Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Campylobacter jejuni flagella as colonization factors for three-day-old chicks: analysis with flagellar mutants

Campylobacter jejuni, an important cause of human gastrointestinal infection, is a major food-borne pathogen in the United States and worldwide. Since poultry becomes colonized and/or contaminated during the early stages of production and is a major food-borne source for this organism, we studied the role of C. jejuni flagella on the ability of the bacterium to colonize the chicken gastrointestinal tract. Three-day-old chicks were orally challenged with a motile wild-type strain of C. jejuni IN9 or with flagellar mutants created from IN9 by disrupting the flagellin genes with a kanamycin resistance cassette by using shuttle mutagenesis (A. Labigne-Roussel, P. Courcoux, and L. Tompkins, J. Bacteriol. 170:1704-1708, 1988). One mutant, IN9-N3, lacked flagella and was nonmotile. The other, IN9-N7, produced a truncated flagellum and was partially motile. Three-day-old chicks were orally challenged with different doses of the wild-type strain and the two mutants. At challenge doses ranging from 3.0 x 10(4) to 6.6 x 10(8) CFU per chick, only the fully motile, wild-type strain colonized the chick ceca. Our results show that intact and motile flagella are important colonization factors for C. jejuni in chicks.
5‐fluorouracil, dacarbazine, and epirubicin in the treatment of patients with neuroendocrine tumors

For patients with surgically untreatable neuroendocrine tumors (NETs), the optimal therapeutic approach remains undefined. Somatostatin analogs and interferons have failed to control neoplastic growth, and chemotherapy has been only moderately more effective. The authors' previous study of the combination of 5‐fluorouracil (FU), dacarbazine (DTIC), and epirubicin (EPI) (the FDE regimen) documented good tolerability, but the results for tumor growth control were disappointing. In an attempt to improve these results, the authors conducted a preliminary trial of an intensified FDE regimen (FU 500 mg/m2 administered intravenously [i.v.], DTIC 200 mg/m2 i.v., and EPI 30 mg/m2 i.v. on Days 1, 2, and 3 every 3 weeks).
Associations of hospital characteristics with nosocomial pneumonia after cardiac surgery can impact on standardized infection rates

SUMMARY To identify hospital-level factors associated with post-cardiac surgical pneumonia for assessing their impact on standardized infection rates (SIRs), we studied 43 691 patients in a cardiac surgery registry (2001–2011) in 16 hospitals. In a logistic regression model for pneumonia following cardiac surgery, associations with hospital characteristics were quantified with adjustment for patient characteristics while allowing for clustering of patients by hospital. Pneumonia rates varied from 0·7% to 12·4% across hospitals. Seventy percent of variability in the pneumonia rate was attributable to differences in hospitals in their long-term rates with the remainder attributable to within-hospital differences in rates over time. After adjusting for patient characteristics, the pneumonia rate was found to be higher in hospitals with more registered nurses (RNs)/100 intensive-care unit (ICU) admissions [adjusted odds ratio (aOR) 1·2, P = 0·006] and more RNs/available ICU beds (aOR 1·4, P < 0·001). Other hospital characteristics had no significant association with pneumonia. SIRs calculated on the basis of patient characteristics alone differed substantially from the same rates calculated on the basis of patient characteristics and the hospital characteristic of RNs/100 ICU admissions. Since SIRs using patient case-mix information are important for comparing rates between hospitals, the additional allowance for hospital characteristics can impact significantly on how hospitals compare.
Transcranial magnetic stimulation: Potential treatment for tinnitus?

Abstract Tinnitus is a common and often severely disabling disorder for which there is no satisfactory treatment. Transcranial magnetic stimulation (TMS) is a new, non‐invasive method of modifying the excitability of the cerebral cortex, which has proven effective in auditory hallucinations and other disorders. Some early studies have been published in which TMS has been trialed in the treatment of tinnitus. The aim of the present paper was to examine the literature and consider the potential for TMS as a therapy in tinnitus. A thorough search of the tinnitus and TMS literature was conducted, and all available relevant material was examined. Discussions were held with leaders in both fields. Tinnitus is common and there are no effective treatments. It is frequently associated with deafness, and may be the result of a pathological plastic process, secondary to loss of innervation of the outer hair cells of the cochlea. Neuroimaging studies demonstrate increase blood flow to the primary and secondary auditory cortices, particularly on the left side. Transcranial magnetic stimulation is a non‐invasive method of perturbing and inducing change in the cerebral cortex. It uses electromagnetic principles and has been successfully employed in the treatment of other conditions associated with increased activity of the cerebral cortex. A small number of studies have suggested that TMS may be effective in the treatment of tinnitus. There is a good theoretical basis and early research evidence suggesting that TMS may have treatment potential in tinnitus. Further, larger studies are necessary.
Prospective BMI category change associated with cardiovascular fitness change.

PURPOSE The objective of this study was to test the relationship of change in body mass index (BMI) percentile score group (from sixth to eighth grade) with change in cardiovascular fitness (CVF), baseline BMIz-score, and CVF. METHODS Children (3998 (92%)) in the HEALTHY trial provided complete data at the beginning of sixth and end of eighth grades. Height and weight were assessed according to standardized protocol. CVF was measured using the 20-m shuttle run. Changes in BMI percentile were categorized into five groups: increased a BMI category, stayed obese, stayed overweight, stayed at a healthy weight, and decreased a BMI category. Data were analyzed separately by sex, controlling for race, parental education, change in pubertal stage, and baseline BMIz-score and CVF. RESULTS Youth (male and female) who lowered their BMI group or remained in the healthy or overweight groups had significantly larger increases in CVF than those in the stayed obese or increased a BMI category groups. However, these relationships accounted for a small percentage of variance (i.e., weak relationship). Staying obese was associated with the highest baseline BMIz-score, with the second highest among those who decreased a BMI category. BMI category change accounted for the most variance in baseline BMIz-score. CONCLUSIONS Changes in BMI categories were substantially more strongly related to sixth-grade values of BMIz-score than to CVF changes. Because preexisting adiposity may inhibit adiposity change, changes in CVF and adiposity should be attempted before middle school.
Morphological and immunohistochemical studies of the lungs and bronchus-associated lymphoid tissue in a rat model of chronic pulmonary infection with Pseudomonas aeruginosa

Pseudomonas aeruginosa is one of the most frequently encountered bacterial pathogens in patients with chronic pulmonary infections, including cystic fibrosis and diffuse panbronchiolitis. Bronchus-associated lymphoid tissue (BALT), noted frequently in patients with cystic fibrosis and diffuse panbronchiolitis, is considered to play an important role in the local immunologic defense mechanisms in the respiratory tract. To investigate the role of BALT in chronic pulmonary infections, we developed an animal model for chronic pulmonary infection and studied the morphological and immunohistochemical characteristics of BALT. Experimental pneumonia was produced in rats by intratracheal inoculation of P. aeruginosa enmeshed in agar beads. The histological changes corresponded to those occurring in chronic bronchiolitis. Immunohistochemically, surface immunoglobulin M-positive (sIgM+) cells and sIgA+ cells were recognized in the inflamed bronchial walls from day 4, and sIgG+ cells were recognized from day 14, W3/25+ cells exceeded OX8+ cells in number until day 14. In the BALT, there was a massive accumulation of lymphocytes in the lymphatics and high endothelial venules. The development of germinal centers was accompanied by increased numbers of sIgM+ and sIgA+ cells. W3/25+ cells exceeded OX8+ cells in number in the BALT until day 14. On the other hand, OX8+ cells were predominant in comparison with W3/25+ cells at day 21, and then both sIgM+ and sIgA+ cells and inflammatory changes in the lung decreased at day 28. These findings suggest that BALT regulates the local immune responses against chronic pulmonary infection due to P. aeruginosa.
Identification of a Novel HLA-B60-Restricted T Cell Epitope of the Minor Histocompatibility Antigen HA-1 Locus1

The polymorphic minor histocompatibility Ag HA-1 locus encodes two peptides, HA-1H and HA-1R, with a single amino acid difference. Whereas the immunogenicity of the HA-1R allele has not yet been shown, the nonameric HA-1H peptide induces HLA-A2-restricted cytotoxic T cells in vivo and in vitro. It is not known whether the mHag HA-1H or HA-1R associates with other HLA class I molecules. Therefore, the polymorphic regions of both HA-1 alleles were analyzed to identify HLA class I binding peptides that are properly processed by proteasomal degradation. Peptide binding analyses were performed for all nonameric HA-1H/R peptides for binding to nine HLA class I molecules with >10% prevalence in the Caucasian population and for seven nonameric/decameric HA-1H/R peptides predicted to bind to HLA-A3, -B14, and -B60. Only the nonameric KECVLH/RDDL and decameric KECVLH/RDDLL peptides showed strong and stable binding to HLA-B60. In vitro digestion of 29-aa-long HA-1 peptides by purified 20S proteasomes revealed proper cleavage at the COOH termini of both HLA-B60 binding HA-1H and HA-1R peptides. In subsequent analyses, dendritic cells pulsed with the nonameric HA-1R peptide did not induce CTLs that recognize the natural HLA-B60/HA-1R ligand. In contrast, dendritic cells pulsed with the nonameric HA-1H peptide induced IFN-γ-secreting T cells specific for the natural HLA-B60/HA-1H ligand in three HLA-B60+ HA-1RR individuals, demonstrating the immunogenicity of the HLA-B60/HA-1H ligand. In conclusion, this study shows a novel HLA-B60-restricted T cell epitope of the minor histocompatibility Ag HA-1 locus.
Ethylene insensitivity conferred by a mutated Arabidopsis ethylene receptor gene alters nodulation in transgenic Lotus japonicus.

BACKGROUND AND AIMS Transgenics are used to demonstrate a causal relationship between ethylene insensitivity of a seedling legume plant, the level of ethylene receptor gene expression, lateral root growth and Mesorhizobium loti-induced nodule initiation. METHODS Lotus japonicus plants expressing the dominant etr1-1 allele of the Arabidopsis thaliana gene encoding a well-characterized mutated ethylene receptor were created by stable Agrobacterium tumefaciens transformation. Single insertion, homozygous lines were characterized for symbiotic properties. KEY RESULTS Transgenic plants were ethylene insensitive as judged by the lack of the 'Triple Response', and their continued ability to grow and nodulate in the presence of inhibitory concentrations of ACC (1-aminocyclopropane-1-carboxylic acid; an ethylene precursor). Transgenic plants with high insensitivity to ACC had significantly fewer lateral roots and exhibited increased nodulation while showing no altered nitrate sensitivity or lack of systemic autoregulation. Whereas ACC-insensitive shoot growth and nodulation were observed in transformants, root growth was inhibited similarly to the wild type. Increased nodulation was caused by increased infection and a seven-fold increase in nodules developing between xylem poles. Bacteroid numbers per symbiosome increased about 1.7-fold in ethylene-insensitive plants. CONCLUSIONS The study further demonstrates multiple roles for ethylene in nodule initiation by influencing root cell infections and radial positioning, independent of autoregulation and nitrate inhibition of nodulation.
Impact of an Online Analytic Skills Course

This article describes the effect of an online analytic skills training course on professional development and practice and discusses recommendations for using this training modality in the public health workforce. The Enhancing Data Utilization Skills Through Information Technology initiative trained professionals in maternal and child health from 13 Southern-tier state and local health departments to collect, analyze, and interpret data via a year-long Web-based course. The evaluation of this initiative was based on a model of change for health professionals that holds that training influences behavior by increasing knowledge, influencing beliefs related to the behavior, enhancing self-efficacy, and improving skills. Participants’ knowledge, beliefs, and self-efficacy all increased significantly during the course. Participants’ self-assessed skill levels increased significantly for each of 12 selected skills and overall for all skills combined. Distance learning is potentially an effective means for professionals to advance their skills while continuing to fulfill their work-related responsibilities.
Carcinogenic human liver fluke: current status of Opisthorchis viverrini metacercariae in Nakhon Ratchasima, Thailand.

BACKGROUND Opisthorchis viverrini infection is a serious public-health problem in Southeast Asia. It is associated with a number of hepatobiliary diseases and the evidence strongly indicates that liver fluke infection is the etiology of cholangiocarcinoma. OBJECTIVES This study aimed to investigate Opisthorchis viverrini metacercarial infection in cyprinoid fish collected from 32 districts of Nakhon Ratchasima province, Northeastern Thailand during one year period from February 2010 to February 2011. METHODS A cross-sectional study was conducted, data being collected with pepsin-HCl digestion and stereomicroscope, respectively. Analysis was performed using SPSS Windows Version 12.0. RESULTS A total of 640 Cyprinidae family fish including 5 species were collected from different study sites, and investigated for O. viverrini metacercariae. The infection rate was 12.3% (79/640), predominantly in Cyclocheilichthys armatus, C. repasson, Puntioplites proctzysron, Hampala macrolepitota and Hampala dispar, respectively. The prevalence of O. viverrini metaceria in Nakhon Ratchasima area was 78.1%, predominantly in Sida and KiaKham Thale So. CONCLUSION This findings stress that natural fish species in rural communities are still a source of O viverrini infection and put local people at risk, therefore public awareness and prevention campaigns are urgently required.
Decision Support Preferences Among Hispanic and Non-Hispanic White Older Adults With Chronic Musculoskeletal Pain.

OBJECTIVES Despite broad recognition that social networks play a key role in the management of chronic musculoskeletal pain (CMP), little is known about when and why older adults with CMP choose to involve others in treatment decisions. This study investigates the types (i.e., informational, emotional, and instrumental) and sources (i.e., formal and informal) of support Hispanic and non-Hispanic White CMP patients desire and receive when making decisions about their pain care. METHOD Semi-structured interviews were conducted with Hispanic and non-Hispanic White older adults with CMP (N = 63) recruited from one medical center and one senior center in New York City. Interviews were transcribed and then analyzed using content analysis. RESULTS CMP patients sought network members who supported their emotional well-being throughout the decision-making process. When considering high-stakes treatment decisions, participants selectively involved individuals who had similar pain conditions or first-hand experience with the procedure. Participants' perceptions of the decision-making process were contingent upon the congruence between the decision they made and the support they received for it. For Spanish-speaking participants, positive perceptions were linked with satisfactory language competence by their providers. On the other hand, lack of language competence among providers hindered Spanish speakers' ability to obtain adequate informational support. DISCUSSION Results reveal the importance of empathic patient-provider exchanges across diverse patient populations and cultural sensitivity for Spanish-speaking patients. Findings suggest that social networks beyond the patient-provider dyad influence patients' decision-making satisfaction.
Experimental Demonstration of a Tiered Power Management System for Economic Operation of Grid-Tied Microgrids

Power management of grid-tied microgrids including distributed generations (DGs) and storage devices can be challenging due to the intermittent and uncontrollable nature of many types of DGs, load variations in time, different grid power tariffs, availability of different options to balance the electric supply and demand, and other parameters. In order to operate a microgrid efficiently, the management system should accomplish two tasks. 1) It needs to be adaptive and optimize the microgrid's performance by defining long-term (daily-based) directives or control strategies. 2) The management system should be able to operate and control the microgrid in real time and satisfy all operational constraints. To address the above-mentioned tasks, a comprehensive power management system that includes two control layers is developed in this paper. Concept for the proposed power management policy was demonstrated on an experimental microgrid system composed of lead-acid batteries, photovoltaic (PV) system, 3-kW peak load, and a utility connection.
Clinical lung xenotransplantation – what donor genetic modifications may be necessary?

Cooper DKC, Ekser B, Burlak C, Ezzelarab M, Hara H, Paris L, Tector AJ, Phelps C, Azimzadeh AM, Ayares D, Robson SC, Pierson RN III. Clinical lung xenotransplantation – what donor genetic modifications may be necessary? Xenotransplantation 2012; 19: 144–158. © 2012 John Wiley & Sons A/S.
A pooled analysis of two placebo-controlled trials of desvenlafaxine in major depressive disorder

The efficacy, safety, and tolerability of desvenlafaxine (administered as desvenlafaxine succinate) were evaluated in two similarly designed, phase 3, randomized, double-blind, placebo-controlled, venlafaxine-extended-release-referenced, flexible-dose studies of outpatients with a primary diagnosis of major depressive disorder. Owing to a high placebo response, the individual studies were underpowered. Therefore, a post-hoc pooled analysis was performed (desvenlafaxine and placebo data were pooled; venlafaxine extended release data were not, owing to different flexible-dose regimens in the two studies). The primary outcome measure was the change from baseline on the 17-item Hamilton Rating Scale for Depression; the Clinical Global Impressions-Improvement item score was a secondary outcome. Analysis of the pooled data (using a mixed-effect model for repeated measures) revealed that after 8 weeks of treatment, desvenlafaxine was significantly better than placebo on 17-item Hamilton Rating Scale for Depression [−14.21 vs. −11.87 for desvenlafaxine and placebo, respectively; magnitude of effect=−2.34 (P<0.001)] and Clinical Global Impressions-Improvement item scores [1.95 vs. 2.32 for desvenlafaxine and placebo, respectively; magnitude of effect=−0.37 (P<0.001)]. Adverse events were comparable to those found with other drugs sharing a similar mechanism of action. These data support the efficacy, safety, and tolerability of desvenlafaxine in the treatment of major depressive disorder.
The benefits of a 5-day dysphagia intensive placement

Abstract Finding practical dysphagia opportunities for students pre-qualification is challenging. Discussions with clinicians led to the development of a new placement model. The placement was just five days and had an accompanying workbook. The current study aimed to evaluate the benefits of the placement. Data were analysed from 40 students who attended an adult dysphagia placement and 13 who attended a paediatric dysphagia placement. Measures included a pre and post self-rating questionnaire, qualitative feedback from clinical educators and students and a pre and post measure of knowledge using concept maps. Student self-rating data indicated gains in experience, awareness, knowledge, clinical skills, competence, confidence and interest in dysphagia. Clinical educators and students also reported a range of benefits from this placement. Students who undertook a placement that focused on adult dysphagia significantly increased their knowledge of adult dysphagia, but this did not generalize to paediatric dysphagia. Despite reporting that they felt they had gained in knowledge of dysphagia, the students who did a paediatric dysphagia placement did not significantly increase their knowledge of dysphagia. The study raises a number of important considerations when designing placements including length, timing, intensity, how best to encourage generalization of knowledge, and how best to measure learning.
Towards next generation CHO cell biology: Bioinformatics methods for RNA‐Seq‐based expression profiling

High throughput, cost effective next generation sequencing (NGS) has enabled the publication of genome sequences for Cricetulus griseus and several Chinese hamster ovary (CHO) cell lines. RNA‐Seq, the utilization of NGS technology to study the transcriptome, is expanding our understanding of the CHO cell biological system in areas ranging from the analysis of transcription start sites to the discovery of small noncoding RNAs. The analysis of RNA‐Seq data, often comprised of several million short reads, presents a considerable challenge. If the CHO cell biology field is to fully exploit the potential of RNA‐Seq, the development of robust data analysis pipelines is critical. In this manuscript, we outline bioinformatics approaches for the stages of a typical RNA‐Seq expression profiling experiment including quality control, pre‐processing, alignment and de novo transcriptome assembly. Algorithms for the analysis of mRNA and microRNA (miRNA) expression as well as methods for the detection of alternative splicing from RNA‐Seq data are also presented. At this relatively early stage of Cricetulus griseus genome assembly and annotation, it is likely that a combination of isoform deconvolution and raw count based methods will provide the most complete picture of transcript expression patterns in CHO cell RNA‐Seq experiments.
A survey of the ASA physical status classification: significant variation in allocation among Finnish anaesthesiologists

Background:The American Society of Anesthesiologists' (ASA) Classification of Physical Health is a widely used grading system for preoperative health of the surgical patient. In previous studies conducted in North America and Great Britain, considerable variation in the ASA classification allocation has been reported. We hypothesised that in smaller and culturally more homogeneous countries there might be less variation in the ASA classification.