bluuebunny/crossref_metadata_2025_split huggingface dataset:
Budding yeast chromatin is dispersed in a crowded nucleoplasmin vivo
Authors: Chen Chen , Lim Hong Hwa , Shi Jian , Tamura Sachiko , Maeshima Kazuhiro , Surana Uttam , Gan Lu 
Published: June 2016

AbstractChromatin organization has an important role in the regulation of eukaryotic systems. While recent studies have refined the 3-D models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin — nucleosomes — are positioned in 3-Din vivo. Here we have used electron cryotomography to study chromatin organization in the budding yeastS. cerevisiae. Direct visualization of yeast nuclear densities shows no evidence of 30-nm chromatin fibers. Aside from pre-ribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an “open” configuration that is conducive to high levels of transcription. In the absence of higher-order chromatin packing, we propose that yeast can regulate its transcription using local nucleosome-nucleosome associations.
Transcriptional activity of TRF2 is telomere length dependent
Authors: Mukherjee Ananda Kishore , Sharma Shalu , Dhapola Parashar , Saha Dhurjhoti , Hussain Tabish , Roy Sumitabho Deb , Purohit Gunjan , Kar Anirban , Singh Ankita , Sengupta Suman , Srivastava Vivek , Kumar Manish , Sengupta Sagar , Chowdhury Shantanu 
Published: June 2016

AbstractTRF2 is a telomere repeat binding factor crucial for telomere maintenance and genome stability. An emerging non-conventional role of TRF2 is as a transcriptional regulator through extra-telomeric bindings. Herein we report that increase in telomere length leads to sequestration of TRF2 at the telomeres leading to reduced extra-telomeric TRF2 occupancy genome wide. Decrease in TRF2 occupancy was found on multiple gene promoters in cells with elongated telomeres, including the cell cycle regulator kinase-p21. We found that TRF2 is a transcriptional repressor ofp21, and, interestingly, TRF2-mediated regulatory control ofp21is telomere length dependent.
Breaking bud: probing the scalability limits of phylogenetic network inference methods
Authors: Hejase Hussein A , Liu Kevin J 
Published: June 2016

AbstractBackgroundBranching events in phylogenetic trees reflect strictly bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a directed acyclic graph known as a phylogenetic network. Both phylogenetic trees and networks are typically reconstructed using computational analysis of multi-locus sequence data. The advent of high-throughput sequencing technologies has brought about two main scalability challenges:(1) dataset size in terms of the number of taxa and (2) the evolutionary divergence of the taxa in a study. The impact of both dimensions of scale on phylogenetic tree inference has been well characterized by recent studies; in contrast, the scalability limits of phylogenetic network inference methods are largely unknown. In this study, we quantify the performance of state-of-the-art phylogenetic network inference methods on large-scale datasets using empirical data sampled from natural mouse populations and synthetic data capturing a wide range of evolutionary scenarios.ResultsWe find that, as in the case of phylogenetic tree inference, the performance of leading network inference methods is negatively impacted by both dimensions of dataset scale. In general, we found that topological accuracy degrades as the number of taxa increases; a similar effect was observed with increased sequence mutation rate. The most accurate methods were probabilistic inference methods which maximize either likelihood under coalescent-based models or pseudo-likelihood approximations to the model likelihood. Furthermore, probabilistic inference methods with optimization criteria which did not make use of gene tree root and/or branch length information performed best-a result that runs contrary to widely held assumptions in the literature. The improved accuracy obtained with probabilistic inference methods comes at a computational cost in terms of runtime and main memory usage, which quickly become prohibitive as dataset size grows past thirty taxa.ConclusionsWe conclude that the state of the art of phylogenetic network inference lags well behind the scope of current phylogenomic studies. New algorithmic development is critically needed to address this methodological gap.
Healthy, wealthy and wise?
Authors: Drury Pauline 
Published: June 2016

Purpose
The purpose of this paper is to explore the effects of introducing an involuntary wellness program (IWP) on employee attitudes and willingness to participate.

Design/methodology/approach
The paper analyzes responses to a survey of office workers employed by a US education and media company when the existing wellness program was replaced by a new IWP.

Findings
It’s estimated that two out of three Americans are now overweight – and that’s bad for business. Having a fit and healthy workforce not only benefits the individual, it also means less time off sick, lower costs and better organizational performance. Firms that encourage a “wellness culture” are showing that they care about their employees – and can expect a payoff in terms of morale, motivation and productivity. What’s harder to predict is whether wellness can be made compulsory – and if compulsory, whether it still delivers a “win-win” result.

Practical implications
The study indicates aspects that may require particular care when introducing an IWP to ensure that employees appreciate the health benefits of this approach rather than joining the program for purely economic reasons.

Social implications
It provides an insight into the effects of expanding health insurance plan wellness incentives under the US Affordable Care Act of 2010.

Originality/value
This paper aims to raise the question of whether individuals can be incentivized to adopt a healthier lifestyle.
Employer branding
Authors: Drury Pauline 
Published: June 2016

Purpose
The purpose of this paper is to examine the effects of employer branding on company attractiveness to younger workers.

Design/methodology/approach
The paper analyzes the relative importance attached to symbolic and functional company attributes using a survey conducted at a large North American university. It considers the impact of differing levels of work experience on responses to employer branding.

Findings
The best employers get nearly twice as many job applications compared with other organizations. So when they are recruiting, they can pick and choose from a bigger talent pool and select the very best applicants. The “baby boomer” generation is retiring from the workforce, and later generations are smaller in size. The result of these demographic factors has been to increase fears of labor shortages. Competition for a shrinking talent pool of younger workers means that employers need to focus on the things that make their company attractive to potential applicants.

Practical implications
The study suggests ways in which human resources professionals can maximize the effectiveness of employer branding as a means of attracting job applications from young workers.

Social implications
It notes that symbolic attributes are more strongly predictive of company attractiveness than functional attributes and that this effect becomes more marked with work experience.

Originality/value
This paper aims to show how marketing concepts can be applied in a human resource context.
Developing individuals, developing business
Authors: Lofthouse Sadie 
Published: June 2016

Purpose
This paper aims to explore the subject of individual development, the benefits it offers to a business and tips for making it a success.

Design/methodology/approach
Sadie Lofthouse is Head of Human Resources at Adnams, the award-winning brewer, distiller and retailer, a company that successfully gained its Gold IIP status in 2013.

Findings
Successfully developing individuals depends on engaging your workforce through tactics such as setting professional Personal Bests and encouraging people to realise new skills through participating in activities outside of their usual remit.

Originality/value
Heading up HR at Adnams, a company that’s ethos is to “do good”, Sadie is passionate about the role business has to play in supporting education, and works with schools, colleges and training providers to help drive standards and prepare young people for work. Her approach embodies the innovation the company employs in every area of the business.
Beyond Bureaucracy: How Prosecutors and Public Defenders Enforce Urban Planning Laws in São Paulo, Brazil
Authors: Coslovsky Salo V. 
Published: June 2016

AbstractCities need law to thrive, but it is not clear how abstract texts become tangible policy outcomes. Existing research on the role of law in urban affairs conceives law as either an algorithm that shapes urban life or a reflection of political disputes. The former assumes that the meaning of law is obvious; the latter claims it is irrelevant. In contrast to these views, I argue that laws are multipurpose instruments that acquire a specific function when enforced by those government agents who operate at the frontlines of public service. To understand what these agents do and why, I conducted a qualitative study of the Ministério Público and the Defensoria Pública in São Paulo, Brazil. Through this process, I found that these government agencies are not cohesive bureaucracies but heterarchies composed of distinct internal factions with different evaluative principles. Moreover, officials within them are not isolated from other entities in society but tightly entangled with them, and these connections influence what these officials do. Finally, enforcement agents are not always resigned to solving conflicts as they arise. Rather, they strive to find acceptable solutions in the interstices of existing conditions or even change the circumstances that created the conflict in the first place.
A Sense of Displacement: Long‐time Residents' Feelings of Displacement in Gentrifying Bushwick, New York
Authors: Valli Chiara 
Published: June 2016

AbstractThis article is a contribution to reinforcing our understanding of gentrification and displacement as neighborhood expressions of inequality. It explores the experiences of gentrification of lower‐income, long‐time residents in the gentrifying neighborhood of Bushwick, Brooklyn, New York City. The focus is on components of displacement beyond the traditional emphasis on outmigration. In particular, the article pinpoints the emotional, affective, psychological reactions of long‐time residents triggered through the encounter with newcomers. While the entry point is the exploration of emotions and affects, the article argues that these feelings are outcomes of material socio‐economic inequalities and, in particular, their powerfully racialized historical foundations, as embodied in the contemporary encounter of long‐time residents with newcomers.
Segregated Networks in the City
Authors: Netto Vinicius M. , Soares Maíra Pinheiro , Paschoalino Roberto 
Published: June 2016

AbstractSegregation has been one of the most persistent features of urban life and, accordingly, one of the main subjects of enquiry in urban studies. Stemming from a tradition that can be traced back to the Chicago School in the early twentieth century, social segregation has been seen as the natural consequence of the social division of space. Such naturalized understanding of segregation as ‘territorial segregation' takes space as a surrogate for social distance. We propose a shift in the focus from the static segregation of places—where social distance is assumed rather than fully explained—to how social segregation is reproduced through embodied urban trajectories. We aim to accomplish this by exploring the spatial behaviour of different social groups as networks of movement that constitute opportunities for co‐presence. This alternative view recasts the original idea of segregation as ‘restrictions on interaction' by concentrating on the spatiality of segregation potentially active in the circumstances of social contact and encounters in the city. This approach to segregation as a subtle process that operates ultimately through trajectories of the body is illustrated by an empirical study in a Brazilian city.
REACTED – Reducing Acute Chest pain Time in the ED: A prospective pre‐/post‐interventional cohort study, stratifying risk using early cardiac multi‐markers, probably increases discharges safely
Authors: Mountain David , Ercleve Tor , Allely Peter , McQuillan Brendan , Yamen Eric , Beilby John , Lim Ee‐Mun , Rogers Jeremy , Geelhoed Elizabeth 
Published: June 2016

AbstractObjectiveED chest pain assessments can be challenging, lengthy and contribute to overcrowding. Rapid accurate risk stratification strategies should improve ED length of stay (EDLOS). Emergency, Biochemistry and Cardiology implemented new guidelines using paired (<3 h) multiple cardiac markers to stratify patients. The intervention would reduce chest pain EDLOS. We observed for safety and disposition effects.MethodsThis is a single‐site, prospective observational, before and after intervention study. In December 2009, paired multiple cardiac markers, the second at least 4 h from pain, replaced late troponins. The 4 h rule (ED flow improvement) started in April 2009 (unplanned confounder). Demographics, clinical features, risk assessment and disposition; preferably prospective. Administrative datasets provided disposition outcomes, 4 months pre‐/post‐intervention. Follow up with partially blinded adjudications assessed for 45 day major adverse cardiac events (MACE). Before intervention, consecutive patients were enrolled with mixed prospective/retrospective data. After, sampling occurred whenever prospective data were collected.ResultsAdjudicated patients were n = 1029 (14.2% MI, 14.9% MACE), 426 before, 603 after. EDLOS reduced 87 min (416–329; P < 0.001), similar to triage 2 patients without chest pain. Possibly, avoidable MACE occurred in five of 598 discharges (0.8%, CI 0.3–1.8%) with non‐significant decreases (0.5%, CI 0.1–1.8%) post‐intervention. Disposition changes included greater observation ward use (3.8–12.3%; P < 0.001), more discharges (47.4–52.9%, P = 0.002), less transfers (9.3–6.9%, P = 0.014) and less late inpatient discharge decisions (15.2–8.7%, P = 0.001).ConclusionPaired cardiac markers performed adequately for avoidable MACE, and disposition improved significantly. A confounding system change meant the reduced EDLOS (primary outcome) was unable to be associated with the intervention.
Effect of S100A12 and soluble receptor for advanced glycation end products on the occurrence of severe acute pancreatitis
Authors: Zhao Bing , Chen Ying , Sun Wen Wu , Chen Wei Wei , Ma Li , Yang Zhi Tao , Huang Jun , Chen Er Zhen , Fei Jian , Mao En Qiang 
Published: June 2016

AbstractObjectiveTo assess whether serum levels of S100A12 and soluble receptor for advanced glycation end products (sRAGE) could predict the severity of acute pancreatitis (AP).MethodsWe conducted a non‐interventional pilot study, including 74 AP patients and 28 healthy volunteers serving as controls. AP patients were further divided into the mild (MAP, n = 22), moderately severe (MSAP, n = 30) and severe (SAP, n = 22) groups. Peripheral blood samples were collected within 72 h after the onset of AP for the determination of S100A12, sRAGE and C‐reactive protein (CRP) levels. The acute physiology and chronic health evaluation II (APACHE II) score, Balthazar computed tomography severity index (CTSI) were calculated at admission.ResultsS100A12 and sRAGE levels in SAP patient were significantly higher than in controls, MAP and MSAP patients. The receiver operating characteristic (ROC) curve analysis demonstrated the predictive ability of S100A12 [sensitivity 91%, specificity 81%, the area under the ROC curve AUROC 0.9047] and sRAGE (sensitivity 57%, specificity 100%, AUROC 0.8304) for evaluating the severity of AP. S100A12 and sRAGE were correlated with APACHE II and CTSI but not with CRP. This combination of new and traditional indicators had higher accuracy than traditional indicators alone. Specifically, S100A12 and sRAGE were positively correlated with the type of organ failure (respiratory and renal failure) and might distinguish transient from persistent organ failure at admission.ConclusionS100A12 and sRAGE could be used as efficient biomarkers for the early identification of SAP.
Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups
Authors: Gauzere J. , Oddou‐Muratorio S. , Gay L. , Klein E. K. 
Published: June 2016

AbstractAccurate estimates of heritability () are necessary to assess adaptive responses of populations and evolution of fitness‐related traits in changing environments. For plants, estimates generally rely on maternal progeny designs, assuming that offspring are either half‐sibs or unrelated. However, plant mating systems often depart from half‐sib assumptions, this can bias estimates. Here, we investigate how to accurately estimate in nonmodel species through the analysis of sibling designs with a moderate genotyping effort. We performed simulations to investigate how microsatellite marker information available for only a subset of offspring can improve estimates based on maternal progeny designs in the presence of nonrandom mating, inbreeding in the parental population or maternal effects. We compared the basic family method, considering or not adjustments based on average relatedness coefficients, and methods based on the animal model. The animal model was used with average relatedness information, or with hybrid relatedness information: associating one‐generation pedigree and family assumptions, or associating one‐generation pedigree and average relatedness coefficients. Our results highlighted that methods using marker‐based relatedness coefficients performed as well as pedigree‐based methods in the presence of nonrandom mating (i.e. unequal male reproductive contributions, selfing), offering promising prospects to investigate in situ heritabilities in natural populations. In the presence of maternal effects, only the use of pairwise relatednesses through pedigree information improved the accuracy of estimates. In that case, the amount of father‐related offspring in the sibling design is the most critical. Overall, we showed that the method using both one‐generation pedigree and average relatedness coefficients was the most robust to various ecological scenarios.
The Influence of Age on the Diagnostic Performance of White Blood Cell Count and Absolute Neutrophil Count in Suspected Pediatric Appendicitis
Authors: Bachur Richard G. , Dayan Peter S. , Dudley Nanette C. , Bajaj Lalit , Stevenson Michelle D. , Macias Charles G. , Mittal Manoj K. , Bennett Jonathan , Sinclair Kelly , Monuteaux Michael C. , Kharbanda Anupam B. 
Published: June 2016

AbstractObjectiveWhite blood cell (WBC) count and absolute neutrophil count (ANC) are a standard part of the evaluation of suspected appendicitis. Specific threshold values are utilized in clinical pathways, but the discriminatory value of WBC count and ANC may vary by age. The objective of this study was to investigate whether the diagnostic value of WBC count and ANC varies across age groups and whether diagnostic thresholds should be age‐adjusted.MethodsThis is a multicenter prospective observational study of patients aged 3–18 years who were evaluated for appendicitis. Receiver operator characteristic curves were developed to assess overall discriminative power of WBC count and ANC across three age groups: <5, 5–11, and 12–18 years of age. Diagnostic performance of WBC count and ANC was then assessed at specific cut‐points.ResultsA total of 2,133 patients with a median age of 10.9 years (interquartile range = 8.0–13.9 years) were studied. Forty‐one percent had appendicitis. The area under the curve (AUC) for WBC count was 0.69 (95% confidence interval [CI] = 0.61 to 0.77) for patients < 5 years of age, 0.76 (95% CI = 0.73 to 0.79) for 5–11 years of age, and 0.83 (95% CI = 0.81 to 0.86) for 12–18 years of age. The AUCs for ANC across age groups mirrored WBC performance. At a commonly utilized WBC cut‐point of 10,000/mm3, the sensitivity decreased with increasing age: 95% (<5 years), 91% (5–11 years), and 89% (12–18 years) whereas specificity increased by age: 36% (<5 years), 49% (5–12 years), and 64% (12–18 years).ConclusionWBC count and ANC had better diagnostic performance with increasing age. Age‐adjusted values of WBC count or ANC should be considered in diagnostic strategies for suspected pediatric appendicitis.
Multifocal and refractory pyoderma gangrenosum: Possible role of cocaine abuse
Authors: Baliu‐Piqué Carola , Mascaró José Manuel 
Published: June 2016

AbstractPyoderma gangrenosum is a rare and severe inflammatory skin condition. There are different variants, including generalised and atypical forms, but the most common presentation is an enlarging ulcer on the lower extremities. Treatment can represent a challenge for physicians and there are no guidelines based on randomised controlled trials. We report an exceptional case of widespread and refractory pyoderma gangrenosum in a middle‐aged woman where cocaine use may have played a role. Treatment with i.v. pulse corticosteroids and cyclosporine was ineffective, and disease control was obtained with oral corticosteroids together with mycophenolic acid, infliximab and abstinence from cocaine consumption. There was a temporal relationship between disease outbreaks and cocaine consumption and improvement after its discontinuation. In the present case such clinical severity without associated pathology and the temporal association with cocaine abuse raises the possibility of cocaine playing an aetiological role as well as accounting for therapy resistance.
IgG4 but no IgG1 antibody production after intralymphatic immunotherapy with recombinant MAT‐Feld1 in human
Authors: Freiberger S. N. , Zehnder M. , Gafvelin G. , Grönlund H. , Kündig T. M. , Johansen P. 
Published: June 2016

AbstractAllergy immunotherapy (AIT) mediates protection against allergen exposure in part due to allergen‐specific antibodies. While immunization typically stimulated IgG1 and IgG2, AIT is often associated with production of IgG4. Here, twenty cat dander‐sensitized patients were randomized to receive three injections of intralymphatic immunotherapy (ILIT) with MAT‐Feld1 adsorbed to aluminum hydroxide or just aluminum hydroxide (placebo) in a double‐blind setting (ClinicalTrials.gov NCT00718679). Whereas the clinical data, showing benefit of Mat‐Feld1 ILIT was published in 2012 (Senti et al., J Allergy Clin Immunol, vol 129(5):1290–1296), the current study investigated the cat allergen‐specific antibody responses. Blood was drawn prior to ILIT, as well as 1, 3, and 12 months after first ILIT. The sera were analyzed to characterize all IgG subclasses and IgE antibody responses. ILIT with MAT‐Feld1 elicited high levels of total IgG that were maintained for at least 12 months. Interestingly, a strong increase in IgG4 and some increase in IgG2 were observed throughout the study, while production of cat‐specific IgG1 and IgG3 was not stimulated by MAT‐Feld1 ILIT. The IgE levels remained constant.