AndreaBozzo/ceres-open-data-index huggingface dataset:
Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins

Background
          Ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. In prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. Duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. However, with the accumulation of numerous complete genome sequences of prokaryotes, several paralogous pairs of ribosomal protein genes have been identified. Here we analyze all such cases and attempt to reconstruct the evolutionary history of these ribosomal proteins.
        
        
          Results
          Complete bacterial genomes were searched for duplications of ribosomal proteins. Ribosomal proteins L36, L33, L31, S14 are each duplicated in several bacterial genomes and ribosomal proteins L11, L28, L7/L12, S1, S15, S18 are so far duplicated in only one genome each. Sequence analysis of the four ribosomal proteins, for which paralogs were detected in several genomes, two of the ribosomal proteins duplicated in one genome (L28 and S18), and the ribosomal protein L32 showed that each of them comes in two distinct versions. One form contains a predicted metal-binding Zn-ribbon that consists of four conserved cysteines (in some cases replaced by histidines), whereas, in the second form, these metal-chelating residues are completely or partially replaced. Typically, genomes containing paralogous genes for these ribosomal proteins encode both versions, designated C+ and C-, respectively. Analysis of phylogenetic trees for these seven ribosomal proteins, combined with comparison of genomic contexts for the respective genes, indicates that in most, if not all cases, their evolution involved a duplication of the ancestral C+ form early in bacterial evolution, with subsequent alternative loss of the C+ and C- forms in different lineages. Additionally, evidence was obtained for a role of horizontal gene transfer in the evolution of these ribosomal proteins, with multiple cases of gene displacement 'in situ', that is, without a change of the gene order in the recipient genome.
        
        
          Conclusions
          A more complex picture of evolution of bacterial ribosomal proteins than previously suspected is emerging from these results, with major contributions of lineage-specific gene loss and horizontal gene transfer. The recurrent theme of emergence and disruption of Zn-ribbons in bacterial ribosomal proteins awaits a functional interpretation.

Tags: bacterial-genomes, gene-duplication, horizontal-gene-transfer, nih, ribosomal-proteins
Organization: U.S. Department of Health & Human Services
A mathematical model of optimized radioiodine-131 therapy of Graves' hyperthyroidism

Background
          The current status of radioiodine-131 (RaI) dosimetry for Graves' hyperthyroidism is not clear. Recurrent hyperthyroidism and iatrogenic hypothyroidism are two problems which interact such that trying to solve one leads to exacerbation of the other. Optimized RaI therapy has therefore begun to be defined just in terms of early hypothyroidism (ablative therapy) as physicians have given up on reducing hypothyroidism.
        
        
          Methods
          Optimized therapy is evaluated both in terms of the greatest separation of cure rate from hypothyroidism rate (non-ablative therapy) or in terms of early hypothyroidism (ablative therapy) by mathematical modeling of outcome after radioiodine and critically discussing the three common methods of RaI dosing for Graves' disease.
        
        
          Results
          Cure follows a logarithmic relationship to activity administered or absorbed dose, while hypothyroidism follows a linear relationship. The effect of including or omitting factors in the calculation of the administered I–131 activity such as the measured thyroid uptake and effective half-life of RaI or giving extra compensation for gland size is discussed.
        
        
          Conclusions
          Very little benefit can be gained by employing complicated methods of RaI dose selection for non-ablative therapy since the standard activity model shows the best potential for cure and prolonged euthyroidism. For ablative therapy, a standard MBq/g dosing provides the best outcome in terms of cure and early hypothyroidism.

Tags: graves-disease, hyperthyroidism, mathematical-model, nih, radioiodine-therapy
Organization: U.S. Department of Health & Human Services
Medical therapy versus interventional therapy in hypertropic obstructive cardiomyopathy

Medical treatment in symptomatic patients with hypertrophic obstructive cardiomyopathy aims to reduce the outflow tract gradients, and to improve diastolic dysfunction and rhythm disorders. Surgical myectomy is the standard treatment in patients with drug refractory symptoms. Since the early 1990s, dual-chamber (DDD)-pacemaker implantation and percutaneous transluminal septal myocardial ablation by alcohol-induced septal branch occlusion have widened treatment options in this subgroup of patients. An overview of medical and interventional treatment is presented.

Tags: hypertrophic-cardiomyopathy, medical-therapy, nih, percutaneous-ablation, septal-myectomy
Organization: U.S. Department of Health & Human Services
United States (US)

This report presents estimates for measures of substance use and mental health based on the combined 2010 and 2011 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 five age groups: 12 to 17, 18 to 25, 26 or older, 18 or older and all persons 12 or older.

Tags: drug-use, mental-health, national-survey, samhsa, substance-use
Organization: U.S. Department of Health & Human Services
Correlation of the score for subjective pain with physical disability, clinical and radiographic scores in recent onset rheumatoid arthritis

Background
          To analyse the relationship between subjective pain score and other measures of clinical, radiographic and functional status; in particular Larsen radiographic scores and Health Assessment Questionnaire (HAQ); in patients with severe rheumatoid arthritis (RA) with a disease duration of less than 3 years.
        
        
          Methods
          In this cross sectional study of 105 patients with RA (76 women, 29 men: mean age 50.93; mean disease duration 15.86 months; 71% rheumatoid factor positive) subjective pain was assessed according to the Visual Analog Scale (VAS). Correlation coefficients between pain score and disease activity measures (patients' global assessment of disease by VAS, number of tender and swollen joints, morning stiffness, erythrocyte sedimentation rate [ESR], C-reactive protein [CRP] and titre of rheumatoid factor, radiographic evaluations (Larsen-Dale scores for radiographic damage of the small joints of the hands, wrist and feet), disability measures (health assessment questionnaire [HAQ]), and demographic variables were calculated; hierarchical regression analysis was done with subjective pain score as the dependent variable.
        
        
          Results
          The Spearman's correlation coefficient comparing subjective pain and HAQ was 0.421 (p < 0.001), between subjective pain and global assessment of disease and morning stiffness was 0.573 (p < 0.001) and 0.427 (p < 0.001) respectively, and between pain and number of tender and swollen joints 0.037 and 0.050 respectively (p > 0.05). In regression analysis, global assessment of disease by patients explained 32.8% of the variation in pain intensity score, morning stiffness 10.7%, CRP 4.0%, HAQ 3.8% and Larsen-Dale scores explained 2.1%; other variables were not significant in the model.
        
        
          Conclusions
          Pain scores of patients with early severe rheumatoid arthritis are correlated at higher levels with patients' global assessment of disease and with morning stiffness rather than with radiographic or other clinical variables such as number of tender and swollen joints.

Tags: disease-activity, nih, pain-assessment, radiographic-damage, rheumatoid-arthritis
Organization: U.S. Department of Health & Human Services
The intein of the Thermoplasma A-ATPase A subunit: Structure, evolution and expression in

Background
          Inteins are selfish genetic elements that excise themselves from the host protein during post translational processing, and religate the host protein with a peptide bond. In addition to this splicing activity, most reported inteins also contain an endonuclease domain that is important in intein propagation.
        
        
          Results
          The gene encoding the Thermoplasma acidophilum A-ATPase catalytic subunit A is the only one in the entire T. acidophilum genome that has been identified to contain an intein. This intein is inserted in the same position as the inteins found in the ATPase A-subunits encoding gene in Pyrococcus abyssi, P. furiosus and P. horikoshii and is found 20 amino acids upstream of the intein in the homologous vma-1 gene in Saccharomyces cerevisiae. In contrast to the other inteins in catalytic ATPase subunits, the T. acidophilum intein does not contain an endonuclease domain.
          T. acidophilum has different codon usage frequencies as compared to Escherichia coli. Initially, the low abundance of rare tRNAs prevented expression of the T. acidophilum A-ATPase A subunit in E. coli. Using a strain of E. coli that expresses additional tRNAs for rare codons, the T. acidophilum A-ATPase A subunit was successfully expressed in E. coli.
        
        
          Conclusions
          Despite differences in pH and temperature between the E. coli and the T. acidophilum cytoplasms, the T. acidophilum intein retains efficient self-splicing activity when expressed in E. coli. The small intein in the Thermoplasma A-ATPase is closely related to the endonuclease containing intein in the Pyrococcus A-ATPase. Phylogenetic analyses suggest that this intein was horizontally transferred between Pyrococcus and Thermoplasma, and that the small intein has persisted in Thermoplasma apparently without homing.

Tags: a-atpase, intein-splicing, nih, protein-structure, thermoplasma-acidophilum
Organization: U.S. Department of Health & Human Services
Somatic frameshift mutations in the Bloom syndrome

Background
          Genomic instability has been reported at microsatellite tracts in few coding sequences. We have shown that the Bloom syndrome BLM gene may be a target of microsatelliteinstability (MSI) in a short poly-adenine repeat located in its coding region. To further characterize the involvement of BLM in tumorigenesis, we have investigated mutations in nine genes containing coding microsatellites in microsatellite mutator phenotype (MMP) positive and negative gastric carcinomas (GCs).
        
        
          Methods
          We analyzed 50 gastric carcinomas (GCs) for mutations in the BLM poly(A) tract aswell as in the coding microsatellites of the TGFβ1-RII, IGFIIR, hMSH3, hMSH6, BAX, WRN, RECQL and CBL genes.
        
        
          Results
          BLM mutations were found in 27% of MMP+ GCs (4/15 cases) but not in any of the MMP negative GCs (0/35 cases). The frequency of mutations in the other eight coding regions microsatellite was the following: TGFβ1-RII (60 %), BAX (27%), hMSH6 (20%),hMSH3 (13%), CBL (13%), IGFIIR (7%), RECQL (0%) and WRN (0%). Mutations in BLM appear to be more frequently associated with frameshifts in BAX and in hMSH6and/or hMSH3. Tumors with BLM alterations present a higher frequency of unstable mono- and trinucleotide repeats located in coding regions as compared with mutator phenotype tumors without BLM frameshifts.
        
        
          Conclusions
          BLM frameshifts are frequent alterations in GCs specifically associated with MMP+tumors. We suggest that BLM loss of function by MSI may increase the genetic instability of a pre-existent unstable genotype in gastric tumors.

Tags: bloom-syndrome, gastric-carcinoma, microsatellite-instability, nih, somatic-mutation
Organization: U.S. Department of Health & Human Services
2017 Uniform Reporting System (URS) Table for Guam

This is the 2017 Uniform Reporting System (URS) Output Tables for Guam. 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: community-mental-health, guam-mental-health, mental-health-services, national-outcome-measures, samhsa
Organization: U.S. Department of Health & Human Services
Risk and Protective Factors and Estimates of Substance Use Initiation: Results from the 2015 National Survey on Drug Use and Health

This report presents data from the 2015 National Survey on Drug Use and Health (NSDUH) regarding the perceived harmfulness of using cigarettes,alcohol, and specific illicit drugs and the perceived availability of substances. Estimates are presented for specific age groups.  Estimates of the perceived great risk of harm associated with the use of marijuana, cocaine, alcohol, and cigarettes also are presented according to whether people initiated use of these substances in the past year. In addition, the report presents estimates for youth-specific protective factors, such as perceptions about parents strongly disapproving of youth substance use. Finally, this report presents the estimated numbers of individuals who initiated substance use in the past year and the average age at first use among people who initiated use in the past year (i.e., past year initiates). Statistically significant differences are noted for these various estimates.

Tags: nsduh-2015, perceived-harmfulness, samhsa, substance-use-initiation, youth-protective-factors
Organization: U.S. Department of Health & Human Services
2014 CMHS Uniform Reporting System (URS) Table for Utah

2014 Center for Mental Health Services (CMHS) 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: block-grant-data, mental-health-services, noms-measures, samhsa, utah-mental-health
Organization: U.S. Department of Health & Human Services
Therapeutic angiogenesis for cardiovascular disease

The identification of angiogenic growth factors, such as vascular endothelial growth factor and fibroblast growth factor, has fueled interest in using such factors to induce therapeutic angiogenesis. The results of numerous animal studies and clinical trials have offered promise for new treatment strategies for various ischemic diseases. Increased understanding of the cellular and molecular biology of vessel growth has, however, prompted investigators and clinicians alike to reconsider the complexity of therapeutic angiogenesis. The realization that formation of a stable vessel is a complex, multistep process may provide useful insights into the design of the next generation of angiogenesis therapy.

Tags: cardiovascular-disease, growth-factors, ischemic-disease, nih, therapeutic-angiogenesis
Organization: U.S. Department of Health & Human Services
Table 26. Had at Least One Major Depressive Episode in the Past Year, by Age Group and State: Percentages, Annual Averages Based on 2010 and 2011 NSDUHs

This report presents State estimates for major depressive episode in the past year based on the combined 2010 and 2011 National Surveys on Drug Use and Health (NSDUHs). Resuts are provided for four age groups: 12 to 17, 18 to 25, 26 or older, and 18 or older.

Tags: depression-prevalence, major-depressive-episode, mental-health, nsduh, samhsa
Organization: U.S. Department of Health & Human Services
Publications Using SAMHSA Data2015 CMHS Uniform Reporting System (URS) Table for Georgia

2015 Center for Mental Health Services (CMHS) Uniform Reporting System (URS) Output Tables for Georgia. 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: georgia-urs-data, mental-health-services, outcome-measures, samhsa, substance-abuse
Organization: U.S. Department of Health & Human Services
Behavioral Health Barometer: HHS Region V, 2014

This is a behavioral health report for HHS Region V of the United States and utilizes data from the National Survey on Drug Use and Health (NSDUH) and the National Survey of Substance Abuse Treatment (N-SSATS), collected annually. The topics addressed in the reports include youth mental health and treatment, adult mental health and treatment, and substance use treatment.

Tags: behavioral-health, hhs-region-v, mental-health, samhsa, substance-use
Organization: U.S. Department of Health & Human Services
2012 Uniform Reporting System (URS) Tables for American Samoa

Center for Mental Health Services (CMHS) Uniform Reporting System (URS) Output Tables for 2012. The Uniform Reporting System (URS) is a state and national reporting system 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: american-samoa, community-mental-health, mental-health-services, noms-data, samhsa
Organization: U.S. Department of Health & Human Services
Publications Using SAMHSA DataTable 17. Alcohol Dependence 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 alcohol dependence based on the combined 2010 and 2011 National Surveys on Drug Use and Health (NSDUHs). Resuts are provided by age group.

Tags: alcohol-dependence, nsduh-data, samhsa, state-alcohol-estimates, substance-use
Organization: U.S. Department of Health & Human Services
Veterans' Primary Substance of Abuse is Alcohol in Treatment Admissions

This spotlight uses 2013 The Treatment Episode Data Set (TEDS) to examine substance abuse treatment admissions among veterans and nonveterans. Substance abuse treatment admissions were analyzed for alcohol, heroin, cocaine, marijuana, methamphetamine, and other opioids and synthetics.

Tags: alcohol-abuse-treatment, samhsa, substance-abuse-admissions, teds-data, veteran-substance-abuse
Organization: U.S. Department of Health & Human Services
Genetic counselling for hypertrophic cardiomyopathy: are we ready for it?

Hypertrophic cardiomyopathy (HCM) is a dominant genetic disorder of the myocardium associated with dysfunctional contractile proteins. The major risk of HCM is sudden cardiac death, which may occur even in asymptomatic carriers. Causes are highly heterogeneous. Over 140 different mutations in nine sarcomeric genes have been described to date. The majority of cases (80% or more) may eventually be traced to one of these genes. Although genetic counselling is suggested even if mutations are not known, molecular diagnosis implies new options such as carrier identification or - theoretically - preclinical risk stratification. A scheme according to which cardiologists and clinical and molecular geneticists could cooperate in counselling patients and managing HCM clinically is proposed.

Tags: genetic-counseling, hypertrophic-cardiomyopathy, nih, sarcomeric-genes, sudden-cardiac-death
Organization: U.S. Department of Health & Human Services
2021 NSDUH Detailed Tables

Get detailed national estimates from the 2021 National Survey on Drug Use and Health (NSDUH). The tables provide comprehensive statistics on substance use, mental health, and treatment in the United States. Unlike previous NSDUH detailed tables, there are no trend tables comparing estimates to previous years for 2021. This is because changes in survey methodology mean the indicators are not comparable to past NSDUH estimates.The tables are based on the NSDUH survey, which interviews people ages 12 or older in the civilian, noninstitutionalized population. In the tables, indicators are broken out by a variety of demographic, geographic, and economic variables.The following topics are covered, among others: drug, alcohol, nicotine, and tobacco product use and initiation; substance use disorder (SUD); substance use risk and protective factors; availability of substance use treatment; any mental illness (AMI) and serious mental illness (SMI); major depressive episode (MDE); suicidal thoughts and behaviors; serious psychological distress (SPD); mental health service utilization; treatment for depression; and co-occurrence of mental health issues and SUDs. In 2021, these tables also present the perceived effects of the Coronavirus Disease 2019 (COVID-19) pandemic on substance use and mental health.All of the tables can be downloaded in a zip file which contains both an html and PDF file containing every table. Alternatively, users can open the clickable Table of Contents to go to a particular section. Click on “PE” to get to a population estimate or percentage table, and “SE” to get a standard error table.

Tags: ami-smi, mental-health, nsduh-survey, samhsa, substance-use
Organization: U.S. Department of Health & Human Services
Utility of routine chest radiographs in a medical–surgical intensive care unit: a quality assurance survey

Objective
          To determine the utility of routine chest radiographs (CXRs) in clinical decision-making in the intensive care unit (ICU).
        
        
          Design
          A prospective evaluation of CXRs performed in the ICU for a period of 6 months. A questionnaire was completed for each CXR performed, addressing the indication for the radiograph, whether it changed the patient's management, and how it did so.
        
        
          Setting
          A 14-bed medical–surgical ICU in a university-affiliated, tertiary care hospital.
        
        
          Patients
          A total of 645 CXRs were analyzed in 97 medical patients and 205 CXRs were analyzed in 101 surgical patients.
        
        
          Results
          Of the 645 CXRs performed in the medical patients, 127 (19.7%) led to one or more management changes. In the 66 surgical patients with an ICU stay <48 hours, 15.4% of routine CXRs changed management. In 35 surgical patients with an ICU stay ≥ 48 hours, 26% of the 100 routine films changed management. In both the medical and surgical patients, the majority of changes were related to an adjustment of a medical device.
        
        
          Conclusions
          Routine CXRs have some value in guiding management decisions in the ICU. Daily CXRs may not, however, be necessary for all patients.

Tags: chest-radiography, icu-patients, medical-surgical, nih, quality-assurance
Organization: U.S. Department of Health & Human Services