Type | Feedback |
|---|---|---|---|---|
| Ernst Handel | Chemistry | 10/03/2019 | Review | Completed |
| Alfreds Futterkiste | Math | 11/14/2019 | Private | Not completed |
| Jessica Valentine | English | 12/11/2019 | Private | Not completed |


Keeping Calm calm.
Implemented automated and modularized terraform 12 deployment pattern using terragrunt and github actions.
Helped various QA teams to automate and modernize the test automation suites.
Shared mindfulness and selfcare practices such as breathing exercises throughout the organization.
Embedded SRE for Web and Mobile team responsible for https://www.flightstats.com/v2/
Kubernetes evangelist with practical production implementations.
Developed deployment pipeline written as Jenkinsfile featuring pull request analysis, automated tests, automated staging deployment, and blue green deployment for production environment for zero downtime deployment.
Transformed manually managed AWS environment into automated infrastructure with terraform and serverless.
Evaluated new tools and provide automation to help other team’s adaption.
Developed CI/CD pipeline automation for AWS Lambda, API Gateway, and ECS with Python.
Automated Docker Swarm cluster creation and CI/CD for containers with Salt Stack.
Integrated Hubot with Slack to enable Chat Ops.
Maintained and improved existing AWS infrastructure provisioned with Chef and Rightscale.
Designed and implemented more automated and event driven infrastructure from scratch with CloudFormation, SaltStack, and Docker. From VPC to Route 53 entries everything was automated.
Researched and implemented new tools such as OpenVPN, Elasticsearch, and AWS RDS with security requirements and restrictions under HIPAA compliance.
Managed BestBuy’s software development lifecycle(SDLC) tools including OpenStack infrastructure, Atlassian stacks, Artifactory, Jenkins, and more.
Used Opscode Chef for configuration management, Jenkins for continuous integration, OpenStack for testing/development environment, and AWS for production environment.
Consulted various teams in BestBuy to enable agile methodology for specific team needs.
Managed security vulnerabilities of 2500 servers in Windows Server environment
{{ . | safeHTML }}
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Welcome! In this third module, you will learn how to multiply and divide fractions and whole numbers. Navigate through the module by clicking through the links.
Navigation
--> 1 - Title2 - Objectives
3 - Music Videos
4 - Multiplication Video
5 - Division Video
6 - Multiplication Activity
7 - Division Activity
8 - Extra Practice
9 - References
10 - Quiz
11 - Certificate
Audio


| Productivity challenges & Coordel solutions | Opportunity challenges & Coordel solutions |
|
My to-do list is so long, I don’t know how and where to start.
The Coordel solution:Current Tasks - Track work you can do right now
Turbo Wizard - Get your day started
|
I have great ideas, but no time to make them happen.
The Coordel solution:Coords - Coordinate work with other people
|
|
Between calendars and to-do lists, how do I keep track of all my deadlines?
The Coordel solution:Deadline Calendar - Track all deadlines in one place
|
I keep reinventing the wheel.
The Coordel solution:Blueprints - Get it right once, then reuse or repeat your successes
|
|
What exactly is my deliverable here?
The Coordel solution:Blocked Tasks - Set it and forget it
Deliverables - Everything you need, where you expect it to be
Blocked Deliverables - Set the order steps in a task are completed
|
I’m really good at …, but my job doesn’t let me use that skill very often.
The Coordel solution:Coords - Coordinate work with other people
People - Choose your own team
Residual Contracts - Build your own business
|
|
My calendar, inbox, to-do lists and calls are overwhelming.
The Coordel solution:Turbo Wizard - Get your day started
Current Tasks - Track work you can do right now
Deferred Tasks - Track work you will start later
Delegated Tasks - Track your delegated work
Blocked Tasks - Set it and forget it
Deadline Calendar - Track all deadlines in one place
|
I like my team, but sometimes I would like to work with others.

The Coordel solution:Explicit Invitations - Agree or decline new work requests
Explicit Agreements - Agree & amend changes to proposed tasks
Explicit Completion - Submit & agree on completed tasks
|
I like my job, but I would like to-do something with more purpose.
The Coordel solution:Coords - Coordinate work with other people
Coordel Business - Build your own business
|
|
My team is struggling to coordinate its efforts.
The Coordel solution:Explicit Invitations - Agree or decline new work requests
Blocked Tasks - Set it and forget it
Deadline Calendar - Track all deadlines in one place
|
I like to be challenged, but my job doesn't always challenge me fully.
The Coordel solution:Coords - Coordinate work with other people
People - Choose your own team
Residual Contracts - Build your own business
|
|
My team spends too much time chasing e-mails.
The Coordel solution:Stream - Spend your time doing work, not writing about it
Alerts - Know what happens when it happens
|
My pay is fine, but what if I can't work?
The Coordel solution:Residual Contracts - Build your own business
|


Though all snapping types are shown here for all target layers, not all are sensible. Points don't have edges, for example.


|
Perception: Human Detection
Group14
Human Detection using OpenCV Haard CAscade Classifier
|
Go to the source code of this file.
Functions | |
| TEST (CamTest, testreadVideo) | |
| TEST (CamTest, testreadVideo1) | |
| TEST (CamTest, testreadFrameImage) | |
| TEST (CamTest, testcolor2gray) | |
| TEST | ( | CamTest | , |
| testcolor2gray | |||
| ) |
Definition at line 57 of file camtest.cpp.
| TEST | ( | CamTest | , |
| testreadFrameImage | |||
| ) |
Definition at line 47 of file camtest.cpp.
| TEST | ( | CamTest | , |
| testreadVideo | |||
| ) |
Definition at line 33 of file camtest.cpp.
| TEST | ( | CamTest | , |
| testreadVideo1 | |||
| ) |
Definition at line 40 of file camtest.cpp.


Module: ActiveRecord::SignedId::ClassMethods
| Relationships & Source Files | |
| Defined in: | activerecord/lib/active_record/signed_id.rb |
Instance Attribute Summary
-
#signed_id_verifier
rw
The verifier instance that all signed ids are generated and verified from.
-
#signed_id_verifier=(verifier)
rw
Allows you to pass in a custom verifier used for the signed ids.
Instance Method Summary
-
#find_signed(signed_id, purpose: nil)
Lets you find a record based on a signed id that’s safe to put into the world without risk of tampering.
-
#find_signed!(signed_id, purpose: nil)
Works like find_signed, but will raise an
::ActiveSupport::MessageVerifier::InvalidSignature
exception if the #signed_id has either expired, has a purpose mismatch, is for another record, or has been tampered with. - #combine_signed_id_purposes(purpose) Internal use only
Instance Attribute Details
#signed_id_verifier (rw)
The verifier instance that all signed ids are generated and verified from. By default, it’ll be initialized with the class-level signed_id_verifier_secret
, which within Rails comes from the Rails.application.key_generator. By default, it’s SHA256 for the digest and JSON for the serialization.
# File 'activerecord/lib/active_record/signed_id.rb', line 71
def signed_id_verifier @signed_id_verifier ||= begin secret = signed_id_verifier_secret secret = secret.call if secret.respond_to?(:call) if secret.nil? raise ArgumentError, "You must set ActiveRecord::Base.signed_id_verifier_secret to use signed ids" else ActiveSupport::MessageVerifier.new secret, digest: "SHA256", serializer: JSON end end end
#signed_id_verifier=(verifier) (rw)
Allows you to pass in a custom verifier used for the signed ids. This also allows you to use different verifiers for different classes. This is also helpful if you need to rotate keys, as you can prepare your custom verifier for that in advance. See ::ActiveSupport::MessageVerifier
for details.
# File 'activerecord/lib/active_record/signed_id.rb', line 87
def signed_id_verifier=(verifier) @signed_id_verifier = verifier end
Instance Method Details
#combine_signed_id_purposes(purpose)
# File 'activerecord/lib/active_record/signed_id.rb', line 92
def combine_signed_id_purposes(purpose) [ base_class.name.underscore, purpose.to_s ].compact_blank.join("/") end
#find_signed(signed_id, purpose: nil)
Lets you find a record based on a signed id that’s safe to put into the world without risk of tampering. This is particularly useful for things like password reset or email verification, where you want the bearer of the signed id to be able to interact with the underlying record, but usually only within a certain time period.
You set the time period that the signed id is valid for during generation, using the instance method signed_id(expires_in: 15.minutes)
. If the time has elapsed before a signed find is attempted, the signed id will no longer be valid, and nil is returned.
It’s possible to further restrict the use of a signed id with a purpose. This helps when you have a general base model, like a User, which might have signed ids for several things, like password reset or email verification. The purpose that was set during generation must match the purpose set when finding. If there’s a mismatch, nil is again returned.
Examples
signed_id = User.first.signed_id expires_in: 15.minutes, purpose: :password_reset
User.find_signed signed_id # => nil, since the purpose does not match
travel 16.minutes
User.find_signed signed_id, purpose: :password_reset # => nil, since the signed id has expired
travel_back
User.find_signed signed_id, purpose: :password_reset # => User.first
# File 'activerecord/lib/active_record/signed_id.rb', line 42
def find_signed(signed_id, purpose: nil) raise UnknownPrimaryKey.new(self) if primary_key.nil? if id = signed_id_verifier.verified(signed_id, purpose: combine_signed_id_purposes(purpose)) find_by primary_key => id end end
#find_signed!(signed_id, purpose: nil)
Works like find_signed, but will raise an ::ActiveSupport::MessageVerifier::InvalidSignature
exception if the ActiveRecord::SignedId#signed_id has either expired, has a purpose mismatch, is for another record, or has been tampered with. It will also raise an ::ActiveRecord::RecordNotFound
exception if the valid signed id can’t find a record.
Examples
User.find_signed! "bad data" # => ActiveSupport::MessageVerifier::InvalidSignature
signed_id = User.first.signed_id
User.first.destroy
User.find_signed! signed_id # => ActiveRecord::RecordNotFound
# File 'activerecord/lib/active_record/signed_id.rb', line 62
def find_signed!(signed_id, purpose: nil) if id = signed_id_verifier.verify(signed_id, purpose: combine_signed_id_purposes(purpose)) find(id) end end


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{% extends "base.html" %} {% block title %}{{ project.display_name }} – {{ block.super }}{% endblock %} {% block content %}
Google Cloud Storage offers a service called AutoML that allows you to train models using image or video data without writing code or preparing data splits. These instructions will help you format your data for Google’s services after Zooniverse’s volunteers have labeled the images.
In the Subject Set Export options below, click Generate to select the subject set for analysis. When it is ready, a link will appear next to the export button.
When the export is complete, copy the subject set export URL that appears next to the subject set into Google Cloud Storage's transfer service to copy your images into the storage bucket you’ll use for AutoML. Producing the export may take some time, especially if you have a large dataset, so please be patient and do not click multiple times.
To prepare the data manifest, run a subject reductions export in Caesar. If you haven’t already, set up a Consensus reducer following these instructions. Then create a new Data Request within Caesar to pull the “most likely” labels assigned by volunteers for model training.
Under Workflow labels export below, select the workflow from which you want to export your data, which should correspond with the workflow accessed in Caesar. Enter the URL of your Google storage, starting with gs://
and without a slash at the end.
Note that any subjects not included in the step 1 export will not be included in this report.
After you download the results for your workflow labels export, upload it to your Google Cloud Storage bucket in order to train your model.


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Doctors Lounge Privacy Statement
June 21, 2007
Welcome. Doctors Lounge would like to thank you for visiting our website.
We are pleased to have the opportunity to help make the Internet a secure,
private, and reliable place to share information and conduct business.
This privacy policy explains how we collect and use information from our
website visitors. All of Doctors Lounge divisions prescribe to essentially
the same information collection and use practices, and all of these practices
are stated in this privacy policy. If a practice is specific to a particular
division in Doctors Lounge, this policy will describe that practice
in detail and refer directly to the appropriate division.
Doctors Lounge Privacy Policy statement, addresses the following
issues:
- The websites and information covered by this Privacy Policy;
- Exactly what information may be collected and how it will be used;
- The consequences, if any, resulting from your refusal to provide
personal information;
- Whether a company uses cookies, tracks IP addresses, or uses other
passive means to collect information;
- Who, if anyone, is collecting your personal information;
- With whom, if anyone, is your personal information shared;
- What is a company's policy regarding links to third party sites;
- What choices you have with regard to the use of your personal information;
- How you can access, and if necessary, change the personal information
a company collects and maintains;
- How a company ensures data security, quality, and integrity; and,
- Where and how to ask questions or file complaints.
What does this Privacy Policy apply to?
This privacy policy applies to the website operated by Doctors
Lounge:
www.doctorslounge.com
Please note that this privacy policy applies only to information submitted
and collected online through the website(s) listed above, and does not
apply to information that may be collected by Doctors Lounge offline.
In addition, this privacy policy applies only to sites maintained by
Doctors Lounge and not to websites maintained by other companies or organizations
to which we link. Doctors Lounge is therefore not responsible for
the content or activities provided on such sites.
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Are you a doctor or a nurse?
Do you want to join the Doctors Lounge online medical community?
Participate in editorial activities (publish, peer review, edit) and
give a helping hand to the largest online community of patients.
Click on the link below to see the requirements:
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What types of information does
Doctors Lounge collect and how
will it be used?
Doctors Lounge only collects information on a voluntary basis.
The personal information Doctors Lounge collects is used almost exclusively
for communications purposes and will usually take the form of: (1)
Doctors Lounge Membership registration form; (2) a consumer complaint
or inquiry directed to the Support Team; (3) Doctors Lounge survey;
(4) Doctors Lounge Medical Forums and other medical services; (5)
Doctors Lounge referral services; (6)
Doctors Lounge's newsletter; and/or, (7) other general information
contained in an email (e.g., comments). The types of information that
may be requested for each activity and the way the information may be
used are detailed below.
Doctors Lounge Membership registration form
Visitors that wish to participate in the activities on the site are required
to complete Doctors Lounge Membership registration form. The requested
information may include the individual's name, address, telephone, electronic
mail (email) address, job, area of specialty, qualifications as well as
demographic data. Doctors Lounge uses this information to contact
the individual regarding participation and, if eligible, to communicate
with such a member on an ongoing basis regarding certification and compliance.
Consumer Complaints Directed to the Support Team
From time to time, the Support Team receives complaints or inquiries regarding
the Doctors Lounge services. When a complaint or inquiry is received,
the Support Team promptly investigates the complaint or inquiry, and then,
when appropriate, responds to the individual who sent the complaint or
inquiry via the e-mail address from where the request originated.
Doctors Lounge Survey
Any one of the Doctors Lounge divisions may conduct surveys. The surveys
are conducted strictly for internal profiling purposes and only keep track
of anonymous demographic data.
Doctors Lounge Medical Services
Doctors Lounge Medical Services are designed to help both physicians
and consumers in extending their knowledge of various medical topics and
keep up to date with current medical information. These services include;
Doctors Lounge Medical Forums. Some of our services are conducted
through a partnership.
Doctors Lounge Newsletter
Visitors who wish to subscribe to the Doctors Lounge newsletter will
be asked to provide their e-mail address as well as demographic data. The submitted e-mail address
is then used to send you, via e-mail, our quarterly newsletter and to
otherwise keep you informed as to what's going on at the Doctors
Lounge.
General Information Contained in Email
Doctors Lounge's website provides a number of links through which
an online visitor can e-mail us. Doctors Lounge collects personal
information contained in the e-mail for the purpose of responding to a
consumer's questions and/or comments.
No matter what method we use to collect information and no matter how
we use that information, we will only collect the information deemed reasonably
necessary to fulfill your online requests and our legitimate business
objectives.
What happens if I refuse to provide my personal information to
Doctors Lounge?
If you choose not to submit personal information when requested, you
may not be able to access certain areas of our site and may considerably
limit the services we can provide you. To simply use our site, however,
you do not need to give us any personal information.
Does Doctors Lounge use cookies, track IP addresses or use other
passive means to collect information?
Cookies
Doctors Lounge uses cookies on its Medical Forums to allow registered
users to use the forums. A "cookie" is a small file or record-keeping
device that websites often store on a user's computer.
IP Addresses
Doctors Lounge may collect your IP address for safety and security
purposes. An IP address is a number that is used by computers on the network
to identify your computer every time you log on to the Internet.
Who is collecting my personal information?
The information that you disclose while visiting our website is collected
by Doctors Lounge or a vendor on Doctors Lounge's behalf, and
is used in the manner specified above.
With whom does Doctors Lounge share my personal information?
From time to time, Doctors Lounge may employ and share your personal
information with vendors who use it solely to provide support for the
internal operations of Doctors Lounge's website(s) (e.g., technical
support, order fulfillment, and newsletter delivery). These entities will
not use your personal information for any other purpose, and have agreed
to maintain the confidentiality, security, and integrity of the personal
information they obtain from us.
It is our policy not to sell or rent your personal information. We may,
however, disclose your personal information to outside third parties as
described in this privacy policy. In addition, we may also disclose your
personal information in the good faith belief that we are required to
do so by law, or that doing so is reasonably necessary to comply with
legal processes; respond to any claims; or, to protect the rights, property,
or personal safety of Doctors Lounge or the public.
Customers may receive information about third party
services that are likely to be of interest. Users of our free
service will initially be opted in to this program while customers
signing up any of our paid service can choose to opt in. Customers
can opt out by clicking on the link provided in the email or by
visiting our site and opting out at any time.
We may also use personally identifiable End-User
information to provide targeted content and commerce opportunities
to End-Users based on their demographic and behavioral information.
This does not apply to the personal medical information collected in
the "Ask a Doctor"/ "Medical Forums" section. We do not share the personal medical
information of our users.
Finally, we never use or share the personally
identifiable information provided to us online in ways or for
reasons unrelated to the ones described above without also providing
an opportunity to opt-out or otherwise prohibit such unrelated uses.
What is the policy of Doctors Lounge regarding links to third party
sites?
You should be aware that while you are on a website operated by
Doctors Lounge, you may be directed to other sites that are beyond our
control and for which we are not responsible. Because we cannot guarantee
that the privacy policies of these websites meet our high standards, we
recommend that you read the privacy policy of the website to which you
link before you submit any personal information.
Can I choose how my personal information is used?
If you wish to opt-out from receiving our newsletter or any other communication,
please contact us, at any time,
via e-mail.
We will be happy to honor your request.
How can I access my personal information?
If you wish to review, update, or delete any personal information that
we may have collected about you, please contact us
via e-mail.
What safeguards does Doctors Lounge use to protect my personal
information?
Doctors Lounge maintains appropriate safeguards that ensure the
security, integrity and privacy of the personal information we collect
from all users. Personal information collected by Doctors Lounge is
stored in secure operating environments that are not available to the
public and is only accessible by authorized employees. We also have security
measures in place to protect the loss, misuse and alteration of the information
under our control.
How do I ask a question or file a complaint?
If you have any questions, complaints or comments regarding our privacy
policy or practices, please contact us
via e-mail.
By using this site, you signify your assent to the Doctors Lounge
Online Privacy Policy. If you do not agree to this Privacy Policy, please
do not use this site. We reserve the right to make changes to this Policy.
Please check back from time to time to ensure you are aware of these changes.
Your continued use of this site will signify your acceptance of these
changes.
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“Upasampadā ca me laddhā,
vimutto camhi anāsavo;
So ca me bhagavā diṭṭho,
vihāre ca sahāvasiṁ.
I’ve received ordination;
I am liberated, without defilements;
I’ve seen the Blessed One myself,
and even stayed together with him.
Bahudeva rattiṁ bhagavā,
abbhokāsetināmayi;
Vihārakusalo satthā,
vihāraṁ pāvisī tadā.
The Blessed One, the teacher,
spent much of the night in the open;
then he, who is so skilled in meditation,
entered his dwelling.
Santharitvāna saṅghāṭiṁ,
seyyaṁ kappesi gotamo;
Sīho selaguhāyaṁva,
pahīnabhayabheravo.
Spreading his outer robe,
Gotama made his bed,
like a lion in a rocky cave,
with fear and dread given up.
Tato kalyāṇavākkaraṇo,
sammāsambuddhasāvako;
Soṇo abhāsi saddhammaṁ,
buddhaseṭṭhassa sammukhā.
Then, with lovely enunciation,
Soṇa, a disciple of the Buddha,
recited the true teaching
before the best of Buddhas.
Pañcakkhandhe pariññāya,
Bhāvayitvāna añjasaṁ;
Pappuyya paramaṁ santiṁ,
Parinibbissatyanāsavo”ti.
… Soṇo kuṭikaṇṇatthero ….
When he has completely understood the five aggregates,
developed the direct route,
and arrived at ultimate peace,
he will realize quenching without defilements.


{% block title %}myApi Flask Pymongo{% endblock %} {% if g.user %} {{ g.user['username'] }} {% else %} No connected user {% endif %} {% block header %}{% endblock %} {% for message in get_flashed_messages() %} {{ message }} {% endfor %} {% block content %} Users Http Method Description Url get_users() GET Return all users http://localhost:5000/users add_user() POST Add user (expected JSON username, email, password) Return JSON(id : username, email, hashed_pwd) http://localhost:5000/users get-user() GET Return JSON(id : username, email, hashed_pwd) http://localhost:5000/user/ modify_user() PUT Modify user (expected JSON username, email, password) Return JSON(id : username, email, hashed_pwd) http://localhost:5000/user/ delete_user() DELETE Return 'deleted' http://localhost:5000/user/ login() POST Login (expected JSON email, password) Return 'logged in' http://localhost:5000/auth/login Articles Http Method Description Url get_articles() GET Return all articles http://localhost:5000/articles write_article() POST Add article (expected JSON title, body) Return JSON(title, body, created, author, modified) http://localhost:5000/articles get_article() GET Return JSON(title, body, created, author, modified) http://localhost:5000/article/<id> modify_article() PUT Modify article (expected JSON title, body) Return JSON(title, body, created, author, modified) http://localhost:5000/article/<id> delete_article() DELETE Return 'deleted' http://localhost:5000/article/<id> Comments Http Method Description Url get_comments_by_article() GET Return all comments for an article <id> http://localhost:5000/article/<id>/comments; get_comments_by_author() DELETE Return all comments for an author <author> http://localhost:5000/article/comments/<author> post_comment() POST Post comment for an article <id> Return JSON(id : content, created, author, modified) http://localhost:5000/article/<id>/comments; edit_comment() PUT Edit comment by comment <id> Return JSON(id : content, created, author, modified) http://localhost:5000/article/comment/<id> delete_comment() DELETE Return 'deleted' http://localhost:5000/article/comment/<id> {% endblock %}


All relevant data are within the paper.
During pregnancy an adequate amino acid supply is essential for embryo development and fetal growth. We have studied amino acid composition and branched chain amino acid (BCAA) metabolism at day 6 p.c. in diabetic rabbits and blastocysts. In the plasma of diabetic rabbits the concentrations of 12 amino acids were altered in comparison to the controls. Notably, the concentrations of the BCAA leucine, isoleucine and valine were approximately three-fold higher in diabetic rabbits than in the control. In the cavity fluid of blastocysts from diabetic rabbits BCAA concentrations were twice as high as those from controls, indicating a close link between maternal diabetes and embryonic BCAA metabolism. The expression of BCAA oxidizing enzymes and BCAA transporter was analysed in maternal tissues and in blastocysts. The RNA amounts of three oxidizing enzymes, i.e. branched chain aminotransferase 2 (Bcat2), branched chain ketoacid dehydrogenase (Bckdha) and dehydrolipoyl dehydrogenase (Dld), were markedly increased in maternal adipose tissue and decreased in liver and skeletal muscle of diabetic rabbits than in those of controls. Blastocysts of diabetic rabbits revealed a higher Bcat2 mRNA and protein abundance in comparison to control blastocysts. The expression of BCAA transporter LAT1 and LAT2 were unaltered in endometrium of diabetic and healthy rabbits, whereas LAT2 transcripts were increased in blastocysts of diabetic rabbits. In correlation to high embryonic BCAA levels the phosphorylation amount of the nutrient sensor mammalian target of rapamycin (mTOR) was enhanced in blastocysts caused by maternal diabetes. These results demonstrate a direct impact of maternal diabetes on BCAA concentrations and degradation in mammalian blastocysts with influence on embryonic mTOR signalling.
Amino acids are essential nutrients for embryo and fetal development and growth [ 1 ]. During pregnancy the availability and concentration of amino acids are vital determinants for trophoblast differentiation and implantation [ 2 , 3 ]. In vitro studies showed the necessity of amino acids for the development of zygotes in vitro (sheep) [ 4 ] and for preimplantation embryos from the golden hamster [ 5 ], bovine [ 6 ], mouse [ 7 ] and human [ 8 ]. In 1966, Gwatkin reported that an absence of the amino acids leucine and arginine in culture medium led to inhibited trophoblast growth [ 9 ].
The branched chain amino acids (BCAA) leucine, isoleucine and valine are of great importance for fetal growth. They are preferentially transported to the embryo via system L [ 10 ] and spread quickly across the placenta [ 11 ]. BCAA are three of the nine essential amino acids and are abundant in foods, accounting for 15 to 20% of total protein intake [ 12 ]. In contrast to other amino acids, BCAA are poorly metabolised in the liver. Sixty percent of them are metabolised in skeletal muscle [ 13 ]. Skeletal muscle and adipose tissue have the highest BCAA degradation capacity [ 14 ]. The BCAA metabolism encompasses three steps: transamination, oxidative decarboxylation and dehydration. The mitochondrial branched chain aminotransferase (BCAT2 or Bcatm) catalyses the transamination reaction as first step. BCAT2 is expressed in most peripheral tissues [ 15 , 16 ]. The branched chain ketoacid dehydrogenase complex (BDKDHC) is required for BCAA oxidation. BCKDHC consists of three catalytic components; the branched chain ketoacid dehydrogenase (BCKDH; alpha and beta subunit), dehydrolipoyl dehydrogenase (DLD) and dehydrolipoyl transacylase (DBT).
BCAA are transported via system L transporter containing a catalytic subunit and a glycoprotein 4F2hc/CD98. The subunit includes two isoforms called light chains LAT1 (gene: SLC7A5) and LAT2 (gene: SLC7A8) with high affinity to the BCAA [ 17 , 18 ].
Pathological high levels of BCAA have a critical influence on fetal growth and development in pregnant women suffering from maple syrup urine disease (MSUD) [ 19 ]. MSUD is an autosomal recessive disease with mutations in the gens Bckdha, Dld or Dbt. This genetic defect leads to a disturbed BCAA degradation. This disorder represents in neonates as a neurologic distress with either ketosis or ketoacidosis and hyperammonaemia.
For metabolic disorders like diabetes mellitus it is well known that the plasma amino acid concentrations are increased [ 20 , 21 ]. Hyperglycaemia in poorly controlled diabetes mellitus is related to high plasma levels of BCAA [ 22 , 23 ]. Likewise in pregnancies with gestational diabetes increases were observed for valine, methionine, phenylalanine, isoleucine, leucine, alanine in umbilical blood. So far, little is known about the effect of maternal diabetes on the embryonic amino acid content during early pregnancy.
We have used a rabbit animal model to investigate the effects of a type 1 diabetes mellitus on maternal and embryonic amino acid metabolism. We assumed that changes in the maternal plasma amino acid concentrations are transferred to the embryo prior to implantation as we had found high BCAA in early pregnant diabetic rabbits. Our study demonstrates that maternal diabetes mellitus type 1 leads to changes in amino acid composition and degradation in rabbits and their blastocysts during the preimplantation period with consequences on embryonic mTOR signalling.
Experimental insulin dependent diabetes (IDD) was induced in female nonpregnant rabbits by alloxan treatment as described before [ 24 ]. The diabetic rabbits were hold in hyperglycaemic conditions with a permanent blood glucose concentration of >20 mmol/L for 9–11 days before mating. The blood glucose level was monitored twice per day. To prevent ketoacidosis insulin was supplemented 3 times per day (Humaninsulin basal, Lilly Deutschland GmbH, Giessen). This insulin supplementation is not enough to lower blood glucose levels to normal as diabetic rabbits should be investigated. For maternal blood and tissue analyses 6 or more pregnant rabbits from three different independent experiments were used. All blood samples were collected at day 6 after mating, at the same time when blastocysts and blastocyst cavity fluids were collected. In the same experiment and at the same time point (day 6.0 p.c.) blastocysts of three stages can be collected from individual donors (non-gastrulated stage 0 and early gastrulation stages 1 and 2).
All animal experiments were in accordance with the principles of laboratory animal care and had been approved by the local ethics committee (Landesverwaltungsamt Dessau, reference number 42502-2-812). All surgery was performed under Ketanest and Dormitor anesthesia and all efforts were made to minimize suffering.
Embryos were collected from sexually mature rabbits (12- to 16-weeks-old). The female rabbits, outbred ZIKA-hybrid New Zealand white, were purchased from a local breeder and were stimulated with 110 I.U. pregnant mare serum gonadotropin (PMSG, Intervet, Unterschleissheim, Germany) three days prior to mating. After mating 75 I.U. human choriongonadotropin (hCG, Intervet, Unterschleissheim, Germany) was intravenously injected to ensure ovulation. The rabbits were killed using an overdose of pentobarbital. Blood samples were collected with S-Monovetten (Sarstedt, Germany) containing EDTA. Plasma probes were centrifuged for 15 minutes at 4400 rpm and the supernatant were stored at -80°C until use. The uterine secretion was collected from the endometrial surface by using absorbing paper strips. The samples were stored at -80°C until use. Adipose tissue, skeletal muscle and liver were prepared and stored at -80°C until use for RNA and protein analyses.
Collection of the cavity fluid was performed as followed: As rabbit blastocysts at day 6 are so big that they can be easily be identified by eye, they were picked up directly from the uterine luminal surface with a “blastocyst spoon”, briefly washed in cold PBS avoiding any storage and put on a 4°C precooled watch glasses. Blastocysts’ surface was then dried by flint-free cellulose paper. The blastocysts were staged and punctured and fluids were taken up with a pipette from the watch glasses and stored at -80°C until use. Overall, pick-up, rinsing and the collection of fluids and samples took less than 2 min and were highly standardized in all experimental replicates.
The embryos were flushed from the oviduct or uteri on day 3, 4 and 6 post coitum ( p. c.), washed two times in basal synthetic medium II (BSM II, serum- and growth factor-free) [ 25 ], pooled and randomly divided amongst the experimental groups. Six days old blastocysts were characterized morphologically and grouped by gastrulation stages in stage 0 (non-gastrulating), 1 (gastrulation stage 1 with anterior marginal crest) and 2 (gastrulation stage 2 with posterior gastrulation extension) [ 26 ]. Flushed embryos were washed with ice-cold phosphate buffered saline (PBS) and their gastrulation stage was determined. Embryos of gastrulation stage 1 and 2 were then transferred on a dry watch glass and washed again. After fluid removal the embryos were punctured and the effluent cavity fluid collected. Blastocyst cavity fluids were stored at -80°C until use.
For RNA isolation the embryos were washed 3 times in PBS containing 0.05% polyvinyl alcohol (PVA) and the extracellular coverings were removed mechanically. Samples of whole embryos or separated embryoblast and trophoblast were stored in PBS at -80°C until RNA isolation for RT-qPCR [ 27 ].
For Western Blot analysis embryos were washed 3 times in PBS and the extracellular coverings were removed mechanically in 0.05% PVA/PBS containing protease and phosphatase inhibitor. 8–10 embryos were pooled in RIPA buffer with protease and phosphatase inhibitor and stored at -80°C until further processing.
To study the effects of insulin or glucose, groups of 3 to 6 blastocysts were cultured in 4 ml BSM II medium [ 25 ] at 37°C in a water saturated atmosphere of 5% O
The concentrations of free amino acids in maternal plasma, uterine secretion and in blastocyst cavity fluid were measured as isoindole derivatives by reversed phase high performance liquid chromatography (HPLC) (Hypersil ODS, 250 mm x 4 mm, 5 μm, Agilent 1100, Agilent Technologies, Waldbronn, Germany) according to Schuster 1988 [ 28 ] with fluorescence detection (337 nm / 454 nm) after pre-column derivatisation with o-phthaldialdehyde and mercaptopropionic acid [ 29 ]. 20 μl of non-diluted plasma samples or 5 μl blastocyst cavity fluid (from single blastocysts) were precipitated with 0.25 vol sulphosalicylic acid (10%) and simultaneously incubated with 1 mM of internal standard nor-valine for 30 minutes at 4°C. Uterine secretions were eluated from the paper by adding of a defined volume of two parts deionized water and one part 1 mM internal standard nor-valine (final dilution 1:4) followed by an incubation in ice cold ultrasonic bath for 5 minutes. Afterwards the samples were centrifuged from the bored reaction tube into an imposed reaction tube for 5 minutes at 10000 g. Twenty μl of the eluates were incubated with 5 μl sulphosalicylic acid (10%) for 30 minutes at 4°C. All samples were centrifuged (18000 g, 10 min, 4°C) and the 1:5 (1:20 for uterine secretion samples) diluted supernatant was used for HPLC measurement.
The mRNA of single blastocysts was extracted with Dynabeads Oligo (dT)
Total RNA from tissues (liver, skeletal muscle, adipose tissue and endometrium) was extracted by using TRIzol reagent (Life Technologies, Darmstadt, Germany) according to a previously described protocol [ 31 ]. Isolated RNA was treated with DNase for 30 minutes. The amount of total RNA was determined spectrophotometrically at 260 nm. Three μg of RNA was diluted in a total of 11.5 μl and preincubated with 1 μmol random pd(N)
For real time analysis (RT-qPCR) duplicates of each cDNA sample and a no template control were measured for any primer set [ 32 ]. The primer sequences used in this study are documented in Table 1 . The housekeeping gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was quantified as endogenous control. Thieme et al. [ 27 ] had shown that GAPDH expression is not affected by the treatments used in current study. The target gene expression was normalized to that of GAPDH in each sample. A calibration curve was included from serial dilutions in a range from 10 8–10 3 copies of primer-specific DNA plasmid standards. Individual data are expressed relative to these standards.
| Gene | Primer sequence | Product [Bp] | Tm | Acc. No. |
|---|---|---|---|---|
| Rabbit GAPDH | fw: GCCGCTTCTTCTCGTGCAG rev: ATGGATCATTGATGGCGACAACAT | 144 | 60°C | L23961 |
| Rabbit Bcat2 | fw: ACTACTCCCTGCAGCTCTTTG rev: GAACCCAGTCCTTGTCCACTC | 191 | 60°C | XM_002723704.2 |
| Rabbit Bckdha | fw: AGACAAGCTCGAGTTCATCCA rev: AGAACTTCAGCACCTTCTCCT | 130 | 60°C | XM_002722294.1 |
| Rabbit Dld | fw: GTGATAGGTTCTGGTCCTGGA rev: CAATTCCCCTAGATGCAAAAT | 198 | 60°C | XR_085085.2 |
| Rabbit Dbt | fw: GATATTGCCACCTGAAGTAGC rev: GAGAAGCGTGACCATTGAAGCA | 155 | 60°C | XM_002715835.1 |
| Rabbit SLC7A8 | fw: GTCCCTTGCATCTGCTAAGACT rev: TCCAAAAAGTAAGGCATCCACT | 234 | 60°C | NM_001082682.1 |
| Rabbit SLC7A5 | fw: CTCTTCCTCATCGCCGTCTC rev: TTTTTCCACCACACCCCGAA | 110 | 60°C | NM_001082120.1 |
Protein samples diluted in RIPA buffer were homogenized with Precellys (Peqlab, Erlangen, Germany), incubated 30 minutes on ice and afterwards centrifuged at 4°C for 20 minutes. The supernatant was used to measure the protein concentration according to Bradford. Western blot analyses were performed with 25 μg protein. After blotting, the nylon membranes were stained with Ponceau S. Molecular weights were determined by comparison with PageRuler prestained molecular weight marker (Fermentas, St. Leon-Rot, Germany). The immunoreactive signals were visualized by enhanced chemiluminescence detection (Millipore, Schwalbach, Germany) and quantified by Fusion Fx7 Imaging System (Peqlab, Erlangen, Germany). The primary antibody against BCAT2 (mouse polyclonal) was purchased from Abcam (ab72850) and diluted 1:1000. An anti-phospho-mTOR (Ser2448) (rabbit Ab, 1:500, #2971) and anti-mTOR (rabbit Ab, 1:500, #2972) antibody (both NEB, Frankfurt, Germany) were used to calculate phosphorylation as ratio of band intensities (p-mTOR vs. mTOR) in the same blot. Protein amount was evaluated by re-blotting with an antibody against the mouse monoclonal beta-actin antibody (Sigma, A-5441, 1:40000) after stripping the membranes. Protein amounts were calculated as ratio of band intensities (BCAT2 vs. beta-actin) in the same blot.
Data are expressed as mean value ± standard error of mean (mean ± SEM). If not stated otherwise, levels of significance between groups were calculated using student’s t-test after proving normal distribution. Multiple comparisons were made by factorial variance analysis (ANOVA) adjusted according to Bonferroni (statistical software: Sigma Plot v. 11.0). Levels of statistical significance are indicated as follows *- p<0.05, **- p< 0.01 and ***- p<0.001. All experiments were carried out at least three times.
The plasma amino acid composition from 11 diabetic rabbits and 11 non-diabetic healthy control females at day 6 of pregnancy was analysed and quantified by HPLC. In plasma samples from diabetic rabbits the concentrations of 12 amino acids were altered in comparison to controls. Alanine, valine, isoleucine, leucine and phenylalanine concentrations were significantly increased, whereas serine, glutamine, glycine, arginine, tyrosine, tryptophan and lysine concentrations were significantly reduced in diabetes ( Table 2 ). Collectively, the concentrations of 5 essential amino acids were modified by maternal diabetes. The branched chain amino acids (BCAA) showed the most obvious effects. Their concentrations were approximately three-fold higher in plasma of diabetic rabbits than in plasma of the control group ( Table 2 ).
| Amino acid concentration [mM] | ||||
|---|---|---|---|---|
| Amino acid | Control | IDD | P | Fold change |
| essential | ||||
| Histidine | 0.118 ± 0.003 | 0.116 ± 0.003 | ||
| Threonine | 0.201 ± 0.011 | 0.248 ± 0.012 | ||
| Methionine | 0.081 ± 0.004 | 0.089 ± 0.006 | ||
| Tryptophan | 0.062 ± 0.002 | 0.055 ± 0.002 | 0.024 | 0.87 |
| Phenylalanine | 0.054 ± 0.001 | 0.061 ± 0.002 | 0.032 | 1.13 |
| Lysine | 0.203 ± 0.011 | 0.169 ± 0.007 | 0.02 | 0.83 |
| Valine | 0.241 ± 0.014 | 0.674 ± 0.095 | 0.001 | 2.8 |
| Isoleucine | 0.080 ± 0.005 | 0.231 ± 0.040 | 0.001 | 2.89 |
| Leucine | 0.108 ± 0.007 | 0.323 ± 0.057 | 0.001 | 2.99 |
| non-essential | ||||
| Asparagine | 0.106 ± 0.005 | 0.091 ± 0.008 | ||
| Serine | 0.247 ± 0.006 | 0.209 ± 0.012 | 0.014 | 0.85 |
| Glutamine | 0.836 ± 0.023 | 0.527 ± 0.017 | 0.001 | 0.63 |
| Glycine | 0.903 ± 0.041 | 0.500 ± 0.042 | 0.001 | 0.55 |
| Arginine | 0.211 ± 0.016 | 0.112 ± 0.014 | 0.001 | 0.53 |
| Alanine | 0.355 ± 0.028 | 0.624 ± 0.065 | 0.01 | 1.75 |
| Taurine | 0.128 ± 0.023 | 0.092 ± 0.009 | ||
| Tyrosine | 0.079 ± 0.002 | 0.053 ± 0.002 | 0.001 | 0.68 |
| Ornithine | 0.063 ± 0.003 | 0.085 ± 0.013 |
Results are given in mM and are from 3 independent experiments including 11 individuals in each group. (mean ± SEM; N = 3; n = 11).
Amino acid composition of uterine secretion from 7 diabetic rabbits and 8 non-diabetic healthy control females at day 6 of pregnancy was analysed and quantified by HPLC. The concentrations of threonine, valine, isoleucine, leucine, glutamine, arginine, alanine and taurine were significantly increased in uterine secretion of diabetic rabbits ( Table 3 ).
| Amino acid concentration [mM] | ||||
|---|---|---|---|---|
| Amino acid | Control | IDD | P | Fold change |
| essential | ||||
| Threonine | 0.651 ± 0.050 | 0.803 ± 0.043 | 0.043 | 1.23 |
| Methionine | 0.205 ± 0.026 | 0.213 ± 0.018 | ||
| Tryptophan | 0.048 ± 0.003 | 0.050 ± 0.005 | ||
| Phenylalanine | 0.151 ± 0.020 | 0.164 ± 0.015 | ||
| Lysine | 0.355 ± 0.034 | 0.342 ± 0.029 | ||
| Valine | 0.350 ± 0.033 | 0.573 ± 0.062 | 0.002 | 1.63 |
| Isoleucine | 0.157 ± 0.019 | 0.238 ± 0.029 | 0.032 | 1.51 |
| Leucine | 0.269 ± 0.023 | 0.454 ± 0.055 | 0.017 | 1.69 |
| non-essential | ||||
| Serine | 1.994 ± 0.148 | 2.032 ± 0.141 | ||
| Glutamine | 0.046 ± 0.008 | 0.100 ± 0.022 | 0.04 | 2.15 |
| Glycine | 34.964 ± 3.136 | 41.073 ± 1.660 | ||
| Arginine | 0.181± 0.025 | 0.262 ± 0.027 | 0.021 | 1.44 |
| Alanine | 4.307 ± 0.413 | 6.884 ± 0.267 | 0.001 | 1.60 |
| Taurine | 0.733 ± 0.066 | 1.008 ± 0.098 | 0.033 | 1.37 |
| Tyrosine | 0.176 ± 0.018 | 0.148 ± 0.015 | ||
| Ornithine | 0.076 ± 0.016 | 0.054 ± 0.005 |
Results are given in mM and are from 4 independent experiments. (mean ± SEM; N = 4; n
Blastocyst cavity fluid (BCF) was collected from embryos at gastrulation stage 1 and 2. BCF of 11 individual blastocysts from diabetic and non-diabetic females was analysed and quantified in each group and stage by HPLC. The amino acid concentrations (Mean±SEM) are listed in Table 4 .
| Amino acid concentration [mM] | ||||
|---|---|---|---|---|
| Stage 1 | Stage 2 | |||
| Amino acid | Control | IDD | Control | IDD |
| essential | ||||
| Histidine | 0.094 ± 0.013 | 0.080 ± 0.007 | 0.094 ± 0.007 | 0.112 ± 0.009 b |
| Threonine | 0.337 ± 0.025 | 0.302 ± 0.028 | 0.387 ± 0.022 | 0.453 ± 0.021 b |
| Methionine | 0.113 ± 0.020 | 0.114 ± 0.023 | 0.143 ± 0.023 | 0.116 ± 0.015 |
| Tryptophan | 0.050 ± 0.004 | 0.040 ± 0.03 | 0.055 ± 0.005 | 0.048 ± 0.006 |
| Phenylalanine | 0.066 ± 0.005 | 0.054 ± 0.003 | 0.073 ± 0.006 | 0.067 ± 0.005 |
| Lysine | 0.438 ± 0.044 | 0.483 ± 0.027 | 0.411 ± 0.050 | 0.582 ± 0.061 a |
| Valine | 0.268 ± 0.030 | 0.586 ± 0.054 a | 0.271 ± 0.026 | 0.595 ± 0.052 a |
| Isoleucine | 0.084 ± 0.010 | 0.265 ± 0.029 a | 0.099 ± 0.011 | 0.240 ± 0.024 a |
| Leucine | 0.112 ± 0.011 | 0.373 ± 0.043 a | 0.133 ± 0.013 | 0.330 ± 0.033 a |
| non-essential | ||||
| Asparagine | 0.341 ± 0.033 | 0.250 ± 0.019 | 0.286 ± 0.024 | 0.367 ± 0.029 b |
| Serine | 0.892 ± 0.108 | 0.720 ± 0.039 | 0.992 ± 0.076 | 1.098 ± 0.069 b |
| Glutamine | 0.491 ± 0.065 | 0.798 ± 0.084 a | 0.522 ± 0.042 | 0.754 ± 0.062 a |
| Glycine | 5.414 ± 0.352 | 7.688 ± 0.767 a | 6.451 ± 0.408 | 7.770 ± 0.029 a |
| Arginine | 0.318 ± 0.050 | 0.316 ± 0.018 | 0.248 ± 0.016 | 0.380 ± 0.038 a |
| Alanine | 2.333 ± 0.311 | 3.949 ± 0.508 a | 2.063 ± 0.234 | 3.851 ± 0.406 a |
| Taurine | 0.093 ± 0.007 | 0.161 ± 0.015 a | 0.086 ± 0.005 | 0.141 ± 0.025 a |
| Tyrosine | 0.090 ± 0.007 | 0.047 ± 0.003 a | 0.092 ± 0.007 | 0.061 ± 0.004 ab |
| Ornithine | 0.089 ± 0.019 | 0.093 ± 0.007 | 0.193 ± 0.027 b | 0.154 ± 0.015 b |
Results are given in mM and are from 3 independent experiments including 11 individuals in each group. (mean ± SEM; ANOVA; N = 3; n = 11; a—significantly different between diabetic and non-diabetic (p< 0.05); b — significantly different in gastrulation stage 1 and 2 (p< 0.05)).
We compared the amino acid composition in blastocyst cavity fluid at gastrulation stage 1 and stage 2. In blastocysts from healthy rabbits only the concentration of the non-essential amino acid ornithine was different with a two-fold increase in stage 2 ( Table 4 ). In blastocysts from diabetic rabbits we found an increase of asparagine, serine, histidine, threonine, tyrosine and ornithine at gastrulation stage 2 ( Table 4 ).
The concentrations of 8 amino acids (3 essential and 5 non-essential amino acids) were altered in the blastocyst cavity fluid from gastrulation stage 1 blastocysts grown in diabetic mothers compared to control blastocysts of the same stage. Concentrations of 7 amino acids (glutamine, glycine, alanine, taurine, valine, isoleucine and leucine) were significantly higher. Tyrosine concentration was decreased. Remarkably, as in maternal plasma, the BCAA showed the strongest differences in BCF of embryos from diabetic rabbits in comparison to the controls. Embryonic BCAA were two- to three-fold increased, while other essential amino acids were not changed. In blastocysts at gastrulation stage 2 the concentrations of 10 amino acids (4 essential and 6 non-essential amino acids) were altered under diabetic conditions ( Table 4 ). Tyrosine was reduced. BCAA and lysine were increased. The non-essential amino acids glutamine, glycine, arginine, alanine and taurine were significantly enhanced in blastocysts of diabetic rabbits. Again, the strongest effect was found in BCAA.
Diabetes showed a strong impact on the BCAA concentrations. We assumed that the increase in BCAA concentrations was caused by a disruption of BCAA degradation due to transcriptional regulation in maternal tissues as described by Herman in mice before [ 33 ]. Consequently, the embryo should adapt its amino acid metabolism to the increased BCAA availability.
The mRNA amounts of the BCAA oxidizing enzymes branched chain aminotransferase 2 (Bcat2), 2-oxoisovalerate dehydrogenase subunit alpha (Bckdha), dehydrolipoyl dehydrogenase (Dld) and dehydrolipoyl transacylase (Dbt) were analysed in various maternal tissues (liver, skeletal muscle and adipose tissue). The lowest expression level of all enzymes was found in the skeletal muscle (Bcat2: 13±1, Bckdha: 2±0.09, Dld: 408±41, Dbt: 26±3 molecules per 10 5 GAPDH molecules) and the highest in liver (Bcat2: 104±11, Bckdha: 123±10, Dld: 38090±2800, Dbt: 14757±1225 molecules per 10 5 GAPDH molecules) and adipose tissue (Bcat2: 275±25, Bckdha: 1666±88, Dld: 19041±1488, Dbt: 3839±172 molecules per 10 5 GAPDH molecules). Bcat2 was higher expressed in adipose tissue than in liver.
In diabetic rabbits the Bcat2 mRNA level was increased in adipose tissue compared to the controls ( Fig 1A). In adipose tissue mRNA amounts of the Bckdha and the Dld were increased, too. However, the expression of most oxidizing enzymes was reduced in liver and skeletal muscle. The analysis of BCAT2 protein amount revealed a two-fold increase in adipose tissue of diabetic rabbits compared to controls ( Fig 1B and 1C).
(A) Transcript amounts of Bcat2, Bckdha, Dld and Dbt were measured in liver, skeletal muscle and adipose tissue from diabetic and non-diabetic (control) rabbits at day 6 p. c. by real time RT-qPCR. The control group is set 100%. Transcript amounts of most oxidizing enzymes were reduced in liver and skeletal muscle and enhanced in adipose tissue of diabetic rabbits in comparison to healthy controls. (B) BCAT2 protein amount was analysed by Western blotting in adipose tissue of diabetic (IDD) and non-diabetic (control) rabbits. A representative Western blot for BCAT2 is shown. Amounts were calculated relative to ß-actin of the same sample. BCAT2 amounts of the control group are set 100%. Diabetic rabbits showed an approximately 2 fold higher BCAT2 protein amount in adipose tissue than healthy controls. (1,2,3,4—individual protein samples isolated from non-diabetic rabbits; 5,6,7,8—individual protein samples isolated from diabetic rabbits; N = 3; n ≥ 6; * = p˂ 0.05; ** = p< 0.01; ***p = <0.001).
Fig 2 documents the ontogenetic pattern of BCAA transporter system L with the subunits LAT1 (gene: SLC7A5) and LAT2 (gene: SLC7A8) in morulae (day 3), early blastocyst (day 4) and expanded blastocyst (day 6). Transcripts of SLC7A5 and SLC7A8 and the BCAA oxidizing enzymes Bcat2, Dld, Dbt and Bckdha were present in all investigated embryo stages ( Fig 2). Bcat2 mRNA amount was quantified by real time RT-PCR in separated embryoblast (16.03±1.43 molecules per 10 3 GAPDH molecules) and trophoblast (15.31±1.63 molecules per 10 3 GAPDH molecules). Bcat2 transcripts were equal in both cell lineages. During gastrulation at day 6, blastocysts Bcat2 transcript levels decreased from stage 1 to 2, whereas Dbt transcripts increased ( Fig 3A and 3D). The mRNA amount of Bckdha and Dld was not affected ( Fig 3B and 3C).
Expression of Bcat2, Bckdha, Dld, Dbt, SLC7A8 and SLC7A5 was determined in preimplantation rabbit embryos at day 3 (d3; morula), 4 (d4; early blastocyst) and 6 p. c. (d6; expanded blastocyst) by RT-qPCR. Transcripts of BCAA oxidizing enzymes and transporters were present in all investigated stages. (ntc—non template control).
The mRNA amounts of Bcat2, Bckdha, Dld and Dbt were quantified by real time RT-qPCR in blastocysts of gastrulation stage 1 and 2 from control (white bars) and diabetic rabbits (black bars). Bcat2 and Dbt transcripts were significantly increased in stage 1 and stage 2 embryos from diabetic rabbits (A+D) compared to control blastocysts; Dld and Bckdha transcripts were not influenced by maternal diabetes (B+C). (ANOVA; N = 3; n≥ 9; * = p˂ 0.05). (E) The relative BCAT2 protein amount was analysed by Western blotting in blastocysts of diabetic (IDD; black bars) and non-diabetic (control; white bars) rabbits. ß-actin was used as loading control. The control group stage 1 is set 100%. Blastocysts of diabetic rabbits revealed an approximately two-fold increase in BCAT2 protein amount in both gastrulation stages. (F) A representative Western Blot for BCAT2 is shown with protein samples from 10 pooled blastocysts per group (1–8). (ANOVA; N = 4; n = 40; * = p< 0.05).
In blastocysts grown in diabetic rabbits the transcript and protein amounts of BCAT2 were significantly increased compared to control blastocysts ( Fig 3). Also Dbt-RNA amount was significantly enhanced in gastrulation stages 1 and 2 compared to corresponding control blastocysts ( Fig 3D). The transcription of Bckdha and Dld was not influenced by maternal diabetes ( Fig 3B and 3C).
The quantification of Bcat2 RNA in blastocysts cultured without insulin showed higher amounts after 4 h in vitro culture ( Fig 4A). A 6 h culture with 0, 10 or 25 mM glucose had no effect on embryonic Bcat2 expression.
Blastocysts were cultured in pools of 3 to 6 embryos with 17 nM insulin (A) or in 0, 10 or 25 mM glucose. The mRNA amount of Bcat2 was quantified by real time RT-qPCR in single blastocysts. The Bcat2 transcript level was unaltered after 1 h culture without or with insulin and increased after 4 h culture in the insulin free group (A). Bcat2 transcript amounts were not altered after culture with glucose for 6h (B). (N = 3; n≥ 11; * = p< 0.05).
SLC7A5 and SLC7A8 mRNA amounts were quantified by real time RT-qPCR in endometrium of diabetic rabbits and their blastocysts at gastrulation stage 2. SLC7A5 and SLC7A8 transcript amounts were not statistically significantly different in endometrium of control and diabetic rabbits ( Fig 5). In blastocysts grown in diabetic rabbits the transcript amount of SLC7A5 was unaltered, whereas SLC7A8 transcripts were significantly increased in blastocysts from diabetic rabbits compared to blastocysts of healthy controls ( Fig 5).
Transcript amounts of SLC7A5 and SLC7A8 were measured in endometrium and blastocysts of the gastrulation stage 2 from diabetic and non-diabetic (control) rabbits at day 6 p.c. by real time RT-qPCR. The control group was set 100%. In blastocysts developed under diabetic conditions the SLC7A8 transcript amount was significantly increased but not SLC7A5 and none in endometrium. (N = 3; n≥ 9; ** = p< 0.005).
Blastocysts from diabetic rabbits revealed an approximately 1.5-fold higher phosphorylation of mTOR compared to healthy controls ( Fig 6). The protein amount of mTOR was not influenced by maternal diabetes.
The relative amount of mTOR phosphorylation was quantified by Western blotting in four samples pooled from a total of 30 blastocysts of gastrulation stage 2. (A) shows a representative Western Blot of two pooled samples (n≥ 7 blastocysts per sample) from blastocysts from control (lanes 1,2) and diabetic (lanes 3,4) rabbits. The amount of phosphorylated protein was related to the non-phosphorylated protein and calculated relative to the healthy blastocysts (set 1). The phosphorylation of mTOR was significantly increased in stage 2 blastocysts of diabetic rabbits compared to controls (B). (N = 4; n = 30; ** = p< 0.005).
In diabetic patients with poorly controlled hyperglycaemia the plasma levels of amino acids are altered. The plasma BCAA levels are increased and serine and glycine concentrations are reduced by a diabetic ketoacidosis [ 34 ]. A comparable change in amino acid pattern was also observed in nonobese patients with insulin-dependent diabetes mellitus [ 35 ]. The plasma amino acid concentrations are comparable between humans and rabbits. In human plasma samples the normal concentrations for leucine, isoleucine and valine are 0.14±0.03 mM, 0.07±0.01 mM and 0.25±0.002 mM, respectively [ 22 ]. In diabetic ketosis the concentrations of BCAA are two-fold increased (0.27–0.28 mM leucine, 0.14–0.15 mM isoleucine, 0.40–0.46 mM valine) [ 22 , 34 ]. In current study, rabbits with an induced diabetes mellitus type 1 showed the same pattern of plasma amino acids as diabetic humans ( Table 2 ). The two-fold increase in BCAA in blood as a consequence of diabetes has also been described in two experimental diabetic rat models, the Zucker diabetic fatty rat [ 36 ] and in streptozotocin induced diabetes [ 37 ].
So far, little is known about amino acid metabolism of mammalian embryos during the pre-implantation period. We used rabbit gastrulating blastocysts at stage 1 and 2 for our study.
In blastocysts from healthy donors the amino acid composition was comparable between both developmental stages, indicating the stability of embryonic amino acid metabolism at those stages. Only ornithine was found in a higher concentration in the cavity fluid of stage 2 blastocysts. Ornithine is required for polyamine synthesis, which is reported to be essential for embryonic growth [ 38 ]. In rabbit blastocysts the concentrations of the gluconeogenic amino acids alanine and glycine were six- to eight-fold higher compared with maternal plasma concentrations. Beside asparagine and glutamic acid the concentrations of alanine and glycine were also the highest in bovine blastocoel fluid compared to control synthetic oviductal fluid [ 39 ]. Early embryos are characterised by elevated levels of both amino acids. In hamster embryos it has been hypothesized that glycine and alanine are important for intracellular pH regulation by acting as proton shuttles [ 40 ]. The rabbit blastocyst is one of the biggest mammalian blastocysts with a strong need for alanine and glycine for expansion.
Current study shows for the first time the influence of maternal diabetes on embryonic amino acid metabolism prior to implantation. In contrast to normal development conditions stage 2 blastocysts grown in a diabetic milieu have an altered amino acid pattern with increased concentrations of BCAA, arginine, alanine, lysine, glutamine, glycine and taurine in blastocoel fluid, indicating that the embryonic amino acid composition is closely related to maternal amino acid plasma levels and uterine supply.
Further, diabetic conditions during gastrulation are characterised by increased ornithine, asparagine, serine, histidine, threonine and tyrosine concentrations in rabbit embryos. The reasons remain unclear. Some of these amino acids are involved in cellular stress protection, indicating that diabetic conditions act as a metabolic stress during this ontogenetic stage.
We hypothesise a disturbed BCAA degradation in skeletal muscle and liver cells as potential reason for BCAA accumulation in maternal plasma, which may lead to an increased catabolism in maternal adipocytes. A scheme of BCAA catabolism in diabetic pregnancy is given in Fig 7. Our analysis revealed a reduced transcription level of all investigated BCAA oxidizing enzymes (Bcat2, Bckdha, Dbt and Dld) in liver and skeletal muscle from diabetic rabbits. The reduced degradation of BCAA in skeletal muscle, which accomplishes 60% of the BCAA oxidizing capacity [ 13 ], and in the liver leads to a BCAA accumulation in plasma during diabetes ( Fig 7). Conversely, the transcript and protein amounts of aminotransferase BCAT2, which catalyses the first step of BCAA degradation, were elevated in adipose tissue. The adipose tissue may benefit from high BCAA. The increase in BCAA oxidizing enzymes may enable adipose tissue to produce more lipids [ 41 ].
Maternal diabetes leads to reduced BCAA catabolism in skeletal muscle and liver and to increased BCAA catabolism in adipose tissue. As a result of the reduced catabolism in muscle tissue the maternal blood plasma BCAA levels are enhanced. This might influence the BCAA levels in uterine secretions as BCAA are transferred via SLC7A8 to the uterine lumen and to embryos. BCAA accumulate in the blastocyst cavity fluid (BCF) and can be used as a source for embryonic metabolism and protein synthesis, increasing the embryonic BCAA supply.
In embryos from diabetic rabbits the changes in expression of BCAA oxidizing enzymes were quantified. These embryos showed higher mRNA amounts of Bcat2 like in maternal adipose tissue. Both, transcripts and protein of BCAT2 were increased, indicating a higher embryonic transamination of BCAA to their corresponding keto acid. Also Dbt expression was enhanced in embryos from diabetic rabbits, while the enzymes of the BCKDH complex were transcriptional unaltered. In conclusion, these data demonstrate a higher embryonic amino acid catabolism in a diabetic pregnancy ( Fig 7).
It is known that BCAA are sensitive to changes in insulin [ 41 ]. For example, in human postoperative patients, diabetic or obese, supplementation of insulin returns plasma BCAA to normal levels [ 42 , 43 , 44 ]. The insulin supplementation in our rabbit model, securing survival under diabetic metabolic conditions, is not high enough to reduce BCAA levels to the normal. In obese mice and human co-twins with normal or high insulin levels the BCAT2 expression was decreased underlying that BCAT2 is regulated by insulin [ 33 , 45 ]. In adipose tissue of diabetic rabbits we measured an increased Bcat2 transcription. This increase was closely correlated with increased plasma BCAA levels. In contrast, Bcat2 transcripts were lower in skeletal muscle and liver tissues, suggesting a tissue specific Bcat2 regulation. As shown by in vitro culture experiments insulin availability regulated Bcat2 transcription in preimplantation embryos, whereas glucose did not. Insulin supplementation in vitro kept the embryonic Bcat2 transcription down, while hypoinsulinaemic conditions in vivo increased Bcat2 transcription in blastocysts from diabetic mothers. We suggest that insulin deficiency is a potential and likely reason for higher Bcat2 transcription in embryos from diabetic mothers.
Changes in maternal metabolism may affect the early embryo by various ways, with uterine epithelia playing key role. Analysis of nutrients in the uterine fluid revealed the presents of amino acids and an increase of amino acids in uterine fluid compared to plasma levels in mice [ 46 , 47 ]. Higher BCAA levels were found in females after fertilisation [ 48 ]. In our study the concentrations of BCAA were increased in uterine secretions of diabetic rabbits, which was reflected by higher BCAA levels in their embryos, too. However, we observed no alterations in endometrial BCAA transporters while in blastocysts of diabetic donors, the LAT2 transporter was transcriptional enhanced. This indicates a higher embryonic BCAA transport, which may have contributed to the higher embryonic BCAA levels.
Maternal metabolic conditions are transferred to the developing embryo as early as during the preimplantation period. Altered patterns of BCAA concentrations as a consequence of metabolic disorders have a potential influence on embryonic development programming mechanisms. The accumulation of leucine or its metabolites appears to be the main cause of neurotoxicity like in MSUD and may result in neurological dysfunction in the long term [ 49 , 50 ]. It has been suggested that the viability of mammalian embryos is associated with a metabolism that is quiet rather than active during early development [ 51 ]. In human early embryos it is known that a reduced amino acid turnover is important for the blastocyst formation in vitro [ 52 ]. Diabetic conditions as shown in current study resulted in an increase in amino acid catabolism, disturbing the “quietness” of the embryo and its developmental competence or/and metabolic imprinting as embryos that are metabolically too active may be of poorer quality/viability.
During maternal protein restriction reduced plasma BCAA levels resulted in intrauterine growth restriction (IUGR) and affected the metabolic health of adult offspring [ 53 ]. BCAA supplementation reverses IUGR impact during pregnancy [ 54 , 55 ]. Mice fed with a low protein diet and their blastocysts at day 3.5 have decreased BCAA levels [ 56 ]. BCAA are necessary for various metabolic activities (energy production as pyruvate, protein synthesis and degradation [ 57 , 58 ]. Especially leucine is a potent activator of the mammalian target of rapamycin (mTOR). We evaluated directly the effect of maternal diabetes on embryonic mTORC1 signalling using antibodies to detect relative pools of phosphorylated and total mTOR. Central finding of this study is the increased activation of mTOR in blastocysts developed under diabetic conditions. Potential effects of altered mTOR signalling on protein synthesis and trophoblast outgrowth have been proposed [ 59 , 60 ]. An altered mTOR signalling based on the high BCAA levels in rabbit preimplantation embryos might be an important mechanism with long-lasting programming effects on pre- and postnatal development.
We thank Michaela Kirstein and Sabine Schrötter for excellent technical assistance.


Provides a progn block with lamdba binding.
Returns the last command character struck. If you have a function bound to many keys, the function may use last-key-struck to determine which key was used to invoke it.
See also:
(left-marker marker-expression)
Takes a marker as a parameter and returns a new marker. The new marker will be at the same position as the original but with left-hand affinity. This means that text inserted at the position of the marker will not move the marker's position. Right-hand affinity markers move to the right as text is inserted.
Example: Set a left marker:
(setq left-hand-end (left-marker (dot))See also:
Moves the cursor into the window that is to the left of the current window. (Unlike next-window, which moves the cursor without regard to the physical position of the windows on the screen).
If the repeat-count is given then the command is repeated that number of times.
left-window reports an error if there is not a window to the left of the current window.
Example: Move to the window at the extreme left:
(while 1 (left-window) ) ; whileSee also:
Returns the length of its string parameter.
Example:
The length of "time" is 4:(length "time")
Moves the line in which dot resides to the top of the window associated with the current buffer.
Enables Lisp Mode, a major mode for editing programs written in the Lisp language and also MLisp programs for Emacs.
For more information, see the User Guide
Creates a buffer called Abbreviation table list and inserts a list of the abbreviation tables that have been defined in Emacs.
See also:
Creates a buffer called Auto Execute list and inserts a list of all the auto-execute patterns and their functions.
Creates a buffer called Breakpoint list and inserts a list of the functions that have breakpoints set.
See also:
- breakpoint
- breakpoint-hook variable
Produces a listing of all existing buffers giving their names, the name of the associated file (if there is one), the number of characters in the buffer and an indication of whether or not the buffer has been modified since it was read from or written to the associated file.
Lists all database search lists and the names of the database files contained in them.
Lists the names of all images referenced by the external-function command. The listing shows the image name, the value of the context and the name of the file that holds the image.
See also:
Lists the names of all existing subprocesses. The list includes the state in which each process is running, the time at which each process entered that state, and some information about the names of buffers and procedures associated with the process.
Processes that have died appear once in this list before completely disappearing.
See also:
Lists all the syntax tables that have been defined.
Loads the nominated file as a series of MLisp expressions executing each in turn. (This function is exactly the same as execute-mlisp-file).
See also:
(local-bind-to-key function key-sequence)
Binds the specified function to the given key sequence. Unlike bind-to-key, the binding has effect in only the current buffer. If called interactively, the function prompts for the name of the function to bind and also for the key.
See bind-to-key for details of key names.
Examples:
A function to insert the time, followed by a tab character, bound to the key Numlock-t:
(defun (time-and-tab (insert-string (current-time) "\t") ) ) (local-bind-to-key "time-and-tab" "\[f1]t")A single binding to do the same thing:
(local-bind-to-key "(insert-string (current-time) \"\\t\")" "\[f1]t")See also:
(local-binding-of key-sequence)
Returns the name of the function that the key sequence provided will invoke using the current local keymap.
See also:
(looking-at regular-expression)
Deprecated: Use ere-looking-at for new code.
Returns 1 if the given regular expression search string matches the text immediately following dot. This is for use in packages that want to do limited parsing.
If a negative prefix argument is supplied, characters to the left of dot are checked, rather than those to the right.
For example, if dot is at the beginning of a line then:
(looking-at "[ \t]*else")is true if the line starts with any number of spaces or tabs, followed by "else".
See re-search-forward for more information about regular expression searches.
See also:


This page tracks the new paper links made to my list of EGSR 2011 papers.
Page maintained by Ke-Sen Huang.
If you have additions or changes, send an e-mail.
October 12, 2011
- Direct Ray Tracing of Phong Tessellation
July 5, 2011
- Guided Image Filtering for Interactive High-quality Global Illumination Filtering
July 4, 2011
- Anaglyph Stereo Without Ghosting
July 3, 2011
- Progressive Expectation-Maximization for Hierarchical Volumetric Photon Mapping
June 27, 2011
- Variable Bit Rate GPU Texture Decompression
June 17, 2011
- Stratified Sampling for Stochastic Transparency
June 16, 2011
- Coherent Out-of-Core Point-Based Global Illumination
June 11, 2011
- Efficient Computation of Blue Noise Point Sets through Importance Sampling
June 8, 2011
- Efficient Packing of Arbitrary Shaped Charts for Automatic Texture Atlas Generation
June 7, 2011
- Importance Point Projection for GPU-based Final Gathering
- A Ray Tracing Approach to Diffusion Curves
- Improved Model- and View-Dependent Pruning of Large Botanical Scenes
- Guided Image Filtering for Interactive High-quality Global Illumination Filtering
- Least Squares Vertex Baking
June 4, 2011
- Efficient Packing of Arbitrary Shaped Charts for Automatic Texture Atlas Generation
- Making Imperfect Shadow Maps View-Adaptive: High-Quality Global Illumination in Large Dynamic Scenes
June 3, 2011
- ManyLoDs: Parallel Many-View Level-of-Detail Selection for Real-Time Global Illumination
- Stone Weathering in a Photograph
- Direct ray tracing of Phong Tessellation
June 2, 2011
- Perceptual Global Illumination Cancellation in Complex Projection Environments
- Improved Stochastic Progressive Photon Mapping with Metropolis Sampling
May 31, 2011
- A Volumetric Approach to Predictive Rendering of Fabrics
- Perception of Visual Artifacts in Image-based Rendering of Facades
- Silhouette-aware Warping for Image-based Rendering
- A Physically Plausible Model for Light Emission from Glowing Solid Objects
May 30, 2011
- An Energy-Conserving Hair Reflectance Model
- Optimizing Environment Maps for Material Depiction
- A Physically Plausible Model for Light Emission from Glowing Solid Objects
May 25, 2011
- ManyLoDs: Parallel Many-View Level-of-Detail Selection for Real-Time Global Illumination
- Silhouette-aware Warping for Image-based Rendering
- Perception of Visual Artifacts in Image-based Rendering of Facades
- Importance Point Projection for GPU-based Final Gathering
- A Ray Tracing Approach to Diffusion Curves
May 24, 2011
- A Volumetric Approach to Predictive Rendering of Fabrics
- Page published
kesen.huang@gmail.com


Jan 2020 Presentation
This is the easiest bulletpoint to add to your resume.
(psst... visit the site... https://webpack.js.org/)
MOST PEOPLE:
Get a starter kit and don't ever think of webpack.
SELECT FEW:
Modify options to set things up.
THE ELITE:
Start from scratch or apply webpack to giant applications.
You can use create-react-app, vue-cli, or copy a config from the internet.
npm install webpack webpack-cli --save-dev
Right out of the box, it should work
If you left it to default setup
What it generates
(psst... click the link)
https://webpack.js.org/concepts/loaders/Babel transpiler, ES2015 to JS, etc
(psst... click the link)
https://github.com/webpack/webpack


Dashboard
Cereals
Legumes
Root Crops
Oil Crops
Vegetables
Fiber
Forages
Sugar/Energy
Fruit Crops
Variuos
| # | Experiment | Description | Modified |
|---|
| Experimental Data |
|---|
| Model Output Files |
|---|
| # | Treatment | Experiment |
|---|
| Actions | Model Output Files |
|---|
| # | Experiment | Description | Modified |
|---|
| Experimental Data |
|---|
| Model Output Files |
|---|
| # | Treatment | Experiment |
|---|
| Actions | Model Output Files |
|---|


{% load i18n staticfiles sekizai_tags %}
{% trans 'Please enable JavaScript to view the comments powered by Disqus.' %}


Positive interval length
Positive interval value
Negative interval length
Negative interval value
Waveform length
Noise amplitude
Signal gain
Number of workers
Start
Cancel


This is
Sortable
It works with Bootstrap...
...out of the box.
It has support for touch devices.
Just drag some elements around.


src/sampleComponent/sample.controller.ts
This sample controller uses a route configuration to map routes to services. Sample module is generic here, and has no dependencies on express, isolating buisness logic.
Properties |
constructor(sampleModule: SampleModule)
|
||||||||
|
Defined in src/sampleComponent/sample.controller.ts:22
|
||||||||
|
Creates an instance of SampleController.
Parameters :
|
| Public path |
Type : string
|
|
Defined in src/sampleComponent/sample.controller.ts:16
|
|
The root mount path for all the routes of the module(sub-application) |
| Public router |
Type : Router
|
|
Defined in src/sampleComponent/sample.controller.ts:22
|
|
The router object for holding all the routes to services of the module. |
import { Router, Request, Response } from "express";
import { SampleModule } from "./sample.module";
/**
* This sample controller uses a route configuration to map routes to services.
* Sample module is generic here, and has no dependencies on express, isolating buisness logic.
* @export
* @class SampleController
*/
export class SampleController {
/**
* The root mount path for all the routes of the module(sub-application)
* @type {string}
* @memberof SampleController
*/
public path: string;
/**
* The router object for holding all the routes to services of the module.
* @type {Router}
* @memberof SampleController
*/
public router: Router;
/**
* Creates an instance of SampleController.
* @param {SampleModule} sampleModule Set of services which can be mapped to routes.
* @memberof SampleController
*/
constructor(sampleModule: SampleModule) {
this.path = '/sample';
this.router = Router();
const configs = [
{ method: 'get', route: '/', handler: sampleModule.sayHelloWorld }
];
configs.forEach((config: any) => {
(this.router as any)[config.method](config.route, async (req: Request, res: Response) => {
const requestDetails = parseExpressRequest(req);
const { status, data } = await config.handler(requestDetails);
res.status(status).send(data);
})
})
}
}
/**
* This function converts an express request into a generic object.
* @param {Request} req
* @returns
*/
function parseExpressRequest(req: Request) {
return {
headers: req.headers,
path: req.params,
query: req.query,
body: req.body
};
}