AndreaBozzo/ceres-open-data-index huggingface dataset:
Genetic polymorphisms in lung disease: bandwagon or breakthrough?

The study of genetic polymorphisms has touched every aspect of pulmonary and critical care medicine. We review recent progress made using genetic polymorphisms to define pathophysiology, to identify persons at risk for pulmonary disease and to predict treatment response. Several pitfalls are commonly encountered in studying genetic polymorphisms, and this article points out criteria that should be applied to design high-quality genetic polymorphism studies.

Tags: disease-susceptibility, genetic-polymorphism, lung-disease, nih, treatment-response
Organization: U.S. Department of Health & Human Services
Can Australian general practitioners effectively screen for diabetic retinopathy? A pilot study

Background
          Diabetes has been identified as one of the national health priority areas in Australia. After 20 years of diabetes most patients can be expected to develop diabetic retinopathy which, if undetected, is likely to cause significant visual loss or blindness. This paper reports on a pilot study aimed to test the ability of Australian GPs to clinically recognise diabetic retinopathy following a brief training intervention.
        
        
          Method
          17 GPs from a Brisbane Division of General Practice were recruited to participate in a clinical upskilling intervention pilot. Participant scores on clinical assessments were used to analyse GP sensitivity and specificity in screening for diabetic retinopathy. Results were compared with the NHMRC guidelines for acceptable screening accuracy.
        
        
          Results
          Ten of the 17 GPs (59%) achieved a screening sensitivity of 25% or less in the pre test, three (18%) a sensitivity of 50%, and four (23%) achieved a sensitivity of ≥ 75%. In the post-test, all seventeen GPs achieved between 50 and 100% sensitivity. In the pre-test, thirteen (76%) GPs achieved a screening specificity of less than or equal to 50%, and four (23%) a specificity of 75 %. In the post test, four GPs (23%) rated a screening specificity of less than 50%, six (35%) achieved a specificity of 66%, and seven (41%) 100% specificity.
        
        
          Conclusion
          24% of GPs met the NHMRC diabetic retinopathy screening criterion prior to the workshop, and 94% following this brief training intervention. Australian GPs are capable of a much more significant role in community screening for diabetic retinopathy.

Tags: clinical-assessment, diabetic-retinopathy, general-practitioners, nih, screening-accuracy
Organization: U.S. Department of Health & Human Services
2015 CMHS Uniform Reporting System (URS) Table for Arkansas

2015 Center for Mental Health Services (CMHS) Uniform Reporting System (URS) Output Tables for Arkansas. The URS state reporting system is collected annually to support the Community Mental Health Services Block Grant program. State Mental Health Authorities report on National Outcome Measures (NOMS), evidence based practices, and utilization measures providing an overview of state mental health delivery systems.

Tags: arkansas, mental-health-services, national-outcome-measures, samhsa, substance-abuse-treatment
Organization: U.S. Department of Health & Human Services
A C-terminal hydrophobic region is required for homo-oligomerization of the hepatitis E virus capsid (ORF2) protein

Hepatitis E virus (HEV) is the causative agent of hepatitis E, an
acute form of viral hepatitis. The open reading frame 2 (ORF2) of HEV encodes the viral capsid protein, which can self-oligomerize into virus-like particles. To understand the domains within this protein important for capsid biogenesis, we have carried out in vitro analyses of association and folding patterns of wild type and mutant ORF2 proteins. When expressed in vitro or in transfected cells, the ORF2
protein assembled as dimers, trimers and higher order forms. While
N-terminal deletions up to 111 amino acids had no effect, the deletion of amino acids 585–610 led to reduced homo-oligomerization. This deletion also resulted in aberrant folding of the protein, as determined by its sensitivity to trypsin. This study suggests that a C-terminal hydrophobic region encompassing amino acids 585–610 of the ORF2 protein might be critical for capsid biogenesis.

Tags: hepatitis-e-virus, homo-oligomerization, nih, orf2-protein, viral-capsid-protein
Organization: U.S. Department of Health & Human Services
Minnesota (MN)

This report presents Minnesota\'s estimates for 25 measures of substance use and mental health based on the combined 2009 and 2010 National Surveys on Drug Use and Health (NSDUHs). Topics covered include past month substance use (e.g., illicit drugs, marijuana, cocaine, pain relievers, alcohol, tobacco), substance dependence, abuse, and treatment need, past year serious mental illness (SMI), any mental illness (AMI), suicidal thoughts, and major depressive episode (MDE). Resuts are provided for Minnesota for five age groups: 12 to 17, 18 to 25, 26 or older, 18 or older and all persons 12 or older.

Tags: mental-health, nsduh-data, samhsa, serious-mental-illness, substance-use
Organization: U.S. Department of Health & Human Services
The identity and distribution of neural cells expressing the mesodermal determinant

Background
          The spadetail (spt) gene of zebrafish is expressed in presomitic mesoderm and in neural cells previously suggested to be Rohon-Beard neurons. The mechanism(s) generating the apparently irregular rostrocaudal distribution of spt-expressing cells in the developing CNS is unknown.
        
        
          Results
          spt-expressing neural cells co-express huC, a marker of neurons. These cells also co-express the genes islet-1, -2 and -3 but not valentino. The islet-1 gene expression, irregular distribution and dorsolateral position of spt-expressing cells in the developing CNS are characteristic of dorsal longitudinal ascending (DoLA) interneurons. Shortly after their birth, these neurons extend processes rostrally into which spt mRNA is transported. At 24 hours post fertilisation(hpf), spt-expressing neurons occur most frequently at rostral levels caudal of the 5th-formed somite pair. There is no apparent bias in the number of spt-expressing cells on the left or right sides of embryos. Extended staining for spt-transcription reveals expression in the dorsocaudal cells of somites at the same dorsoventral level as the spt-expressing neurons. There is frequent juxtaposition of spt-expression in newly formed somites and in neurons. This suggests that both types of spt-expressing cell respond to a common positional cue or that neurons expressing spt are patterned irregularly by flanking somitic mesoderm.
        
        
          Conclusions
          spt-expressing cells in the developing CNS appear to be DoLA interneurons. The irregular distribution of these cells along the rostrocaudal axis of the spinal cord may be due to "inefficient" patterning of neural spt expression by a signal(s) from flanking, regularly distributed somites also expressing spt.

Tags: developmental-neurobiology, dola-interneurons, nih, spadetail-gene, zebrafish-neural-cells
Organization: U.S. Department of Health & Human Services
Behavioral Health Barometer: United States, 2014

This is a behavioral health report for the United States. The report utilizes data from the National Survey on Drug Use and Health (NSDUH), the Youth Risk Behavior Survey (YRBS), the Monitoring of the Future Survey (MtF) sponsored by the National Institute on Drug Abuse. The topics addressed in the report include youth substance use, youth mental health and treatment, adult mental health and treatment, substance use and substance use treatment.

Tags: behavioral-health, mental-health, samhsa, substance-use, youth-risk-behavior
Organization: U.S. Department of Health & Human Services
2020 Uniform Reporting System (URS) Table For Utah

This is the 2020 Uniform Reporting System (URS) Output Tables for Utah. The URS state reporting system is collected annually to support the Community Mental Health Services Block Grant program. State Mental Health Authorities report on National Outcome Measures (NOMS), evidence based practices, and utilization measures providing an overview of state mental health delivery systems.

Tags: mental-health-services, national-outcome-measures, samhsa, substance-abuse-treatment, utah-health-data
Organization: U.S. Department of Health & Human Services
Relatedness of baculovirus and

Background
          Current evidence suggests that lepidopteran baculoviruses may be divided into two phylogenetic groups based on their envelope fusion proteins. One group utilizes gp64, a low pH-dependent envelope fusion protein, whereas the other employs a protein family (e.g. LD130 in the Lymantria dispar nucleopolyhedrovirus) unrelated to gp64, but that is also low pH-dependent. Database searches with members of the LD130 protein family often record significant levels of homology to envelope proteins from a number of insect retrovirus-like transposable elements of the gypsy class. In this report, the significance of the homology between these two types of envelope proteins is analyzed.
        
        
          Results
          The significance of the alignment scores was evaluated using Z-scores that were calculated by comparing the observed alignment score to the distribution of scores obtained for alignments after one of the sequences was subjected to 100 random shuffles of its sequence. These analyses resulted in Z-scores of >9 for members of the LD130 family when compared to most gypsy envelope proteins. Furthermore, in addition to significant levels of sequence homology and the presence of predicted signal sequences and transmembrane domains, members of this family contain a possible a furin cleavage motif, a conserved motif downstream of this site, predicted coiled-coil domains, and a pattern of conserved cysteine residues.
        
        
          Conclusions
          These analyses provide a link between envelope proteins from a group of insect retrovirus-like elements and a baculovirus protein family that includes low-pH-dependent envelope fusion proteins. The ability of gypsy retroelements to transpose from insect into baculovirus genomes suggests a pathway for the exchange of this protein between these viral families.

Tags: baculovirus-gp64, envelope-fusion-proteins, insect-retrovirus, nih, phylogenetic-analysis
Organization: U.S. Department of Health & Human Services
Genetic snapshots of the

Background:
          In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing.
        
        
          Results:
          Homology searches of public databases with 2,275 random sequences of strain ANU265 resulted in the identification of 1,130 putative protein-coding sequences, of which 922 (41%) could be classified into functional groups. In contrast to the 18% of insertion-like sequences (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun sequences represent known ISs, suggesting that pNGR234a is enriched in such elements. Hybridization data also indicate that the density of known transposable elements is higher in pNGR234b (the megaplasmid) than on the chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously thought to be present only in Rhizobium meliloti. As non-overlapping shotgun sequences together represent approximately 10% of ANU265 genome, the chromosome and megaplasmid may carry a total of over 200 RIMEs.
        
        
          Conclusions:
          'Skimming' the genome of Rhizobium sp. NGR234 sheds new light on the fine structure and evolution of its replicons, as well as on the integration of symbiotic functions in the genome of a soil bacterium. Although most putative coding sequences could be distributed into functional classes similar to those in Bacillus subtilis, functions related to transposable elements were more abundant in NGR234. In contrast to ISs that accumulated in pNGR234a and pNGR234b, the hundreds of RIME elements seem mostly attributes of the chromosome.

Tags: bacterial-genetics, legume-symbiosis, nih, nitrogen-fixation, rhizobium-genomes
Organization: U.S. Department of Health & Human Services
NSDUH 2019 Field Interviewer Manual

This detailed manual was used as a training guide for the Field Interviewers (FIs) who conducted the in-person 2019 National Survey on Drug Use and Health (NSDUH). It covers the information presented at the intensive training for new FIs. Although it is written for NSDUH FIs, researchers may find it helpful for learning about data collection challenges that could affect data quality. It also may be helpful for those designing their own field operations.The manual includes:An introduction to the survey;A guide to what is expected of FIs;Copies of materials that were mailed or given to respondents;FI instructions for locating sample dwelling units, contacting residents, obtaining participation, conducting the screening and interview, documenting their experiences; andQuality control and administrative procedures for FIs.

Tags: data-collection, mental-health, samhsa, substance-use, survey-methodology
Organization: U.S. Department of Health & Human Services
Consensus guidelines on analgesia and sedation in dying intensive care unit patients

Background
          Intensivists must provide enough analgesia and sedation to ensure dying patients receive good palliative care. However, if it is perceived that too much is given, they risk prosecution for committing euthanasia. The goal of this study is to develop consensus guidelines on analgesia and sedation in dying intensive care unit patients that help distinguish palliative care from euthanasia.
        
        
          Methods
          Using the Delphi technique, panelists rated levels of agreement with statements describing how analgesics and sedatives should be given to dying ICU patients and how palliative care should be distinguished from euthanasia. Participants were drawn from 3 panels: 1) Canadian Academic Adult Intensive Care Fellowship program directors and Intensive Care division chiefs (N = 9); 2) Deputy chief provincial coroners (N = 5); 3) Validation panel of Intensivists attending the Canadian Critical Care Trials Group meeting (N = 12).
        
        
          Results
          After three Delphi rounds, consensus was achieved on 16 statements encompassing the role of palliative care in the intensive care unit, the management of pain and suffering, current areas of controversy, and ways of improving palliative care in the ICU.
        
        
          Conclusion
          Consensus guidelines were developed to guide the administration of analgesics and sedatives to dying ICU patients and to help distinguish palliative care from euthanasia.

Tags: analgesia-sedation, delphi-method, end-of-life-care, icu-patients, nih
Organization: U.S. Department of Health & Human Services
Table 22. Needing But Not Receiving Treatment for Alcohol Use in the Past Year, by Age Group and State: Percentages, Annual Averages Based on 2010 and 2011 NSDUHs

This report presents State estimates for measures of needing but not receiving treatment for past year alcohol use based on the combined 2010 and 2011 National Surveys on Drug Use and Health (NSDUHs). Resuts are provided by age group.

Tags: alcohol-use-disorder, nsduh-survey, samhsa, substance-abuse-treatment, unmet-treatment-need
Organization: U.S. Department of Health & Human Services
2016 Mental Health Client-level Data (MH-CLD) Annual Report

This report presents results from the Mental Health Client Level Data (MH-CLD) and Mental Health Treatment Episode Data Set (MH-TEDS) for individuals receiving mental health treatment services in 2016, as well as selected trends in data collected from such individuals between 2013 and 2016. The report provides information on mental health diagnoses, mental health treatment services, and demographic and substance use characteristics of individuals in mental health treatment in facilities that reported to individual state administrative data systems.

Tags: client-level-data, mental-health, samhsa, substance-use, treatment-episodes
Organization: U.S. Department of Health & Human Services
The concentration of three anti-seizure medications in hair: the effects of hair color, controlling for dose and age

Background
          This paper assess the relationship between the quantity of three anti-seizure medications in hair and the color of the analyzed hair, while controlling for the effects of dose, dose duration, and patient age for 140 clinical patients undergoing anti-seizure therapy. Three drugs are assessed: carbamazepine (40 patients), valproic acid (40 patients), and phenytoin (60 patients). The relationship between hair assay results, hair color, dose, dose duration, and age is modeled using an analysis of covariance. The covariance model posits the hair assay results as the dependent variable, the hair color as the qualitative categorical independent variable, and dose, dose duration, and age as covariates. The null hypothesis assessed is that there is a no relationship between hair color and the quantity of analyte determined by hair assay such that darker colored hair will demonstrate higher concentrations of analyte than lighter colored hair.
        
        
          Results
          The analysis reveals that there is a significant relationship between dose and concentration for all hair color categories independent of the other covariates or the categorical independent variable.
        
        
          Conclusion
          There does not appear to be any relationship between carbamazepine concentration and hair color. There is a weak relationship between hair color and valproic acid concentration, which the data suggest may be mediated by age. There is a significant, moderate relationship between phenytoin concentration and hair color such that darker colored hair has greater concentration values than lighter colored hair.

Tags: anti-seizure-medications, carbamazepine, hair-analysis, nih, pharmacokinetics
Organization: U.S. Department of Health & Human Services
Virginia: 2011-2012 NSDUH

This report presents Virginia\'s estimates for 25 measures of substance use and mental health based on the combined 2011 and 2012 National Surveys on Drug Use and Health (NSDUHs). Topics covered include past month substance use (e.g., illicit drugs, marijuana, cocaine, pain relievers, alcohol, tobacco), substance dependence, abuse, and treatment need, past year serious mental illness (SMI), any mental illness (AMI), suicidal thoughts, and major depressive episode (MDE). Resuts are provided by State and for five age groups: 12 to 17, 18 to 25, 26 or older, 18 or older and all persons 12 or older.

Tags: major-depressive-episode, mental-health, samhsa, substance-use, virginia-nsduh
Organization: U.S. Department of Health & Human Services
Table 2. Marijuana Use in the Past Year, by Age Group and State: Percentages, Annual Averages Based on 2010 and 2011 NSDUHs

This report presents State estimates for measures of past year marijuana use based on the combined 2010 and 2011 National Surveys on Drug Use and Health (NSDUHs). Resuts are provided by age group.

Tags: adolescent-health, marijuana-use, nsduh, samhsa, substance-use
Organization: U.S. Department of Health & Human Services
2010 State Profile — West Virginia

This state profile includes data from facilities in West Virginia that reported to N-SSATS for the survey reference date March 31, 2010. Data were collected on the location, characteristics, services offered, and number of clients in treatment at alcohol and drug abuse treatment facilities (both public and private) in West Virginia. In West Virginia, 82 substance abuse treatment facilities were included in the 2010 N-SSATS, reporting that there were 10,132 clients in substance abuse treatment on March 31, 2010. The survey response rate in West Virginia was 92.4%.

Tags: addiction-services, n-ssats, samhsa, substance-abuse-treatment, west-virginia
Organization: U.S. Department of Health & Human Services
Mental Health Annual Report 2014

This report presents results from the Mental Health Client-Level Data (MH-CLD) and Mental Health Treatment Episode Set (MH-TEDS) for individuals receiving mental health treatment services in 2014, as well as selected data collection trends for such individuals from 2011 to 2014. The report provides information on mental health diagnoses, mental health treatment services, and demographic and substance use characteristics of individuals in mental health treatment in facilities that reported to individual state administrative data systems.

Tags: client-level-data, mental-health, samhsa, substance-use, treatment-episodes
Organization: U.S. Department of Health & Human Services
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins

Background
          Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat).
        
        
          Results
          Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment.
        
        
          Conclusions
          Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

Tags: functional-diversification, nih, orthologous-proteins, protein-evolution, sequence-analysis
Organization: U.S. Department of Health & Human Services