bluuebunny/crossref_metadata_2025_split huggingface dataset:
A real-time PCR for the differentiation of typhoidal and non-typhoidal Salmonella
Authors: Nair Satheesh , Patel Vineet , Hickey Tadgh , Maguire Clare , Greig David R , Lee Winnie , Godbole Gauri , Grant Kathie , Chattaway Marie Anne 
Published: February 2019

AbstractRapid and accurate differentiation of Salmonella spp. causing enteric fever from non-typhoidal Salmonella is essential for clinical management of cases, laboratory risk management and implementation of public health measures. Current methods used for confirmation of identification including biochemistry and serotyping as well as whole genome sequencing analyses, takes several days. Here we report the development and evaluation of a real-time PCR assay that can be performed directly on crude DNA extracts from bacterial colonies, for the rapid identification of typhoidal and non-typhoidal Salmonella.This novel two-hour assay identifies the genus Salmonella by detecting the ttr gene, encoding tetrathionate reductase, and defines typhoidal Salmonella by the detection of S. Typhi and Paratyphi-specific gene combinations. PCR assay performance was determined using 211 clinical cultures of Salmonella (114 non-typhoidal and 97 Typhoidal strains) and 7 clinical non-Salmonella cultures. In addition, the specificity of the assay was evaluated in silico using a diverse in-house collection of 1882 Salmonella whole genome sequences. The real-time PCR results for 218 isolates and the genomic analysis of the 1882 isolates produced 100% sensitivity and 100% specificity (based on a 7 gene profile) for identifying typhoidal Salmonella compared to the Salmonella whole genome sequening identification methods currently used at Public Health England.This paper describes a robust real-time PCR assay for the rapid, accurate identification of typhoidal and non-typhoidal Salmonella which will be invaluable for the urgent screening of isolates from symptomatic individuals, the safe processing of isolates in laboratories and for assisting the management of public health risks.
Peripheral axonal ensheathment is regulated by Ral GTPase and the exocyst complex
Authors: Silva-Rodrigues Joana F. , Patrício-Rodrigues Cátia F. , Sousa-Xavier Vicente de , Augusto Pedro M. , Fernandes Ana C. , Farinho Ana R. , Teodoro Rita O. 
Published: February 2019

AbstractAxon ensheathment is fundamental for fast impulse conduction and the normal physiological functioning of the nervous system. Defects in axonal insulation lead to debilitating conditions, but despite its importance, the molecular players responsible are poorly defined. Here, we identify Ral GTPase as a key player in axon ensheathment inDrosophilalarval peripheral nerves. We demonstrate through genetic analysis that Ral action through the exocyst complex is sufficient and necessary in wrapping glial cells to regulate their growth and development. We suggest that the Ral-exocyst pathway controls the targeting of secretory vesicles for membrane growth or for the secretion of a wrapping glia-specific factor that itself regulates growth. In summary, our findings provide a new molecular understanding of the process by which axons are ensheathedin vivo, a process critical for normal neuronal function.
Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: Is disturbance an alternative explanation?
Authors: Griffin Eric A. , Harrison Joshua G. , Kembel Steven W. , Carrell Alyssa A. , Joseph Wright S. , Carson Walter P. 
Published: February 2019

AbstractBacterial endophytes may be fairly host‐specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community‐wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity.We tested the following four non‐mutually exclusive hypotheses: (a)The Host Identity Hypothesis: endophytes vary substantially among different host‐plant species. (b)The Core Microbiome Hypothesis: a subset of microbial taxa will be shared among all host‐plant species. (c).The Soil Resource Supply Hypothesis: endophytes vary substantially among habitats with experimentally elevated levels of macronutrients. (d)The Disturbance–Disruption Hypothesis: disturbances created by the periodic application of antibiotics structure bacterial endophyte communities.We tested these hypotheses by characterizing endophytes using high‐throughput sequencing among seedlings of five phylogenetically diverse tree species nested within a long‐term, full factorial nitrogen, phosphorus and potassium soil fertilization experiment. We artificially disturbed one of our focal species by applying antibiotics every 10–14 days for 29 months within the soil (N, P, K) fertilization experiment.While we detected a significant effect of host identity and soil nutrient additions,togetherthey explained little variation in endophyte community composition (<10%). We found unequivocal evidence for a core microbiome shared by all species. Specifically, we inferred that nine OTUs were present among 95% or more of all control saplings, representing a third of the total reads. These bacterial taxa belonged to the Actinobacteria.In contrast, disturbance (antibiotics) explained more endophyte variation than all nutrient addition combinationscombinedand twice the variation explained by host identity for all five tree species.Synthesis. Our results challenge the idea that host identity is a primary filter shaping bacterial endophyte communities; this suggests that many of the same bacterial taxa occur inside plant hosts even if those host plants are phylogenetically diverse. Moreover, we documented a distinct core microbiome shared among our five focal tree species. Finally, we found that disturbance rather than host identity and soil nutrient availability was an important driver of microbial community composition, which parallels the importance of disturbance in other areas of community ecology.
Identification of three podoviruses infecting Klebsiella encoding capsule depolymerases that digest specific capsular types
Authors: Pan Yi‐Jiun , Lin Tzu‐Lung , Chen Yi‐Yin , Lai Peng‐Hsuan , Tsai Yun‐Ting , Hsu Chun‐Ru , Hsieh Pei‐Fang , Lin Yi‐Tsung , Wang Jin‐Town 
Published: February 2019

SummaryKlebsiella pneumoniae is an important human pathogen causing opportunistic nosocomial and community‐acquired infections. A major public health concern regarding K. pneumoniae is the increasing incidence of multidrug‐resistant strains. Here, we isolated three novel Klebsiella bacteriophages, KN1‐1, KN3‐1 and KN4‐1, which infect KN1, KN3 and K56, and KN4 types respectively. We determined their genome sequences and conducted a comparative analysis that revealed a variable region containing capsule depolymerase‐encoding genes. Recombinant depolymerase proteins were produced, and their enzymatic activity and specificity were evaluated. We identified four capsule depolymerases in these phages that could only digest the capsule types of their respective hosts. Our results demonstrate that the activities of these capsule depolymerases were correlated with the host range of each phage; thus, the capsule depolymerases are host specificity determinants. By generating a capsule mutant, we demonstrate that capsule was essential for phage adsorption and infection. Further, capsule depolymerases can enhance bacterial susceptibility to serum killing. The discovery of these phages and depolymerases lays the foundation for the typing of KN1, KN3, KN4 and K56 Klebsiella and could be useful alternative therapeutics for the treatment of K. pneumoniae infections.
Scholarly Productivity and Impact: Developing a Quantifiable, Norm‐based Benchmarking Methodology for Academic Emergency Medicine
Authors: Boudreaux Edwin D. , Higgins Stephen E. , Reznik‐Zellen Rebecca , Wang Bo , Volturo Gregory 
Published: February 2019

AbstractBackgroundQuantifying and benchmarking scholarly productivity of emergency medicine faculty is challenging. While performance indicators including publication and citation counts are available, use of indicators to create normative references has lagged. The authors developed methodology to benchmark emergency medicine academician scholarly productivity (e.g., publications over time) and impact (e.g., citations per publication over time) against an appropriate reference group.MethodsThe methodology includes: 1) define time frame and scholarly metrics; 2) identify representative population; 3) reconcile alternative author names; 4) use analytic tool to identify scholarly output; 5) build database containing metrics; and 6) create benchmarking statistics, including subsamples. This study included emergency medicine faculty from 2011 to 2015, with total peer‐reviewed publications and citations per publication as scholarly metrics.ResultsIn the United States at the time of the search (2016) there were 200 academic emergency departments, 186 with public faculty listings, which yielded 6,727 academicians. For each academician, the authors calculated statistics about peer‐reviewed publications and average citations per publication from 2011 to 2015 and created benchmarking rulers using percentile ranks. Productivity by year of graduation with terminal degree was compared within each subsample, finding that newly graduated faculty demonstrated higher productivity than their within‐rank peers who graduated earlier. Finally, benchmarking tables were created that allow comparison of peer‐reviewed publication counts and citations per publication for individual academicians against the norm.ConclusionsThis benchmarking method can serve as a model for norm‐based scaling of scholarly productivity for emergency medicine. This has important implications for performance review, promotion and hiring, and evaluating group productivity.
Forecasting wildlife die‐offs from extreme heat events
Authors: Ratnayake H. U. , Kearney M. R. , Govekar P. , Karoly D. , Welbergen J. A. 
Published: February 2019

AbstractExtreme heat events pose increasing challenges to biodiversity conservation worldwide, yet our ability to predict the time, place and magnitude of their impacts on wildlife is limited. Extreme heat events in Australia are known to kill thousands of flying‐foxes (Pteropus spp.), and such die‐offs are expected to become more frequent and widespread in the future under anthropogenic climate change. There is a growing need for predicting when and where such heat‐related die‐offs would occur, to facilitate short‐term wildlife management and conservation actions. In this study, we used gridded hourly air temperature forecasts [Australian Community Climate and Earth‐System Simulator (ACCESS‐R) Numerical Weather Prediction (NWP) model] from the Australian Bureau of Meteorology to predict flying‐fox heat‐related mortality based on an empirically determined threshold of 42.0°C. We tested the accuracy and precision of this model using a twofold evaluation of the ACCESS‐R NWP forecast air temperature during a recorded extreme heat event with in situ air temperature measurements and interpolated weather station data. While our results showed a slight discrepancy between the modelled and measured air temperatures, there was no significant difference in the forecast's accuracy to predict die‐offs during an extreme heat event and the overall summer period. We evaluated the accuracy of mortality predictions based on different air temperature thresholds (38.0, 40.0, 42.0 and 44.0°C). Our results revealed a significant probability of flying‐fox mortality occurrence when forecast air temperature was ≥42.0°C, while the 24‐ and 48‐h forecasts accurately predicted 77 and 73% of the die‐offs, respectively. Thus, the use of 42.0°C forecast air temperature from the ACCESS‐R NWP model can predict flying‐fox mortality reliably at the landscape scale. In principle, the forecaster can be used for any species with known thermal tolerance data and is therefore a promising new tool for prioritizing adaptation actions that aim to conserve biodiversity in the face of climate change.
Control of the banded fruit weevil Phlyctinus callosus (Coleoptera: Curculionidae) using entomopathogenic nematodes
Authors: Dlamini Bonginkhosi E , Malan Antoinette P , Addison Pia 
Published: February 2019

AbstractPhlyctinus callosus (Schönherr), the banded fruit weevil, is a key pest of deciduous fruit and grapevine in the Western Cape province of South Africa. Entomopathogenic nematodes (EPNs), as a biocontrol agent, are found to be effective in controlling both soilborne and above‐ground insect pests. Different EPN species were screened for virulence against different life stages of P. callosus, followed by a field trial, in which Steinernema yirgalemense was applied at different concentrations. S. yirgalemense, Heterorhabditis noenieputensis and the exotic Steinernema feltiae gave good control of P. callosus larvae at 100 infective juveniles per insect, with no significant difference between treatments. In the case of P. callosus pupae, Heterorhabditis indica (70%) and Heterorhabditis baujardi (67%) differed significantly (P < 0.05) in their control, compared with H. noenieputensis (55%). H. indica (95%) and S. yirgalemense (94%) gave significantly higher (P < 0.05) control of P. callosus adults, compared with the three other nematode species tested. In the field trials, S. yirgalemense, at 20 and 40 infective juveniles/cm2, gave 69% and 78% control of P. callosus larvae after 48 h of exposure, respectively. The results indicated that all EPNs tested were effective against the immature and adult stages of P. callosus, with differences in mortality among the EPN species tested. S. yirgalemense, at low concentration, can effectively control P. callosus under field conditions, but large‐scale field trials are recommended to demonstrate the potential use of this biocontrol agent within integrated pest management programmes.
Surveillance colonoscopies frequently booked earlier than the National Health and Medical Research Council guidelines: findings of a single centre audit
Authors: Bunjo Zachary , Koh Yu Han , Leopardi Lisa , Reid Jessica , Maddern Guy J. , Hewett Peter J. 
Published: February 2019

BackgroundTo assess the adherence rate of surveillance colonoscopy booking intervals to recommended National Health and Medical Research Council guidelines at The Queen Elizabeth Hospital, Adelaide, Australia.MethodsPatients on The Queen Elizabeth Hospital colorectal unit surveillance colonoscopy waiting list were included in this audit. Patient demographics, colonoscopy findings, follow‐up plans and pathology results were analysed. Patients were categorized as normal/non‐neoplastic finding, low‐risk adenomas, high‐risk adenomas, personal history of colorectal cancer (CRC) and family history of CRC. Booked colonoscopy within 2 months of guideline recommended interval was considered correct.ResultsA total of 467 patients were included (59.1% male; mean age 60 years). Two hundred and fifty‐one (53.7%) patients had an incorrect surveillance colonoscopy booking. Twenty‐seven patients with a normal/non‐neoplastic previous colonoscopy not requiring surveillance colonoscopy were incorrectly booked for a colonoscopy. For the 222 patients booked incorrectly and requiring surveillance colonoscopy, 88.7% were early and 11.3% were late. The proportions of incorrect bookings were highest in the low‐risk finding (66.1%) and history of CRC (67.6%) groups. For the 186 patients requiring a 3‐year surveillance interval, 38.7% were booked incorrectly. For the 197 patients requiring a 5‐year surveillance interval, 63.5% were booked incorrectly, of which 99.2% were early. More 5‐year surveillance interval patients were booked at 3 years (n = 79), than at the correct interval of 5 years (n = 72).ConclusionAdherence to the National Health and Medical Research Council guidelines for surveillance colonoscopy is poor. The majority of deviations represent early follow‐up, which is most common among patients with low‐risk findings or history of CRC. There is a tendency towards 3‐year surveillance among low‐risk patients.
Systematic review with meta‐analysis: cholecystectomy for biliary dyskinesia—what can the gallbladder ejection fraction tell us?
Authors: Gudsoorkar Vineet S. , Oglat Ayah , Jain Amita , Raza Ali , Quigley Eamonn M. M. 
Published: February 2019

SummaryBackgroundGallbladder dyskinesia (gallbladder spasm, biliary dyskinesia or chronic acalculous cholecystitis) is a poorly defined entity which presents as biliary‐type pain without any identifiable organic pathology. Abnormal gallbladder ejection fraction (GBEF) is used by some to select those likely to benefit from cholecystectomy. The validity of this approach has been questioned.AimTo systematically review the literature and summarise the evidence surrounding the practice of cholecystectomy based on GBEF for gallbladder dyskinesia.MethodsWe conducted a systematic search of PubMed/MEDLINE and SCOPUS from 1980 to 2016 to identify the relevant literature.ResultsTwenty‐nine studies including 2891 patients were included in the final analysis. In comparing cholecystectomy with medical management, patients with a normal GBEF did not benefit from cholecystectomy; whereas those with low GBEF had a higher chance (RR, relative risk = 2.37) of symptomatic improvement following surgery. When those classified as “low” and “normal” GBEF were compared in terms of outcome following cholecystectomy, the rate of improvement following surgery was similar in the two groups (RR 1.09) which suggests a placebo effect of surgery.ConclusionsWhile a low GBEF may provide some guidance in identifying those with gallbladder dyskinesia who may benefit from cholecystectomy, the available data are inconsistent and based on studies of poor quality which are often subject to bias and the impact of confounding factors. For these reasons, we conclude that the role of scintigraphy and cholecystectomy in the definition and management of this disorder remain unclear pending definitive study.
Blockage of SLC31A1‐dependent copper absorption increases pancreatic cancer cell autophagy to resist cell death
Authors: Yu Ze , Zhou Rongtao , Zhao Yicheng , Pan Yi , Liang Hao , Zhang Jin‐San , Tai Sheng , Jin Liang , Teng Chun‐Bo 
Published: February 2019

AbstractObjectivesClinical observations have demonstrated that copper levels elevate in several cancer types, and copper deprivation is shown to inhibit tumour angiogenesis and growth in both animal models and preclinical trials. However, the content of copper in pancreatic duct adenocarcinoma (PDAC) and whether it is a potential therapy target is still unknown.Materials and MethodsThe levels of copper in PDAC specimens were detected by ICP‐MS assays. Copper depletion in Panc‐1 or MiaPaCa‐2 cells was conducted via copper transporter 1 (SLC31A1) interference and copper chelator tetrathiomolybdate (TM) treatment. The effects of copper deprivation on cancer cells were evaluated by cell proliferation, migration, invasion, colony formation and cell apoptosis. The mechanism of copper deprivation‐caused cancer cell quiescence was resolved through mitochondrial dysfunction tests and autophagy studies. The tumour‐suppression experiments under the condition of copper block and/or autophagy inhibition were performed both in vitro and in xenografted mice.ResultsSLC31A1‐dependent copper levels are correlated with the malignant degree of pancreatic cancer. Blocking copper absorption could inhibit pancreatic cancer progression but did not increase cell death. We found that copper deprivation increased mitochondrial ROS level and decreased ATP level, which rendered cancer cells in a dormant state. Strikingly, copper deprivation caused an increase in autophagy to resist death of pancreatic cancer cells. Simultaneous treatment with TM and autophagy inhibitor CQ increased cell death of cancer cells in vitro and retarded cancer growth in vivo.ConclusionsThese findings reveal that copper deprivation‐caused cell dormancy and the increase in autophagy is a reason for the poor clinical outcome obtained from copper depletion therapies for cancers. Therefore, the combination of autophagy inhibition and copper depletion is potentially a novel strategy for the treatment of pancreatic cancer and other copper‐dependent malignant tumours.
Interannual variation of the diet shifts and their effects on the fatness and growth of age‐0 Pacific bluefin tuna (Thunnus orientalis) off the southwestern Pacific coast of Japan
Authors: Hiraoka Yuko , Fujioka Ko , Fukuda Hiromu , Watai Mikio , Ohshimo Seiji 
Published: February 2019

AbstractWe investigated the effect of feeding habits on the fatness (length–weight relationship (LW)) and otolith growth of age‐0 Pacific bluefin tuna (PBF) (fork length (FL) of 15.0–29.9 cm) collected off the southwestern Pacific coast of Japan from July to August during 2010–2015. The feeding rate on Clupeiformes (FRc) was substantially influenced by the path of the Kuroshio Current during early summer. We suggest that the following patterns occurred in the feeding habits of PBF. In 2012 and 2014, the short distance from the coast to the Kuroshio provided high overlap between PBF and Clupeiformes and increased the opportunity for feeding, and this pattern likely caused the observed diet shift from Crustacea to Clupeiformes by smaller PBF in the studied years than those in other years. In 2011 and 2015, the encounter probability for Clupeiformes might have been low due to the long distance to the Kuroshio Current, which led PBF to actively consume non‐Clupeiformes Teleostei. In contrast, in August 2010 and 2015, PBF did not encounter Clupeiformes or other Teleostei and may have been forced to feed on a large number of Crustacea; this effect was likely due to high water temperatures. Despite the interannual fluctuation in the timing of the diet shift and the feeding intensity (FI), these factors did not contribute to growth in length; rather, they contributed to fatness. Considering size‐dependent mortality in the larval stage, these results suggest that only fast‐growing individuals survive, even if the feeding conditions drastically change.
Resilience and affect balance of empty‐nest older adults with mild cognitive impairment in poor rural areas of Hunan province, China
Authors: Xie LiQin , Zhou Jun , Deng YunLong , Richmond Christopher J , Na Jiang 
Published: February 2019

AimTo evaluate the prevalence of mild cognitive impairment (MCI) within the empty‐nest older adults population in poor rural areas of the Hunan province of China, and to explore the effects of resilience and affective balance on cognitive functioning within this specific population.MethodsA cross‐sectional, multistage, random cluster survey was administered to participants from March 2013 to December 2014 in the Hunan province. There were a total of 1164 participants. These participants were empty‐nest older adults who were residing in poor rural areas of the Hunan province. The data was collected in two stages. In stage 1, the participants were administered the Montreal Cognitive Assessment for screening cognitive impairment. In stage 2, the participants were screened for any potential cognitive impairment, were administered a series of neuropsychological tests and received a definitive diagnosis for MCI, if the criteria were met. Resilience and affect balance were assessed by the Chinese modified version of the Stress Resilience Quotient and the Affect Balance Scale.ResultsThe prevalence of MCI was 38.40% within this empty‐nest older adult population. Significant differences were found between MCI and non‐MCI empty‐nest older adults specific to resilience and affect balance. Path analysis showed that resilience mediated the relationship between MCI and affect balance.ConclusionsResilience and affect balance were less prominent within the MCI empty‐nest older adults than those in the non‐MCI group. The results suggest that resilience is a mediating variable between MCI and affect balance. Geriatr Gerontol Int 2019; 19: 222–227.