bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical risk factors, bacterial aetiology, and outcome of urinary tract infection in children hospitalized with diarrhoea in Bangladesh
Authors: DAS R. , AHMED T. , SAHA H. , SHAHRIN L. , AFROZE F. , SHAHID A. S. M. S. B. , SHAHUNJA K. M. , BARDHAN P. K. , CHISTI M. J. 
Published: December 2016

SUMMARYUrinary tract infection (UTI) is common in children aged <5 years with diarrhoea, but little is known about risk factors, aetiology and outcome of such children. We aimed to evaluate these knowledge gaps of UTI in children aged <5 years with diarrhoea. We enrolled all children aged <5 years with diarrhoea admitted to Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh, between May 2011 and April 2013, who had history of fever (⩾38 °C) and obtained a urine sample for culture. Diarrhoea with UTI (confirmed by culture) constituted cases (n= 26) and those without UTI constituted controls (n= 78). Threefold controls were randomly selected. The case-fatality rate was comparable in cases and controls (4%vs. 1%,P= 0·439).Escherichia coli(69%) andKlebsiella(15%) were the most commonly isolated pathogens. Persistent diarrhoea, pneumonia and prior antibiotics use were identified as risk factors for UTI in logistic regression analysis (P< 0·05 for all). Thus, children with diarrhoea presenting with persistent diarrhoea, pneumonia, and prior antibiotic use should be investigated for UTI for their prompt management that may reduce morbidity.
Two levels of specialization in bacteraemicEscherichia colistrains revealed by their comparison with commensal strains
Authors: CLERMONT O. , COUFFIGNAL C. , BLANCO J. , MENTRÉ F. , PICARD B. , DENAMUR E. ,   the COLIVILLE and COLIBAFI groups
Published: December 2016

SUMMARYBacteraemia caused byEscherichia coliare particularly frequent and severe, contrasting with the commensal character of the strains found in the digestive tract. A better understanding of the relationships between strains of both origins is needed to unravel the pathogenesis of this disease. Two hundred and forty-three commensal strains were compared to 243 bacteraemic strains isolated from adult hosts matched in terms of gender and age, and from similar location and epoch. Phylogenetic grouping, O-type determination, virulence factor content and antibiotic resistance were compared. Compared to commensal strains, the bacteraemic strains were characterized by a higher proportion of B2, C and D phylogroups, and a lower proportion of A, E and F phylogroups. They also had a lower proportion of the B2 subgroup IV (STc141), a higher proportion of virulence factors, and a higher frequency of antibiotic resistance. These differences were more marked for the bacteraemic strains of urinary tract origin with the presence of specific clones, whereas the bacteraemic strains of digestive origin remained non-significantly different from the commensal strains, except for their antibiotic resistance. Thus, two levels of specialization from commensal strains were demonstrated in the bacteraemic strains: resistance to antibiotics in all cases, and virulence for those of urinary tract origin.
Impact of national policies on the microbial aetiology of surgical site infections in acute NHS hospitals in England: analysis of trends between 2000 and 2013 using multi-centre prospective cohort data
Authors: ELGOHARI S. , WILSON J. , SAEI A. , SHERIDAN E. A. , LAMAGNI T. 
Published: December 2016

SUMMARYOur study aimed to evaluate changes in the epidemiology of pathogens causing surgical site infections (SSIs) in England between 2000 and 2013 in the context of intensified national interventions to reduce healthcare-associated infections introduced since 2006. National prospective surveillance data on target surgical procedures were used for this study. Data on causative organism were available for 72% of inpatient-detected SSIs meeting the standard case definitions for superficial, deep and organ-space infections (9767/13 531) which were analysed for trends. A multivariable logistic linear mixed model with hospital random effects was fitted to evaluate trends by pathogen. Staphylococcus aureus was the predominant cause of SSI between 2000 (41%) and 2009 (24%), decreasing from 2006 onwards reaching 16% in 2013. Data for 2005–2013 showed that the odds of SSI caused by S. aureus decreased significantly by 14% per year [adjusted odds ratio (aOR) 0·86, 95% confidence interval (CI) 0·83–0·89] driven by significant decreases in methicillin-resistant S. aureus (MRSA) (aOR 0·71, 95% CI 0·68–0·75). However a small significant increase in methicillin-sensitive S. aureus was identified (aOR 1·06, 95% CI 1·02–1·10). Enterobacteriaceae were stable during 2000–2007 (12% of cases overall), increasing from 2008 (18%) onwards, being present in 25% of cases in 2013; the model supported these increasing trends during 2007–2013 (aOR 1·12, 95% CI 1·07–1·18). The decreasing trends in S. aureus SSIs from 2006 and the increases in Enterobacteriaceae SSIs from 2008 may be related to intensified national efforts targeted at reducing MRSA bacteraemia combined with changes in antibiotic use aimed at controlling C. difficile infections.
Up the Value Chain: Transition from Law Librarian to Research Analyst
Authors: Marshall Helen , Taylor Kelly 
Published: December 2016

AbstractThis paper is based on a parallel session at the BIALL Conference 2016 which was given by Helen Marshall and Kelly Taylor from Pinsent Masons. Pinsent Masons has a ground-breaking team of research analysts providing the firm with in-depth sector and market analysis. This innovative approach has benefits for Pinsent Masons and also for the research team. These include increased visibility within the firm and developing a role as a trusted adviser to the business. The team are drawn from a variety of backgrounds, including experienced law librarians. In this article, Kelly and Helen, who are both from a law librarian background, will explain Pinsents' unique approach to business and sector insight. The article covers how the team adds value to the firm and charts the development of our existing skillsets to meet this new challenge. The article also includes some practical insight into approaching business research and how to overcome common obstacles, notably the challenge in expanding our output from traditional legal research to more business and commercially aware pieces.
Land rights and neoliberalism: an irreconcilable conflict for indigenous peoples in India?
Authors: Sigamany Indrani 
Published: December 2016

AbstractDoes legislation that grants land rights necessarily ensure justice? The Forest Rights Act of 2006 (FRA) in India, a landmark social justice law, aims to enhance land security for forest peoples. Increasingly displaced by development and extractive industries that intensify impoverishment, indigenous peoples in India should, with the FRA, be able to protect their land, their livelihoods and their culture. Continued government violations of forest land rights in the name of development highlight that economically vulnerable populations lack the power to take advantage of legislation. I examine the tension of current indigenous land struggles in the context of the legal frameworks of the FRA and the neoliberal culture of India.
Twenty years after Novye Atagi: A call to care for the carers
Authors: Hensch Christoph 
Published: December 2016

AbstractWorking in the humanitarian sector as an aid worker has become a dangerous endeavour, with attacks against humanitarian workers becoming more common. In this personal story by a former head of office at an International Committee of the Red Cross (ICRC) surgical hospital, a short, violent encounter leads to a long journey of recovery. There is an important role for the community in supporting the healing process; the author suggests that an integral and collaborative involvement by organizations like the ICRC is effective in addressing the impact of violence directed towards humanitarian aid workers.
Dysphagia in Persons with Dementia: The Dual Diagnosis Challenge
Authors: Tristani Michelle 
Published: December 2016

“While there is life, we must provide quality of life.” Paul Raia
Swallowing and cognition have always been considered two major contributors to quality of life. It's interesting to note, for example, when someone asks for directions, instructions are often provided by using favorite restaurants as landmarks. It is customary for many people spend significant amounts of time and effort accessing executive functions to plan, organize, and cook daily meals as well as to prepare for special occasions and holidays. The enjoyment experienced by sharing a meal with friends and family members is positively anticipated.
The evaluation of functional and quality of life outcomes continues to emerge as a vital component of state-of-the-art health care. Specific to the field of medical speech-language pathology, any discussions pertaining to dementia and/or dysphagia bring quality of life issues to the forefront. Dysphagia as a sequelae of dementia is understood to have significant negative impacts on quality of life due to the challenges associated with its management in persons with progressive, degenerative neuropathology and resulting cognitive, sensory, and motor decline.
Altered Regional Myocardial Mechanics in Transplanted Hearts: Influence of Time and Transplantation
Authors: Stephan Anna , Grundmann Sebastian , Föll Daniela , Beyersdorf Friedhelm , Bode Christoph , Geibel Annette , Wengenmayer Tobias 
Published: December 2016

Background Global longitudinal strain is reduced in heart transplant recipients, but little is known about regional contractility of the transplanted heart. Moreover, it is unclear if factors such as time after transplant and ischemic time have an influence on regional contractility. To test for regional changes in myocardial deformation, we assessed regional myocardial deformation using three-dimensional speckle tracking echocardiography in heart transplant recipients and controls.
Methods Global and regional longitudinal, circumferential, and radial strain was assessed in 51 heart transplant recipients and a control group of healthy individuals (n = 26). Moreover, we correlated regional contractility with clinical characteristics and compared subgroups of heart transplant recipients with normal (n = 32) and reduced left ventricular ejection fraction (n = 32).
Results Global longitudinal and circumferential strain was significantly reduced in all heart transplant recipients, as well as in the transplant group with normal ejection fraction compared with the control group (p < 0.001). Global radial strain (GRS) was elevated in both transplant groups, but was significantly higher in transplant recipients with normal ejection fraction compared with the control group (p < 0.01). Both transplant groups revealed lower longitudinal and circumferential strain values in the mid- and apical regions (p < 0.001), whereas longitudinal and circumferential strain was higher in the basal region (p < 0.01). In both groups, transplanted hearts showed increased radial strain in the basal (p < 0.05, p < 0.01) and midregions (p = 0.22; p < 0.01) and did not differ in the apical regions. Cold ischemic time (150 ± 12.6 minutes) was independently associated with reduction in circumferential strain. Time since transplantation ranging from 18 days to 21 years had no effect on myocardial deformation parameters.
Conclusion Left ventricular mechanics in transplanted hearts display significantly different systolic deformation patterns than native hearts. Strain capability forms a regional gradient from the base toward the apex. The presence of a time-independent deformation pattern and the correlation with cold ischemic time suggest damage induced by the transplantation itself. These findings might be important for understanding pseudo-abnormal echocardiograms in heart transplant patients.
Nrf2 mitigates LRRK2- and α-synuclein–induced neurodegeneration by modulating proteostasis
Authors: Skibinski Gaia , Hwang Vicky , Ando Dale Michael , Daub Aaron , Lee Alicia K. , Ravisankar Abinaya , Modan Sara , Finucane Mariel M. , Shaby Benjamin A. , Finkbeiner Steven 
Published: December 2016

Significance
The prevailing view of nuclear factor erythroid 2-related factor (Nrf2) function in the central nervous system is that it acts by a cell-nonautonomous mechanism to activate a program of gene expression that mitigates reactive oxygen species and the damage that ensues. Our work significantly expands the biological understanding of Nrf2 by showing that Nrf2 mitigates toxicity induced by α-synuclein and leucine-rich repeat kinase 2 (LRRK2), by potently promoting neuronal protein homeostasis in a cell-autonomous and time-dependent fashion. Nrf2 accelerates the clearance of α-synuclein, shortening its half-life and leading to lower overall levels of α-synuclein. By contrast, Nrf2 promotes the aggregation of LRRK2 into inclusion bodies, leading to a significant reduction in diffuse mutant LRRK2 levels elsewhere in the neuron.
Relationship between local structure and relaxation in out-of-equilibrium glassy systems
Authors: Schoenholz Samuel S. , Cubuk Ekin D. , Kaxiras Efthimios , Liu Andrea J. 
Published: December 2016

Significance
A key stumbling block in the study of out-of-equilibrium systems is that their properties depend not only on their current state but also on the manner in which the systems were prepared. Therefore, to understand generic systems out of equilibrium one must take into account the entire history of their preparation. Here we show that the history dependence of a widely studied model of a glass is captured by a quantity that depends only on the positions of the constituent particles. This quantity, called softness, is designed to be a structural order parameter for dynamics in glassy liquids. Our results suggest that a large class of out-of-equilibrium glasses can be understood by augmenting the usual state variables by the instantaneous softness distribution.
Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core
Authors: Chen Yujie , Tokuda Joshua M. , Topping Traci , Meisburger Steve P. , Pabit Suzette A. , Gloss Lisa M. , Pollack Lois 
Published: December 2016

Significance
Nucleosomes are fundamental protein–DNA structures through which eukaryotes package and organize DNA inside the nucleus. Nucleosomes are disassembled to gain access to the critical information stored in DNA. Here, we describe a new experimental approach that characterizes the kinetics of nucleosome disassembly and the synergy between DNA conformation and protein components. Using NaCl to disrupt electrostatic interactions, we identify kinetic pathways and transient intermediates that reveal how DNA unwrapping and protein dissociation are linked in this macromolecular complex. These dynamic structures may provide new insight into the regulation of DNA access during transcription, replication, and repair.
High fishery catches through trophic cascades in China
Authors: Szuwalski Cody S. , Burgess Matthew G. , Costello Christopher , Gaines Steven D. 
Published: December 2016

Significance
Fishing marine ecosystems indiscriminately and intensely can have negative impacts on biodiversity, but it may increase the biomass of fish available for capture in the system. We explore the possibility that China’s high fishery catches are a result of predator removal using an ecosystem model of the East China Sea (ECS). We show that China’s high fishery catches can be explained by the removal of larger predatory fish and consequent increases in the production of smaller fish. We project that single-species management would decrease catches in the ECS by reversing these ecosystem effects. Fisheries similar to those in China produce a large fraction of global catch; management reform in these areas must consider the entire ecosystem, rather than individual species.
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
Authors: Janouškovec Jan , Gavelis Gregory S. , Burki Fabien , Dinh Donna , Bachvaroff Tsvetan R. , Gornik Sebastian G. , Bright Kelley J. , Imanian Behzad , Strom Suzanne L. , Delwiche Charles F. , Waller Ross F. , Fensome Robert A. , Leander Brian S. , Rohwer Forest L. , Saldarriaga Juan F. 
Published: December 2016

Significance
We created a dataset of dinoflagellate transcriptomes to resolve internal phylogenetic relationships of the group. We show that the dinoflagellate theca originated once, through a process that likely involved changes in the metabolism of cellulose, and suggest that a late origin of dinosterol in the group is at odds with dinoflagellates being the source of this important biomarker before the Mesozoic. We also show that nonphotosynthetic dinoflagellates have retained nonphotosynthetic plastids with vital metabolic functions, and propose that one of these may be the evolutionary source of dinoflagellate bioluminescence. Finally, we reconstruct major molecular and morphological transitions in dinoflagellates and highlight the role of horizontal gene transfer in the origin of their unique nuclear architecture.
Synthesis of arborane triterpenols by a bacterial oxidosqualene cyclase
Authors: Banta Amy B. , Wei Jeremy H. , Gill Clare C. C. , Giner José-Luis , Welander Paula V. 
Published: December 2016

SignificancePolycyclic lipids produced by bacteria and eukaryotes can be preserved in sedimentary rocks for millions of years. These ancient lipids can function as “molecular fossils” or biomarkers that can inform us about the types of organisms and environments on early Earth. However, proper interpretation of these biomarkers requires a comprehensive understanding of the taxonomic distribution, biosynthesis, and physiological function of these lipids in modern organisms. In this study, we discover that a marine bacterium produces two arborinols, a class of lipids previously identified only in flowering plants. This discovery addresses a current incongruity in biomarker signatures and also provides insight into the evolution of the biosynthetic pathways of biomarker lipids.
Suppression of 19S proteasome subunits marks emergence of an altered cell state in diverse cancers
Authors: Tsvetkov Peter , Sokol Ethan , Jin Dexter , Brune Zarina , Thiru Prathapan , Ghandi Mahmoud , Garraway Levi A. , Gupta Piyush B. , Santagata Sandro , Whitesell Luke , Lindquist Susan 
Published: December 2016

Significance
In previous work, we used genome-wide screening to uncover a counterintuitive mechanism by which cells can acquire resistance to inhibitors of the proteasome’s catalytic core through experimentally induced imbalances in the composition of its regulatory particle. However, in many cases, mechanisms uncovered in vitro for acquired resistance often do not translate to the context of actual clinical cancers. Here, we show that this mechanism is actually deployed spontaneously and naturally in diverse human cancer lines and is associated not only with increased resistance to proteasome inhibitors both in vitro and in the clinic but also is symptomatic of a much more broadly altered state with a unique gene signature and drug targetable vulnerabilities.
Stable population coding for working memory coexists with heterogeneous neural dynamics in prefrontal cortex
Authors: Murray John D. , Bernacchia Alberto , Roy Nicholas A. , Constantinidis Christos , Romo Ranulfo , Wang Xiao-Jing 
Published: December 2016

Significance
Working memory (WM) is a core cognitive function thought to rely on persistent activity patterns in populations of neurons in prefrontal cortex (PFC), yet the neural circuit mechanisms remain unknown. Single-neuron activity in PFC during WM is heterogeneous and strongly dynamic, raising questions about the stability of neural WM representations. Here, we analyzed WM activity across large populations of neurons in PFC. We found that despite strong temporal dynamics, there is a population-level representation of the remembered stimulus feature that is maintained stably in time during WM. Furthermore, these population-level analyses distinguish mechanisms proposed by theoretical models. These findings inform our fundamental understanding of circuit mechanisms underlying WM, which may guide development of treatments for WM impairment in brain disorders.
Bio-physical connectivity patterns of benthic marine species used in the designation of Scottish nature conservation marine protected areas
Authors: Gallego Alejandro , Gibb Fiona M. , Tullet David , Wright Peter J. 
Published: December 2016

Abstract
Connectivity is a key consideration in the development of networks of marine protected areas (MPAs). However, little is known about the early life history of many of the epi-benthic animals that these spatial measures try to conserve. Here, a pragmatic approach to consider connectivity in such organisms is adopted, as part of the Scottish nature conservation MPA designation process. The primary tool for the study was a basic bio-physical model, forced by a circulation climatology. In the general absence of comprehensive ecological information, the model accounted for the main biological characteristics of the benthic organisms under consideration of relevance to connectivity, namely, presence, spawning season and pelagic larval duration (PLD). The results showed that some degree of connectivity between MPAs is possible even for species with short PLD although those organisms are more likely to be vulnerable to local pressures, particularly in the case of less widely distributed species and those inhabiting less dispersive inshore locations. For MPAs further offshore and species with longer PLD, our simulations suggested large-scale advection patterns crossing large-scale environmental management boundaries. Although the study was an appropriate contribution to the MPA designation process, further refinements encompassing better basic ecological information, enhanced oceanographic resolution, more realistic representation of biological processes (e.g. spawning, larval behaviour) in the model, species presence within and outside MPAs and substrate suitability maps would provide future useful confidence boundaries around the general patterns derived from our study.