bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adenosine Triphosphate Prevents Serum Deprivation-Induced Apoptosis in Human Mesenchymal Stem Cells via Activation of the MAPK Signaling Pathways
Authors: Berlier Jessica L. , Rigutto Sabrina , Dalla Valle Antoine , Lechanteur Jessica , Soyfoo Muhammad S. , Gangji Valerie , Rasschaert Joanne 
Published: September 2014

Abstract
Human mesenchymal stem cells (hMSC) are multipotent cells derived from various sources including adipose and placental tissues as well as bone marrow. Owing to their regenerative and immunomodulatory properties, their use as a potential therapeutic tool is being extensively tested. However, one of the major hurdles in using cell-based therapy is the use of fetal bovine serum that can trigger immune responses, viral and prion diseases. The development of a culture medium devoid of serum while preserving cell viability is therefore a major challenge. In this study, we demonstrated that adenosine triphosphate (ATP) restrained serum deprivation-induced cell death in hMSC by preventing caspases 3/7 activation and modulating ERK1/2 and p38 MAPK signaling pathways. We also showed that serum deprivation conditions triggered dephosphorylation of the proapoptotic protein Bad leading to cell death. Adjunction of ATP restored the phosphorylation state of Bad. Furthermore, ATP significantly modulated the expression of proapoptopic and antiapoptotic genes, in favor of an antiapoptotic profile expression. Finally, we established that hMSC released a high amount of ATP in the extracellular medium when cultured in a serum-free medium. Collectively, our results demonstrate that ATP favors hMSC viability in serum deprivation conditions. Moreover, they shed light on the cardinal role of the MAPK pathways, ERK1/2 and p38 MAPK, in promoting hMSC survival. Stem Cells 2015;33:211–218
Use of Micellar Solutions as Draw Agents in Forward Osmosis
Authors: Roach Jim D. , Al‐Abdulmalek Abdulrahman , Al‐Naama Alaa , Haji Mohammed 
Published: September 2014

AbstractRecent advances in membrane technologies have enhanced the viability of water treatment strategies that employ semipermeable barriers. Forward osmosis (FO), which exploits the natural osmotic pressure gradient between a “draw” solution and a “feed” solution to produce potable water, offers a low‐energy, low‐cost alternative to more conventional treatment methods. Surfactants, because of their tendencies to aggregate into micelles and to adsorb at interfaces, provide intriguing osmotic pressures and offer exploitable properties by which draw solutions can be regenerated. The effectiveness of surfactant‐based FO using cellulose triacetate membranes has been assessed in terms of water flux and reverse surfactant diffusion using cetylpyridinium chloride, sodium dodecylsulfate, and Triton X‐100. The ratios of water flux to surfactant flux exceeded 600 L mol−1 for all surfactants studied. Surfactant recoveries of over 99 % were achieved by ultrafiltration using regenerated cellulose membranes.
The dynamics of European regulatory regimes in higher education — Challenged prerogatives and evolutionary change
Authors: Gornitzka Åse , Stensaker Bjørn 
Published: September 2014

AbstractEuropean higher education has witnessed a substantial growth in regulatory arrangements in external quality assurance (EQA) during the last couple of decades. This current article describes the central characteristics and trajectories of this expansion, and discusses drivers of this development drawing on an institutional perspective. Empirically, three distinct, although overlapping, stages in the building up of a regulatory regime are identified — from formalization and agencification of EQA at national level, establishment of common standards at a European level, to the current stage of an emerging global market-based system. This combination of institutional layering, path-dependency, and conversion can be explained by the nature of political context and the ambiguities of regulation of quality in higher education. In the conclusion it is argued that the development of external quality assurance as a regulatory field is an example of how the dynamics of an evolving regulatory regime may in an unexpected way limit the public control of highly institutionalized fields.
Flow phenomena in the very near wake of a flat plate with a circular trailing edge
Authors: Rai Man Mohan 
Published: September 2014

AbstractThe very near wake of a flat plate with a circular trailing edge, exhibiting pronounced shedding of wake vortices, is investigated with data from direct numerical simulations (DNSs). Computations were performed for two cases. In the first case the Reynolds numbers based on plate length and thickness were $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}1.255 \times 10^{6}$ and $1.0 \times 10^{4}$, respectively. In the second case the two Reynolds numbers were $3.025 \times 10^{5}$ and $5.0 \times 10^{3}$, respectively. The separating boundary layers are turbulent and statistically identical thus resulting in a wake that is symmetric in the mean. The focus here is on the instability of the detached shear layers and the evolution of rib-vortex-induced localized regions of reverse flow. These regions detach from the main body of reverse flow in the trailing edge region and are convected downstream. The detached shear layers intermittently exhibit unstable behaviour, sometimes resulting in the development of shear-layer vortices as seen in earlier cylinder flow investigations with laminar separating boundary layers. Only a small fraction of the separated turbulent boundary layer experiences this instability, and also rolls up into the initial shed vortices. The instability causes a broadband peak in pressure spectra computed within the shear layers. Phase-averaged intensity and shear stress distributions of the randomly fluctuating component of velocity in the very near wake are also provided here and compared with those obtained in the near wake. The distributions of the production terms in the transport equations for the turbulent stresses are also provided.
Changes in oxidative stress in response to different levels of energy restriction in obese ponies
Authors: Bruynsteen Lien , Janssens Geert P. J. , Harris Patricia A. , Duchateau Luc , Valle Emanuela , Odetti Patrizio , Vandevelde Kimberley , Buyse Johan , Hesta Myriam 
Published: September 2014

The present study evaluated the effect of different levels of energy restriction on metabolic parameters in obese ponies. Relative weight changes, markers of lipid metabolism and oxidant/antioxidant balance were monitored. A total of eighteen obese (body condition score ≥ 7/9) Shetland ponies were studied over a 23·5-week trial, which was divided into three periods. The first period involved a 4-week adaptation period in which each animal was fed 100 % of their maintenance energy requirements needed to maintain a stable obese body weight (MERob). This was followed by a 16·5-week weight-loss period in which ponies were assigned to receive either 100 % (control group, CONTROL), 80 % (slow weight-loss (SLOW) group) or 60 % (rapid weight-loss (RAPID) group) of their MERob. During the 3-week end-phase period, all ponies were again fed 100 % of their MERob. Relative weight loss was higher in the RAPID group (P< 0·001) compared with the SLOW group. No linear relationship was found as a doubling of the percentage of energy restriction was accompanied by a tripling of the percentage of weight loss. Relative weight gain afterwards in the end-phase period was higher in the RAPID group (P< 0·001) compared with the SLOW and CONTROL groups. During the weight-loss period, TAG and NEFA concentrations were highest in the RAPID group, as were α-tocopherol and ferric-reducing ability of plasma concentrations. After 8 weeks of weight loss, the concentrations of advanced oxidation protein products were higher in the RAPID group compared with the SLOW and CONTROL groups (P< 0·001). In conclusion, the level of energy restriction influences the extent of changes in oxidant/antioxidant balance. Practically, more severe energy restriction regimens may be associated with a greater regain of weight after the restriction period.
Domestic and sexual violence against patients with severe mental illness
Authors: Khalifeh H. , Moran P. , Borschmann R. , Dean K. , Hart C. , Hogg J. , Osborn D. , Johnson S. , Howard L. M. 
Published: September 2014

BackgroundDomestic and sexual violence are significant public health problems but little is known about the extent to which men and women with severe mental illness (SMI) are at risk compared with the general population. We aimed to compare the prevalence and impact of violence against SMI patients and the general population.MethodThree hundred and three randomly recruited psychiatric patients, in contact with community services for ⩾1 year, were interviewed using the British Crime Survey domestic/sexual violence questionnaire. Prevalence and correlates of violence in this sample were compared with those from 22 606 general population controls participating in the contemporaneous 2011/12 national crime survey.ResultsPast-year domestic violence was reported by 27% v. 9% of SMI and control women, respectively [odds ratio (OR) adjusted for socio-demographics, aOR 2.7, 95% confidence interval (CI) 1.7–4.0], and by 13% v. 5% of SMI and control men, respectively (aOR 1.6, 95% CI 1.0–2.8). Past-year sexual violence was reported by 10% v. 2.0% of SMI and control women respectively (aOR 2.9, 95% CI 1.4–5.8). Family (non-partner) violence comprised a greater proportion of overall domestic violence among SMI than control victims (63% v. 35%, p < 0.01). Adulthood serious sexual assault led to attempted suicide more often among SMI than control female victims (53% v. 3.4%, p < 0.001).ConclusionsCompared to the general population, patients with SMI are at substantially increased risk of domestic and sexual violence, with a relative excess of family violence and adverse health impact following victimization. Psychiatric services, and public health and criminal justice policies, need to address domestic and sexual violence in this at-risk group.
VALIDATION OF SURROGATE ENDPOINTS IN ADVANCED SOLID TUMORS: SYSTEMATIC REVIEW OF STATISTICAL METHODS, RESULTS, AND IMPLICATIONS FOR POLICY MAKERS
Authors: Ciani Oriana , Davis Sarah , Tappenden Paul , Garside Ruth , Stein Ken , Cantrell Anna , Saad Everardo D. , Buyse Marc , Taylor Rod S. 
Published: September 2014

Objectives: Licensing of, and coverage decisions on, new therapies should rely on evidence from patient-relevant endpoints such as overall survival (OS). Nevertheless, evidence from surrogate endpoints may also be useful, as it may not only expedite the regulatory approval of new therapies but also inform coverage decisions. It is, therefore, essential that candidate surrogate endpoints be properly validated. However, there is no consensus on statistical methods for such validation and on how the evidence thus derived should be applied by policy makers.Methods: We review current statistical approaches to surrogate-endpoint validation based on meta-analysis in various advanced-tumor settings. We assessed the suitability of two surrogates (progression-free survival [PFS] and time-to-progression [TTP]) using three current validation frameworks: Elston and Taylor's framework, the German Institute of Quality and Efficiency in Health Care's (IQWiG) framework and the Biomarker-Surrogacy Evaluation Schema (BSES3).Results: A wide variety of statistical methods have been used to assess surrogacy. The strength of the association between the two surrogates and OS was generally low. The level of evidence (observation-level versus treatment-level) available varied considerably by cancer type, by evaluation tools and was not always consistent even within one specific cancer type.Conclusions: Not in all solid tumors the treatment-level association between PFS or TTP and OS has been investigated. According to IQWiG's framework, only PFS achieved acceptable evidence of surrogacy in metastatic colorectal and ovarian cancer treated with cytotoxic agents. Our study emphasizes the challenges of surrogate-endpoint validation and the importance of building consensus on the development of evaluation frameworks.
Choosing and using multiple traits in functional diversity research
Authors: LEFCHECK JONATHAN S. , BASTAZINI VINICIUS A. G. , GRIFFIN JOHN N. 
Published: September 2014

SUMMARYSpecies are different, but they are not equally different. Yet many indices of biodiversity assume species vary to identical degrees. This notion does not meet with intuition: some species vary greatly in terms of their morphology, behaviour and ecology, while others vary only a little. One way to reconcile the dissimilarity between species is by collecting information on their functional traits (FTs), descriptors of how organisms interact with their environment and each other. Functional diversity (FD) is the total variation in one or more FTs across all species within a community, and provides a powerful complement to species diversity. There are several challenges facing the application of FD to conservation science, including lack of rigorous trait data for many organisms, and sparse details on how to select available traits to generate meaningful inferences for the various summary metrics of FD. This Comment provides a brief discussion on choosing and using FTs, and recommendations for best practice. Ultimately, researchers need to consider using a variety of traits when hypotheses are multifaceted or could potentially evolve, at the same time thinking critically about trait selection to avoid redundant information.
The Wire as speculative research
Authors: Leclair-Paquet Benjamin 
Published: September 2014

Created by David Simon in 2002, the HBO series The Wire presents the established moral code of a society that lies outside mainstream America and depicts institutions designed to maintain the status quo. Terry Eagleton suggests of Dickens, that his ‘grotesque realism is a stylistic distortion in the service of truth, a kind of astigmatism which allows us to see more accurately.’ The content of Simon's programme operates in a similar way. It proposes an alternative to academic narratives able to disseminate knowledge beyond the closed-off world of peer review.The richness, uniqueness and intricacy of The Wire has made it difficult to trace its thematic and stylistic heritage. The programme has been referred to as a ‘lyrical sociology’, ‘a type of urban sociology’, ‘a rendering of urban theory’, a ‘fontless social science’, a ‘theoretical archetype’, a ‘Dickensian show’, and more. At an aesthetic level, The Wire has been qualified as a work of ‘psychological realism’, ‘social realism’, as something aspiring to Fredric Jameson's aesthetics of ‘cognitive mapping’, or even a ‘rich counterpart to actor-network-theory’.
Positional Correlative Anatomy of Invertebrate Model Organisms Increases Efficiency of TEM Data Production
Authors: Kolotuev Irina 
Published: September 2014

AbstractTransmission electron microscopy (TEM) is an important tool for studies in cell biology, and is essential to address research questions from bacteria to animals. Recent technological innovations have advanced the entire field of TEM, yet classical techniques still prevail for most present-day studies. Indeed, the majority of cell and developmental biology studies that use TEM do not require cutting-edge methodologies, but rather fast and efficient data generation. Although access to state-of-the-art equipment is frequently problematic, standard TEM microscopes are typically available, even in modest research facilities. However, a major unmet need in standard TEM is the ability to quickly prepare and orient a sample to identify a region of interest. Here, I provide a detailed step-by-step method for a positional correlative anatomy approach to flat-embedded samples. These modifications make the TEM preparation and analytic procedures faster and more straightforward, supporting a higher sampling rate. To illustrate the modified procedures, I provide numerous examples addressing research questions inCaenorhabditis elegansandDrosophila. This method can be equally applied to address questions of cell and developmental biology in other small multicellular model organisms.
Technical Advances Toward an Endoscopic–Phototransducer Approach to Investigation of Velopharyngeal Physiology
Authors: Karnell Michael , Moon Jerald 
Published: September 2014

Purpose
This study aimed to examine the response characteristics of a new generation phototransducer and to test new recording and processing procedures when used with endoscopy to track velopharyngeal closure during normal speech.

Method
Integrated phototransducer–endoscopy response linearity was laboratory tested using a wide range of simulated velopharyngeal orifice areas. In vivo speech testing was completed to determine the effect of endoscope to light receptor distance on measurements documenting variations in normal velopharyngeal closure.

Results

Phototransducer response linearity was excellent (
r
= .99) provided an indirect (reflected light) orientation was used between the endoscope and the light-sensing fiber coupled with the phototransducer. Phototransducer response time exceeded expected velopharyngeal movement rates by an order of magnitude. In vivo speech measurements were affected by the distance between the light-emitting endoscope and the light-receiving tip of the light-sensing fiber. Data normalization to a light-out condition effectively controlled for this expected phenomenon. Patterns of velopharyngeal valving during speech were found to be stable and appropriate given the phonetic content of the utterance.

Conclusions
Technological and data-processing advances support further exploration of an integrated phototransducer–endoscopic approach to studying velopharyngeal closure for speech. Additional studies involving normal speakers are under way.
Survival Time of Methicillin-Resistant Staphylococcus aureus–Free Status after Institutional Clearance
Authors: Valencia-Rey Paula A. , Strymish Judith , Robillard Ernest , Evans Martin , Weinberg Janice , Gupta Kalpana 
Published: September 2014

Objective.To determine the durability of methicillin-resistant Staphylococcus aureus (MRSA)–free status after patients are removed from contact precautions and the association of specific clearance policy variables with survivalDesign.Retrospective cohort study from October 2007 to April 2013.Setting.Veteran Affairs Boston Healthcare System.Participants.Patients with a prior history of MRSA who were removed from contact precautions after deemed cleared of their MRSA status by infection prevention.Methods.Active nasal screening results and clinical data from acute, long-term, and outpatient care facilities were evaluated to determine survival of MRSA-free status in a time-to-event analysis.Results.A total of 351 unique patients were followed for 107,112 patient-days. The median age was 68 years. Overall, 249 (71%) of patients remained MRSA-free, and 102 (29%) reverted to MRSA positive. The median MRSA-free survival was 880 days. Comorbidities, presence of indwelling devices, and the use of systemic antibiotics at the time of clearance screening were not associated with MRSA-free survival. More than 21,000 days of inpatient isolation days were avoided during the study period.Conclusions.The majority of patients removed from contact precautions remained MRSA-free for more than 2 years. Antibiotic use at the time of clearance was not associated with reductions in MRSA-free survival. These findings can be used to simplify clearance criteria, promote clearance policies, and reduce patient isolation days.
Dealing with Uncertainty in Agent‐Based Simulation: Farm‐Level Modeling of Adaptation to Climate Change in Southwest Germany
Authors: Troost Christian , Berger Thomas 
Published: September 2014

AbstractClimate change will most likely confront agricultural producers with natural, economic, and political conditions that have not previously been observed and are largely uncertain. As a consequence, extrapolation from past data reaches its limits, and a process‐based analysis of farmer adaptation is required. Simulation of changes in crop yields using crop growth models is a first step in that direction. However, changes in crop yields are only one pathway through which climate change affects agricultural production. A meaningful process‐based analysis of farmer adaptation requires a whole‐farm analysis at the farm level. We use a highly disaggregated mathematical programming model to analyze farm‐level climate change adaptation for a mountainous area in southwest Germany. Regional‐level results are obtained by simulating each full‐time farm holding in the study area. We address parameter uncertainty and model underdetermination using a cautious calibration approach and a comprehensive uncertainty analysis. We deal with the resulting computational burden using efficient experimental designs and high‐performance computing. We show that in our study area, shifted crop management time slots can have potentially significant effects on agricultural supply, incomes, and various policy objectives promoted under German and European environmental policy schemes. The simulated effects are robust against model uncertainty and underline the importance of a comprehensive assessment of climate change impacts beyond merely looking at crop yield changes. Our simulations demonstrate how farm‐level models can contribute to a process‐based analysis of climate change adaptation if they are embedded into a systematic framework for treating inherent model uncertainty.
Prediction of Indel flanking regions in protein sequences using a variable-order Markov model
Authors: Al-Shatnawi Mufleh , Ahmad M. Omair , Swamy M.N.S. 
Published: September 2014

Abstract
Motivation : Insertion/deletion (indel) and amino acid substitution are two common events that lead to the evolution of and variations in protein sequences. Further, many of the human diseases and functional divergence between homologous proteins are more related to indel mutations, even though they occur less often than the substitution mutations do. A reliable identification of indels and their flanking regions is a major challenge in research related to protein evolution, structures and functions.
Results : In this article, we propose a novel scheme to predict indel flanking regions in a protein sequence for a given protein fold, based on a variable-order Markov model. The proposed indel flanking region (IndelFR) predictors are designed based on prediction by partial match (PPM) and probabilistic suffix tree (PST), which are referred to as the PPM IndelFR and PST IndelFR predictors, respectively. The overall performance evaluation results show that the proposed predictors are able to predict IndelFRs in the protein sequences with a high accuracy and F1 measure. In addition, the results show that if one is interested only in predicting IndelFRs in protein sequences, it would be preferable to use the proposed predictors instead of HMMER 3.0 in view of the substantially superior performance of the former.
Contact : m_alshat@ece.concordia.ca or omair@ece.concordia.ca or swamy@ece.concordia.ca .
Supplementary information: Supplementary data are available at Bioinformatics online.