bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maturation of 6S regulatory RNA to a highly elongated structure
Authors: Fadouloglou Vasiliki E. , Lin Hong‐Tin V. , Tria Giancarlo , Hernández Helena , Robinson Carol V. , Svergun Dmitri I. , Luisi Ben F. 
Published: September 2015

As bacterial populations leave the exponential growth phase and enter the stationary phase, their patterns of gene expression undergo marked changes. A key effector of this change is 6S RNA, which is a highly conserved regulatory RNA that impedes the transcription of genes associated with exponential growth by forming an inactivating ternary complex with RNA polymerase and sigma factor σ70 (σ70–RNAP). In Escherichia coli, the endoribonuclease RNase E generates 6S RNA by specific cleavage of a precursor that is nearly twice the size of the 58 kDa mature form. We have explored recognition of the precursor by RNase E, and observed that processing is inhibited under conditions of excess substrate. This finding supports a largely distributive mechanism, meaning that each round of catalysis results in enzyme dissociation and re‐binding to the substrate. We show that the precursor molecule and the mature 6S share a structural core dominated by an A‐type helix, indicating that processing is not accompanied by extensive refolding. Both precursor and mature forms of 6S have a highly stable secondary structure, adopt an elongated shape, and show the potential to form dimers under specific conditions; nonetheless, 6S has a high structural plasticity that probably enables it to be structurally adapted upon binding to its cognate protein partners. Analysis of the 6S‐σ70–RNAP complex by native mass spectrometry reveals a stable association with a stoichiometry of 1 : 1 : 1. A theoretical 3D model of mature 6S is presented, which is consistent with the experimental data and supports a previously proposed structure with a small stem‐loop inside the central bubble.
Why do we lose protected areas? Factors influencing protected area downgrading, downsizing and degazettement in the tropics and subtropics
Authors: Symes William S. , Rao Madhu , Mascia Michael B. , Carrasco L. Roman 
Published: September 2015

AbstractProtected areas (PAs) are an essential tool for the conservation of biodiversity globally. Previous studies have focussed on the effectiveness of PAs and the design of optimal PA networks. However, not all PAs remain intact permanently; many PAs undergo downgrading, downsizing and/or degazettement (PADDD), a fact largely ignored until recently. The drivers of enacted PADDD events and the factors influencing its spatial occurrence are poorly understood, potentially undermining the efficacy of PAs and PA networks. Here we examine the spatial relationship between PADDD and economic, demographic and structural variables, using a 110‐year data set of 342 enacted PADDD events across 44 countries in the tropics and subtropics. We find that the probability of an enacted PADDD event increases with the size of the PA and through a synergistic interaction between PA size and local population densities. Our results are robust to the under‐reporting of enacted PADDD events that occur among smaller PAs and in regions with lower population density. We find an economic motive for PADDD events, given that the opportunity costs associated with larger PAs are higher, on average, than smaller PAs. Our findings suggest a need for conservation practitioners to better consider PA characteristics, as well as the social, economic and political context in which PAs are situated, to aid the creation of more efficient and sustainable PA networks. In particular, the dynamics of enacted PADDD events highlight the need to explicitly consider PA robustness as a core component of systematic conservation planning for PA networks.
Biotic homogenization of three insect groups due to urbanization
Authors: Knop Eva 
Published: September 2015

AbstractCities are growing rapidly, thereby expected to cause a large‐scale global biotic homogenization. Evidence for the homogenization hypothesis is mostly derived from plants and birds, whereas arthropods have so far been neglected. Here, I tested the homogenization hypothesis with three insect indicator groups, namely true bugs, leafhoppers, and beetles. In particular, I was interested whether insect species community composition differs between urban and rural areas, whether they are more similar between cities than between rural areas, and whether the found pattern is explained by true species turnover, species diversity gradients and geographic distance, by non‐native or specialist species, respectively. I analyzed insect species communities sampled on birch trees in a total of six Swiss cities and six rural areas nearby. In all indicator groups, urban and rural community composition was significantly dissimilar due to native species turnover. Further, for bug and leafhopper communities, I found evidence for large‐scale homogenization due to urbanization, which was driven by reduced species turnover of specialist species in cities. Species turnover of beetle communities was similar between cities and rural areas. Interestingly, when specialist species of beetles were excluded from the analyses, cities were more dissimilar than rural areas, suggesting biotic differentiation of beetle communities in cities. Non‐native species did not affect species turnover of the insect groups. However, given non‐native arthropod species are increasing rapidly, their homogenizing effect might be detected more often in future. Overall, the results show that urbanization has a negative large‐scale impact on the diversity specialist species of the investigated insect groups. Specific measures in cities targeted at increasing the persistence of specialist species typical for the respective biogeographic region could help to stop the loss of biodiversity.
Visceral fat enhances blood pressure reactivity to physical but not mental challenges in male adolescents
Authors: Van Woudenberg M. , Abrahamowicz M. , Leonard G. , Perron M. , Richer L. , Veillette S. , Gaudet D. , Paus T. , Pausova Z. 
Published: September 2015

SummaryBackgroundExcess visceral fat is a major risk factor for hypertension. Enhanced blood pressure (BP) reactivity and delayed BP recovery from physical and mental challenges predict future hypertension.ObjectivesDetermine whether visceral fat is associated with higher BP reactivity and delayed BP recovery from physical and mental challenges during adolescence.MethodsIn a community‐based sample of 283 male and 308 female adolescents, we measured visceral fat with magnetic resonance imaging, total body fat with bioimpedance, and beat‐by‐beat BP with a Finometer at rest and during physical (10‐min standing) and mental (2‐min math stress) challenges.ResultsMales vs. females showed greater BP reactivity and no differences in BP recovery from either type of challenges. Visceral fat was positively associated with BP reactivity to standing up only and in males only (+8.4 ± 3.6 mmHg per 1 log cm3 of visceral fat, P = 0.008), and this association was independent of total body fat. No association was seen between visceral fat and BP recovery from either type of challenge in either sex. All these associations were independent of age, puberty stage, height and initial BP.ConclusionsAdolescent males vs. females demonstrate greater BP reactivity but similar BP recovery from physical and mental challenges. Excess visceral fat enhances BP reactivity to physical but not mental challenges in males only.
Integrative review of benefit levers’ characteristics for system‐wide spread of best healthcare practices
Authors: ten Ham Wilma , Minnie Karin , van der Walt Christa 
Published: September 2015

AbstractAimTo critically analyse the characteristics of the benefit levers that are required for effective system‐wide spread of evidence‐based practice.BackgroundEvidence‐based nursing practice is the cornerstone of quality patient care and merits system‐wide implementation. Achieving system‐wide spread of evidence‐based innovations requires adoption of four benefit levers (the facilitators for spreading innovations), conceptualized by Edwards and Grinspun: alignment, leadership for change, permeation plans and supporting and reinforcing structures. Although these concepts have been explored and described in primary studies, they were only recently identified as benefit levers and their characteristics have not been reviewed in the context of health care using an integrative literature review.DesignAn integrative literature review using an adapted Whittemore and Knafl design.Data sourcesA comprehensive search using multiple sites such as Scopus, EBSCOhost, ProQuest, ScienceDirect, Cochrane Library, Nexus, SAePublications, Sabinet, Google Scholar and grey literature was conducted (January‐March 2012) and updated (December 2014). After reading the abstracts, titles and full‐text articles, forty (N = 40) research and non‐research documents met the inclusion criteria.Review methodsThirty‐five documents remained after critical appraisal. A systematic approach was used to analyse and synthesize the data and formulate concluding statements.ResultsData revealed characteristics about alignment (personal, organizational and contextual attributes), permeation plans (phases), leadership for change (types, strategies, position, attitude and support) and supporting and reinforcing structures (types and requirements).ConclusionBenefit levers should be used to promote the spread of evidence‐based practices. However, more studies concerning benefit levers, specifically regarding ‘alignment’ and ‘permeation plans’, are required to promote system‐wide spread of best healthcare practices.
Lack of haplotype structuring for two candidate genes for trypanotolerance in cattle
Authors: Álvarez I. , Pérez‐Pardal L. , Traoré A. , Fernández I. , Goyache F. 
Published: September 2015

SummaryBovine trypanotolerance is a heritable trait associated to the ability of the individuals to control parasitaemia and anaemia. The INHBA (BTA4) and TICAM1 (BTA7) genes are strong candidates for trypanotolerance‐related traits. The coding sequence of both genes (3951 bp in total) were analysed in a panel including 79 Asian, African and European cattle (Bos taurus and B. indicus) to identify naturally occurring polymorphisms on both genes. In general, the genetic diversity was low. Nineteen of the 33 mutations identified were found just one time. Seventeen different haplotypes were defined for the TICAM1 gene, and 9 and 12 were defined for the exon 1 and the exon 2 of the INHBA gene, respectively. There was no clear separation between cattle groups. The most frequent haplotypes identified in West African taurine samples were also identified in other cattle groups including Asian zebu and European cattle. Phylogenetic trees and principal component analysis confirmed that divergence among the cattle groups analysed was poor, particularly for the INHBA sequences. The European cattle subset had the lowest values of haplotype diversity for both the exon1 (monomorphic) and the exon2 (0.077 ± 0.066) of the INHBA gene. Neutrality tests, in general, did not suggest that the analysed genes were under positive selection. The assessed scenario would be consistent with the identification of recent mutations in evolutionary terms.
Practical Aspects of Traceability in Small Food Businesses with Implemented Food Safety Management Systems
Authors: Dzwolak Waldemar 
Published: September 2015

AbstractAn effective traceability system is very important for food safety and public health. This paper presents results from studies carried out in 2013–2014 on internal traceability in sixPolish small food businesses with implemented food safety management systems (FSMSs). In this paper, two key performance indicators are proposed related to available traceability records (ITR) and traceability time (tT), which can be valuable in the continuous improvement of internal traceability in small food businesses. Both indicators were applied in food businesses before and after certification of theFSMS, which influenced both indices. Before and after certification of theFSMS, theITRvalues were 0.39–0.92 and 0.71–1.00, whereastTvalues were 65–187 and 48–145 min, respectively. After direct observation of recalls and withdrawals, and analysis of records in the studied organizations, a generic mass balance was developed. Additionally, an algorithm includingITR,tTindicators and mass balance was established, which can be useful in practical testing and improving internal traceability systems in small food businesses.Practical ApplicationsThe results can be very useful to food safety/quality managers, practitioners, regulatory bodies and internal/external auditors as fundamentals of the rational improvement of the effectiveness and accuracy of internal traceability systems in small food businesses. The practical application also relates to the application of the algorithm, including available traceability records and traceability time indicators, as well as mass balance developed in this study. All the results can enhance the recall and withdrawal of nonconforming and/or unsafe food products, and can also facilitate the practical simulation of withdrawals as required by some private standards, such as BRC Global Standard for Food Safety and International Food Standard.
Role of platinum DNA damage‐induced transcriptional inhibition in chemotherapy‐induced neuronal atrophy and peripheral neurotoxicity
Authors: Yan Fang , Liu Johnson J , Ip Virginia , Jamieson Stephen M F , McKeage Mark J 
Published: September 2015

AbstractPlatinum‐based anticancer drugs cause peripheral neurotoxicity by damaging sensory neurons within the dorsal root ganglia (DRG), but the mechanisms are incompletely understood. The roles of platinum DNA binding, transcription inhibition and altered cell size were investigated in primary cultures of rat DRG cells. Click chemistry quantitative fluorescence imaging of RNA‐incorporated 5‐ethynyluridine showed high, but wide ranging, global levels of transcription in individual neurons that correlated with their cell body size. Treatment with platinum drugs reduced neuronal transcription and cell body size to an extent that corresponded to the amount of preceding platinum DNA binding, but without any loss of neuronal cells. The effects of platinum drugs on neuronal transcription and cell body size were inhibited by blocking platinum DNA binding with sodium thiosulfate, and mimicked by treatment with a model transcriptional inhibitor, actinomycin D. In vivo oxaliplatin treatment depleted the total RNA content of DRG tissue concurrently with altering DRG neuronal size. These findings point to a mechanism of chemotherapy‐induced peripheral neurotoxicity, whereby platinum DNA damage induces global transcriptional arrest leading in turn to neuronal atrophy. DRG neurons may be particularly vulnerable to this mechanism of toxicity because of their requirements for high basal levels of global transcriptional activity.
imageFindings point to a new stepwise mechanism of chemotherapy‐induced peripheral neurotoxicity, whereby platinum DNA damage induces global transcriptional arrest leading in turn to neuronal atrophy. Dorsal root ganglion neurons may be particularly vulnerable to this neurotoxicity because of their high global transcriptional outputs, demonstrated in this study by click chemistry quantitative fluorescence imaging.
Prothymosin‐alpha preconditioning activates TLR4–TRIF signaling to induce protection of ischemic retina
Authors: Halder Sebok Kumar , Matsunaga Hayato , Ishii Ken J. , Ueda Hiroshi 
Published: September 2015

AbstractProthymosin‐alpha protects the brain and retina from ischemic damage. Although prothymosin‐alpha contributes to toll‐like receptor (TLR4)‐mediated immnunopotentiation against viral infection, the beneficial effects of prothymosin‐alpha‐TLR4 signaling in protecting against ischemia remain to be elucidated. In this study, intravitreal administration of prothymosin‐alpha 48 h before induction of retinal ischemia prevented retinal cellular damage as evaluated by histology, and retinal functional deficits as evaluated by electroretinography. Prothymosin‐alpha preconditioning completely prevented the ischemia‐induced loss of ganglion cells with partial survival of bipolar and photoreceptor cells, but not amacrine cells, in immunohistochemistry experiments. Prothymosin‐alpha treatment in the absence of ischemia caused mild activation, proliferation, and migration of retinal microglia, whereas the ischemia‐induced microglial activation was inhibited by prothymosin‐alpha preconditioning. All these preventive effects of prothymosin‐alpha preconditioning were abolished in TLR4 knock‐out mice and by pre‐treatments with anti‐TLR4 antibodies or minocycline, a microglial inhibitor. Prothymosin‐alpha preconditioning inhibited the retinal ischemia‐induced up‐regulation of TLR4‐related injury genes, and increased expression of TLR4‐related protective genes. Furthermore, the prothymosin‐alpha preconditioning‐induced prevention of retinal ischemic damage was abolished in TIR‐domain‐containing adapter‐inducing interferon‐β knock‐out mice, but not in myeloid differentiation primary response gene 88 knock‐out mice. Taken together, the results of this study suggest that prothymosin‐alpha preconditioning selectively drives TLR4–TIR‐domain‐containing adapter‐inducing interferon‐β signaling and microglia in the prevention of retinal ischemic damage.
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We propose the following mechanism for prothymosin‐alpha (ProTα) preconditioning‐induced retinal prevention against ischemia: ProTα preconditioning‐induced prevention of retinal ischemic damage is mediated by selective activation of the TIR‐domain‐containing adapter‐inducing interferon‐β (TRIF)– interferon regulatory factor 3 (IRF3) pathway downstream of toll‐like receptor 4 (TLR4) in microglia, resulting in up‐regulation of TRIF‐IRF3‐dependent protective genes and down‐regulation of myeloid differentiation primary response gene 88 (MyD88)‐Nuclear factor (NF)κB‐dependent injury genes. Detailed investigations would be helpful to test the efficacy of ProTα as a therapeutic agent for the prevention of ischemic disorders.
Pertussis toxin reduces calcium influx to protect ischemic stroke in a middle cerebral artery occlusion model
Authors: Tang Zhiwei , Li Shiping , Han Pengcheng , Yin Junxiang , Gan Yan , Liu Qingwei , Wang Jinkun , Wang Chongqian , Li Yu , Shi Jiong 
Published: September 2015

AbstractIncreased calcium influx secondary to glutamate induced excitotoxicity initiates and potentiates devastating pathological changes following ischemic stroke. Pertussis toxin (PTx), a G‐protein blocker, is known to suppress intracellular calcium accumulation. We hypothesize that PTx can protect against stroke by blocking calcium influx. In a permanent middle cerebral artery occlusion model, PTx (1000 ng) was given intraperitoneally 30 min after inducing stroke. Magnetic Resonance Imaging of perfusion and T2‐weighted brain scans were obtained to evaluate cerebral blood flow (CBF) and infarct volume. Primary neuronal culture was used to test glutamate induced excitotoxicity and calcium influx. We established a non‐linear exponential curve model to minimize variations in animal cerebrovasculature. A reduction of 40–60% in relative CBF was a critical window where infarct volume started to increase as rCBF reduced. PTx showed maximal effects in reducing infarct volume at this window. In vitro studies further demonstrated PTx increased neuronal cell survival by decreasing glutamate‐induced calcium influx into neurons and preventing neurons from apoptosis. PTx salvages the ischemic penumbra by blocking calcium influx. This provides us a new mechanism upon which experimental therapies can be explored to treat ischemic stroke.
imageIn ischemic stroke, excessive glutamate binds to AMPA receptor that depolarizes calcium channel and/ or NMDA receptor. Both of them allow calcium to enter the cell. The overload of calcium triggers cellular cascade that includes Caspase activation and release, leading to pre‐mature cell death. We have demonstrated that PTx, a G‐protein inhibitor, blocks calcium entry which in turn prevents further cellular damage.
Spinal Nerve Root Enhancement on MRI Scans in Children: A Review
Authors: Kontzialis Marinos , Poretti Andrea , Michell Hans , Bosemani Thangamadhan , Tekes Aylin , Huisman Thierry A.G.M. 
Published: September 2015

ABSTRACTSpinal nerve root enhancement in pediatric patients is generally nonspecific, and clinical and laboratory correlation is essential. Nerve root enhancement indicates lack of integrity of the blood‐nerve barrier. In this review, we will present a range of pediatric conditions that can present with spinal nerve root enhancement including inflammatory, infectious, hereditary, and neoplastic causes. Familiarity with the various pathologic entities associated with spinal nerve root enhancement is important for a concise differential diagnosis in the appropriate clinical setting. This will avoid unnecessary additional investigations.
Daily affective experiences predict objective sleep outcomes among adolescents
Authors: Tavernier Royette , Choo Sungsub B. , Grant Kathryn , Adam Emma K. 
Published: September 2015

SummaryAdolescence is a sensitive period for changes in both sleep and affect. Although past research has assessed the association between affect and sleep among adolescents, few studies have examined both trait (typical) and day‐to‐day changes in affect, and fewer still have specifically examined negative social evaluative emotions (e.g. embarrassment) in relation to sleep. Both between‐ and within‐person variations in daily affect were examined in relation to four objectively‐measured sleep outcomes (sleep hours; sleep latency; sleep efficiency; and length of wake bouts) among adolescents. Participants (N = 77 high‐school students; 42.9% female; M = 14.37 years) wore an actiwatch and completed daily‐diaries for 3 days. The results of hierarchical linear models (controlling for age, gender, race, ethnicity, parental employment status, income, puberty and caffeine) indicated that negative social evaluative emotions and high‐arousal affective experiences generally predicted poor sleep outcomes, whereas low‐arousal affective experiences were associated with good sleep outcomes. Specifically, at the person level, adolescents reporting higher negative social evaluative emotions had shorter average sleep hours, and those experiencing higher anxiety–nervousness had longer wake bouts. In addition, individuals experiencing more dysphoria (sad, depressed, lonely) had longer average sleep hours and shorter wake bouts, while those experiencing more calmness had shorter sleep latencies. At the within‐person level, individuals had longer sleep latencies following days that they had experienced high‐arousal positive affect (e.g. excitement), and had longer wake bouts following days they had experienced more negative social evaluative emotions. The results highlight the detrimental effects of negative social evaluative emotions and high‐arousal affective states for adolescent sleep.