List all Reports for an Institute or Center for a particular year
All Annual Reports for NIMH for reporting year 2011
122 Annual Reports
Investigator-Initiated Project
1.
MH000274 (2011) Methods In Mass Spectrometry
Sanford P. Markey, PhD
Mass spectrometric methods for the analysis of protein structures are being improved, applied and tested in independent and collaborative research projects in proteomics. Projects in separation methods and data processing are in progress. In the past year, progress has been made on implementation of ...
2.
MH000279 (2011) Proteomics in neurotoxicology
Sanford P. Markey, PhD
We are applying proteomic methodology to unresolved problems in neuropathologic diseases. Progress continues in studies on the structure of the postsynaptic density and its remodeling by drugs used in the treatment of mood disorders, on protein complexes implicated by genomic studies of schizophreni ...
3.
MH000332 (2011) Genetic Animal Models for the Study of Serotonin Function and Behavior
Dennis L Murphy, MD
As recently reviewed by us, SERT-deficient +/- and -/- mice have gene-proportionate increases in extracellular fluid serotonin concentrations, i.e., 3- or 6-fold excesses respectively over wildtype +/+ mice. At the same time, SERT -/- mice have a marked deficit of intracellular, releasable serotonin ...
4.
MH000336 (2011) The Genetics Of Obsessive Compulsive Disorder
Dennis L Murphy, MD
OCD is a severe, heritable condition with a lifetime prevalence of about two percent of world populations. The mode of inheritance is incompletely understood but is likely complex, involving multiple genetic loci of small to moderate effect. Our laboratory has played a leading role in studies of OCD ...
5.
MH000478 (2011) Neural Mechanisms Of Stimulus Memory And Habit Formation
Mortimer Mishkin, PhD
The essential circuit for both item and associative stimulus recognition in any given sensory modality consists of the relevant cortical sensory processing stream(s), the medial temporal periallocortex (i.e. parahippocampal, rhinal cortices), the ventromedial prefrontal cortex, and the medial dorsal ...
6.
MH000889 (2011) Studies On Protein Synthesis And Long-Term Adaptive Responses in the CNS
Carolyn E Beebe, PhD
During the 2011 funding period, we addressed the following:
1) We studied the effects of chronic dietary lithium treatment on robust behavioral and morphological phenotypes in Fmr1 KO mice and found that lithium treatment reversed behavioral and mitigated morphological phenotypes (Liu Z-H et al. ...
7.
MH001090 (2011) Studies Of Central Nervous System Functional Anatomy
Miles Herkenham, PhD
Our work currently falls into three major but related areas. The first area is focused on the study in mice of central determinants of psychosocial stress-induced depressive-like behaviors and the amelioration or prevention of these behavioral states by environmental enrichment supplemented with ph ...
8.
MH001101 (2011) Cortical Mechanisms Of Auditory Perception And Memory
Mortimer Mishkin, PhD
Evidence from neuroimaging studies in monkeys from our lab and those of others have raised the possibility that, like occipitotemporal visual areas, superior temporal auditory areas send highly processed stimulus quality information to downstream targets via a multisynaptic corticocortical pathway. ...
9.
MH002032 (2011) Neural Coding Of Visual Stimuli
Barry J Richmond, MD
Two primary processes that are critical for normal higher level visual performance are memories for items we have seen recently, and, second, the ability to distinguish one from another while recognizing that that the items are similar, e.g. distinguishing 2 cats is different than distinguishing cat ...
10.
MH002035 (2011) Functional Anatomy Of Perceptual and Attentional Systems in the Primate Brain
Leslie G Ungerleider, PhD
A typical scene contains many different objects that compete for neural representation due to the limited processing capacity of the visual system. At the neural level, competition among multiple stimuli is evidenced by the mutual suppression of their visually evoked responses and occurs most strong ...
11.
MH002039 (2011) Pharmacology Of Stimulus Memory And Habit Formation
Mortimer Mishkin, PhD
The importance of the cholinergic system in memory function was first recognized because the memory impairment characteristic of Alzheimers disease was associated with the loss of large cholinergic neurons of the basal forebrain and pathophysiology of the entorhinal/perirhinal, or rhinal cortex. We ...
12.
MH002179 (2011) Animal Models Of Neuropsychiatric Disorders
Jacqueline N Crawley, PhD
Autism is a neurodevelopmental disorder that affects approximately 1% of the U.S. population. The causes of autism spectrum disorders are under intense investigation, with strong evidence for genetic substrates. Lifetime costs of caring for autistic individuals are high, both in terms of a) qualit ...
13.
MH002228 (2011) Genetic Neurobiology Of Drosophila
David John Sandstrom, PhD; Howard A. Nash, MD, PhD
To identify dosage-sensitive genes that influence the response to anesthetics, we previously screened for changes in sensitivity to halothane in lines that were missing one copy of a large block of DNA. We found that the anesthetic phenotypes resulting from deleting two regions, ED1 (75 kb) and ED40 ...
14.
MH002240 (2011) Neurobiology Of Disruptive Behavior Disorders
Judith L Rapoport, MD
Over the past year several key findings have emerged.
(1) In a longitudinal analysis, a total of 193 typically developing children with 389 neuroanatomic magnetic resonance images and varying levels of symptoms of hyperactivity and impulsivity were contrasted with 197 children with ADHD with 337 ...
15.
MH002344 (2011) Neuropsychiatric Disorders--protein Structure/activity Studies
Brian M Martin, PhD; Sanford P. Markey, PhD
The unambiguous identification of proteins/peptides is crucial for the definition of the proteome. Using ProteinChip Array technology (SELDI) we have developed experimental protocols and probed test conditions required for protein identification on ProteinChip Arrays. We are able to directly digest ...
16.
MH002386 (2011) Chemical Coding Of Neurotransmission
Lee E Eiden, PhD
The neuropeptide slow transmitter PACAP (pituitary adenylate cyclase activating polypeptide) is released at synapses that transduce stress responses to the brain, and mediate homeostatic adjustments to stress by the organism. Allostatic responses to systemic and psychogenic stressors at multiple poi ...
17.
MH002399 (2011) Postmortem Brain Tissue Examination in Neuropsychiatric Disorders
Joel Kleinman, MD, PhD
It is well known there are difficulties in identifying functional mutations with small effects for complex genetic disorders, so we continue to partner validated genetic associations with biological data of specific genetic variations that affect aspects of brain function and molecular biology. Assu ...
18.
MH002468 (2011) Mechanisms Of Action Of Psychoactive Drugs
De Maw Chuang, PhD
The research in the Section on Molecular Neurobiology focuses on mechanisms of actions of mood stabilizers, notably lithium and valproic acid (VPA). The central hypothesis is that lithium and VPA, by inhibiting glycogen synthase kinase-3 (GSK-3) and histone deacetylases (HDACs), respectively, induce ...
19.
MH002497 (2011) Functional Organization Of The Basal Ganglia
Charles R Gerfen, PhD
Further work on the cellular mechanisms underlying neurologic and pscyhiatric disorders is limited by the fact that neurons throughout the brain utilize common mechanisms for critical functions such as synaptic plasticity, whereas specific neural systems are affected in different disorders. A large ...
20.
MH002498 (2011) Regulation Of Gene Expression In The Brain
Walter Scott Young, MD, PhD
--We have continued this fiscal year to study our gene knockouts (KO) of the mouse oxytocin (Oxt) and vasopressin (Avp) 1a and 1b receptors (Oxtr, Avpr1a and Avpr1b, respectively) to investigate their specific roles in mediating behavior. We are also continuing to analyze whether we were successful ...
21.
MH002537 (2011) Psychobiology And Treatment Of Perimenopausal Mood Disorders
Peter J Schmidt, MD
A role of estradiol withdrawal in the onset of mood disorders in some perimenopausal women has been suggested indirectly by the clustering of depressive episodes during the late menopause transition (the stage of ovarian aging associated with maximal decline of ovarian estradiol secretion) and by es ...
22.
MH002581 (2011) Childhood Onset Schizophrenia
Judith L Rapoport, MD
We continue to refine the differential diagnosis of this rare but devastating condition. The best indicator of true disorder compared to pediatric bipolar and depressive disorder is the extreme severity of psychotic symptoms (Gochman et al 2011). In comparison with adult patients, childhood onset pa ...
23.
MH002585 (2011) Role of Neuroendocrine Stress Response in Inflammatory and Behavioral Illness.
Esther M Sternberg, MD
PROJECT I. Sweat Patch Biomarkers: Clinical Studies. This is currently the main focus of the SNIB. We previously showed that neural and immune biomarkers are detectable in sweat and strongly correlate with plasma levels in a group of women with major depressive disorder (MDD) in clinical remission ( ...
24.
MH002588 (2011) The Neural Foundations for Memory and Social Cognition In The Human Brain
Alex Martin, PhD
This past year we have continued to focus on a major part of long-term memory, termed semantic memory, that is composed of general information, such as facts, ideas, and the meaning of objects and words. We are particularly interested in characterizing the neural substrate mediating object and word ...
25.
MH002592 (2011) Viral And Cellular Factors Governing Efficient Gene Delivery
Maribeth V Eiden, PhD
The Section on Directed Gene Delivery assesses the ability of retroviral vectors to deliver efficiently deliver genes to appropriate target cells with the end goal of transferring therapeutic genes to cells of the central nervous system. Our section has developed vectors based on gibbon ape leukemia ...
26.
MH002619 (2011) Neural Mechanisms Of Motivation And Reward
Barry J Richmond, MD
Efficiently allocating resources to meet many and varied needs is a hallmark of adaptive behavior. To maximize the return on these limited resources, one must estimate the expected value of an outcome before engaging in a particular action. Expected value can be signaled either explicitly through s ...
27.
MH002629 (2011) HIV Nef Function and Early Events in Macrophage and Microglia Infection
Jon W. Marsh, PhD
The objective of this study is to elucidate those early events in HIV infection that may lead to pathogenesis.
Macrophages are infected in the circulatory system as well as in the brain. We have identified the early innate immunological responses following HIV infection of primary human macrop ...
28.
MH002652 (2011) Imaging of Neuropsychiatric Disorders with Developmental and Genetic Mechanisms
Karen F Berman, MD
The Section on Integrative Neuroimaging continues to make advances toward its goals of understanding the nature, molecular underpinnings, underlying neurochemistry, and clinical correlates of neural systems-level dysfunction in schizophrenia. This year, we have made substantial progress in furtheri ...
29.
MH002666 (2011) Evaluation and Treatment of Obsessive Compulsive and Related Disorders
Susan Elizabeth Swedo, MD
Obsessive-compulsive disorder (OCD) affects 1-2% of children and adolescents, causing significant distress and impairments from the unrelenting obsessional thoughts and compulsive behaviors. In some cases, childhood-onset OCD appears to arise as a consequence of common childhood infections, in ...
30.
MH002685 (2011) Peptide Receptor Systems
Theodore B Usdin, MD, PhD
Summary:A current major focus of the laboratory is investigation of the physiological functions of the neuropeptide Tuberoinfundibular Peptide of 39 residues (TIP39) and its receptor, the Parathyroid Hormone 2 (PTH2) receptor. These molecules were discovered in this laboratory several years ago. In ...
31.
MH002711 (2011) Analytic Strategies and Cognitive Task Design to Study Neuropsychiatric Disorder
Daniel R. Weinberger, MD
Longenecker, et al 2010 investigated mechanisms underlying work list recall in patients with schizophrenia and healthy controls. Our group used the California Verbal Learning Test (CVLT), a widely used neuropsychological word list learning task, to examine recall strategies. The CVLT list consist of ...
32.
MH002712 (2011) Characterization Of Neuropsychological Impairment In Schizophrenia
Daniel R. Weinberger, MD
This year our group was the first to examine characteristics, specifically depression history and sex, that may influence cognitive phenotypes seen in unaffected siblings of patients with schizophrenia. Non-psychotic siblings share about half the genes with their affected sister or brother and show ...
33.
MH002716 (2011) MRI Studies of Brain Function and Metabolism
Daniel R. Weinberger, MD
This report briefly describes our findings as mentioned in our objectives. Interesting MRI findings emerged related to the identification of a new intermediate phenotype and cortical circuitry. We tested whether altered dorso-lateral-prefrontal cortex (DLPFC) connectivity is heritable, independent o ...
34.
MH002717 (2011) Neuroimaging of Brain Circuits and Neurogenetic Mechanisms in Normal Cognition
Karen F Berman, MD
Over the past year, in the service of its core scientific agenda, the Section on Integrative Neuroimaging (SoIN) has continued its long-standing commitment to characterizing the neurochemical, neurogenetic, and neuropsychological contributions to neural systems relevant to mental illness. The Secti ...
35.
MH002734 (2011) Genetic Basis Of Cortical Malfunction In Schizophrenia
Daniel R. Weinberger, MD
Potential treatments in neuropsychiatry (cognitive dysfunction) are the targets of psychostimulants. Cognitive dysfunction is a core feature of complex mental disorders like schizophrenia. Modafinil, a psychostimulant, differs from other arousal-enhancing agents in chemical structure, neurochemical ...
36.
MH002736 (2011) Neural Substrates Of Stimulus Recognition And Association Memory
Elisabeth Adams Murray, PhD
The prevailing model of conscious memory holds that a group of loosely related structures, collectively called the medial temporal lobe (MTL), work together as a single functional unit. According to this current orthodoxy, the structures in the MTL are thought to store the memory of specific objects ...
37.
MH002762 (2011) Mechanistic studies on stress, brain inflammation and neuroprotection
Juan M. Saavedra, MD
Our first specific aim is to clarify the mechanisms involved in the beneficial effects of compounds which have not, until very recently, been considered of interest to the therapy of brain disorders. The second specific aim is to further establish the extent of therapeutic benefits of such compounds ...
38.
MH002768 (2011) Subcellular Compartmentilization of Neuronal Gene Expression
Barry Bernard Kaplan, PhD
Axons and nerve terminals are unique subcellular structures of the neuron that play a critical role in the development and maintenance of neural connectivity. One of the central tenets in neuroscience is that the protein constituents of these distal neuronal compartments are synthesized in the nerve ...
39.
MH002778 (2011) The Phenomenology And Neurophysiology Of Juvenile Bipolar Disorder
Ellen Leibenluft, MD
Since the beginning of this project we have screened over 1200 subjects for this study. We have enrolled approximately 150 youth with bipolar disorder (BD), 140 subjects at risk for BD because they have a parent or sibling with the illness, and 100 adults with BD. This year, approximately 20 new sub ...
40.
MH002780 (2011) Fmri Studies Of Emotional Development
Daniel Pine, MD
Work in the current set of projects has major public impact because it shapes understandings of the boundaries of normal development. In the absence of such understanding, it is impossible to precisely demarcate the boundaries of abnormal development.
This set of projects relies on functional ...
41.
MH002781 (2011) fMRI Studies Of Pediatric Mood And Anxiety Disorders
Daniel Pine, MD
Through a series of three protocols, we are using functional magnetic resonance imaging (fMRI) to examine neurocognitive correlates of pediatric anxiety disorders. Through ongoing collaborative studies, we also have increasingly compared findings in these syndromes with findings in adult anxiety di ...
42.
MH002782 (2011) Fmri Studies Of Risk For Mood And Anxiety Disorders In Children
Daniel Pine, MD
In this project, our group is examining biological aspects of risk for mood and anxiety disorders in children. Such work has major public impact. By identifying biological risks in children, information on novel treatments and preventative interventions will emerge. Given the understanding of mos ...
43.
MH002783 (2011) Functional MRI Method Development
Peter A Bandettini, BS, PhD
The Section on Functional Imaging Methods (SFIM) continues to develop cutting edge methods at the interface of functional MRI (fMRI) technology, image processing, interpretation of the signal, and neuroscience applications. The goal of SFIM is to fill the much-needed gap of improving fMRI from b ...
44.
MH002784 (2011) Neurogenesis in the Adult Brain
Heather A Cameron, PhD
We study the regulation and function of adult neurogenesis in rats and mice, which show continued production of new neurons throughout adulthood similar to that in primates, including humans. During the past year, we completed a study examining the function of neurogenesis in adult mice. We made a t ...
45.
MH002786 (2011) The Pathophysiology and Treatment Of Children With Severe Mood Dysregulation
Ellen Leibenluft, MD
As noted above, in response to the concern about the appropriate diagnosis for children with chronic, severe irritability, we defined a group of children whom we described as having severe mood dysregulation (SMD). These children have extremely severe irritability and symptoms of hyperarousal (the ...
46.
MH002793 (2011) PET Radiopharmaceutical Sciences
Victor W Pike, PhD
The Molecular Imaging Branch (MIB) aims to exploit positron emission tomography (PET) as a radiotracer imaging technique for investigating neuropsychiatric disorders, such as depression, addiction, schizophrenia and Alzheimer's disease. Fundamental to the mission of the MIB is the development of nov ...
47.
MH002794 (2011) Pediatric Brain Imaging
Jay Giedd, MD
A unifying theme emerging from our work is that in neuroimaging, as in life, the journey is often as important as the destination. Trajectories of brain morphometry, as opposed to snapshots in time, are more highly correlated with cognitive parameters, are better predictors of clinical outcome, and ...
48.
MH002795 (2011) Preclinical Evaluation Of PET Radiotracers
Robert Innis, MD
Examples of progress made during the prior year are summarized below.
1) We demonstrated that the function of permeability glycoprotein (P-gp) could be selectively measured using a combination of tariquidar (a P-gp inhibitor) and the radiotracer 11CN-desmethyl-loperamide (dLop) (Kannan et al 2011 ...
49.
MH002797 (2011) Neuronal avalanches in the neocortex
Dietmar Plenz, PhD
During the last year, we made several major advances in neuronal avalanche research:
1. We demonstrated for the first time that cortical networks with avalanche dynamics maintain a balance of excitation and inhibition at which information capacity and information processing is optimized (Shew et ...
50.
MH002798 (2011) The Psychophysiology Of Fear And Anxiety
Christian Grillon, PhD
Our objective is to determine the extent to which various aspects of defense mechanisms and conditioned fear are relevant to features of particular forms of normal and abnormal anxiety in humans. Our previous work focused mainly on the mechanisms underlying the expression of fear and anxiety (acquis ...
51.
MH002800 (2011) Identifying Neural Substrates of Behavior in Drosophila Melanogaster
Benjamin H White, PhD
The goal of this research is to define and characterize the neural networks governing two sequentially-linked behavioral programs in the fly. The first is an adaptive, environmentally-sensitive program that mediates the search for safe surroundings, and the second is a hormonally-driven program that ...
52.
MH002803 (2011) Magnetic Resonance Spectroscopy and Imaging Studies of Brain Functions
Jun Shen, PhD
The goals of this research are to develop advanced magnetic resonance spectroscopy (MRS) and imaging techniques and to apply them and other complementary methods to studying brain metabolism, neurotransmission and enzyme activity. MRS allows measurement of neurotransmission of glutamate and GABA in ...
53.
MH002804 (2011) Family Study of Affective and Anxiety Spectrum Disorders
Kathleen R Merikangas, PhD
The major aims of this project have been accomplished through establishment of a large community based family study of adult probands who participate in comprehensive clinical and biologic assessments followed by comparable evaluations of their adult and child relatives. Recruitment of probands and ...
54.
MH002806 (2011) National Comorbidity Survey - Replication (NCS-R)
Kathleen R Merikangas, PhD
During the past year, we have continued to investigate the spectrum of mood disorders and mental-physical comorbidity in this national survey of U.S. adults, and to expand our network of collaborators.
We oversaw a successful completion of a paper on the prevalence and correlates of bipolar spectr ...
55.
MH002807 (2011) Zurich Cohort Study of Young Adults
Kathleen R Merikangas, PhD
During the past year, we have analyzed the data from the latest wave of this prospective cohort study that now covers a total observation period of 30 years for this cohort of young adults who have been followed since the age of 18.
The major topic that we have addressed this year is the prev ...
56.
MH002808 (2011) National Comorbidity Survey - Adolescent (NCS-A)
Kathleen R Merikangas, PhD
During the past year, we have continued to process the diagnostic data, develop codebooks, and create secondary variables for analysis. Several active NCS-A work groups have been formed, including experts in the field from both intramural and extramural collaborators. Working with these expe ...
57.
MH002810 (2011) Mapping genes that contribute to bipolar disorder
Francis Joseph McMahon, MD
In collaboration with 10 academic centers across the United States, we have recruited a large sample of families in which at least 2 siblings suffer from bipolar disorder or related mood disorders. This is the largest sample ever to participate in a genetic study of bipolar disorder. All research pa ...
58.
MH002813 (2011) Cholinergic Modulation of Cognition and Emotion in Mood Disorders
Maura L Furey, PhD; Carlos Alberto Zarate, MD
Multiple neurotransmitter systems are implicated in depressive disorders including the cholinergic systems, which has been found to be hypersensitive in depression whereby depressed patients show exaggerated neuroendocrine and pupillary responses to cholinergic agents, and experience forms of sleep ...
59.
MH002826 (2011) Control of Fear/Defensive Behavior by Brain Derived Neurotrophic Factor
Alexei Y Morozov, PhD
The main goal of this project is to understand how changes in the hippocampus may cause pathological aggression. We have previously found that mice with the conditional knockout (KO) of Brain Derived Neurotrophic Factor (BDNF) restricted to the hippocampal area CA3 are more aggressive than their wil ...
60.
MH002828 (2011) Efficacy of an Antiglutamatergic Agents in Treament-Resistant Deprepression
Carlos Alberto Zarate, MD
The glutamatergic study may be important to the pathophysiology and treatment of mood disorders. Lamotrigine, an inhibitor of glutamate release, is an approved treatment for bipolar disorder. We found in two separate open studies that the glutamate modulating agent riluzole (inhibitor of glutamate r ...
61.
MH002832 (2011) Role of adult neurogenesis in regulation of the HPA axis and stress resiliency
Miles Herkenham, PhD
The hippocampus has been identified as a site of structural and functional pathology in a variety of mental disorders. For example, depression, schizophrenia and post-traumatic stress disorder have been correlated with decreased hippocampal volume, deficits in learning and memory as well as mo ...
62.
MH002835 (2011) Neuronal-Glial Interaction in the Treatment of Bipolar Disorder
Miles Herkenham, PhD
Pro-inflammatory cytokines, such as TNFalpha, IL-1, IL-6, were first discovered in the context of cellular activation and pro-inflammatory responses in the immune system. Early studies on the role of cytokines in the brain suggested that their expression and activity are induced in response to an i ...
63.
MH002838 (2011) Neurophysiology of Visual Perception
David A Leopold, PhD
Our visual perception of the world around us is so immediate and intuitive that it is not obvious that the brain needs to solve any problem at all. However, more than 50% of the cerebral cortex, the prominent outer covering of the brain, is devoted to seeing. Humans and other primates rely more heav ...
64.
MH002843 (2011) Genetic Linkage and Association in Bipolar Disorder
Francis Joseph McMahon, MD
This collaboration has developed a bipolar disorder family resource that has proven to be uniquely valuable in testing clinically-based hypotheses about the genetic heterogeneity of the illness. We have ascertained and assessed about 150 nuclear families with a bipolar I proband and two or more sibl ...
65.
MH002844 (2011) Genetic Determinants of Antidepressant Response in the STAR*D Cohort
Francis Joseph McMahon, MD
Strong evidence from family and twin studies demonstrates that major depressive disorder (MDD) is heritable, yet there has been limited progress in identifying the actual genes involved. A separate, perhaps overlapping set of genes is expected to play a role in individual variation in treatment resp ...
66.
MH002851 (2011) Generalized Anxiety Disorder and Social Anxiety Disorder:
Robert James Richard Blair, PhD
There are three important strands to our work with patients with GSP and GAD. The first of these strands is determining the degree to which the pathology seen in GAD differs from that seen in GSP. In the first study of its kind, we presented patients with GSP, patients with GAD, patients with both G ...
67.
MH002852 (2011) Clinical Evaluation of PET Radiotracers
Robert Innis, MD
Examples of progress made during the prior year are summarized below.
1) We demonstrated that, in human brain, binding of 11C(R)-rolipram to phosphodiesterase 4 (PDE4) could be quantified using kinetic modeling and an arterial input function. Furthermore, image input function from carotid arterie ...
68.
MH002857 (2011) Glutamatergic Modulators for Rapid & Sustained Antidepressant Effect
Carlos Alberto Zarate, MD
Recent preclinical and clinical studies suggest that the glutamatergic system is involved in the mechanism of action of antidepressants. We found that the non-competitive NMDA antagonist (ketamine) was effective in treatment-resistant major depression. Ketamine resulted in rapid, robust and relative ...
69.
MH002860 (2011) Emotional dysfunction and childhood behavioral disturbance
Robert James Richard Blair, PhD
This project has established a series of core neuro-biological findings regarding the basis of Conduct Disorder (CD), particularly CD with Callous-Unemotional traits (reduced guilt and empathy); CD+CU:
(i) CD+CU is associated with impaired processing of the fear of others and this impairment is a ...
70.
MH002862 (2011) The role of serotonin in emotional processing
Robert James Richard Blair, PhD
Our work thus far has investigated the effects of altering serotonergic systems in humans using acute tryptophan depletion on behavioral performance during emotional processing tasks. Moreover, we have begun to determine how acute tryptophan depletions effects on emotional processing vary as a func ...
71.
MH002863 (2011) Multimodal Neuroimaging of Gene-Brain Relationships in Williams Syndrome
Karen F Berman, MD
The Section on Integrative Neuroimaging has made substantial progress toward elucidating specific genetic contributions to brain structure and function through multimodal neuroimaging studies of Williams Syndrome (WS) individuals and carefully matched comparison volunteers. As discussed extensively ...
72.
MH002865 (2011) Reproductive Endocrine Related Mood Disorders-Differential Sensitivity
Peter J Schmidt, MD
In our earlier studies we have developed experimental models for the triggering of symptoms in both premenstrual dysphoric disorder (PMD) and postpartum depression that we continue to employ in our efforts to identify both the underlying biology of these conditions as well as the development of new ...
73.
MH002868 (2011) Clinical and Behavioral Phenotyping of Autism and Related Disorders
Susan Elizabeth Swedo, MD
Autism is currently defined as a single disorder characterized by impairments in communication and social interaction and the presence of restricted interests and repetitive behaviors. However, there is mounting evidence that autism represents a collection of overlapping neurodevelopmental dis ...
74.
MH002869 (2011) Characterization of Dentate Mossy Cell-restricted Genetic Manipulation Mice
Kazutoshi Nakazawa, MD, PhD
Earlier, we generated a conditional transgenic mouse line in which diphtheria toxin receptor was selectively expressed in mossy cells using the Cre/loxP system. Within one week after diphtheria toxin injection, we observed 80% loss of mossy cells throughout the longitudinal axis. We found no obvio ...
75.
MH002870 (2011) National Health And Nutrition Examination Survey (NHANES)
Kathleen R Merikangas, PhD
During the past year we have completed extensive analyses of the data from both the child and adult components of the NHANES surveys. We have examined a U-shaped association between sleep duration and cardiovascular diseases (CVD). We included an adult sample of the 2005 to 2008 NHANES surveys and d ...
76.
MH002874 (2011) The Neuroregulatory Effects of Gonadal Steroids in Humans
Peter J Schmidt, MD
In our earlier studies of regional cerebral blood flow using PET, we reported for the first time in humans that induced hypogonadism was associated with the elimination of the normal pattern of cortical activation in the dorsolateral prefrontal cortex (DLPFC); whereas both estradiol and progesterone ...
77.
MH002881 (2011) Molecular mechanisms of synapse development and plasticity
Zheng Li, PhD
By using gene knockdown and knockout mice, we demonstrated that the BAD-BAX-caspase-3 cascade is to induce NMDA receptor-dependent LTD and AMPA receptor endocytosis, but not for mGluR-LTD or long-term potentiation of synaptic transmission (Li et al., Cell 2010; Jiao et al., Neuron 2011). Unlike in a ...
78.
MH002882 (2011) Characterization of miRNAs on neural development and plasticity
Zheng Li, PhD
miRNAs regulate protein synthesis by suppressing translation or destabilizing mRNAs. Their role in the development and function of the nervous system is not well understood. In this year, we identified several miRNAs that regulates the development and function of synapses in the hippocampus. We foun ...
79.
MH002886 (2011) Neural mechanisms of reward processing and emotion
Elisabeth Adams Murray, PhD
Damage within the OFC, MFC or amygdala leads to altered emotion and social behavior as well as disrupted autonomic responses to highly valued foods. The amygdala, the OFC and the MFC are key sites for processing reward information and for generating autonomic responses. All three areas are reciproca ...
80.
MH002887 (2011) Neural substrates of reward processing and emotion
Elisabeth Adams Murray, PhD
Previous work on this project has demonstrated that reward-based decision making requires the OFC to be intact. The OFC is comprised of several anatomically distinct areas, however, and these areas have been grouped into two major networks based on their patterns of connectivity: a sensory network a ...
81.
MH002890 (2011) Integrating EEG/MEG and fMRI: 99-M-0172
Richard Coppola, SB, DSc
Development of MEG data recording and signal processing methods has been very successful. Studies of working memory tasks and auditory processing tasks have shown the ability to localize brain activation and to address issues of phasic versus tonic activity. We are investigating phenotype measures t ...
82.
MH002892 (2011) Synaptic mechanisms of amygdala-dependent behaviors
Alexei Y Morozov, PhD
Amygdala operates by analyzing incoming information and triggering defensive responses. The first question of our investigation is how amygdala distinguishes, at the synaptic level, between signals which arrive from different areas of the brain, those which process sensory information, and those whi ...
83.
MH002893 (2011) Learning and plasticity in the human brain
Christopher Ian Baker, PhD
The primary goals of this research are i) to establish the changes in brain processing arising from nervous system damage or dysfunction, ii) to understand how brain plasticity contributes to these changes, and iii) to determine how learning may ameliorate the negative consequences of such changes. ...
84.
MH002895 (2011) Forebrain GABAergic cell-selective genetic manipulation in mice
Kazutoshi Nakazawa, MD, PhD
Building upon our previous work this year we have focused on the following four research questions.
(1) Are there any other phenotypes which are reminiscent of schizophrenia in Ppp1r2-Cre/NR1 mutants? In human schizophrenia, impaired gamma oscillations are consistently reported and are thought to ...
85.
MH002896 (2011) The Neural Basis of Functional MRI Responses
David A Leopold, PhD
To study the link between fMRI and electrophysiology, one must be able to conduct both invasive recordings and fMRI scanning on the same animal subjects. The Intramural Research Program at the National Institute of Mental Health is one of the only sites in the world at which such measurements can b ...
86.
MH002897 (2011) Molecular and Cellular Mechanisms of Experience-Dependent Cortical Processing
Kuan Hong Wang, PhD
Our lab produced Activity-Regulated Cytoskeleton-Associated (ARC) knockout mice to be used in a collaborative project studying how the loss of the ARC protein may alter the effects of sensory experience or deprivation in the visual cortex (V1), McCurry et al (Nature Neuroscience 2010). The data indi ...
87.
MH002898 (2011) Visual Adaptation and Neuronal Selectivity
David A Leopold, PhD
Flexible visual recognition, such as that required for social perception, is a notoriously difficult problem for the brain to solve. Ultimately, visual recognition is based on the decoding of the retinal imaging. However, the retinal image cast by a given person's face is never the same twice, and ...
88.
MH002904 (2011) Biological Characterization of Genetic Mechanisms in Neuropsychiatric Disorders
Daniel R. Weinberger, MD
Our group explored neurobiological mechanisms related to risk genes for SZ in Bigos, Arch Gen Psych 2010 and Kao, PNAS 2010. We studied the association of CACNA1C gene, voltage-gated calcium channel, and the clinical implication of potential brain-related phenotypes. A genetic variant of CACNA1C inc ...
89.
MH002907 (2011) Blood Genomics and Cell Model Approaches for Neuropsychiatric Disorders
Daniel R. Weinberger, MD
This year, our group collaborated with the GCAP transgenic lab to study the distribution and orientation of catechol-O-methyltransferase (COMT). COMT is a schizophrenia risk gene and its enzyme product is critical for the inactivation and metabolism of dopamine and other catechol compounds. COMT pro ...
90.
MH002909 (2011) Object, face and body representations in the human brain
Christopher Ian Baker, PhD
The goal of this research is to understand how we see what we see: how does the brain analyze the light falling on the retina of the eye to encode a world full of objects, people and things?
During the past year we have completed two projects investigating i) visual mental imagery, and ii) scene ...
91.
MH002910 (2011) Role of the p75NTR, LTD and the cholinergic system in mediating coping mechanism
Miles Herkenham, PhD
The cellular and molecular mechanisms underlying development of stress-related anxiety disorders remain largely unknown. It is clear that exposure to stress contributes to the development of anxiety disorders, including post-traumatic stress disorder (PTSD). One approach to studying the pathogenes ...
92.
MH002913 (2011) Trial of a Glutamate Antagonist in the Treatment of OCD and Autistic Disorders
Susan Elizabeth Swedo, MD
The serotonin reuptake blocking medications (SSRIs, such as fluoxetine, fluvoxamine and sertraline) have been demonstrated to be efficacious in the treatment of obsessive-compulsive disorder (OCD), but many patients fail to respond to therapy. Treatment-refractory cases are particularly common amon ...
93.
MH002914 (2011) Treatment of Medical Conditions among Individuals with Autism Spectrum Disorders
Susan Elizabeth Swedo, MD
Autism spectrum disorders are defined by deficits of communication and socialization and the presence of restrictive and/or repetitive behaviors. Recent epidemiologic studies have documented an increase in the number of children identified with autism spectrum disorder (ASD) over the past decade and ...
94.
MH002915 (2011) Neuroimmunologic Investigations of Autism Spectrum Disorders (ASD)
Susan Elizabeth Swedo, MD
Autism is defined by its behavioral manifestations: social deficits, impairments in communication and the presence of restricted or repetitive behaviors. The cause of these abnormalities is unknown, but it is strongly suspected that autism spectrum disorders (ASD) result from a combination of genet ...
95.
MH002917 (2011) Office of the Scientific Director
Richard Nakamura
The NIMH Division of Intramural Research (DIR) scientists conduct research ranging from studies into the mechanisms of normal brain function, conducted at the behavioral, systems, cellular, and molecular levels, to clinical investigations into the diagnosis, treatment and prevention of mental illnes ...
96.
MH002918 (2011) Functional Anatomy of Face Processing in the Primate Brain
Leslie G Ungerleider, PhD
Lesions of the inferior temporal (IT) cortex in humans can result in the clinical syndrome termed prosopagnosia, an inability to recognize familiar faces. Single-cell recordings from the IT cortex of monkeys have revealed the existence of neurons that are selectively activated by visual images of fa ...
97.
MH002919 (2011) Subcellular Microdissection for the Identification of Organelle Proteins
Sanford P. Markey, PhD
Microscopic pathology defines many human diseases, but the chemical composition of most histologically observed subcellular structures remains largely uncharacterized. Currently, there is no method for isolating subcellular areas of interest without disrupting the cells and thus distorting naturally ...
98.
MH002920 (2011) The Cognitive Neuroscience of Autism Spectrum Disorders
Alex Martin, PhD
This past year we have completed several behavioral and brain imaging studies of social perception and social communication in adolescents with Autism Spectrum Disorders (ASD). Our behavioral studies have confirmed that adolescents with ASD have difficulty perceiving specific emotional states from f ...
99.
MH002921 (2011) Molecular regulators of mood and mood disorders
Miles Herkenham, PhD
Bipolar disorder is a devastating illness that is marked by recurrent episodes of mania and depression. There is growing evidence that the disease is correlated with disruptions in synaptic plasticity cascades involved in cognition and mood regulation. Alleviating the symptoms of bipolar disorder in ...
100.
MH002922 (2011) Psychiatry Consultation Liaison Service Research
Maryland Pao, MD
The NIMH Psychiatric Consultation Liaison Service (PCLS) provides important psychiatric services to the many constituencies of the NIH. While providing such services to the NIH Community, PCLS clinicians conduct research and collaborate with NIH investigators by providing expertise in the areas of p ...
101.
MH002927 (2011) Target validation of novel therapeutic agents in mood disorders
Carlos Alberto Zarate, MD
Project 1: Enkephalinergic compounds for major depression: There is increasing evidence that patients with anxious major depressive disorder (AMDD) have a greater depressive severity, functional impairment, increased risk of suicidality, worse social distress, higher incidence of alcohol and drug ab ...
102.
MH002928 (2011) Frontal striatal systems and dopamine in normal and pathological behavior
Bruno B Averbeck
Our lab is engaged in collaborations with clinical groups to examine behavior in patients with schizophrenia and Parkinsons disease, using tasks which engage frontal-striatal systems to see if patients show deficits in these tasks. Our strategy is to identify behavioural deficits in patient groups, ...
103.
MH002929 (2011) Developing new methods to discover pathways involved in complex diseases
Yin Yao Shugart, PhD
Nasopharyngeal carcinoma (NPC) has a unique global distribution pattern -- Southeast Asia and some other localized regions of the eastern hemisphere that suggests the disease risk is driven by a combination of environmental exposures and specific genetic factors. Earlier studies have implicated man ...
104.
MH002930 (2011) Developing Stats Methods to Detect Rare Genetics Variants in Human Pedigrees
Yin Yao Shugart, PhD
Next-generation sequencing technologies coupled with the efficient DNA capture methods provide exome sequencing approach to investigate the genetic basis of complex phenotypes. Unlike whole genome association studies (GWAS) which can only discover variation in DNA that is frequent in the population ...
105.
MH002931 (2011) Neurodevelopmental Genomics
Kathleen R Merikangas, PhD
During the past year, 7,500 youth have been enrolled in the study and undergone the clinical and medical interviews, and cognitive testing, and 750 have completed the neuroimaging component of the project. The NIMH and U Penn teams have worked closely in the development of the diagnostic measu ...
106.
MH002932 (2011) Cohort study of Lausanne (COLAUS) on cardiovascular diseases and depression
Kathleen R Merikangas, PhD
The collection of data from this cohort has now been completed and analyses of the data are now underway. The National Institute of Mental Health (NIMH) family study of affective spectrum disorder has included numerous comparable measures of psychiatric and cardiovascular phenotypes that can be anal ...
Scientific Core
1.
MH002884 (2011) Functional MRI Core Facility
Peter A Bandettini, BS, PhD
Space Utilization:
The Functional MRI Facility (FMRIF) currently occupies approximately 4800 sq. ft of space, divided between the scanner bays, control rooms and electronics/machine rooms for 3TA, 3TB, 3TC, and 1.5T MRI scanners located within the NMR center and office space on the second floor a ...
2.
MH002888 (2011) Scientific and Statistical Computing Core
Robert Cox, PhD
The main mission of the Core is to help NIH researchers with analyses of their functional MRI (brain activation mapping) data. Along the way, we also help non-NIH investigators. Several levels of help are provided, from short-term immediate aid to long-term development and planning.
Consultation ...
3.
MH002889 (2011) NIMH MEG Core Facility
Richard Coppola, SB, DSc
We have over 50 user accounts representing numerous NIMH, NINDS and NIDCD protocols. There is continual interest from additional groups that are working on protocols and planning studies.
The MEG Core staff has been working interactively with these users in terms of study design, task pr ...
4.
MH002894 (2011) Magnetic Resonance Spectroscopy Core Facility
Jun Shen, PhD
As a noninvasive method for measuring concentration and distribution of chemicals in the living brain MRS is an important tool for studying brain function and disorders. However, robust measurement of MRS signals requires highly sophisticated design, implementation and maintenance of various MRS tec ...
5.
MH002899 (2011) Neurophysiology Imaging Facility Core: Functional and Structural MRI
David A Leopold, PhD
Magnetic resonance imaging, or MRI, is based on the nuclear spin properties of protons comprising different brain tissues. Through a remarkable set of engineering achievements, MRI is now routinely used to visualize the internal structure of the entire body, including the brain, in three dimensions. ...
6.
MH002901 (2011) Transgenic resources for neuroscience research
James M Pickel, AB, PhD
SUMMARY
The NIMH transgenic core facility has several major functions: 1) to produce transgenics for neuroscience research at NIH 2) develop new transgenic techniques and model systems 3) support research with associated techniques in genetic research in neuroscience and 4) engage in collaborative ...
7.
MH002902 (2011) NIMH Non-Human Primate Research Core
Pamela Noble
-Assessment of neural and behavioral alterations associated with chronic fluoxetine administration in adolescence.
Summary: A primate differential rearing model is used to assess the effects of chronic fluoxetine treatment of juvenile monkeys. Treatment and rearing history are hypothesized to i ...
8.
MH002903 (2011) Procurement and Characterization of Postmortem Brain Tissue
Joel Kleinman, MD, PhD
Since September, 2010 we have collected 95 brains.
To date, our collection consists of 1,160 brains.
Diagnosis: Schizophrenia 170; Bipolar 75; Major Depressive Disorder 151; Other Mood Disorder 33; Alzheimer 58; Adult Control 250;Substance Abuse 57; Neonate to Teen 82; Fetal Brain 66; Others 5 ...
9.
MH002905 (2011) Neuroimaging Core Facility
Venkata S. Mattay, MD; Daniel R. Weinberger, MD
The GCAP Neuroimaging Core implements quality control procedures, optimizes and updates imaging protocols, and collects all clinical imaging data from the CBDB sibling and inpatient studies, and maintains and analyzes all structural, spectroscopy, DTI, and large scale archival fMRI data used in thes ...
10.
MH002906 (2011) Transgenic Mouse and Cellular Models to Characterize Mental Disorders
Jingshan Chen; Daniel R. Weinberger, MD
Dysbindin-1 is encoded by the dystrobrevin-binding protein-1 gene and is located in pre- and postsynaptic sites throughout human and mouse brain. Genetic variations in DTNBP1 affect human cognition and have been associated with risk for schizophrenia. Reduced dysbindin gene and protein expression ha ...
11.
MH002908 (2011) Genetics and Bioinformatics Core Laboratory
Richard Straub, PhD; Daniel R. Weinberger, MD
Our group aims to use evidence of genetic association with measures of brain development and function as a basis for further characterization of molecular pathways. One study which demonstrates this is looking at the genetic protection in healthy siblings of subjects with schizophrenia. Through the ...
12.
MH002911 (2011) NIMH Instrumentation Core Facility
George Raphael Dold, MME, BSEE
This past year, our Section had the unique opportunity to support the research from more than 60 different Labs & Sections within NIMH, NINDS and NICHD. During the past twelve months, investigators from these labs and branches requested 462 formal projects from our staff. Each of these requests was ...
Clinical Support Services
1.
MH002912 (2011) Office of the Clinical Director
Maryland Pao, MD
The NIMH OCD coordinates a wide range of essential clinical, administrative, and research-related support services including: 1)administrative oversight of NIMH inpatient units and outpatient clinics through audits of FDA regulated studies, monitoring of high risk protocols, chart auditing, monthly ...
Animal Research Infrastructure
1.
MH002924 (2011) Veterinary Medicine Research Branch
James Raber, DVM, PhD
The NIMH Veterinary Medicine Research Branch (VMRB) has successfully provided support to veterinary medical, husbandry and research support to over thirty-three (33) principal investigators in the NIMH IRP with over eighty-two (82) active animal study protocols. In addition, the Branch has provided ...
Education and Outreach
1.
MH002916 (2011) Office Of Fellowship Training
Barry Bernard Kaplan, PhD
An Executive Summary of the full length Annual Report is provided below
The Office of Fellowship Training (OFT) organized and managed several educational events and programs for the DIRP and the extramural research communities. These events, geared to service the needs of a multidisciplinary b ...
Technology Transfer
1.
MH002925 (2011) Office of Technology Transfer
Suzanne L Winfield, PhD
The Office of Technology Transfer (OTT) negotiates Material Transfer Agreements, Cooperative Research Development Agreements, Confidential Agreements, Clinical Trial Agreements, etc. We also provide guidance and assistance to NIMH researchers, evaluate employee inventions for their patentability and ...


Planned |
In Progress |
Options...


class: center, middle, inverse, title-slide # Maching Learning in R with mlr3 ## with mlr3 ### Matt Dube ### 2019/09/26 (updated: 2019-10-01) --- # Intro and a few notes Topic Overview - what we won't be covering - this is not a machine learning how-to - we won't be going in-depth on feature engineering, resampling, model selection, etc. - what we will be covering - overview of mlr3 and the mlr3 family of packages - several small demos, and - a bigger demo that puts it all together - the dataset we'll be using for the demos is the attrition dataset from the rsample package. - I've set aside 15% of the dataset to be used as "new data" Keep in mind: - mlr3 (and extension packages) are under active development - examples today may not work next week - if something breaks, the [documention](https://mlr3.mlr-org.com/index.html) is very good, and updated often - this is a BIG topic, we won't cover it all - read the docs, and check the references at the end of this deck - there is some different terminology and syntax - don't get hung up on the differences and quirks - some of this may offend your normal R sensibilities --- # Machine Learning in R: Current State .pull-left[ .large[Individual Packages - C5.0 - earth - glm - glmnet - keras - randomForest - ranger - rpart - xgboost - many others!] ] .pull-right[ .large[Meta Packages Current Generation - Caret - mlr Next Generation - tidymodels - mlr3] ] R does not define a standardized interface for its machine-learning algorithms. Therefore, for any non-trivial experiments, you need to write lengthy, tedious and error-prone wrappers to call the different algorithms and unify their respective output. Additionally you need to implement infrastructure to: - resample your models - optimize hyperparameters - select features - cope with pre- and post-processing of data and compare models in a statistically meaningful way. --- # Why mlr3? mlr - mlr was first released to CRAN in 2013 - now has over 30,000 lines of code - over 120 direct dependencies and over 1400 indirect dependencies - dependency API changes break mlr - unit testing takes a long time, and most tests are disabled to comply with CRAN policies - S3 object oriented (OO) toolkit has limitations in large projects - NAMESPACE has > 1200 lines, > 440 export functions and objects. - only works on in-memory data - no nested parallelization - too difficult to extend, maintain, and add new features - complex code base makes it difficult for new contributors --- # mlr3 architectural changes mlr3 - utilizes R6 OO toolkit - truly object-oriented: data and methods together - inheritance - reference semantics - embrace data.table, both for arguments and internal data structures - light on dependencies - ~ 10 packages – 4 of which are developed by mlr team - R6, data.table, Metrics, lgr, digest, uuid, mlbench - utilizes future and future.apply for parallelization - only basic building blocks are in the core mlr3 package - extra packages contain additional features and capabilities --- # mlr3 workflow .pull-left[ The mlr3 package provides R6 classes for the essential building blocks of the machine learning workflow: - A task encapsulates the data along with additional information, such as what the prediction target is. - A learner encapsulates one of R’s many machine learning algorithms and allows to train models and make predictions. Most learners have hyperparameters that affect their operation. - A measure computes a numeric score based on predicted and ground-truth values and their difference. - A resampling strategy specifies a series of train and test sets and is used to assess the performance of an algorithm. ] .pull-right[ ![mlr3 workflow.](media/workflow.png) ] --- # mlr3 and its extension packages | Package | Functionality | | :- | :------------ | | `mlr3` | Framework for machine learning: `Task`, `Learner`, `resample()` and `benchmark()` | | `mlr3learners` | Concrete `Learner`s for many popular machine learning implementations | | `mlr3pipelines` | Dataflow programming of machine learning workflows. | | `mlr3tuning` | Hyperparameter tuning for machine learning algorithms. | | `mlr3filter` | Feature filtering | | `mlr3viz` | Visualisations and plots | | `paradox` | Auxiliary package providing (hyper)parameter handling | | `mlr3misc` | Auxiliary functions | | `mlr3fswrap` | Variable selection wrappers | | `mlr3survival` | Extensions for survival analysis | | `mlr3ordinal` | Extensions for ordinal regression | | `mlr3spatiotemporal` | Extensions for spatiotemporal resampling methods | | `mlr3hyperband` | Implements the "hyperband" approach for hyperparameter tuning | ??? mlr3fswrap Variable selection wrappers like sequential forward/backward search, exhaustive search, or genetic algorithms. --- # mlr3 extension packages planned | Package | Functionality | | :- | :------------ | | `mlr3cluster` | Extensions for cluster analysis | | `mlr3fda` | Extensions for functional data analysis | | `mlr3forecasting` | Extensions for forecasting | | `mlr3keras` | Extnensions for deep learning via keras | | `mlr3extralearners` | Extension to source additional learners from remote sources | --- # mlr3 overview pre-defined tasks, learners, resamplings, and measures are stored in the following R6 dictionaries: - mlr_tasks - mlr_learners - mlr_resamplings - mlr_measures mlr_tasks: built-in data sets ```r as.data.table(mlr_tasks)[,.(key, task_type)] ``` ``` ## key task_type ## 1: boston_housing regr ## 2: german_credit classif ## 3: iris classif ## 4: mtcars regr ## 5: pima classif ## 6: sonar classif ## 7: spam classif ## 8: wine classif ## 9: zoo classif ``` --- # mlr3 learners: base package ```r as.data.table(mlr_learners)[,list(key,packages, predict_types)] ``` ``` ## key packages predict_types ## 1: classif.debug response,prob ## 2: classif.featureless response,prob ## 3: classif.rpart rpart response,prob ## 4: regr.featureless stats response,se ## 5: regr.rpart rpart response ``` --- # mlr3 learners: extension package loaded ```r library(mlr3learners) as.data.table(mlr_learners)[,list(key,packages, predict_types)] ``` ``` ## key packages predict_types ## 1: classif.debug response,prob ## 2: classif.featureless response,prob ## 3: classif.glmnet glmnet response,prob ## 4: classif.kknn withr,kknn response,prob ## 5: classif.lda MASS response,prob ## 6: classif.log_reg stats response,prob ## 7: classif.naive_bayes e1071 response,prob ## 8: classif.qda MASS response,prob ## 9: classif.ranger ranger response,prob ## 10: classif.rpart rpart response,prob ## 11: classif.svm e1071 response,prob ## 12: classif.xgboost xgboost response,prob ## 13: regr.featureless stats response,se ## 14: regr.glmnet glmnet response ## 15: regr.kknn withr,kknn response ## 16: regr.km DiceKriging response,se ## 17: regr.lm stats response,se ## 18: regr.ranger ranger response,se ## 19: regr.rpart rpart response ## 20: regr.svm e1071 response ## 21: regr.xgboost xgboost response ## key packages predict_types ``` --- # mlr3 resamplings ```r as.data.table(mlr_resamplings) ``` ``` ## key params iters ## 1: bootstrap stratify,repeats,ratio 30 ## 2: custom 0 ## 3: cv stratify,folds 10 ## 4: holdout stratify,ratio 1 ## 5: repeated_cv stratify,repeats,folds 100 ## 6: subsampling stratify,repeats,ratio 30 ``` --- # mlr3 measures .pull-left[ ```r as.data.table(mlr_measures)[task_type == "classif"][,.(key)] ``` ``` ## key ## 1: classif.acc ## 2: classif.auc ## 3: classif.ce ## 4: classif.costs ## 5: classif.dor ## 6: classif.f_score ## 7: classif.fdr ## 8: classif.fn ## 9: classif.fnr ## 10: classif.for ## 11: classif.fp ## 12: classif.fpr ## 13: classif.npv ## 14: classif.ppv ## 15: classif.precision ## 16: classif.recall ## 17: classif.sensitivity ## 18: classif.specificity ## 19: classif.tn ## 20: classif.tnr ## 21: classif.tp ## 22: classif.tpr ## key ``` ] .pull-right[ ```r as.data.table(mlr_measures)[task_type != "classif", .(key)] ``` ``` ## key ## 1: regr.mae ## 2: regr.mse ## 3: regr.rmse ``` ] --- # mlr3 filters |Name | Task Type | Feature Types | Package | | :- | :---------| :-------------| :-------| | `anova` | Classif | Integer, Numeric | stats | | `auc` | Classif | Integer, Numeric | Metrics| | `carscore` | Regr | Numeric | care | `cmim` | Classif & Regr | Integer, Numeric, Factor, Ordered | praznik | | `correlation` | Regr | Integer, Numeric | stats | | `disr` | Classif | Integer, Numeric, Factor, Ordered | praznik | | `importance` | Universal | Logical, Integer, Numeric, Character, Factor, Ordered | rpart| | `information_gain` | Classif & Regr | Integer, Numeric, Factor, Ordered | FSelectorRcpp| | `jmi` | Classif | Integer, Numeric, Factor, Ordered | praznik | | `jmim` | Classif | Integer, Numeric, Factor, Ordered | praznik | | `kruskal_test` | Classif | Integer, Numeric | stats | | `mim` | Classif | Integer, Numeric, Factor, Ordered | praznik | | `mrmr` | Classif & Regr | Numeric, Factor, Integer, Character, Logical | praznik | | `njmim` | Classif Integer, Numeric, Factor, Ordered | praznik | | `performance` | Universal | Logical, Integer, Numeric, Character, Factor, Ordered | rpart | | `variance` | Classif & Regr | Integer, Numeric | stats | --- # installation Install the mlr3 packages from [Github](https://github.com/mlr-org): ```r remotes::install_github("mlr-org/mlr3") remotes::install_github("mlr-org/mlr3db") remotes::install_github("mlr-org/mlr3viz") remotes::install_github("mlr-org/mlr3learners") remotes::install_github("mlr-org/mlr3tuning") remotes::install_github("mlr-org/mlr3filters") remotes::install_github("mlr-org/mlr3pipelines") ``` .footnote[ [1] Check [mlr3 github page](https://github.com/mlr-org/mlr3) for current installation instructions [2] See current list of [mlr3 extension packages](https://github.com/mlr-org/mlr3/wiki/Extension-Packages) on github ] --- # modeling Considering how we are going to tackle the problem relates closely to what `mlr3` entities we will use. - What is the problem we are trying to solve? - i.e. what **Task** do we use? - Binary classification. - `\(\Rightarrow\)` We use `TaskClassif`. - What are appropriate learning algorithms? - i.e. what **Learner** do we use? - Logistic regression, CART, Random Forest - `\(\Rightarrow\)` `lrn("classif.log_reg")`, `lrn("classif.rpart")`, `lrn("classif.ranger")` - How do we evaluate "good" performance? `\(\Rightarrow\)` Depends on many things! Cost of false positive vs. false negative, legal requirements, ... - i.e. what **Measure** do we use? - We start with misclassification error and will also consider AUC. - `\(\Rightarrow\)` `msr("classif.ce")`, `msr("classif.auc")` --- # create task a new classification task is created with: `task = TaskClassif$new(id = "GermanCredit", backend = credit, target = "class")` - id = task identifier, optional - backend = backend sets the dataset for the task. - target = target variable in the backend dataset. - positive = optional - which factor of the target variable is the positive class. The created task is an R6 object. There are several methods that can be used to review the task details. | method/field | outputs | | :- | :------------ | | `task` | review task properties | | `task$ncol` | number of columns in task (dataset)| | `task$nrow` | number of rows in task (dataset) | | `task$formula()` | default modeling formula | | `task$feature_names` | list of feature names | | `task$feature_types` | feature data types | | `task$class_names` | target variable classes | | `task$col_roles` | role of each column (typically features and target) | | `task$data()` | dataset defined in task | --- # create learners `lrn("classif.ranger")` `lrn("classif.xgboost")` You can query a list of learners with `as.data.table(mlr_learners)` Review learner: ```r lrn("classif.xgboost") ``` ``` ## <LearnerClassifXgboost:classif.xgboost> ## * Model: - ## * Parameters: nrounds=1, verbose=0 ## * Packages: xgboost ## * Predict Type: response ## * Feature types: integer, numeric ## * Properties: importance, missings, multiclass, twoclass, weights ``` --- # split data In mlr3, we do not create train and test data sets, but instead keep only a vector of train and test indices. `set.seed(4411)` `train.idx <- sample(seq_len(task$nrow), 0.7 * task$nrow)` `test.idx <- setdiff(seq_len(task$nrow), train.idx)` --- class: inverse, middle, center # Deck not Complete Need links to: - demo markdown html files - additional online resources ---


While we are on the subject of other worlds (or at least other places), it is worth remembering that Dobson once wrote a pamphlet entitled Netherlands, Holland, Dutch—What's That About? The opening lines provide a summary of its subject matter:
We call China China and its people Chinese. We call Finland Finland and its people Finns. We call Germany Germany and its people Germans. I could go on, but I won't. What I want to know is, why do we have two interchangeable names—the Netherlands and Holland—for the country whose inhabitants we call Dutch? Why don't we say Netherlanders or Hollanders? What's all that about?
It's a remarkable pamphlet, chiefly because Dobson, having posed an interesting linguistic question, blathers on for over forty pages trying desperately to conceal the fact that he has done no research whatsoever. He simply makes things up and veers off at tangents. One such tangent is Dobson's brief look at what other nationalities call themselves. For example, the Chinese call China Zhongguo, the Finns call Finland Suomi, and, most enticingly, Shqiperi is where Albanians live and breathe and have their being.
 Perhaps a kind reader can enlighten me.


Dog Based SVG MarketPlace
Vauge Brown
Italian Greyhound
Pug
Chihuahua?
Vauge Brown 2 Electric Boogaloo
Husky
Boston Terrier
BullDog
BloodHound
Doberman?
Vauge Brown
Italian Greyhound
Pug
Chihuahua?
Vauge Brown 2 Electric Boogaloo
Husky
Boston Terrier
BullDog
BloodHound
Doberman?


This example uses a generic sortable that produces drop events that include the originating and destination list ids. There are two kinds of sortable in play here:
- One horizontal one, whose 'cards' are the vertical lists. Try grabbing a whole list by its header, and reordering.
- Many vertical ones, which contain the kanban cards. Try moving the cards between lists.


Version 2 (under construction)
This is a MATLAB software package for the denoising of 1D signals using the SASS approach. In the SASS approach, the signal of interest x(t) is modeled as the sum of a low-pass component f(t) and a sparse order-K derivative component g(t) [x(t) = f(t) + g(t)]. It is assumed that the observed data is corrupted by additive white Gaussian noise (AWGN) w(t) [y(t) = x(t) + w(t)].
Sparsity-Assisted Signal Smoothing Ivan W. Selesnick Web: http://eeweb.poly.edu/iselesni/sass
Ivan Selesnick Email<EMAIL_ADDRESS>Electrical and Computer Engineering Dept. NYU Polytechnic School of Engineering Brooklyn, New York, USA
This research was support by the NSF under Grant No. CCF-1018020.


This Borough map shows the 9 explanatory variables that are found significant in correlation to the target variable: Percentage of child overweight. The variables are listed in descending order of their absolute values of Pearson correlation coefficient.
They are variables found to have positive values of coefficients, in descending order. Labels with a (%) indicate that their values are a percentage of the total purchase in the year 2015, while 'avg. Weight' indicates the actual average grams purchased.
They are variables found to have negative values of coefficients, in descending order. Labels with a (%) indicate that their values are a percentage of the total purchase in the year 2015, while 'avg. Fibre' indicates the actual average grams purchased.
X


MIRROR Spaces Service - CHANGELOG
0.6.2-SNAPSHOT
- [FIX] Fixed NPE caused when node is created dunring health check.
- [FIX] Nodes with long names no longer break pubsub node creation
0.6.1 -- January 9, 2014
0.6 -- October 2, 2013
- [NEW] Runs with Openfire 3.8.2. This version is NOT compatible with previous versions of Openfire.
- [NEW] Added server configuration check to administration console.
- [NEW] Repairs broken pubsub subscriptions.
- [UPDATE] Changed plugin identifier.
0.5 -- April 15, 2013
- [FIX] Pubsub node subscriptions are now validated an repaired when the service is initialized.
- [UPDATE] Changed name displayed in administration console and service discovery.
- [UPDATE] Changed description displayed in administration console.
- [NEW] Added support for MIRROR Persistence Service.
- [NEW] Data objects with more than 64k characters are now rejected.
- [NEW] Added support for Interop Data Models.
- [NEW] Added interface to request version information.
0.4.3 -- October 10, 2012
- Expected schema location will now also be to data object published on private/team spaces, too.
- Fixed bug breaking CDM attribute update on private spaces.
0.4.2 -- October 10, 2012
- Fixed bug breaking the model validation.
0.4.1 -- September 4, 2012
- Fixed bug preventing data objects to be published on orga spaces.
0.4.0 -- Milestone 5 -- August 24, 2012
- Tagged milestone release.
0.4.0 RC2 -- August 17, 2012
- Added support for organizational spaces.
- Release candidate.
0.3.0 -- July 16, 2012
- Added support for CDM version 1.0.
- Base implementation for packet filtering added.
0.2.2 -- July 12, 2012
- Fix: Set pubsub#max_items=0 when space is configured to be non-persistent.
- Improved space consistency validation.
0.2.1 -- April 26, 2012
- Fix: Set pubsub#max_items=MAX_INT when a space is reconfigured to be persistent.
0.2.0 -- Milestone 2 -- March 16, 2012
- Fix: Nickname handling in MUC rooms.
- Minor updates.
0.1.5 -- March 11, 2012
- Added integrity check for spaces. The check is performed during startup.
<IP_ADDRESS> -- March 5, 2012
- Fix: PubSub nodes will now be available after server restart.
- Fix: MUC rooms will now be available after server restart.
- Fix: MUC rooms persistence settings corrected.
0.1.3 -- February 29, 2012
- Added support for the configuration of team spaces.
0.1.2 -- February 27, 2012
- Added support for the creation of team spaces.
- Added support for the discovery of team spaces.
<IP_ADDRESS> -- February 17, 2012
0.1.0 -- Milestone 1 -- February 17, 2012
- First milestone release.
- Fixed configuration field mapping.
- Fixed persistence handling.
- Fixed authorization issues with node discovery.
- Several bug fixes.
0.0.4 -- February 13, 2012
- Added configuration validation.
- Changed membership from user node-id to bare JID.
- Several bug fixes.
0.0.3 -- February 6, 2012
- Added name configuration of private spaces.
- Added deletion of spaces.
0.0.2 -- February 2, 2012
- Add creation of private spaces.
- Added space discovery as specified in XEP-0030.
0.0.1 -- January 31, 2012
- Requires Openfire 3.7.0.
- Initial release.


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KICKING AND SCREAMING A film review by Larry McGillicuddy Copyright 1996 Larry McGillicuddy
**** Dir.-Noah Baumbach Cast- Josh Hamilton, Olivia D' Abo, Chris Eigeman, Carlos Jacott, Eric Stoltz, Jason Wiles, Parker Posey, Elliott Gould, Cara Buono, Jessica Hecht
Review- This wonderful surprise was hands down the funniest movie of 1995. This film tells the stry of four friends who just graduated from college but are uncertain what to do with their lives. The plot may sound similar andf this story has been botched many times before, but this time it is perfect. I loved every minute of this film.
Josh Hamilton stars as Grover, who on graduation night learns that his girlfriend, Jane, is moving to Prague. Grover asks "So how will that work if you're living with me in Brooklyn?" Jane responds, "It'll be the same, except I'll be in Prague." Jane leaves for Prague, and in a futile attempt to get over her, he sleeps with a different freshman each night it seems. Jane continues to leave messages on the answering machine, and Grover tries not to listen, but he does. The film shows the beginnings of their relationship in flashbacks, after we have already seen them breakup. This is an intelligent device, and makes the flashbacks all the more poignant.
Chris Eigeman plays Max, the cynical wisecracking Matthew Perry-ish best friend of Grover. Max graduates and realizes he has to start all over again. "8 hours ago I was Max Beaumont, English major, college senior. Now I'm Max Beaumont who does nothing." Max always seems to have a self deprecating manner, and apparently is never happy with himself. Enter into his life a 16 year old high school student (Buono). They make an odd couple, but thats probably what Max likes about her. He couldn't stand being with someone like him, so he has to be with someone different.
Carlos Jacott plays Otis, the dopey one. He is supposed to go to graduate school, but doesn't have enough confidence and decides to take a year off. He is constantly doing strange things such as wearing his pajamas during the day, coming out of the bathroom unbuckled, and putting mascara on. He takes a job at a huge Blockbuster style video store that has numerous confusing movie categories such as Dog - Buddy pictures and Interesting Failures. This is an obvious attempt at spoofing Blockbuster and it is very funny, but seems out of place in this film which otherwise mines its humor from real life situations. This is a very minor nitpick in an otherwise perfect film.
Jason Wiles plays Skippy, the naive and carefree one who re-enrolls in school after graduating so he has an excuse to stay in town with his undergraduate girlfriend, Miami (Posey). This is a very entertainig relationship between the two that suffers a crisis, and at the end we understand why he has put up with her, and why she has put up with him. The last scene between the two is wonderful. We realize their annoyances, but we understand their significant charms.
In the middle of all this is the bartender Chet, played by Eric Stoltz. He has been going to college for 10 years. "I did skip a semester my sophomore year," he helpfully informs us. Chet is comfortable with what he does in life, and isn't looking for a career.
"Kicking and Screaming" was written and directed by Noah Baumbach in a stunning debut. The depth he puts into each and every character is astonishing. Notice for example the scene in the Creative Writing class where some characters that only have one or two lines have fully developed personalities, especially the teacher, who says only one word. The dialogue is highly entertaining and realistic.  The acting is terrific. There isn't one imperfect performance in the bunch, and Jacott's uproarious deadpan portrayal of Otis deserved the Oscar for best supporting actor. Elliot Gould has a very effective small role as Grover's dad. This little independent feature didn't even make 1 million in its theatrical release, so I beg you to rent this so we will get to see more from Noah Baumbach in the future. This is one of the funniest movies of the decade.
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Deep Vein Thrombosis and Pulmonary Embolism
Executive summary
Introduction
Deep venous thrombosis (DVT) and pulmonary embolism (PE) are both manifestations of venous thromboembolism. DVT can be defined as the formation of a blood clot (thrombus) within a deep vein, with the most common site of affectation being the lower limbs. PE, on the other hand, is a potentially life-threatening complication of DVT in which the thrombus formed becomes dislodged and migrates to occlude an artery within the lung.
Target users
- Nurses
- Doctors
Target area of use
- Gate Clinic
- Outpatient Department
- Ward
Key areas of focus / New additions / Changes
This guideline provides information on the diagnosis and treatment of deep vein thrombosis and pulmonary embolism. A large proportion of patients with pulmonary embolism are asymptomatic. History and examination should seek for risk factures and clinical features of these conditions. The Wells scoring systems should be used to assess clinical probability of DVT and PE respectively. Patients should be initially managed on the ward with heparin, warfarin (non-pregnant patients only) and supportive care. Anticoagulation status should be reviewed using coagulation studies. Warfarin if used should be given for at least 3 months.
Limitations
Facilities for monitoring and treating venous thromboembolism are not available at Keneba and Basse. Patients presenting there with these conditions should be stabilized and referred.
Presenting symptoms and signs
Risk factors for venous thromboembolism should be ruled out.
· Malignancy
· Prolonged bed rest
· Smoking
· Stroke
· Obesity
· Pregnancy
· Recent long-distance travel
Symptoms and signs of DVT usually occur distal to the site of venous occlusion and include:
· Pain in affected limb: occurs in about 50% of cases
· Limb swelling: most specific symptom. DVT should be ruled out in all patients presenting with unilateral pedal swelling
In as many as 40% of patients, PE is silent without obvious symptoms. Those who are symptomatic may present with sudden onset of:
· Shortness of breath
· Chest pain worse on inspiration
· Haemoptysis
· Cough
· Syncope
· Death
Examination findings
In suspected DVT, a general examination should be carried out, followed by examination of the affected limb. Presence of any of the following should raise suspicion of the presence of a DVT.
· Unilateral pitting oedema
· Homans sign: calf pain on foot dorsiflexion with the knee extended
· Pratt sign: Tenderness over calf muscle on palpation
PE may present with:
· Deranged vitals:
· Low saturation of oxygen
· Tachypnea
· Tachycardia
· Hypotension
Chest examination
· Maybe normal in the majority of patients.
· Occasionally, a pleural friction rub may be heard over the affected area
Cardiovascular examination (may be normal apart from tachycardia):
· Parasternal heave
· Loud pulmonary component of the second heart sound
· Raised jugular venous pressure
Wells scores
If the diagnosis of DVT is suspected following history and physical examination, the two-level DVT Wells score should be used to estimate the clinical probability of DVT.
Two-Level DVT Wells Score
|
Clinical Feature |
Points |
|
Active cancer (treatment ongoing, within 6 months or palliative) |
1 |
|
Paralysis, paresis or recent plaster immobilization of the lower extremities |
1 |
|
Recently bedridden for 3 days or more or major surgery within 12 weeks requiring general or regional anaesthesia |
1 |
|
Localized tenderness along the distribution of the deep venous system |
1 |
|
Entire leg swollen |
1 |
|
Calf swelling at least 3cm larger than asymptomatic side |
1 |
|
Pitting oedema confined to the asymptomatic leg |
1 |
|
Collateral superficial veins (non-varicose) |
1 |
|
Previously documented DVT |
1 |
|
Alternative diagnosis at least as likely as a DVT |
-2 |
Interpretation:
|
DVT Likely |
2 Points Or More |
|
DVT Unlikely |
1 Point Or Less |
If the diagnosis of PE is suspected following history and physical examination, the two-level PE Wells score should be used to estimate the clinical probability of PE.
Two-Level PE Well’s Score
|
Clinical Feature |
Points |
|
Clinical signs and symptoms of DVT (minimum of leg swelling and pain with palpation of the deep veins) |
3 |
|
An alternative diagnosis is less likely than PE |
3 |
|
Heart rate >100 beats per minute |
1.5 |
|
Immobilisation for more than 3 days or surgery in the previous 4 weeks |
1.5 |
|
Previous DVT/PE |
1.5 |
|
Hemoptysis |
1 |
|
Malignancy (on treatment, treated in the last 6 months, or palliative) |
1 |
Interpretation:
|
PE Likely |
More Than 4 Points |
|
PE Unlikely |
4 Points Or Less |
Differential diagnoses
· Cellulitis
· Lymphoedema
· Soft tissue injury
· Dependent oedema
· Congestive cardiac failure
· Renal failure
· Nephritic syndrome
· Swelling in a paralysed limb
Investigations
All patients with suspected DVT should be offered:
· Doppler ultrasonography: to confirm the presence of a clot
· Coagulation studies: INR, PT, PTTK to investigate for hypercoagulability if indicated.
In suspected PE, the following should be done:
· CXR: findings might include: Enlarged pulmonary artery(Fleischner sign), peripheral wedge of airspace opacity which implies lung infarction(Hampton’s Hump), regional oligaemia (Westermark sign) or pleural effusion
· ECG: May show sinus tachycardia (most common), right heart strain pattern: seen as a right bundle branch block pattern or right axis deviation or SIQIIITIII pattern: this refers to a deep S wave in lead I, Q wave and T wave inversion in lead III
· Echocardiography: Right ventricular wall hypokinesis, right ventricular dilatation, and pulmonary artery hypertension may be seen
· INR: Done to get baseline value before the commencement of warfarin therapy
Management
Management in Gate Clinic
All patients with features of a DVT or PE should be referred immediately to the ward for urgent review by a doctor.
Management on the Ward
In suspected acute PE, commence intravenous fluid and oxygen (if oxygen saturation <88%).
Heparin and warfarin should be started as soon as possible for prophylaxis in high-risk patients or treatment after confirmed DVT or PE. Heparin should be continued for at least 5 days or until 2 consecutive target INR results are obtained. In pregnancy, only heparin is used
Unfractionated heparin can be given subCutaneously as 250 units/kg stat then every 12 hours. It is the preferred option in patients with kidney disease. Enoxaparin can be given subCutaneously as 1.5mg/kg/ dose OD.
Monitor APTT(ideally, every 6 hours)and adjust unfractionated heparin dose accordingly.
Warfarin can be initiated with a once-daily dose between 2mg and 5mg. The maintenance dose of warfarin is usually between 2mg and 10mg once daily.
Daily INR monitoring should start from day 3 of initiation of therapy until INR is at target for more than 2 consecutive readings.
|
Condition |
Target INR |
|
DVT prophylaxis |
2 – 2.5 |
|
DVT or PE treatment |
2 – 3 |
Thereafter, the frequency of INR monitoring is twice weekly but can be reduced gradually to once-weekly, once every 2 weeks, and then once monthly as long as the patient’s INR remains within the therapeutic range. Warfarin doses should be adjusted according to the INR results. More frequent monitoring is needed after any dose adjustment until stable readings are obtained.
Warfarin should be continued for at least 3 months. Warfarin therapy should be extended beyond 3 months for patients with unprovoked proximal DVT or PE if their risk of recurrence is high and there is no additional risk of major bleeding.
Paracetamol can be prescribed for pain in DVT
Key Issues for Nursing care
· Monitor vital signs every hour initially in acute PE. This frequency may be reduced to every 4 hours as patient stabilizes.
· Monitor vital signs once every shift in DVT.
· Nurse with affected leg elevated
· Avoid IM injections on the affected limb
· Strict fluid charts
· Ensure enoxaparin is given at the same time every day.
· Be wary of heparin concentrations when calculating doses
· Call the doctor if:
· Temperature > 38.5ºC
· Pulse < 50 or > 120 bpm
· Systolic blood pressure < 90 or >160 mmHg
· Diastolic blood pressure< 60 or >90 mmHg
· Oxygen saturation < 90%
References
NICE Guidance for Venous Thromboembolic Diseases https://www.nice.org.uk/guidance/cg144/chapter/recommendations#diagnosis-2
Aggarwal V, Nicolais CD, Lee A; Bashir R. et al. Acute management of pulmonary embolism. https://www.acc.org/latest-in-cardiology/articles/2017/10/23/12/12/acute-management-of-pulmonary-embolism
Medscape. Pulmonary Embolism https://emedicine.medscape.com/article/300901-overview
Diagnosis and Management of Acute Deep Vein Thrombosis: A Joint Consensus Document From the European Society of Cardiology Working Groups of Aorta and Peripheral Circulation and Pulmonary Circulation and Right Ventricular Function. Eur Heart J 2017; Feb 17:[Epub ahead of print].
Antithrombotic therapy and prevention of thrombosis, 9th ed: American College of Chest Physicians evidence-based clinical practice guidelines. Chest. 2012;141(suppl 2).
|
Written by: |
Name: Azeezat Sallahdeen |
Date: 24 November 2018 |
|
Reviewed by: |
Name: Fatai Akemokwe |
Date: 30 January 2019 |
|
Version: |
Change history: |
Review due date: |
|
1.0 |
New document |
31 January 2021 |
|
1.1 |
Executive summary added |
31 January 2021 |
|
Review Comments (if applicable) |
|
|


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3 February 2012 - In December 2011, the Ministry of Health of Cameroon notified WHO of a yellow fever outbreak in the North Region of the country.
A total of 23 cases, including 7 deaths, have been reported to have occurred since October 2011 in Guider, Bibemi, Gaschiga, Lagdo, Mayo Oulo and Golombe districts. These cases were identified as part of the surveillance system, with fever and jaundice within the 14 days of onset.
At least 13 cases from six health districts were laboratory confirmed at the Institute Pasteur of Cameroon by IgM ELISA test, which was followed by the seroneutralizing test (PRNT), the most specific test for yellow fever, and by differential diagnostic for dengue and West Nile Virus conducted in the WHO regional reference laboratory for yellow fever, the Institute Pasteur of Dakar, Senegal.
WHO country office has been working with the government/health authorities in the outbreak field investigation to confirm the cases and assess the extent of the outbreak.
GAVI Alliance, UN Central Emergency Response Fund (CERF) and the International Coordinating Group on Yellow Fever Vaccine Provision (YF-ICG) are supporting a reactive mass vaccination campaign which aims to cover over 1.2 million people in 8 health districts considered at high risk, namely Guider, Bibemi, Gaschiga, Lagdo, Mayo Oulo, Garoua I Garoua II, and Golombe.
The vaccination campaign began on 23 January 2012, covering these 8 health districts which were not covered in the 2009 preventive mass vaccination campaign because they have no history of yellow fever outbreak or yellow fever virus circulation.


What does the following code print?
a = 1
b = 2
c = a + b
b = 4
a = b
c = a
print c
1. Create a plot showing the standard deviation of the inflammation data for each day across all patients.
2. Modify plot.py to display the three plots on top of one another instead of side by side.
What does the following piece of code display when run - and why?
f = 0
k = 0
def f2k(f):
  k = ((f-32)*(5.0/9.0)) + 273.15
  return k
f2k(8)
f2k(41)
f2k(32)
print k
273.15
270.15
278.15
273.15
0
270.15
278.15
273.15
0
1. "Adding" two strings produces their concatention: 'a' + 'b' is 'ab'. Write a function called fence that takes two parameters called original and wrapper and returns a new string that has the wrapper character at the beginning and end of the original; so print fence('ATATA', 'G') would print GATATAG.
2. If the variable s refers to a string, then s[0] is the string's first character and s[-1] is its last. Write a function called outer that returns a string made up of just the first and last characters of its input, so that print outer('GATATAG') would print GG.
Write a function called rev that takes a string as input, and produces a new string with the characters in reverse order. So, print rev('Newton') would print out notweN. As always, be sure to include a docstring.
Hint: the function len(string) returns the length of the string argument; so, len('UBC') returns 3. Alternatively, you can count backwards from the end of a string using negative indices; for example, print 'UBC'[-1] prints 'C'.
Python has a built-in function called range that creates a list of numbers: range(3) produces [0, 1, 2], range(2, 5) produces [2, 3, 4]. Using range, write a function that prints the natural numbers from 1 to N.
Write a function called analyze_all that takes a filename pattern as its sole argument and runs analyze for each file whose name matches the pattern.
Write a function called near that returns True if its first parameter is within 10% of its second and False otherwise. Compare your implementation with your partner's; do you return the same answer for all possible pairs of numbers?
True and False aren't the only values in Python that are true and false. In fact, any value can be used in an if or elif. After reading and running the code below, explain what the rule is for which values are considered true and which are considered false. (Note that if the body of a conditional is a single statement, we can write it on the same line as the if.)
if '': print 'empty string is true'
if 'word': print 'word is true'
if []: print 'empty list is true'
if [1, 2, 3]: print 'non-empty list is true'
if 0: print 'zero is true'
if 1: print 'one is true'
Suppose you are writing a function called average that calculates the average of the numbers in a list. What assertions would you write for it? Compare your answer to your neighbour's: can you think of a function that will past your tests but not hers or vice versa?
Fix range_overlap. Re-run test_range_overlap after each change you make.


hospital beds
Ambulance
Teleconsultation
Testing
Covid care at home
Food/Med Delivery
Oxygen
Medicines


gwt-diagrams demoProject homepage: http://code.google.com/p/gwt-diagrams/. Demo source code download. Demo utilizes gwt-dnd library, so as to add drag and drop functionality. But it is not necessary to use it, and gwt-diagrams do not depends on gwt-dnd. |


Isar735.github.io
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The pinyin vowel a has a rather uniform pronunciation in Chinese, very similar to the "a" sound in the English "father". (The two exceptions to this pronunciation rule are ian and üan, both covered in later sections.)
The most basic syllable involving the pinyin vowel a is the sound alone, pronounced as "ah", as in the sound you make for the doctor when he examines your tonsils.
The vowel a can also combine with other vowels in a single syllable. Basic examples of this include ai and ao. Pinyin ai sounds very much like the name of the English letter "I", although if you draw out the English letter "I" you will notice an "ee" sound at the end. This sound is cut off a bit sooner in Mandarin ai.Pinyin ao sounds like the vowel sound in the English "now." Just make sure not to drag out the "oo" sound at the end. This way the a sound is more dominant than the o sound and more closely resembles Mandarin speakers’ pronunciation.
Mandarin Chinese does not have many syllable-final sounds, but pinyin vowel a can take them all, giving us an and ang.The syllable ang sounds very much like the second half of the English word "song." The an syllable sounds like the second half of the man's name "Don," but not like the woman's name "Dawn." Avoid putting an "aw" sound into the syllable, keeping to a pure "ah" sound.
Linguist's Note:
The following are the IPA symbols for this section's pinyin vowel sounds:
| a | [ɑ] | |
| ai | [ai] | |
| ao | [ɑu] | |
| an | [ɑn] | |
| ang | [ɑŋ] |
The following pinyin consonants are very similar (if not identical) to their English equivalents and should not give you much trouble: b, p, m, f, d, t, n, l.
The two notable exceptions to this rule are b and d. You may find it difficult at first to distinguish between Mandarin's b and p sounds as well as its d and t sounds. This is because in English "b" and "d" sounds are voiced,meaning that the vocal chords are used when producing the sound. This creates a somewhat more forceful consonant sound. In Mandarin Chinese, the only difference between the b sound and the p sound is that the p sound is aspirated, meaning that a puff of air comes from the mouth when pronouncing the p sound. (In English, the "p" sound is also aspirated.) This makes the difference between Mandarin b and p seem subtler, since aspiration and non-aspiration is the only difference, as opposed to aspiration and voicing, as in English.
Just like b and p, the only difference between Mandarin's d and t sounds is that the d sound is not aspirated while the t sound is. Neither consonant sound is voiced in Mandarin, while the "d" sound is voiced in English.
While difficult to distinguish at first, this subtle difference will become more and more apparent with prolonged exposure.
Linguist’s Note:
The following are the IPA symbols for this section’s pinyin consonant sounds:
| b | [p] | |
| p | [ph] | |
| m | [ɑu] | |
| d | [t] | |
| t | [th] | |
| n | [n] | |
| l | [l] |
Listen to the sounds of this section and try repeating them by clicking on the syllables below:
| a | ai | ao | an | ang | |
| a |
ai |
ao |
an |
ang |
|
| b | ba |
bai |
bao |
ban |
bang |
| p | pa |
pai |
pao |
pan |
pang |
| m | ma |
mai |
mao |
man |
mang |
| f | fa |
fan |
fang |
||
| d | da |
dai |
dao |
dan |
dang |
| t | ta |
tai |
tao |
tan |
tang |
| n | na |
nai |
nao |
nan |
nang |
| l | la |
lai |
lao |
lan |
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