bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producingEnterobacter hormaechei
Authors: Roberts Leah W. , Harris Patrick N. A. , Forde Brian M. , Ben Zakour Nouri L. , Stanton-Cook Mitchell , Catchpoole Elizabeth , Phan Minh-Duy , Sidjabat Hanna E. , Bergh Haakon , Heney Claire , Gawthorne Jayde A. , Lipman Jeffrey , Allworth Anthony , Chan Kok-Gan , Chong Teik Min , Yin Wai-Fong , Schembri Mark A. , Paterson David L. , Beatson Scott A. 
Published: August 2017

AbstractCarbapenem-resistant Enterobacteriaceae (CRE) represent one of the most urgent threats to human health posed by antibiotic resistant bacteria.Enterobacter hormaecheiand other members of theEnterobacter cloacaecomplex are the most commonly encounteredEnterobacterspp. within clinical settings, responsible for numerous outbreaks and ultimately poorer patient outcomes. Here we applied three complementary whole genome sequencing (WGS) technologies to characterise a hospital cluster ofblaIMP-4carbapenemase-producingE. hormaechei.In response to a suspected CRE outbreak in 2015 within an Intensive Care Unit (ICU)/Burns Unit in a Brisbane tertiary referral hospital we used Illumina sequencing to determine that all outbreak isolates were sequence type (ST)90 and near-identical at the core genome level. Comparison to publicly available data unequivocally linked all 10 isolates to a 2013 isolate from the same ward, confirming the hospital environment as the most likely original source of infection in the 2015 cases. No clonal relationship was found to IMP-4-producing isolates identified from other local hospitals. However, using Pacific Biosciences long-read sequencing we were able to resolve the complete context of theblaIMP-4gene, which was found to be on a large IncHI2 plasmid carried by all IMP-4-producing isolates. Continued surveillance of the hospital environment was carried out using Oxford Nanopore long-read sequencing, which was able to rapidly resolve the true relationship of subsequent isolates to the initial outbreak. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90E. hormaecheiand the IncHI2 plasmid within the hospital plumbing.Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak, including the transmission dynamics of a carbapenemase-producingE. hormaecheicluster, identification of possible hospital reservoirs and the full context ofblaIMP-4on a multidrug resistant IncHI2 plasmid that appears to be widely distributed in Australia.
Clearance of senescent decidual cells by uterine natural killer cells drives endometrial remodeling during the window of implantation
Authors: Brighton Paul J , Maruyama Yojiro , Fishwick Katherine , Vrljicak Pavle , Tewary Shreeya , Fujihara Risa , Muter Joanne , Lucas Emma S , Yamada Taihei , Woods Laura , Lucciola Raffaella , Lee Yie Hou , Takeda Satoru , Ott Sascha , Hemberger Myriam , Quenby Siobhan , Brosens Jan J 
Published: August 2017

SummaryIn cycling human endometrium, menstruation is followed by rapid estrogen-dependent growth. Upon ovulation, progesterone and rising cellular cAMP levels activate the transcription factor Forkhead box O1 (FOXO1) in endometrial stromal cells (EnSCs), leading to cell cycle exit and differentiation into decidual cells that control embryo implantation. Here we show that FOXO1 also causes acute senescence of a subpopulation of decidualizing EnSCs in an IL-8 dependent manner. Selective depletion or enrichment of this subpopulation revealed that decidual senescence drives the transient inflammatory response associated with endometrial receptivity. Further, senescent cells prevent differentiation of endometrial mesenchymal stem cells in decidualizing cultures. As the cycle progresses, IL-15 activated uterine natural killer (uNK) cells selectively target and clear senescent decidual cells through granule exocytosis. Our findings reveal that acute decidual senescence governs endometrial rejuvenation and remodeling at embryo implantation, and suggest a critical role for uNK cells in maintaining homeostasis in cycling endometrium.
Structural Basis of Mitochondrial Receptor Binding and GTP-Driven Conformational Constriction by Dynamin-Related Protein 1
Authors: Kalia Raghav , Wang Ray Yu-Ruei , Yusuf Ali , Thomas Paul V. , Agard David A. , Shaw Janet M. , Frost Adam 
Published: August 2017

AbstractMitochondrial inheritance, genome maintenance, and metabolic adaptation all depend on organelle fission byDynamin-RelatedProtein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogsMitochondrialDynamics 49 and 51 (MID49/MID51) andMitochondrialFissionFactor (MFF), but the mechanisms by which these proteins recruit DRP1 and regulate its activities are unknown. Here we present a cryoEM structure of human, full-length DRP1 bound to MID49 and an analysis of structure- and disease-based mutations. We report that GTP binding allosterically induces a remarkable elongation and rotation of the G-domain, Bundle-Signaling Element (BSE) and connecting hinge loops of DRP1. In this nucleotide-bound conformation, a distributed network of multivalent interactions promotes DRP1 copolymerization into a linear filament with MID49, MID51 or both. Subsequent GTP hydrolysis and exchange within the filament leads to receptor dissociation, shortening through disassembly, and concomitant curling of DRP1 oligomers into closed rings. The dimensions of the closed DRP1 rings are consistent with DRP1-constricted mitochondrial tubules observed in human cells. These structures are the first views of full-length, receptor- and nucleotide-bound dynamin-family GTPases and—in comparison with nucleotide-free crystal structures—teach us how these molecular machines perform mechanical work through nucleotide-driven allostery.
Edge effects on components of diversity and above‐ground biomass in a tropical rainforest
Authors: Razafindratsima Onja H. , Brown Kerry A. , Carvalho Fabio , Johnson Steig E. , Wright Patricia C. , Dunham Amy E. 
Published: August 2017

Abstract

Edge effects are among the most significant consequences of forest fragmentation. Therefore, understanding the impacts of edge creation on biodiversity is crucial for forest management and biological conservation.

In this study, we used trait‐based and phylogenetic approaches to examine the effects of fragmentation on components of diversity and above‐ground biomass of rainforest tree communities in Madagascar in forest edge vs. interior habitats.

Tree communities in forest edges showed lower phylogenetic diversity relative to those in interior habitats, suggesting that some clades may be more vulnerable to environmental filtering than others. Functional diversity was also significantly lower on the edge for productivity traits, but not for dispersal traits. Tree communities in the forest edge showed higher divergence of dispersal traits and lower divergence in productivity traits than expected, while functional diversity in interior forest did not differ from random expectations. This suggests that separate mechanisms affect productivity traits vs. dispersal traits in edge habitats.

There was no significant difference in above‐ground biomass between edge and interior habitats, suggesting that edge effects have not yet negatively influenced the forest's potential for carbon storage. However, these changes may not have occurred yet, given the slow turnover of tree communities.

Synthesis and applications. Our results highlight the role of edge effects in the erosion of functional and phylogenetic diversity of highly diverse tree communities. While above‐ground biomass did not appear to be affected by forest edge in our study, we suggest long‐term monitoring of forests for potential changes in ecosystem functioning. These findings also indicate the need to reduce edge creation and buffer existing edges for holistic biodiversity conservation.
Current Status of Gender and Racial/Ethnic Disparities Among Academic Emergency Medicine Physicians
Authors: Madsen Tracy E. , Linden Judith A. , Rounds Kirsten , Hsieh Yu‐Hsiang , Lopez Bernard L. , Boatright Dowin , Garg Nidhi , Heron Sheryl L. , Jameson Amy , Kass Dara , Lall Michelle D. , Melendez Ashley M. , Scheulen James J. , Sethuraman Kinjal N. , Westafer Lauren M. , Safdar Basmah 
Published: August 2017

AbstractObjectiveA 2010 survey identified disparities in salaries by gender and underrepresented minorities (URM). With an increase in the emergency medicine (EM) workforce since, we aimed to 1) describe the current status of academic EM workforce by gender, race, and rank and 2) evaluate if disparities still exist in salary or rank by gender.MethodsInformation on demographics, rank, clinical commitment, and base and total annual salary for full‐time faculty members in U.S. academic emergency departments were collected in 2015 via the Academy of Administrators in Academic Emergency Medicine (AAAEM) Salary Survey. Multiple linear regression was used to compare salary by gender while controlling for confounders.ResultsResponse rate was 47% (47/101), yielding data on 1,371 full‐time faculty: 33% women, 78% white, 4% black, 5% Asian, 3% Asian Indian, 4% other, and 7% unknown race. Comparing white race to nonwhite, 62% versus 69% were instructor/assistant, 23% versus 20% were associate, and 15% versus 10% were full professors. Comparing women to men, 74% versus 59% were instructor/assistant, 19% versus 24% were associate, and 7% versus 17% were full professors. Of 113 chair/vice‐chair positions, only 15% were women, and 18% were nonwhite. Women were more often fellowship trained (37% vs. 31%), less often core faculty (59% vs. 64%), with fewer administrative roles (47% vs. 57%; all p < 0.05) but worked similar clinical hours (mean ± SD = 1,069 ± 371 hours vs. 1,051 ± 393 hours). Mean overall salary was $278,631 (SD ± $68,003). The mean (±SD) salary of women was $19,418 (±$3,736) less than men (p < 0.001), even after adjusting for race, region, rank, years of experience, clinical hours, core faculty status, administrative roles, board certification, and fellowship training.ConclusionsIn 2015, disparities in salary and rank persist among full‐time U.S. academic EM faculty. There were gender and URM disparities in rank and leadership positions. Women earned less than men regardless of rank, clinical hours, or training. Future efforts should focus on evaluating salary data by race and developing systemwide practices to eliminate disparities.
Ecological momentary analysis of the relations among stressful events, affective reactivity, and smoking among smokers with high versus low depressive symptoms during a quit attempt
Authors: Minami Haruka , Frank Brandon E. , Bold Krysten W. , McCarthy Danielle E. 
Published: August 2017

AbstractAimsTo assess whether individuals trying to quit smoking who have high depressive symptoms (HD), compared with low depressive symptoms (LD): (1) report more frequent stressful events (SEs), (2) are more likely to smoke after SEs, (3) experience greater acute or persistent changes in affect after an SE, and (4) are at greater risk of smoking following affective changes.DesignSmoking cessation data were analyzed using multi‐level path modeling to examine the moderating effects of depressive symptoms on relations among SEs, subsequent affect, and smoking.SettingAn academic research center in Central New Jersey, USA.ParticipantsSeventy‐one adult treatment‐seeking daily smokers recruited from 2010 to 2012.MeasurementsBaseline depressive symptoms [HD: Center for Epidemiological Studies Depression Scale (CES‐D) ≥ 16 versus LD: CES‐D < 16]; and real‐time ecological momentary assessment (EMA) reports of SEs, affect, and smoking assessed during 21 days post‐quit.FindingsMulti‐level models indicated that HD smokers were more likely than LD smokers to report stressful events [odds ratio (OR) = 2.323, P = 0.009], but had similar post‐stress acute affective changes (negative affect: b = −0.117, P = 0.137, positive affect: b = 0.020, P = 0.805). Only HD smokers reported increased negative affect (NA) (b = 0.199, P = 0.030) and decreased positive affect (PA) up to 12 hours later (b = −0.217, P = 0.021), and greater lapse risk up to 24 hours after an SE (OR = 3.213, P = 0.017). The persistence of elevated NA and suppressed PA was partially explained by increased odds of subsequent SEs among HD smokers. However, the heightened stress–lapse association over 24 hours found in HD smokers was not fully explained by sustained aversive affect or subsequent SEs.ConclusionsDepressed and non‐depressed smokers trying to quit appear to experience similar acute affective changes following stress: however, depressed smokers experience higher rates of exposure to stress, longer‐lasting post‐stress affective disturbance and greater risk of smoking lapse 12–24 hours after a stressful event than non‐depressed smokers.
Prenatal early food and multiple micronutrient supplementation trial reduced infant mortality in Bangladesh, but did not influence morbidity
Authors: Kallioinen Maija , Ekström Eva‐Charlotte , Khan Ashraful Islam , Lindström Emma , Persson Lars Åke , Rahman Anisur , Selling Katarina Ekholm 
Published: August 2017

AbstractAimA previous maternal and infant nutrition intervention in rural Matlab, Bangladesh, showed that prenatal nutrient supplements improved child survival, but had no effect on size at birth. This secondary analysis examined whether prenatal multiple micronutrient supplements (MMS), on their own or combined with an early invitation to receive prenatal food supplements, affected child morbidity.MethodsThis randomised trial enrolled 4436 pregnant women from November 2001 to October 2003 and allocated them to early or standard invitations to food supplements, in the ninth and 20th weeks of pregnancy, respectively, and supplements of either the standard 60 mg iron with 400 μg folic acid, 30 mg iron with 400 μg folic acid or MMS. Quasi‐Poisson regression was used to analyse morbidity.ResultsThere were 3560 single live births and 3516 had morbidity data. The incidence rates of fever, diarrhoea and acute lower respiratory tract infection were 15.3, 3.6 and 2.3 episodes per person‐year, respectively. The separate or combined interventions had no effect on morbidity up to 24 months.ConclusionEarly invitations to prenatal food supplements or prenatal MMS had no effect on common infections in rural Bangladesh, suggesting that earlier findings on improved child survival were not mediated by an effect on child morbidity.
Longitudinal tracking of academic progress during teacher preparation
Authors: Corcoran Roisin P. , O'Flaherty Joanne 
Published: August 2017

BackgroundGiven that the ultimate academic goal of many education systems in the developed world is for students to graduate from college, grades have a considerable bearing on how effective colleges are in meeting their primary objective. Prior academic performance informs predominantly the selection and retention of teacher candidates. However, there remains a dearth of evidence linking academic performance with outcomes in teacher preparation or the workplace.AimThis study examined pre‐service teachers' trajectories of academic growth during teacher preparation.SampleThe sample comprised 398 pre‐service teachers – 282 (70.8%) males and 116 (29.1%) females.MethodAcademic growth was measured across eight time points over the course of 4 years. Pre‐service teachers' academic growth was analysed using linear and nonlinear latent growth models.ResultsResults indicate that academic growth was quadratic and, over time, decelerated, with no evidence of the Matthew effect or the compensatory effect. There was evidence of a connection between prior academic attainment and current grades.ConclusionGreater attention to academic growth during the college years, and particularly among pre‐service teachers, may enable greater achievement support for students.
Tectono‐sedimentary evolution of the Plio‐Pleistocene Corinth rift, Greece
Authors: Gawthorpe Robert L. , Leeder Mike R. , Kranis Haralambos , Skourtsos Emmanuel , Andrews Julian E. , Henstra Gijs A. , Mack Greg H. , Muravchik Martin , Turner Jenni A. , Stamatakis Michael 
Published: August 2017

AbstractThe onshore central Corinth rift contains a syn‐rift succession >3 km thick deposited in 5–15 km‐wide tilt blocks, all now inactive, uplifted and deeply incised. This part of the rift records upward deepening from fluviatile to lake‐margin conditions and finally to sub‐lacustrine turbidite channel and lobe complexes, and deep‐water lacustrine conditions (Lake Corinth) were established over most of the rift by 3.6 Ma. This succession represents the first of two phases of rift development – Rift 1 from 5.0–3.6 to 2.2–1.8 Ma and Rift 2 from 2.2–1.8 Ma to present. Rift 1 developed as a 30 km‐wide zone of distributed normal faulting. The lake was fed by four major N‐ to NE‐flowing antecedent drainages along the southern rift flank. These sourced an axial fluvial system, Gilbert fan deltas and deep lacustrine turbidite channel and lobe complexes. The onset of Rift 2 and abandonment of Rift 1 involved a 30 km northward shift in the locus of rifting. In the west, giant Gilbert deltas built into a deepening lake depocentre in the hanging wall of the newly developing southern border fault system. Footwall and regional uplift progressively destroyed Lake Corinth in the central and eastern parts of the rift, producing a staircase of deltaic and, following drainage reversal, shallow marine terraces descending from >1000 m to present‐day sea level. The growth, linkage and death of normal faults during the two phases of rifting are interpreted to reflect self‐organization and strain localization along co‐linear border faults. In the west, interaction with the Patras rift occurred along the major Patras dextral strike‐slip fault. This led to enhanced migration of fault activity, uplift and incision of some early Rift 2 fan deltas, and opening of the Rion Straits at ca. 400–600 ka. The landscape and stratigraphic evolution of the rift was strongly influenced by regional palaeotopographic variations and local antecedent drainage, both inherited from the Hellenide fold and thrust belt.
Cytokine responses to exercise and activity in patients with chronic fatigue syndrome: case–control study
Authors: Clark L V , Buckland M , Murphy G , Taylor N , Vleck V , Mein C , Wozniak E , Smuk M , White P D 
Published: August 2017

SummaryChronic fatigue syndrome (CFS) is characterized by fatigue after exertion. A systematic review suggested that transforming growth factor (TGF)-β concentrations are often elevated in cases of CFS when compared to healthy controls. This study attempted to replicate this finding and investigate whether post-exertional symptoms were associated with altered cytokine protein concentrations and their RNA in CFS patients. Twenty-four patients fulfilling Centers for Disease Control criteria for CFS, but with no comorbid psychiatric disorders, were recruited from two CFS clinics in London, UK. Twenty-one healthy, sedentary controls were matched by gender, age and other variables. Circulating proteins and RNA were measured for TGF-β, tumour necrosis factor (TNF), interleukin (IL)-8, IL-6 and IL-1β. We measured six further cytokine protein concentrations (IL-2, IL-4, IL-5, IL-10, IL-12p70, and interferon (IFN)-γ). Measures were taken at rest, and before and after both commuting and aerobic exercise. CFS cases had higher TGF-β protein levels compared to controls at rest (median (quartiles) = 43·9 (19·2, 61·8) versus 18·9 (16·1, 30·0) ng/ml) (P = 0·003), and consistently so over a 9-day period. However, this was a spurious finding due to variation between different assay batches. There were no differences between groups in changes to TGF-β protein concentrations after either commuting or exercise. All other cytokine protein and RNA levels were similar between cases and controls. Post-exertional symptoms and perceived effort were not associated with any increased cytokines. We were unable to replicate previously found elevations in circulating cytokine concentrations, suggesting that elevated circulating cytokines are not important in the pathophysiology of CFS.
A randomized double‐blind controlled trial comparing three sedation regimens during flexible bronchoscopy: Dexmedetomidine, alfentanil and lidocaine
Authors: Riachy Moussa , Khayat Georges , Ibrahim Ihab , Aoun Zeina , Dabar Georges , Bazarbachi Taha , Khalil Nadine , Habr Bassem 
Published: August 2017

AbstractIntroductionNo standardized sedation protocol is available for flexible bronchoscopy (FB).ObjectivesThe aim of this study was to evaluate the efficacy and safety of three regimens used for sedation during FB.MethodsThis randomized double‐blind controlled trial assessed patients undergoing bronchoscopy and receiving lidocaine alone (C) or combined with dexmedetomidine (D) or alfentanil (A). Tolerance was assessed using the bronchoscopy score, and level of sedation was assessed using the Nursing Instrument for the Communication of Sedation. Safety was evaluated in terms of pulmonary function and vital signs.ResultsA total of 162 patients were enrolled. The bronchoscopy score was identical in all groups. Group D subjects were the most sedated (P = .013), whereas group A subjects were the least agitated. Linear regression showed a negative association between bronchoscopy score and age in A (β = –0.06; P = .001). Positive predictors of bronchoscopy score were female gender (β = 1.96; P = .003) in D and obesity (β = 2.41; P = .012), longer procedures (β = 0.08; P = .009) and female gender (β = 1.15; P = .038) in C. Longer procedures (β = –0.12; P = .010) was a negative predictor of bronchoscopy score in D. Desaturation, hypoxia and heart rate changes were most prevalent in group A. Hypotension was mostly observed in D.ConclusionsNo consistent differences were present between the three regimens; however, each was more appropriate in certain patient profiles. We consequently proposed a protocol as a first step towards standardizing sedation practice in FB in a patient‐tailored manner. A more comprehensive and detailed protocol including other sedative agents with their corresponding doses should be developed.
How is chronic non‐communicable respiratory conditions research reported in European newspapers? An impact assessment for policy
Authors: Pallari Elena , Lewison Grant , Sullivan Richard 
Published: August 2017

AbstractBackgroundNewspapers are an important means for the communication of medical research findings to policy‐makers and the public, but may distort their views on the relative importance of research into, and burden from, different respiratory diseases.MethodsA systematic search strategy based on respiratory‐related keywords was developed and translated into 15 European languages to identify relevant stories in 26 newspapers from eight countries in 2002‐2013. Details of the stories were recorded on Excel and coded based on the reported respiratory conditions (asthma, chronic obstructive pulmonary disease (COPD) and other) and research types. Each cited research study was identified on the Web of Science and downloaded for analysis.FindingsThere were far more stories about asthma than on COPD, although the amount of research was only modestly greater, and the disease burden far less. Epidemiology, lifestyle and genetics research received the most media attention but not in all newspapers, while means of diagnosis and quality of life were under‐reported in all newspapers. Journalists tended to over‐cite research from their country by a factor averaging four times more than other researchers. About 10% of stories included a quote from a commentator, especially those in the two UK newspapers, with most of the quotes from UK charities.ConclusionsThe balance between disease areas reported in European newspaper stories is very misleading. European policy‐makers and public may perceive asthma as more burdensome than it is and COPD much less. The study also showed that UK charities, but not those in other European countries, gained significant publicity from their contributions to these stories.