bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bodyweight change aids prediction of survival in chronic equine grass sickness
Authors: Jago R. C. , Handel I. , Hahn C. N. , Pirie R. S. , Keen J. A. , Waggett B. E. , McGorum B. C. 
Published: December 2015

SummaryReasons for performing studyObjective criteria for predicting survival of chronic grass sickness cases are currently lacking.ObjectivesTo determine whether the rate and/or magnitude of bodyweight change during hospitalisation of chronic grass sickness cases can provide an objective predictor of survival to discharge from hospital. Clinicians’ recorded indication(s) for euthanasia were also reviewed.Study designSingle centre retrospective observational study.MethodsCase records of all horses admitted for management of chronic grass sickness to The Dick Vet Equine Hospital between 1998 and 2013 were analysed. Case background, survival to hospital discharge, indication(s) for euthanasia, disease duration at admission and bodyweight changes during the hospitalisation period were analysed, and data for survivors and nonsurvivors compared. Percentage weight change was calculated for 7 day intervals up to 28 days (0–7, 7–14, 14–21, 21–28 days) and for entire periods from the first weight recorded (0–7, 0–14, 0–21, 0–28 days). These results were used to estimate survival probability conditional on weight change.ResultsThe study sample comprised 213 horses, with 114 survivors (53.5%) and 99 (46.5%) nonsurvivors. Compared with nonsurvivors, survivors had significantly lower median maximum bodyweight loss as a percentage of first weight (survivors 5.9%, interquartile range 1.8–13.5; nonsurvivors 12.7%, 6.4–17.3). Throughout all time periods analysed, survivors had significantly lower median bodyweight loss than nonsurvivors, but no specific time period was more predictive of survival. Highest percentages of total bodyweight loss for individual horses were comparable for survivors (36%) and nonsurvivors (37%). Survival prediction curves reporting percentage survival rates for all time periods analysed provided data to aid prediction of chronic grass sickness survival.ConclusionsOverall, nonsurvivors had greater bodyweight loss than survivors. Rapidity and magnitude of bodyweight loss were equally predictive of outcome. Percentage survival prediction curves provide objective data to aid discussion of prognosis, but greater predictive specificity with associated sensitivity is required for clinical decision making in individual cases.
Evidence‐based medicine teaching requirements in the USA: taxonomy and themes
Authors: Shaughnessy Allen F. , Torro John R. , Frame Kara A. , Bakshi Munish 
Published: December 2015

AbstractBackgroundIn the USA, recent changes to oversight of residency training codify the requirements for teaching evidence‐based medicine and information mastery (lifelong learning) knowledge, skills, and attitudes.ObjectiveThe goal of this project is to determine current requirements for teaching of evidence‐based medicine (EBM) and information mastery (IM) in specialty residency education in the USA.MethodsThe project was a qualitative thematic analysis using content analysis. The source of the requirements for EBM and IM were the “milestone” statements for all 28 major specialties and transition year programs. Milestone descriptors related to EBM/IM were extracted and codes were developed and applied to each descriptor by four researchers. The resulting codes were coalesced into themes and tested against the milestone descriptors.ResultsThe coding process identified 15 content areas comprising five themes. Two themes related to the knowledge and skills of EBM and three themes related to the knowledge, skills, and attitudes of IM. EBM themes encompassed basic critical appraisal skills and knowledge of clinical epidemiology principles and statistics. IM themes centered on identifying one's information needs for patient‐specific information, using information sources, and using current awareness services to remain abreast of changes in medicine. In general, they align well with the Sicily Statement on Evidence‐Based Practice. No specialty required competence in all areas.ConclusionNew training requirements for specialties in the USA require the development of both classic EBM skills as well as skills for managing information. However, there is marked variation in the requirements among specific specialties.
Isotopologue profiling of the listerial N‐metabolism
Authors: Kutzner Erika , Kern Tanja , Felsl Angela , Eisenreich Wolfgang , Fuchs Thilo M. 
Published: December 2015

SummaryThe nitrogen (N‐) sources and the relative contribution of a nitrogenous nutrient to the N‐pool of the gram‐positive pathogen Listeria monocytogenes are largely unknown. Therefore, 15N‐isotopologue profiling was established to study the N‐metabolism of L. monocytogenes. The pathogen was grown in a defined minimal medium supplemented with potential 15N‐labeled nutrients. The bacteria were harvested and hydrolysed under acidic conditions, and the resulting amino acids were analysed by GC‐MS, revealing 15N‐enrichments and isotopomeric compositions of amino acids. The differential 15N‐profiles showed the substantial and simultaneous usage of ammonium, glutamine, methionine, and, to a lower extent, the branched‐chain amino acids valine, leucine, and isoleucine for anabolic purposes, with a significant preference for ammonium. In contrast, arginine, histidine and cysteine were directly incorporated into proteins. L. monocytogenes is able to replace glutamine with ethanolamine or glucosamine as amino donors for feeding the core N‐metabolism. Perturbations of N‐fluxes caused by gene deletions demonstrate the involvement of ethanolamine ammonia lyase, and suggest a role of the regulator GlnK of L. monocytogenes distinct from that of Escherichia coli. The metabolism of nitrogenous nutrients reflects the high flexibility of this pathogenic bacterium in exploiting N‐sources that could also be relevant for its proliferation during infection.
Ubiquitin regulates TORC1 in yeastSaccharomyces cerevisiae
Authors: Hu Kejin , Guo Shuguang , Yan Gonghong , Yuan Wenjie , Zheng Yin , Jiang Yu 
Published: December 2015

SummaryIn the yeastSaccharomyces cerevisiaethe TOR complex 1 (TORC1) controls many growth‐related cellular processes and is essential for cell growth and proliferation. Macrolide antibiotic rapamycin, in complex with a cytosol protein named FKBP12, specifically inhibits TORC1, causing growth arrest. The FKBP12‐rapamycin complex interferes with TORC1 function by binding to the FRB domain of the TOR proteins. In an attempt to understand the role of the FRB domain in TOR function, we identified a single point mutation (Tor2W2041R) in the FRB domain of Tor2 that renders yeast cells rapamycin resistant and temperature sensitive. At the permissive temperature, the Tor2 mutant protein is partially defective for binding with Kog1 and TORC1 is impaired for membrane association. At the restrictive temperature, Kog1 but not the Tor2 mutant protein, is rapidly degraded. Overexpression of ubiquitin stabilizes Kog1 and suppresses the growth defect associated with thetor2mutant at the nonpremissive temperature. We find that ubiquitin binds non‐covalently to Kog1, prevents Kog1 from degradation and stabilizes TORC1. Our data reveal a unique role for ubiquitin in regulation of TORC1 and suggest that Kog1 requires association with the Tor proteins for stabilization.
A Candida albicans regulator of disseminated infection operates primarily as a repressor and governs cell surface remodeling
Authors: Böhm Lena , Muralidhara Prathibha , Pérez J. Christian 
Published: December 2015

SummaryVirulence traits are often controlled by transcription regulators, i.e. sequence‐specific DNA‐binding proteins. The regulators that sustain microbial proliferation in the host typically work by promoting the expression of the genes that mediate such traits. Here, we report a singular example in the human fungal pathogen Candida albicans in which a transcription regulator functions by repressing the expression of virulence genes, yet its overall role is to promote virulence. We explain this apparent paradox by establishing that a major function of this protein, Zcf21p, is to set a default state of low expression of multiple cell wall components which include virulence determinants. These components comprise GPI‐anchored proteins, adhesins and enzymes that synthesize cell wall sugar decorations. Deletion or overexpression of ZCF21 results in cell wall structure modifications that influence recognition and elimination of the fungus by macrophages. By leveling off the expression of adhesins, ZCF21 also prevents C. albicans self‐aggregation. Balancing the expression of cell wall components – virulence determinants included – is, therefore, critical for C. albicans to assemble a cell surface configuration that is suitable to colonize mammalian tissues and evade immune surveillance.
Silencing of the gibberellin receptor homolog, CsGID1a, affects locule formation in cucumber (Cucumis sativus) fruit
Authors: Liu Bin , Liu Xingwang , Yang Sen , Chen Chunhua , Xue Shudan , Cai Yanling , Wang Dandan , Yin Shuai , Gai Xinshuang , Ren Huazhong 
Published: December 2015

Summary

Gibberellins are phytohormones with many roles, including the regulation of fruit development. However, little is known about the relationship between GA perception and fleshy fruit ontogeny, and particularly locule formation.

We characterized the expression of cucumber (Cucumis sativus) GA receptor gene (CsGID1a) using quantitative real‐time PCR, in situ hybridization and a promoter::β‐glucuronidase (GUS) assay. CsGID1a‐RNAi cucumber fruits were observed by dissecting microscope, scanning electron microscopy and transmission electron microscopy. Finally, genome‐wide gene expression in young fruits from a control and the RNAi line was compared using a digital gene expression (DGE) analysis approach.

The expression pattern of CsGID1a was found to be closely correlated with fruit locule formation, and silencing CsGID1a in cucumber resulted in fruits with abnormal carpels and locules. Overexpression of CsGID1a in the Arabidopsis thaliana double mutant (gid1a gid1c) resulted in ‘cucumber locule‐like’ fruits. The DGE analysis suggested that expression of genes related to auxin synthesis and transport, as well as the cell cycle, was altered in CsGID1a‐RNAi fruits, a result that was supported by comparing the auxin content and cellular structures of the control and transgenic fruits.

This study demonstrates a previously uncharacterized GA signaling pathway that is essential for cucumber fruit locule formation.
Foetal and infant growth patterns, airway resistance and school‐age asthma
Authors: Sonnenschein‐van der Voort Agnes M.M. , Gaillard Romy , de Jongste Johan C. , Hofman Albert , Jaddoe Vincent W.V. , Duijts Liesbeth 
Published: December 2015

AbstractBackground and objectivePreterm birth, low birth weight and rapid infant weight gain are associated with increased risks of asthma symptoms in childhood. The underlying mechanism may include persistently higher airway resistance (Rint). The aim of our study was to examine the associations of longitudinally measured foetal and infant growth characteristics with Rint and asthma outcomes in school‐age children.MethodsThis study was embedded in a population‐based prospective cohort study in Rotterdam, The Netherlands. Foetal growth was estimated by ultrasound in the second and third trimesters. Infant growth was measured at birth, 3, 6 and 12 months. At age 6 years, Rint was measured, and information about wheezing and asthma was obtained by questionnaires. The number of subjects per analysis differed per available outcome (3954–5066 subjects).ResultsLongitudinal growth analyses showed that school‐age children with increased Rint had lower foetal length growth and weight gain, and lower infant length growth. Children with persistent wheezing until age 6 years and physician‐diagnosed asthma had a higher Rint compared with children who never wheezed or without asthma (difference z‐scores Rint: 0.58 (0.19, 0.97) and 0.55 (0.15, 0.95), respectively).ConclusionRint in school‐age children is influenced by foetal growth restriction and is associated with asthma outcomes.See Editorial, page 574
Seroprevalence of HTLV‐1 and HTLV‐2 amongst mothers and children in Malawi within the context of a systematic review and meta‐analysis of HTLV seroprevalence in Africa
Authors: Fox James M. , Mutalima Nora , Molyneux Elizabeth , Carpenter Lucy M. , Taylor Graham P. , Bland Martin , Newton Robert , Martin Fabiola 
Published: December 2015

AbstractObjectivesHuman T‐lymphotropic virus (HTLV)‐1 causes T‐cell leukaemia and myelopathy. Together with HTLV‐2, it is endemic in some African nations. Seroprevalence data from Malawi are scarce, with no reports on associated disease incidence. HTLV seroprevalence and type were tested in 418 healthy mothers from Malawi. In addition, we tested the sera of 534 children to investigate mother‐to‐child transmission. To provide context, we conducted a systematic review and meta‐analysis of HTLV seroprevalence in African women and children.MethodsStored samples from a previous childhood cancer and BBV study were analysed. ELISA was used for HTLV screening followed by immunoblot for confirmation and typing. Standard methods were used for the systematic review.ResultsHTLV seroprevalence was 2.6% (11/418) in mothers and 2.2% (12/534) in children. Three mothers carried HTLV‐1 alone, seven had HTLV‐2 and one was dually infected. Three children carried HTLV‐1 alone, seven had HTLV‐2 and two were dually infected. Only two corresponding mothers of the 12 HTLV‐positive children were HTLV positive. The systematic review included 66 studies of women and 13 of children conducted in 25 African countries. Seroprevalence of HTLV‐1 varied from 0 to 17% and of HTLV‐2 from 0 to 4%.ConclusionsIn contrast to findings from other studies in Africa, the seroprevalence of HTLV‐2 was higher than that of HTLV‐1 in Malawi and one of the highest for the African region. The lack of mother–child concordance suggests alternative sources of infection among children. Our data and analyses contribute to HTLV prevalence mapping in Africa.
New Commercially Available IgG Kits and Time-Resolved Fluorometric IgE Assay for Diagnosis of Allergic Bronchopulmonary Aspergillosis in Patients with Cystic Fibrosis
Authors: Barrera Coralie , Richaud-Thiriez Bénédicte , Rocchi Steffi , Rognon Bénédicte , Roussel Sandrine , Grenouillet Frédéric , Laboissière Audrey , Dalphin Jean-Charles , Reboux Gabriel , Millon Laurence 
Published: December 2015

ABSTRACT

Allergic bronchopulmonary aspergillosis (ABPA) is difficult to diagnose; diagnosis relies on clinical, radiological, pathological, and serological criteria. Our aim was to assess the performance of two new commercially available kits and a new in-house assay: an
Aspergillus fumigatus
enzyme-linked immunosorbent assay (ELISA) IgG kit (Bordier Affinity Products), an
Aspergillus
Western blotting IgG kit (LDBio Diagnostics), and a new in-house time-resolved fluorometric IgE assay (dissociation-enhanced lanthanide fluorescent immunoassay, or DELFIA) using recombinant proteins from an
Aspergillus
sp. recently developed by our laboratory for ABPA diagnosis in a retrospective study that included 26 cystic fibrosis patients.
Aspergillus fumigatus
-specific IgG levels measured by a commercial ELISA kit were in accordance with the level of precipitins currently used in our lab. The ELISA kit could accelerate and help standardize ABPA diagnosis.
Aspergillus fumigatus
-specific IgE levels measured by ImmunoCAP (Phadia) with
A. fumigatus
M3 antigen and by DELFIA with a purified protein extract of
A. fumigatus
were significantly correlated (
P
< 10
−6
). The results with recombinant antigens glucose-6-phosphate isomerase and mannitol-1-phosphate dehydrogenase were encouraging but must be confirmed with sera from more patients. The DELFIA is an effective tool that can detect specific IgE against more fungal allergens than can be detected with other commercially available tests.
Draft Genome Sequence of
Arthrobacter
sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium
Authors: Gkorezis Panagiotis , Bottos Eric M. , Van Hamme Jonathan D. , Thijs Sofie , Rineau Francois , Franzetti Andrea , Balseiro-Romero Maria , Weyens Nele , Vangronsveld Jaco 
Published: December 2015

ABSTRACT

We report here the 4.7-Mb draft genome of
Arthrobacter
sp. SPG23, a hydrocarbonoclastic Gram-positive bacterium belonging to the
Actinobacteria
, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations.
Complete Genome Sequence of a Tomato-Infecting Tomato Mottle Mosaic Virus in New York
Authors: Padmanabhan Chellappan , Zheng Yi , Li Rugang , Martin Gregory B. , Fei Zhangjun , Ling Kai-Shu 
Published: December 2015

ABSTRACT
The complete genome sequence of an isolate of tomato mottle mosaic virus (ToMMV) infecting tomatoes in New York was obtained using small RNA (sRNA) deep sequencing. ToMMV_NY-13 shared 99% sequence identity with isolates from Mexico and Florida. Broader distribution of this emerging virus is a cause for concern to the tomato industry.
Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks
Authors: Fitzpatrick Margaret A. , Ozer Egon A. , Hauser Alan R. 
Published: December 2015

ABSTRACT

Acinetobacter baumannii
frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical
Acinetobacter
isolates and analyzing a carbapenem-resistant
A. baumannii
(CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148
Acinetobacter calcoaceticus-A. baumannii
complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three
Acinetobacter
species within this collection. Four major
A. baumannii
clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished
A. baumannii
isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for
A. baumannii
strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.
Two Listeria monocytogenes Pseudo-outbreaks Caused by Contaminated Laboratory Culture Media
Authors: Matanock Almea , Katz Lee S. , Jackson Kelly A. , Kucerova Zuzana , Conrad Amanda R. , Glover William A. , Nguyen Von , Mohr Marika C. , Marsden-Haug Nicola , Thompson Deborah , Dunn John R. , Stroika Steven , Melius Beth , Tarr Cheryl , Dietrich Stephen E. , Kao Annie S. , Kornstein Laura , Li Zhen , Maroufi Azarnoush , Marder Ellyn P. , Meyer Rebecca , Perez-Osorio Ailyn C. , Reddy Vasudha , Reporter Roshan , Carleton Heather , Tweeten Samantha , Waechter HaeNa , Yee Lisa M. , Wise Matthew E. , Davis Kim , Jackson Brendan R. 
Published: December 2015

ABSTRACT

Listeriosis is a serious foodborne infection that disproportionately affects elderly adults, pregnant women, newborns, and immunocompromised individuals. Diagnosis is made by culturing
Listeria monocytogenes
from sterile body fluids or from products of conception. This report describes the investigations of two listeriosis pseudo-outbreaks caused by contaminated laboratory media made from sheep blood.
Culture-Based and Culture-Independent Bacteriologic Analysis of Cystic Fibrosis Respiratory Specimens
Authors: Mahboubi Mona A. , Carmody Lisa A. , Foster Bridget K. , Kalikin Linda M. , VanDevanter Donald R. , LiPuma John J. 
Published: December 2015

ABSTRACT

Cystic fibrosis (CF) is characterized by chronic infection and inflammation of the airways.
In vitro
culture of select bacterial species from respiratory specimens has been used to guide antimicrobial therapy in CF for the past few decades. More recently, DNA sequence-based, culture-independent approaches have been used to assess CF airway microbiology, although the role that these methods will (or should) have in routine microbiologic analysis of CF respiratory specimens is unclear. We performed DNA sequence analyses to detect bacterial species in 945 CF sputum samples that had been previously analyzed by selective CF culture. We determined the concordance of results based on culture and sequence analysis, highlighting the comparison of the results for the most prevalent genera. Although overall prevalence rates were comparable between the two methods, results varied by genus. While sequence analysis was more likely to detect
Achromobacter
,
Stenotrophomonas
, and
Burkholderia
, it was less likely to detect
Staphylococcus
.
Streptococcus
spp. were rarely reported in culture results but were the most frequently detected species by sequence analysis. A variety of obligate and facultative anaerobic species, not reported by culture, was also detected with high prevalence by sequence analysis. Sequence analysis indicated that in a considerable proportion of samples, taxa not reported by selective culture constituted a relatively high proportion of the total bacterial load, suggesting that routine CF culture may underrepresent significant segments of the bacterial communities inhabiting CF airways.
Urine Galactomannan-to-Creatinine Ratio for Detection of Invasive Aspergillosis in Patients with Hematological Malignancies
Authors: Reischies Frederike M. J. , Raggam Reinhard B. , Prattes Juergen , Krause Robert , Eigl Susanne , List Agnes , Quehenberger Franz , Strenger Volker , Wölfler Albert , Hoenigl Martin 
Published: December 2015

ABSTRACT
Galactomannan (GM) testing of urine specimens may provide important advantages, compared to serum testing, such as easy noninvasive sample collection. We evaluated a total of 632 serial urine samples from 71 patients with underlying hematological malignancies and found that the urine GM/creatinine ratio, i.e., (urine GM level × 100)/urine creatinine level, which takes urine dilution into account, reliably detected invasive aspergillosis and may be a promising diagnostic tool for patients with hematological malignancies. (This study has been registered at ClinicalTrials.gov under registration no. NCT01576653.)