bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal Variation of Common Surgical Site Infections: Does Season Matter?
Authors: Durkin Michael J. , Dicks Kristen V. , Baker Arthur W. , Lewis Sarah S. , Moehring Rebekah W. , Chen Luke F. , Sexton Daniel J. , Anderson Deverick J. 
Published: May 2015

OBJECTIVETo evaluate seasonal variation in the rate of surgical site infections (SSI) following commonly performed surgical procedures.DESIGNRetrospective cohort study.METHODSWe analyzed 6 years (January 1, 2007, through December 31, 2012) of data from the 15 most commonly performed procedures in 20 hospitals in the Duke Infection Control Outreach Network. We defined summer as July through September. First, we performed 3 separate Poisson regression analyses (unadjusted, multivariable, and polynomial) to estimate prevalence rates and prevalence rate ratios of SSI following procedures performed in summer versus nonsummer months. Then, we stratified our results to obtain estimates based on procedure type and organism type. Finally, we performed a sensitivity analysis to test the robustness of our findings.RESULTSWe identified 4,543 SSI following 441,428 surgical procedures (overall prevalence rate, 1.03/100 procedures). The rate of SSI was significantly higher during the summer compared with the remainder of the year (1.11/100 procedures vs 1.00/100 procedures; prevalence rate ratio, 1.11 [95% CI, 1.04–1.19];P=.002). Stratum-specific SSI calculations revealed higher SSI rates during the summer for both spinal (P=.03) and nonspinal (P=.004) procedures and revealed higher rates during the summer for SSI due to either gram-positive cocci (P=.006) or gram-negative bacilli (P=.004). Multivariable regression analysis and sensitivity analyses confirmed our findings.CONCLUSIONSThe rate of SSI following commonly performed surgical procedures was higher during the summer compared with the remainder of the year. Summer SSI rates remained elevated after stratification by organism and spinal versus nonspinal surgery, and rates did not change after controlling for other known SSI risk factors.Infect. Control Hosp. Epidemiol.2015;36(9):1011–1016
A fast direct numerical simulation method for characterising hydraulic roughness
Authors: Chung D. , Chan L. , MacDonald M. , Hutchins N. , Ooi A. 
Published: May 2015

We describe a fast direct numerical simulation (DNS) method that promises to directly characterise the hydraulic roughness of any given rough surface, from the hydraulically smooth to the fully rough regime. The method circumvents the unfavourable computational cost associated with simulating high-Reynolds-number flows by employing minimal-span channels (Jiménez & Moin,J. Fluid Mech., vol. 225, 1991, pp. 213–240). Proof-of-concept simulations demonstrate that flows in minimal-span channels are sufficient for capturing the downward velocity shift, that is, the Hama roughness function, predicted by flows in full-span channels. We consider two sets of simulations, first with modelled roughness imposed by body forces, and second with explicit roughness described by roughness-conforming grids. Owing to the minimal cost, we are able to conduct direct numerical simulations with increasing roughness Reynolds numbers while maintaining a fixed blockage ratio, as is typical in full-scale applications. The present method promises a practical, fast and accurate tool for characterising hydraulic resistance directly from profilometry data of rough surfaces.
GAS EXCHANGE, GROWTH, FLOWERING AND FRUIT PRODUCTION IN SWEET PEPPER (CAPSICUM CHINENSE JACQ) ALONG A THERMAL GRADIENT DETERMINED BY ALTITUDINAL DIFFERENCES IN A TROPICAL REGION
Authors: JAIMEZ R. E. , RADA F. 
Published: May 2015

SUMMARYA common practice in some South American countries consists in moving around Capsicum chinense cultivars between regions where edaphoclimatic conditions differ notably. The purpose of this research was to compare and relate gas exchange responses with assimilate allocation patterns and flower and fruit production dynamics in a cultivar of C. chinense in three locations with different mean temperatures (19, 24 and 28 °C) along a gradient from 140–1855 m. Leaf gas exchange (leaf conductance, CO2 assimilation and transpiration rates) was measured at 60–70, 110–120 and 140–150 days after transplanting (dat) from seed beds. Dry weight per plant of leaves, stems and roots were determined at 50, 73, 96, 114 and 196 dat. Flowering dynamics and fruit production were followed weekly. A marked reduction (50%) in mean Gs was found at the site with the lowest mean temperature in relation to plants grown at the highest temperature site. Mean daily CO2 assimilation rate was higher for plants in the intermediate site and a reduction of 18 and 42% was found for sites with highest and lowest mean temperature, respectively. We report an adverse effect of low temperatures on growth of C. chinense. Flowering initiation and fruit production was delayed at lower temperatures. An increase in temperature (between 26–30 °C) led to an increase in the number of flowers; below this temperature it remained unchanged. Fruit production is drastically reduced at the lower temperature site due to a large number of aborted flowers and small fruits.
Urban growth and police reform in Marseille (1855–1908)
Authors: REGNARD CÉLINE 
Published: May 2015

ABSTRACT:This article deals with Marseille's social and political history between the 1850s and 1910s. During this period of extensive economic and demographic growth, the municipal government and police never seemed able to handle the consequences of these rapid changes. The case of Marseille thus allows us to test the connection between a growth situation interpreted as a ‘permanent crisis’ and police reform. The persistence of the crisis discourse invites us to examine the connection between the alarmist rhetoric and reforms in law enforcement. Is the first the cause of the second and, if not, how do we interpret the continuing complaints of a crisis for more than half a century, when they must have lost their effectiveness? This article examines the weakness and discontinuity of the relationship between claims of a crisis and police reforms and situates these reforms within the political context of tensions between the national and local levels.
Autologous iPSC-derived dopamine neuron transplantation in a nonhuman primate Parkinson’s disease model
Authors: Wang Shuyan , Zou Chunlin , Fu Linlin , Wang Bin , An Jing , Song Gongru , Wu Jianyu , Tang Xihe , Li Mo , Zhang Jian , Yue Feng , Zheng Chengyun , Chan Piu , Zhang Y Alex , Chen Zhiguo 
Published: May 2015

AbstractAutologous dopamine (DA) neurons are a new cell source for replacement therapy of Parkinson’s disease (PD). In this study, we tested the safety and efficacy of autologous induced pluripotent stem cell (iPSC)-derived DA cells for treatment of a cynomolgus monkey PD model. Monkey bone marrow mesenchymal cells were isolated and induced to iPSCs, followed by differentiation into DA cells using a method with high efficiency. Autologous DA cells were introduced into the brain of a cynomolgus monkey PD model without immunosuppression; three PD monkeys that had received no grafts served as controls. The PD monkey that had received autologous grafts experienced behavioral improvement compared with that of controls. Histological analysis revealed no overgrowth of grafts and a significant number of surviving A9 region-specific graft-derived DA neurons. The study provided a proof-of-principle to employ iPSC-derived autologous DA cells for PD treatment using a nonhuman primate PD model.
Translational regulation shapes the molecular landscape of complex disease phenotypes
Authors: Schafer Sebastian , Adami Eleonora , Heinig Matthias , Rodrigues Katharina E. Costa , Kreuchwig Franziska , Silhavy Jan , van Heesch Sebastiaan , Simaite Deimante , Rajewsky Nikolaus , Cuppen Edwin , Pravenec Michal , Vingron Martin , Cook Stuart A. , Hubner Norbert 
Published: May 2015

AbstractThe extent of translational control of gene expression in mammalian tissues remains largely unknown. Here we perform genome-wide RNA sequencing and ribosome profiling in heart and liver tissues to investigate strain-specific translational regulation in the spontaneously hypertensive rat (SHR/Ola). For the most part, transcriptional variation is equally apparent at the translational level and there is limited evidence of translational buffering. Remarkably, we observe hundreds of strain-specific differences in translation, almost doubling the number of differentially expressed genes. The integration of genetic, transcriptional and translational data sets reveals distinct signatures in 3′UTR variation, RNA-binding protein motifs and miRNA expression associated with translational regulation of gene expression. We show that a large number of genes associated with heart and liver traits in human genome-wide association studies are primarily translationally regulated. Capturing interindividual differences in the translated genome will lead to new insights into the genes and regulatory pathways underlying disease phenotypes.
Membrane tension controls the assembly of curvature-generating proteins
Authors: Simunovic Mijo , Voth Gregory A. 
Published: May 2015

AbstractProteins containing a Bin/Amphiphysin/Rvs (BAR) domain regulate membrane curvature in the cell. Recent simulations have revealed that BAR proteins assemble into linear aggregates, strongly affecting membrane curvature and its in-plane stress profile. Here, we explore the opposite question: do mechanical properties of the membrane impact protein association? By using coarse-grained molecular dynamics simulations, we show that increased surface tension significantly impacts the dynamics of protein assembly. While tensionless membranes promote a rapid formation of long-living linear aggregates of N-BAR proteins, increase in tension alters the geometry of protein association. At high tension, protein interactions are strongly inhibited. Increasing surface density of proteins leads to a wider range of protein association geometries, promoting the formation of meshes, which can be broken apart with membrane tension. Our work indicates that surface tension may play a key role in recruiting proteins to membrane-remodelling sites in the cell.
A review of epidemiological parameters from Ebola outbreaks to inform early public health decision-making
Authors: Van Kerkhove Maria D. , Bento Ana I. , Mills Harriet L. , Ferguson Neil M. , Donnelly Christl A. 
Published: May 2015

AbstractThe unprecedented scale of the Ebola outbreak in West Africa has, as of 29 April 2015, resulted in more than 10,884 deaths among 26,277 cases. Prior to the ongoing outbreak, Ebola virus disease (EVD) caused relatively small outbreaks (maximum outbreak size 425 in Gulu, Uganda) in isolated populations in central Africa. Here, we have compiled a comprehensive database of estimates of epidemiological parameters based on data from past outbreaks, including the incubation period distribution, case fatality rate, basic reproduction number (R0), effective reproduction number (Rt) and delay distributions. We have compared these to parameter estimates from the ongoing outbreak in West Africa. The ongoing outbreak, because of its size, provides a unique opportunity to better understand transmission patterns of EVD. We have not performed a meta-analysis of the data, but rather summarize the estimates by virus from comprehensive investigations of EVD and Marburg outbreaks over the past 40 years. These estimates can be used to parameterize transmission models to improve understanding of initial spread of EVD outbreaks and to inform surveillance and control guidelines.
Open science resources for the discovery and analysis of Tara Oceans data
Authors: Pesant Stéphane , Not Fabrice , Picheral Marc , Kandels-Lewis Stefanie , Le Bescot Noan , Gorsky Gabriel , Iudicone Daniele , Karsenti Eric , Speich Sabrina , Troublé Romain , Dimier Céline , Searson Sarah ,   Tara Oceans Consortium Coordinators, Acinas Silvia G. , Bork Peer , Boss Emmanuel , Bowler Chris , De Vargas Colomban , Follows Michael , Gorsky Gabriel , Grimsley Nigel , Hingamp Pascal , Iudicone Daniele , Jaillon Olivier , Kandels-Lewis Stefanie , Karp-Boss Lee , Karsenti Eric , Krzic Uros , Not Fabrice , Ogata Hiroyuki , Pesant Stéphane , Raes Jeroen , Reynaud Emmanuel G. , Sardet Christian , Sieracki Mike , Speich Sabrina , Stemmann Lars , Sullivan Matthew B. , Sunagawa Shinichi , Velayoudon Didier , Weissenbach Jean , Wincker Patrick 
Published: May 2015

AbstractThe Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.
An overhang-based DNA block shuffling method for creating a customized random library
Authors: Fujishima Kosuke , Venter Chris , Wang Kendrick , Ferreira Raphael , Rothschild Lynn J. 
Published: May 2015

AbstractWe present an overhang-based DNA block shuffling method to create a customized random DNA library with flexible sequence design and length. Our method enables the efficient and seamless assembly of short DNA blocks with dinucleotide overhangs through a simple ligation process. Next generation sequencing analysis of the assembled DNA library revealed that ligation was accurate, directional and unbiased. This straightforward DNA assembly method should fulfill the versatile needs of both in vivo and in vitro functional screening of random peptides and RNA created with a desired amino acid and nucleotide composition, as well as making highly repetitive gene constructs that are difficult to synthesize de novo.
TPC: the NAADP discovery channel?
Authors: Morgan Anthony J. , Davis Lianne C. , Ruas Margarida , Galione Antony 
Published: May 2015

The Ca2+-mobilizing second messenger, NAADP (nicotinic acid adenine dinucleotide phosphate), has been with us for nearly 20 years and yet we still cannot fully agree on the identity of its target Ca2+-release channel. In spite of some recent robust challenges to the idea that two-pore channels (TPCs) represent the elusive “NAADP receptor”, evidence continues to accumulate that TPCs are important for NAADP-mediated responses. This article will briefly outline the background and review more recent work pertaining to the TPC story.
Cell communication across gap junctions: a historical perspective and current developments
Authors: Evans W. Howard 
Published: May 2015

Collaborative communication lies at the centre of multicellular life. Gap junctions (GJs) are surface membrane structures that allow direct communication between cells. They were discovered in the 1960s following the convergence of the detection of low-resistance electrical interactions between cells and anatomical studies of intercellular contact points. GJs purified from liver plasma membranes contained a 27 kDa protein constituent; it was later named Cx32 (connexin 32) after its full sequence was determined by recombinant technology. Identification of Cx43 in heart and later by a further GJ protein, Cx26 followed. Cxs have a tetraspan organization in the membrane and oligomerize during intracellular transit to the plasma membrane; these were shown to be hexameric hemichannels (connexons) that could interact end-to-end to generate GJs at areas of cell-to-cell contact. The structure of the GJ was confirmed and refined by a combination of biochemical and structural approaches. Progress continues towards obtaining higher atomic 3D resolution of the GJ channel. Today, there are 20 and 21 highly conserved members of the Cx family in the human and mouse genomes respectively. Model organisms such as Xenopus oocytes and zebra fish are increasingly used to relate structure to function. Proteins that form similar large pore membrane channels in cells called pannexins have also been identified in chordates. Innexins form GJs in prechordates; these two other proteins, although functionally similar, are very different in amino acid sequence to the Cxs. A time line tracing the historical progression of wide ranging research in GJ biology over 60 years is mapped out. The molecular basis of channel dysfunctions in disease is becoming evident and progress towards addressing Cx channel-dependent pathologies, especially in ischaemia and tissue repair, continues.
Design of simple and compact tunable fibre laser
Authors: Fujimoto Y. , Ishii O. , Yamazaki M. 
Published: May 2015

A novel design of a simple and compact tunable fibre laser that uses the chromatic aberration of the lens relay and a slit‐like effect of the optical fibre core is proposed and demonstrated. The tunability of 20 nm is obtained by 130 µm of cavity output mirror adjustment.
The Value of Total antioxidant Status and Serum Tumor Necrosis Factor-α Levels at 24–28 Weeks of Gestation in the Prediction of Optimal Treatment Protocol in Gestational Diabetes Mellitus
Authors: Ozler S. , Oztas E. , Uygur D. , Ersoy A. O. , Ergin M. , Koca C. , Danisman N. , Erkaya S. 
Published: May 2015

Abstract
Aim: The aim of this study was to investigate the serum oxidative stress markers, antioxidant enzyme and tumor necrosis factor-α (TNF-α) levels at 24–28 weeks of gestation and to evaluate the predictive value of them on the subsequent treatment protocol in gestational diabetes mellitus (GDM).
Methods: A total of 58 GDM patients (30 treated with only conventional healthy dietary recommendation (CHDR), 28 treated with insulin) and 30 healthy pregnant women at 24–28 weeks of gestation, were enrolled in this prospective case-control study. The oxidative status, antioxidant enzyme and TNF-α levels were evaluated to determine if there is an association with the need of insulin therapy for glycemic control by using multivariable logistic regression analysis.
Results: TNF-α (OR=11.976, 95%CI: 2.441–58.754, P=0.002) and total antioxidant status (TAS) (OR=12.769, 95%CI: 2.464–66.182, P=0.002) were found to be predictive for GDM at 24–28 weeks of gestation. Besides, further evaluation considering the treatment modality showed that increased TNF-α (OR=18.615, 95%CI: 2.338–148.240, P=0.006) and lower TAS levels (OR=99.471, 95%CI: 2.865–3 453.061, P=0.011) were independent predictors of the need for insulin treatment in GDM patients.
Conclusions: Increased TNF-α levels and low TAS are significantly associated with the increased risk of insulin requirement for achieving good glycemic control in GDM.
The Effect of Age and Gender on Pressure Pain Thresholds and Suprathreshold Stimuli
Authors: Petrini Laura , Matthiesen Susan Tomczak , Arendt-Nielsen Lars 
Published: May 2015

Objectives: The study investigates the impact of age and gender on (1) experimental pressure pain detection thresholds (PPDT) and pressure pain tolerance thresholds (PPTolT) and (2) participants' self-reports of pain intensity and unpleasantness at suprathreshold and subthreshold levels. Methods: twenty young (20–34, mean age = 24.6 ± 3.6 years, ten female) and twenty elderly (65–88, mean age = 73.6 ± 6.6 years, ten female) healthy volunteers were compared. Mini-Mental State Examination (MMSE 28–30) assessed intact cognitive functioning. Pain thresholds were assessed together with the sensory intensity ratings to 1.3 x PPDT (pain) and 0.2 x PPDT (no pain). Results: PPDT and PPTolT significantly decreased with age and were lower in young females as compared with young males. No gender differences were observed in the elderly group. PPDT decreased significantly with age in males but not in females. Conversely, the intensity and unpleasantness of the pain stimulus were significantly rated lower in the elderly as compared with the young. No gender differences were observed in the report of intensity and unpleasantness of the stimulations. Discussion: a mismatch in pain sensitivity, tolerance, and pain self-reports was observed. Findings suggest that pain experiences in the elderly differ from the experiences in the young on multiple dimensions: sensory, affective, and cognitive. Findings may also indicate that the elderly appraise pain experiences using different psychological strategies.
15-Deoxy-Δ12,14-prostaglandin J2 as an electrophilic mediator
Authors: Shibata Takahiro 
Published: May 2015

Abstract
Lipid-derived electrophilic molecules are endogenously generated and are causally involved in many pathophysiological effects. Prostaglandin D2, a major cyclooxygenase product in a variety of tissues and cells, readily undergoes dehydration to yield the J-series PGs such as 15-deoxy-Δ12,14-PGJ2 (15d-PGJ2). Because of the electrophilic α,β-unsaturated ketone moiety present in its cyclopentenone ring, 15d-PGJ2 acts as an endogenous electrophile. 15d-PGJ2 can covalently react via the Michael addition reaction with critical cellular nucleophiles, such as the free cysteine residues of proteins that play a key role in the regulation of the intracellular signaling pathways. Covalent modification of cellular proteins by 15d-PGJ2 may be one of the most important mechanisms by which 15d-PGJ2 induces many biological responses involved in the pathophysiological effects associated with inflammation. This current review is intended to provide a comprehensive summary of 15d-PGJ2 as an endogenous electrophilic mediator of biological activities.
Structural and physical properties of collagen extracted from moon jellyfish under neutral pH conditions
Authors: Miki Ayako , Inaba Satomi , Baba Takayuki , Kihira Koji , Fukada Harumi , Oda Masayuki 
Published: May 2015

Abstract
We extracted collagen from moon jellyfish under neutral pH conditions and analyzed its amino acid composition, secondary structure, and thermal stability. The content of hydroxyproline was 4.3%, which is lower than that of other collagens. Secondary structure analysis using circular dichroism (CD) showed a typical collagen helix. The thermal stability of this collagen at pH 3.0 was lower than those from fish scale and pig skin, which also correlates closely with jellyfish collagen having lower hydroxyproline content. Because the solubility of jellyfish collagen used in this study at neutral pH was quite high, it was possible to analyze its structural and physical properties under physiological conditions. Thermodynamic analysis using CD and differential scanning calorimetry showed that the thermal stability at pH 7.5 was higher than at pH 3.0, possibly due to electrostatic interactions. During the process of unfolding, fibrillation would occur only at neutral pH.