bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring and simulating morphology gradients in injection‐molded talc‐reinforced isotactic polypropylene
Authors: Granlund Håvard , Andreassen Erik , Skjønsfjell Eirik Torbjørn Bakken , Høydalsvik Kristin , Diaz Ana , Breiby Dag Werner 
Published: June 2014

ABSTRACTInjection molded polymer parts are known to exhibit structural gradients of crystallinity, crystallite phases and crystallite orientations. The structural variations depend on the geometry, the material properties, and the processing conditions, and affect the mechanical properties of the molded part. We explore the use of raster‐scanning small‐ and wide‐angle X‐ray scattering (SAXS, WAXS) for mapping the microstructure in dogbone specimens of an isotactic polypropylene (PP) homopolymer and a talc‐reinforced isotactic PP compound. The specimens were injection molded with different mold temperatures and injection speeds, and the mapping approach revealed systematic structural heterogeneities and asymmetries. Accompanying numerical simulations of the injection molding process yielded predictions of the flow pattern, including the shear rate distribution and the resulting orientation of the flake‐shaped talc particles. We found a clear correspondence between the experimentally observed data and the simulations, in particular regarding the asymmetry of the orientation distributions relative to the center of the dogbone cross section, caused by asymmetric flow through the entrance of the mold. Furthermore, the shear rate distribution correlated with the occurrence of α‐ and β‐phases. Subtle differences in the crystallized structures along the long axis of the dogbones suggest an explanation to the observation that the specimens studied always tended to break at the same position in tensile tests. The results clearly demonstrate the potential of mapping experiments which combine lateral resolution on macroscopic length scales with the molecular‐scale resolution from scattering. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys.2014,52, 1157–1167
Molecular basis for bacterial peptidoglycan recognition by LysM domains
Authors: Mesnage Stéphane , Dellarole Mariano , Baxter Nicola J. , Rouget Jean-Baptiste , Dimitrov Jordan D. , Wang Ning , Fujimoto Yukari , Hounslow Andrea M. , Lacroix-Desmazes Sébastien , Fukase Koichi , Foster Simon J. , Williamson Michael P. 
Published: June 2014

AbstractCarbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM–peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms.
‘Fullye Bente to Fighte Oute the Matter’: Reconsidering Cornwall’s Role in the Western Rebellion of 1549
Authors: Stoyle Mark 
Published: June 2014

Abstract
This article brings new evidence to bear on the Western Rebellion—the popular insurrection which convulsed Devon, Cornwall and areas of West Somerset during the summer of 1549 and which is today more commonly known as the ‘Prayer Book Rebellion’. The article argues that, while the rising is one of the most famous mass protests to have occurred during the Tudor period and has been very widely written about and discussed, the standard narrative of events—which was first laid down by Frances Rose-Troup a century ago—is in need of fundamental revision, particularly in so far as it pertains to Cornwall. More specifically, it argues that the orthodox view which holds that the insurrection began in Cornwall on 6 June, that the Cornish rebel forces quickly suppressed all resistance in their own county, and that they then marched into Devon just a few days later, is almost certainly wrong. Instead, it is suggested here that rebellion did not break out in Cornwall until some time subsequent to 26 June; that at least one loyalist garrison in the county remained stubbornly defiant thereafter; and that the Cornish rebel host did not advance across the Tamar until early to mid-July—a full month later than the standard interpretation suggests. The article concludes by casting fresh light on the government’s defeat of the insurrectionists in August, and by considering some of the wider implications of the revised chronology of events which has been put forward here.
Determining predator identity from attack marks left in model caterpillars: guidelines for best practice
Authors: Low Petah A. , Sam Katerina , McArthur Clare , Posa Mary Rose C. , Hochuli Dieter F. 
Published: June 2014

AbstractThe use of model caterpillars to assess relative rates of predation has risen in popularity in recent years. Among the various benefits of the technique is its capacity to provide information on the identity of attackers through the impressions left in the modelling clay from which the model prey is constructed. However, there currently exists no detailed information on how to assign attack marks to particular predators. We aimed to address this gap by collating a comprehensive reference collection of the types of marks made by different predators to serve as a guide for researchers wanting to identify the predators responsible for attacks. To determine what level of resolution in identification may be considered reliable, we also tested the consistency of predator assignments made by different individuals. We found that predator identification at a coarse taxonomic level (i.e., bird, mammal, arthropod) was reasonably consistent. In contrast, when more fine‐scale identification was attempted, the level of consistency and therefore also confidence in the accuracy of an identification was dramatically reduced, reflecting the difficulty of distinguishing between attacks made not only by different arthropod groups but also by differently sized birds and mammals. We recommend that identifications be made at a coarse taxonomic level and, where possible, by multiple individuals. We also suggest that our collection of images of representative attack marks from each of the coarse predator categories, and descriptions of their defining characteristics, can serve as a guide to assist with identifications and this will be complemented by a good knowledge of the locally occurring and abundant predators.
NMR evidence for oligosaccharide release from the dendritic‐cell specific intercellular adhesion molecule 3‐grabbing non‐integrin‐related (CLEC4M) carbohydrate recognition domain at low pH
Authors: Probert Fay , Mitchell Daniel A. , Dixon Ann M. 
Published: June 2014

Dendritic cell‐specific intercellular adhesion molecule 3‐grabbing non‐integrin‐related (DC‐SIGNR), also known as liver/lymph node‐specific intercellular adhesion molecule 3‐grabbing non‐integrin, CLEC4M, CD209L, and CD299, is a Ca2+‐dependent lectin that has been implicated in increasing the infection rates of several viruses, including HIV, but the physiological role of DC‐SIGNR in healthy cells is currently not known with certainty. A close homologue of DC‐SIGNR, dendritic‐cell specific intercellular adhesion molecule 3‐grabbing non‐integrin, has been shown to act as a recycling endocytic receptor, which binds pathogens at the cell's surface and then releases them in the low pH environment of endosomal compartments. However, it is currently under debate in the literature as to whether DC‐SIGNR plays a similar role. In this work, we used NMR to explore whether the DC‐SIGNR carbohydrate recognition domain (CRD) shows any pH dependence in its ability to bind carbohydrates and Ca2+. We found clear evidence of reduced or abolished CRD‐binding affinities for three different glycans at low pH (4.2) as compared to neutral pH (6.8). We also report the assignment of the DC‐SIGNR CRD in the apo form, and use these new results to characterize the degree of structural rearrangement upon binding (or release) of Ca2+. Finally, we report a differential effect of pH on the affinities of glycans containing mannose exclusively versus glycans containing GlcNAc moieties. Our results lead us to propose that the DC‐SIGNR CRD rapidly and reversibly releases glycan ligands and Ca2+ at reduced pH (behaviour that would be expected for an endocytic receptor), and that the binding of mannose‐containing oligosaccharides is more strongly affected by pH than the binding of GlcNAc‐containing oligosaccharides.
Escherichia coli ST131, an Intriguing Clonal Group
Authors: Nicolas-Chanoine Marie-Hélène , Bertrand Xavier , Madec Jean-Yves 
Published: June 2014

SUMMARY

In 2008, a previously unknown
Escherichia coli
clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant
E. coli
lineage among extraintestinal pathogenic
E. coli
(ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131
E. coli
isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of
E. coli
ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131.
A qualitative study of informal caregivers’ perspectives on the effects of idiopathic pulmonary fibrosis
Authors: Belkin Amanda , Albright Karen , Swigris Jeffrey J 
Published: June 2014

BackgroundIdiopathic pulmonary fibrosis (IPF) is a life-shortening lung disease that leads to significant morbidity in patients. The devastation IPF imposes extends beyond patients: it affects their spouses, loved ones and any other person who might take on the role of informal caregiver (IC) to the patient.ObjectiveThe aim of this study was to capture ICs’ perspectives on how they are affected by having a loved one with IPF. Given ICs’ vantage, data were also collected on their perceptions of how IPF impacted their patient-loved ones over the course of the disease.MethodsReflexive team analysis was used to analyse the transcripts from semistructured focus groups conducted with ICs of patients with IPF. Based on the analyses, a conceptual framework of the IC's journey with a patient with IPF was developed and includes suggestions for interventions that might ease the burdens ICs endure while caring for their patient-loved ones.Results14 ICs included in this study experienced several hardships throughout the course of their loved ones’ illness, from emotional devastation at the time of diagnosis to living with an ‘impatient,’ ‘cranky’ loved one and being forced to exist in a ‘smaller world’ because of the physical limitations IPF imposed on their partners. The threat of patients needing supplemental oxygen was central to creating angst among patients and ICs, and supplemental oxygen use by patients prohibited them and their ICs from living the ‘normal’, carefree lives they desired.ConclusionsBeing an IC to a patient with IPF is extremely challenging (as 1 IC put it: “…harder on the spouse than the patient in some ways”). As patients attempt to adapt to the ‘sick person’ role, ICs face a struggle between performing their duties as caregiver and maintaining their own identities and independence.
Childhood adversity and asthma prevalence: evidence from 10 US states (2009–2011)
Authors: Bhan Nandita , Glymour M Maria , Kawachi Ichiro , Subramanian S V 
Published: June 2014

BackgroundExisting evidence on stress and asthma prevalence has disproportionately focused on pregnancy and postpregnancy early life stressors, largely ignoring the role of childhood adversity as a risk factor. Childhood adversity (neglect, stressful living conditions and maltreatment) may influence asthma prevalence through mechanisms on the hypothalamic-pituitary axis.MethodsData from the Center for Disease Control's (CDC's) Behavioral Risk Factor Surveillance System (BRFSS) surveys were used to examine cross-sectional associations of adverse childhood experiences (ACE) with lifetime and current asthma prevalence. Information on childhood adversity was available from 84 786 adult respondents in 10 US states. Poisson regression models (with robust SE) were used to estimate prevalence ratios (PRs) relating overall ACE score and dimensions of exposure ACE to asthma prevalence, adjusting for socioeconomic status.ResultsGreater ACE was associated with a higher prevalence of asthma (adjusted PRcat 4=1.78 (95% CI 1.69 to 1.87), adjusted PRcat 1=1.21 (95% CI 1.16 to 1.27)). Reported experiences of sexual abuse (adjusted PR=1.48* (1.42 to 1.55)) and physical abuse (adjusted PR=1.38* (1.33 to 1.43)) were associated with a higher asthma prevalence. No clear socioeconomic gradient was noted, but those reporting lowest education and income levels reported high rates of asthma and adversity. Sensitivity analyses indicated that ACE exposures were interrelated.ConclusionsReport of childhood adversity predicts asthma prevalence among US adults. Frameworks for asthma prevention need to recognise and integrate aspects related to childhood adversity. Further investigation into specific time periods of exposure would provide meaningful inferences for interventions.
A general railway data model for simulations and simulators
Authors: Öztürk Veysi , Rende Ferhat Şükrü , İnce Onur , Soyer Burak Selçuk 
Published: June 2014

According to new regulations, railway employees require computer-based training before they get a driver license. Training with simulators is now a must to increase the safety and efficiency of railway transportation. In this study, a train driving simulator with full cab and motion platform, called TRENSIM, was developed for Turkish State Railways. It was realized that constructing a data model of the railway was one of the most important aspects of the project. Many modules of TRENSIM make use of this data model in real time. We developed a general railway data model, called OpenRailway, expressed in Extensible Markup Language for logical description of railway networks. OpenRailway includes a railway model, which consists of signals, railway elements (catenaries, switches, etc.), road properties, surroundings near the railway road and their parameters. OpenRailway can also be modified to be used in the development of other vehicle training simulators. Data from real trains was collected in 4 ms periods for the validation of the dynamic and visualization models (about 200 GB). It was seen that data generated by models are appropriate to the collected real data.
Long-acting bronchodilators in COPD: where are we now and where are we going?
Authors: Cazzola Mario , Page Clive 
Published: June 2014

Educational aimsTo discuss fundamental questions relating to the use of bronchodilators that can lead to an optimisation of their utilisation.To describe new bronchodilators that have recently been approved in some countries or are currently undergoing clinical developmentSummaryBronchodilators are central to the treatment of chronic obstructive pulmonary disease (COPD) because they alleviate bronchial obstruction and airflow limitation, reduce hyperinflation, and improve emptying of the lung and exercise performance. For this reason, all guidelines highlight that inhaled bronchodilators are the mainstay of the current management of all stages of COPD.However, there are still fundamental questions regarding their use that require clarification to optimise utilisation of these drugs. It is crucial to address the following questions. Is it appropriate to treat all COPD patients with long-acting bronchodilators? Is it better to start treatment with a β2-agonist or with an anti-muscarinic agent in patients with stable mild/moderate COPD? Is it useful to use a bronchodilator with rapid onset of action? Is it preferable to administer a bronchodilator on a once- or twice-daily basis? Can a second bronchodilator can be introduced for patients with stable COPD (“dual” bronchodilator therapy), and if so when? Are inhaled corticosteroids (ICSs) really useful in COPD patients without chronic bronchitis, since long-lasting bronchodilators may prevent exacerbations even in the absence of an ICS in frequent exacerbators? Finally, is combined therapy really useful in non-frequent exacerbators?Due to the the central role of bronchodilators in the treatment of COPD, there is still considerable interest in finding novel classes of bronchodilator drugs. However, new classes of bronchodilators have proved difficult to develop because either new emerging targets are not really important and/or it is difficult to find substances capable of interacting with them. As a consequence, many research groups have sought to improve the existing classes of bronchodilators.
IVT-seq reveals extreme bias in RNA sequencing
Authors: Lahens Nicholas F , Kavakli Ibrahim Halil , Zhang Ray , Hayer Katharina , Black Michael B , Dueck Hannah , Pizarro Angel , Kim Junhyong , Irizarry Rafael , Thomas Russell S , Grant Gregory R , Hogenesch John B 
Published: June 2014

Abstract
Background
RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value.

Results
We present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. We created a pool of over 1,000 in vitro transcribed RNAs from a full-length human cDNA library and sequenced them with polyA and total RNA-seq, the most common protocols. Because each cDNA is full length, and we show in vitro transcription is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find 50% of transcripts have more than two-fold and 10% have more than 10-fold differences in within-transcript sequence coverage. We also find greater than 6% of transcripts have regions of dramatically unpredictable sequencing coverage between samples, confounding accurate determination of their expression. We use a combination of experimental and computational approaches to show rRNA depletion is responsible for the most significant variability in coverage, and several sequence determinants also strongly influence representation.

Conclusions
These results show the utility of IVT-seq for promoting better understanding of bias introduced by RNA-seq. We find rRNA depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation. These biases suggest exon-level expression analysis may be inadvisable, and we recommend caution when interpreting RNA-seq results.
Nurse-led PICC insertion: is it cost effective?
Authors: Walker Graham , Todd Alistair 
Published: June 2014

Aims: Repeated attempts to cannulate small veins can cause considerable distress for patients and expend substantial staff time. For longer term venous access, a peripherally inserted central catheter (PICC) may be used instead of a peripheral cannula. Previous studies indicate that insertion of a PICC costs three times more than a cannula but the lifespan is substantially longer. This study aimed to compare insertion cost, patient satisfaction, and infection rates of PICCs for the two main staff groups (trained nurses and radiologists) inserting these devices in a district general hospital. Materials and Methods: The study took place over 4 months in 2012–13. A questionnaire was attached to all identified PICCs in stock at Raigmore Hospital to collect details of the date of insertion, patient involved, time taken, attendant staff grade and experience level, consumables used and insertion success. The lead author's personal observation of PICC insertion by different staff groups allowed estimation of staff time, costs and success rates. Patient experience and satisfaction was assessed before and after insertion using a patient questionnaire. PICC longevity, infection rates and failures were assessed by review of patient notes. Results: The radiologist group had a statistically significant (p< 0.01) increased cost (42%) over the nurse group. Patient satisfaction regarding explanation of treatment before insertion was higher in the nurse group. Insertion success and infection rates were higher in the radiologist group. Conclusion: The authors conclude that the majority of PICCs can be safely performed without x-ray screening in a ward-based environment. This is likely to be the most cost-effective solution for large volume services.
Oil Yield Components of Maize Crops Exposed to Heat Stress during Early and Late Grain‐Filling Stages
Authors: Mayer Luis I. , Rattalino Edreira Juan I. , Maddonni Gustavo A. 
Published: June 2014

ABSTRACTHeat stress frequently limits grain yield of summer crops. Most research on maize (Zea mays L.) has analyzed heat stress effects on crop physiology and kernel set but little attention has been given to kernel weight and its composition. The objectives of this work were (i) to assess the response of maize oil yield components (kernel number and weight, embryo oil concentration, and embryo/kernel ratio) to postflowering heat stress and (ii) to explore changes in the sensitivity to this constraint across developmental stages and genotypes. Hybrids with different kernel types (flint, popcorn, and semident) were exposed to contrasting temperature regimes (nonheated and heated: air temperature at ear level > 35°C) during early or late stages of the effective grain filling. Oil yield was affected by early (up to −60%), and to a lesser extent, late (up to −40%) heat‐stress episodes. These effects were mediated by lighter kernels (r2 = 0.94; P < 0.001) and lower kernel oil concentrations (r2 = 0.80; P < 0.001). Reductions of kernel weight were related to shorter grain‐filling periods (r2 = 0.48; P < 0.01), and those of kernel oil concentration were mainly associated with lower embryo oil concentrations (r2 = 0.64; P < 0.001). Kernels of semident hybrids were the most prone to alter their weights and oil concentrations in the face of a wide range of heat stress intensities. Variations in kernel oil concentration due to high temperature became notorious when kernel weight reductions were larger than 20%.