AndreaBozzo/ceres-open-data-index huggingface dataset:
The process of genome shrinkage in the obligate symbiont

Background
          Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.
        
        
          Results
          The reconstructed ancestral genome contained 2,425 open reading frames (ORFs). The Buchnera genome, containing 564 ORFs, consists of 153 fragments of 1-34 genes that are syntenic with reconstructed ancestral regions. On the basis of this reconstruction, 503 genes were eliminated within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements. Lost regions are sometimes large, and often span functionally unrelated genes. In addition, individual genes and regulatory regions have been lost or eroded. For the categories of DNA repair genes and rRNA genes, most lost loci fall in regions between syntenic fragments. This history of gene loss is reflected in the sequences of intergenic spacers at positions where genes were once present.
        
        
          Conclusions
          The most plausible interpretation of this reconstruction is that Buchnera lost many genes through the fixation of large deletions soon after the acquisition of an obligate endosymbiotic lifestyle. An implication is that final genome composition may be partly the chance outcome of initial deletions and that neighboring genes influence the likelihood of loss of particular genes and pathways.

Tags: buchnera-aphidicola, endosymbiont-genome, genome-reduction, nih, obligate-symbiont
Organization: U.S. Department of Health & Human Services
Alteration in expression of the rat mitochondrial ATPase 6 gene during

Background
          Pneumocystis carinii causes pneumonia in immunocompromised patients with a high morbidity and mortality rate, but the interaction between this organism and the host cell is not well understood. The purpose of this research was to study the response of host cells to P. carinii infection on a molecular level.
        
        
          Results
          The technique of mRNA differential display was used to detect genes whose expression may be affected by P. carinii infection. The nucleotide sequence of one differentially displayed DNA fragment was found to be identical to that of the rat mitochondrial ATPase 6 gene, which is a subunit of the F0F1-ATP synthase complex. A four-fold increase in expression of this gene was verified by Northern blot analysis of total RNA extracted from P. carinii-infected rat lung versus that from mock-infected rat lung. Localization of the cells containing ATPase 6 mRNA was accomplished by in situ hybridization. In sections of non-infected rat lung, these cells were found lining the distal parts of the respiratory tree and in apical areas of the alveoli. Histological location of these cells suggested that they were Clara cells and type II pneumocytes. This hypothesis was confirmed by co-localizing the mRNAs for ATPase 6 and surfactant protein B (SP-B) to the same cells by two-color fluorescent in situ hybridization.
        
        
          Conclusions
          The ATPase 6 gene is over expressed during P. carinii infection, and type II pneumocytes and Clara cells are the cell types responsible for this over-expression.

Tags: atpase-6-gene, mitochondrial-function, nih, pneumocystis-carinii, rat-lung
Organization: U.S. Department of Health & Human Services
Purification and partial characterization of bacillocin 490, a novel bacteriocin produced by a thermophilic strain of

Background
          Applications of bacteriocins as food preservatives have been so far limited, principally because of their low antimicrobial activity in foods. Nisin is the only bacteriocin of significant use, but applications are restricted principally because of its very low activity at neutral or alkaline pH. Thus the isolation of new bacteriocins active in foods is desirable.
        
        
          Results
          We isolated a Bacillus licheniformis thermophilic strain producing a bacteriocin with some novel features, named here bacillocin 490. This bacteriocin was inactivated by pronase E and proteinase K and was active against closely related Bacillus spp. both in aerobic and in anaerobic conditions. Bactericidal activity was kept during storage at 4°C and was remarkably stable in a wide pH range. The bacteriocin was partially purified by elution after adhesion to cells of the food-isolated strain Bacillus smithii and had a rather low mass (2 KDa). Antimicrobial activity against B. smithii was observed also when this organism was grown in water buffalo milk.
        
        
          Conclusions
          Bacillocin 490 is a novel candidate as a food anti-microbial agent since it displays its activity in milk, is stable to heat treatment and during storage, is active in a wide pH range and has bactericidal activity also at high temperature. These features may allow the use of bacillocin 490 during processes performed at high temperature and as a complementary antimicrobial agent of nisin against some Bacillus spp. in non-acidic foods. The small size suggests its use on solid foods.

Tags: antimicrobial-peptides, bacillus-licheniformis, bacteriocin-activity, food-preservatives, nih
Organization: U.S. Department of Health & Human Services
Preferences of Mexican anesthesiologists for vecuronium, rocuronium, or other neuromuscular blocking agents: a survey

Background
          Several neuromuscular blocking (NMB) agents are available for clinical use in anesthesia. The present study was performed in order to identify preferences and behaviors of anesthesiologists for using vecuronium, rocuronium or other NMB agents in their clinical practice.
        
        
          Material and methods
          The cross-sectional survey was applied at the Updated Course of the Colegio Mexicano de Anestesiología performed last year. Of 989, 282 (28.5%) surveys were returned.
        
        
          Results
          Most anesthesiologists were working at both public and private hospitals, performed anesthetic procedures for hospitalized and ambulatory patients, and anesthetized children as well as adults. Respondents did not consider mechanomyography as the gold standard method for neuromuscular monitoring. The T25 was not recognized as a pharmacodynamic parameter that represents the clinical duration of the neuromuscular block. Most answered that vecuronium induces less histamine release than rocuronium, had never used any neuromuscular monitor, did not know the cost of vecuronium and rocuronium, and preferred rocuronium in multiple-sampling vials and vecuronium in either a vial for single or multiple sampling. Rocuronium was preferred for emergency surgery in patients with full stomach only. Almost all of anesthesiologists that conserve the unused drug did it without refrigeration and more than 30% conserve the unused drug in one syringe for further use.
        
        
          Conclusion
          Vecuronium was preferred for most clinical situations, and the decision for this choice was not based on costs. Storage of unused drugs without refrigeration in a single syringe for purpose of future use in several patients represented a dangerous common practice.

Tags: anesthesiologist-preferences, mexican-anesthesiology, neuromuscular-blockers, nih, vecuronium-rocuronium
Organization: U.S. Department of Health & Human Services
California (CA)

This report uses 2008 to 2010 National Survey on Drug Use and Health (NSDUH) to assess past year alcohol use disorder and illicit drug use disorder among persons aged 12 or older for California overall and for substate regions within California. 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).

Tags: california-health-survey, mental-health-indicators, nsduh-data, samhsa, substance-use-disorder
Organization: U.S. Department of Health & Human Services
Tribal Federal Medical Assistance Percentage Reference Table for FYs 2016-2017

This report provides the Federal Medical Assistance Percentages (FMAPs) for fiscal years 2016 and 2017 as well as relevant per capita income data for tribes expressing interest in operating title IV-E programs.

Metadata-only record linking to the original dataset. Open original dataset below.

Tags: affair, data, fiscal, policy, social
Organization: U.S. Department of Health & Human Services
Red blood cell transfusion does not increase oxygen consumption in critically ill septic patients

Background
          Red blood cell (RBC) transfusion is commonly used to increase oxygen transport in patients with sepsis. However it does not consistently increase oxygen uptake at either the whole-body level, as calculated by the Fick method, or within individual organs, as assessed by gastric intra-mucosal pH.
        
        
          Aim
          This study evaluates the hemodynamic and oxygen utilization effects of hemoglobin infusion on critically ill septic patients.
        
        
          Methods
          Fifteen septic patients undergoing mechanical ventilation whose hemoglobin was <10 g% were eligible. Ten patients (APACHE II: 25.5 ± 7.6) received an infusion of 1 unit of packed RBC over 1 h while sedated and paralyzed. The remaining five control patients (APACHE II: 24.3 ± 6.0) received a 5% albumin solution (500 ml) over 1 h. Hemodynamic data, gastric tonometry and calorimetry were obtained prior to and immediately after RBC transfusion or 5% albumin infusion.
        
        
          Results
          Transfusion of RBC was associated with an improvement in left ventricular systolic work index (38.6 ± 12.6 to 41.1 ± 13.0 g/min/m2; P = 0.04). In the control group there was no significant change in the left ventricular systolic work index (37.2 ± 14.3 to 42.2 ± 18.9 g/min/m2). An increase in pulmonary vascular resistance index (203 ± 58 to 238 ± 49 dyne/cm5/m2; P = 0.04) was also observed, while no change was produced by colloid infusion (237 ± 87.8 to 226.4 ± 57.8 dyne/cm5/m2). Oxygen utilization did not increase either by Fick equation or by indirect calorimetry in either group. Gastric intramucosal pH increased only in the control group but did not reach statistical significance.
        
        
          Conclusion
          Hemoglobin increase does not improve either global or regional oxygen utilization in anemic septic patients. Furthermore, RBC transfusion may hamper right ventricular ejection by increasing the pulmonary vascular resistance index.

Tags: hemodynamics, nih, oxygen-consumption, red-blood-cell-transfusion, sepsis
Organization: U.S. Department of Health & Human Services
The DAWN Report: Emergency Department Visits Involving Buprenorphine

This Drug Abuse Warning Network (DAWN) short report shows the estimated number of emergency room visits involving buprenorphine between 2005 and 2011. Buprenorphine is used to treat dependence on heroin and narcotic pain medications. The report also shows buprenorphine-related visits broken out by non-medical use, adverse reactions and seeking detoxification or treatment. The report talks about emergency room visits for buprenorphine alone and in combination with other drugs such as marijuana, cocaine, heroin and benzodiazepines.

Tags: buprenorphine-overdose, emergency-department-visits, opioid-dependence, samhsa, substance-abuse-treatment
Organization: U.S. Department of Health & Human Services
Percutaneous tracheostomy: comparison of Ciaglia and Griggs		  techniques

Endoscopic percutaneous dilatational tracheostomy is at least as			 safe as standard open tracheostomy in the operating room (OR). Recently, a			 single dilator was introduced to accomplish dilatation of the tracheal aperture			 in one step, thus obviating the need for multiple graduated dilators.			 Experience with endoscopic percutaneous tracheostomy (PCT) using the single			 dilator in 40 patients to date supports the premise that the procedure is safe,			 rapid, and technically simple. In the study by Añon et al, two			 very different techniques, are compared: the Ciaglia percutaneous dilatational			 tracheostomy technique using multiple dilators and the Griggs percutaneous			 technique using guidewire-dilating forceps. Although relative complication			 rates for the two techniques are not significantly different, both procedures			 are performed in a 'blind' fashion, without the benefit of a			 bronchoscope. The reported incidence of serious complications in this study is			 high, and almost certainly avoidable with the addition of direct bronchoscopic			 visualization. Operative time is reported to be shorter with the Griggs			 technique, but this finding is unlikely to hold true for the single dilator			 technique, which reduces procedure time to less than 15 min. This author's			 experience with bedside endoscopic PCT using the single dilator indicates that			 it is a safe, rapid and cost-effective procedure with a low complication			 rate.

Tags: ciaglia-technique, griggs-technique, nih, percutaneous-tracheostomy, tracheostomy-complications
Organization: U.S. Department of Health & Human Services
Compound 525383: 2-(Isopropyldisulfanyl)butane

Chemical compound data from PubChem database. IUPAC Name: 2-(propan-2-yldisulfanyl)butane. Molecular Formula: C7H16S2. Molecular Weight: 164.3. This dataset contains comprehensive chemical information including structural data, physical properties, and biological activities. Useful for drug discovery, chemical research, and educational purposes.

Tags: chemistry, compound, pubchem, research, science
Organization: U.S. Department of Health & Human Services
National Survey of Substance Abuse Treatment Services: State Profiles 2002

The 2002 National Survey of Substance Abuse Treatment Services (N-SSATS) is an annual survey of facilities providing substance abuse treatment. The N-SSATS, conducted by the Substance Abuse and Mental Health Services Administration (SAMHSA), is designed to collect data on the location, characteristics, services offered, and number of clients in treatment at alcohol and drug abuse facilities (both public and private) throughout the 50 states, the District of Columbia, and other U.S. jurisdictions.

Tags: alcohol-drug-abuse, n-ssats, samhsa, substance-abuse-treatment, treatment-facilities
Organization: U.S. Department of Health & Human Services
2011 CMHS Uniform Reporting System (URS) Output Tables for Michigan

Center for Mental Health Services (CMHS) Uniform Reporting System (URS) Output Tables for 2011. 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: community-mental-health, mental-health-services, outcome-measures, samhsa, urs-data
Organization: U.S. Department of Health & Human Services
The Siblings With Ischemic Stroke Study (SWISS) Protocol

Background
          Family history and twins studies suggest an inherited component to ischemic stroke risk. Candidate gene association studies have been performed but have limited capacity to identify novel risk factor genes. The Siblings With Ischemic Stroke Study (SWISS) aims to conduct a genome-wide scan in sibling pairs concordant or discordant for ischemic stroke to identify novel genetic risk factors through linkage analysis.
        
        
          Methods
          Screening at multiple clinical centers identifies patients (probands) with radiographically confirmed ischemic stroke and a family history of at least 1 living full sibling with stroke. After giving informed consent, without violating privacy among other family members, the proband invites siblings concordant and discordant for stroke to participate. Siblings then contact the study coordinating center. The diagnosis of ischemic stroke in potentially concordant siblings is confirmed by systematic centralized review of medical records. The stroke-free status of potentially discordant siblings is confirmed by validated structured telephone interview. Blood samples for DNA analysis are taken from concordant sibling pairs and, if applicable, from 1 discordant sibling. Epstein-Barr virus-transformed lymphoblastoid cell lines are created, and a scan of the human genome is planned.
        
        
          Discussion
          Conducting adequately powered genomics studies of stroke in humans is challenging because of the heterogeneity of the stroke phenotype and the difficulty of obtaining DNA samples from clinically well-characterized members of a cohort of stroke pedigrees. The multicentered design of this study is intended to efficiently assemble a cohort of ischemic stroke pedigrees without invoking community consent or using cold-calling of pedigree members.

Tags: genetic-risk-factors, genome-wide-scan, ischemic-stroke, nih, sibling-study
Organization: U.S. Department of Health & Human Services
Compound 528576: (1,1-Dimethylethyl)dimethylsilyl 2-(((1,1-dimethylethyl)dimethylsilyl)oxy)acetate

Chemical compound data from PubChem database. IUPAC Name: [tert-butyl(dimethyl)silyl] 2-[tert-butyl(dimethyl)silyl]oxyacetate. Molecular Formula: C14H32O3Si2. Molecular Weight: 304.57. This dataset contains comprehensive chemical information including structural data, physical properties, and biological activities. Useful for drug discovery, chemical research, and educational purposes.

Tags: chemistry, compound, pubchem, research, science
Organization: U.S. Department of Health & Human Services
Chicago: Drug-Related Emergency Department Visits, 2004-2011 - Illicits (excluding alcohol)

Excel file with estimates, rates, relative standard errors, trends and confidence intervals for all drug-related emergency department (ED) visits involving illicit drugs for the Chicago metropolitan area, covering 2004-2011. These visits involve the use of drugs that have limited or no therapeutic value and are generally illegal if taken without a prescription. It also includes visits involving the inhalation of substances for their psychoactive properties (e.g., sniffing model airplane glue).

Tags: drug-related-ed-visits, emergency-department-data, illicit-drug-use, samhsa, substance-abuse-trends
Organization: U.S. Department of Health & Human Services
2022 Uniform Reporting System (URS) Table For Maine

This is the 2022 Uniform Reporting System (URS) Output Tables for Maine. 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-program, mental-health-services, national-outcome-measures, samhsa, substance-abuse-treatment
Organization: U.S. Department of Health & Human Services
Comparison of serum and bronchoalveolar lavage fluid sialic acid levels between malignant and benign lung diseases

Background
          It is known that tissue and serum sialic acid levels may be altered by malignant transformation. In this study, sialic acid levels were determined in bronchoalveolar lavage fluid (BAL) and serum in two groups of patients with lung cancer and non-malignant diseases of the lung.
        
        
          Methods
          Colorimetric methods were used for determination sialic acid in serum and in BAL samples. Flexible bronchoscopy was used to obtain the latter.
        
        
          Results
          Sialic acid levels in bronchoalveolar lavage fluid and serum did not show any statistically significant difference between subjects with malignant and the non-malignant lung diseases (p > 0.05). Sialic acid levels were also unrelated to the stage and localization of the tumor (p > 0.05).
        
        
          Conclusions
          Sialic acid levels do not appear to be a good marker for discriminating malignant from non-malignant diseases of the lung.

Tags: biomarker-study, bronchoalveolar-lavage, lung-cancer-diagnosis, nih, sialic-acid
Organization: U.S. Department of Health & Human Services
Behavioral Health Barometer: Indiana, 2015

This is a behavioral health report for the state of California. The report utilizes data from the National Survey on Drug Use and Health (NSDUH), and the Uniform Reporting System. The topics addressed in the report include youth substance use, youth mental health and treatment, mental health and treatment, substance use and substance use treatment.

Tags: behavioral-health, indiana, mental-health, samhsa, substance-use
Organization: U.S. Department of Health & Human Services
Handheld computers in critical care

Background
          Computing technology has the potential to improve health care management but is often underutilized. Handheld computers are versatile and relatively inexpensive, bringing the benefits of computers to the bedside. We evaluated the role of this technology for managing patient data and accessing medical reference information, in an academic intensive-care unit (ICU).
        
        
          Methods
          Palm III series handheld devices were given to the ICU team, each installed with medical reference information, schedules, and contact numbers. Users underwent a 1-hour training session introducing the hardware and software. Various patient data management applications were assessed during the study period. Qualitative assessment of the benefits, drawbacks, and suggestions was performed by an independent company, using focus groups. An objective comparison between a paper and electronic handheld textbook was achieved using clinical scenario tests.
        
        
          Results
          During the 6-month study period, the 20 physicians and 6 paramedical staff who used the handheld devices found them convenient and functional but suggested more comprehensive training and improved search facilities. Comparison of the handheld computer with the conventional paper text revealed equivalence. Access to computerized patient information improved communication, particularly with regard to long-stay patients, but changes to the software and the process were suggested.
        
        
          Conclusions
          The introduction of this technology was well received despite differences in users' familiarity with the devices. Handheld computers have potential in the ICU, but systems need to be developed specifically for the critical-care environment.

Tags: critical-care, handheld-computers, medical-informatics, nih, point-of-care
Organization: U.S. Department of Health & Human Services