bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concrete ensemble Kalman filters with rigorous catastrophic filter divergence
Authors: Kelly David , Majda Andrew J. , Tong Xin T. 
Published: August 2015

Significance
Understanding ensemble-based data assimilation methods, including their performance when applied to high-dimensional nonlinear models with low ensemble size, is a crucial problem in science and engineering. Catastrophic filter divergence is a well-documented but mechanistically mysterious phenomenon whereby ensemble-state estimates explode to machine infinity despite the true state remaining in a bounded region. We provide breakthrough insight into the phenomenon by proposing a simple forecast model that experiences catastrophic filter divergence under all ensemble-based methods. This is the first instance to our knowledge of a forecast model that plainly and rigorously illustrates that simple mechanisms can lead to such a drastic filter malfunction and thereby sheds light on when catastrophic filter divergence should be expected and how it can be avoided.
Loss of diphthamide pre-activates NF-κB and death receptor pathways and renders MCF7 cells hypersensitive to tumor necrosis factor
Authors: Stahl Sebastian , da Silva Mateus Seidl Ana Rita , Ducret Axel , Kux van Geijtenbeek Sabine , Michel Sven , Racek Tomas , Birzele Fabian , Haas Alexander K. , Rueger Ruediger , Gerg Michael , Niederfellner Gerhard , Pastan Ira , Brinkmann Ulrich 
Published: August 2015

SignificanceDiphthamide is a conserved modification on eukaryotic translation elongation factor 2 (eEF2). Analyses of genetically defined diphthamide-deficient cell lines indicate that this modification determines not only sensitivity of cells to the ADP-ribosylating toxinsPseudomonasexotoxin A and diphtheria toxin, but it also modulates nuclear factor of kappa light polypeptide gene enhancer in B cells (NF-κB) and TNF receptor signaling pathways.
Effects of Stocking Density on Production Traits of Channel Catfish×Blue Catfish Hybrids
Authors: Bosworth Brian , Ott Brian , Torrans Les 
Published: August 2015

Abstract
Channel Catfish Ictalurus punctatus × Blue Catfish I. furcatus hybrid fingerlings (mean weight, 47 g) were stocked in 0.4-ha ponds at densities of 7,425, 12,375, 17,325, 22,275, and 27,225 fish/ha in three replicate earthen ponds for each density. Fish were fed a 28% protein diet to apparent satiation once daily. Ponds were equipped with electric paddlewheel aerators (12.5 hp/ha) that were turned on when dissolved oxygen (DO) levels reached &lt;5.0 mg/L; additional aeration was provided by power-takeoff tractor-driven paddlewheels at DO &lt; 2.5 mg/L. Feeding was terminated at the end of October and fish were harvested and weighed. Stocking density had no significant effect on feed conversion (overall average, 1.97), survival (≥93% in all treatments), or processing yield (carcass yield = 66.2%, shank fillet yield = 34.8%, nugget yield = 10.5%). Harvest weight was not significantly different between 7,425 and 22,275 fish/ha (average, 0.85 kg) but was less at 27,225 fish/ha (0.72 kg). Net production increased significantly with increased density from 7,425 to 22,275 fish/ha but was not different between 22,275 and 27,225 fish/ha. Percentage of submarketable fish (&lt;0.45 kg) was not significantly different from pond densities of 7,425 through 22,275 fish/ha (average, 2.3%), but was higher at 27,225 fish/ha (8.8%). Aeration hours increased and minimum DO levels decreased significantly as stocking density increased. The smaller average weight at 27,225 fish/ha may have been due to fish behavior associated with crowding, lack of equal access to feed, or degraded water quality. However, past research has demonstrated a “threshold” relationship between minimum DO levels and catfish feeding and growth. Data from this study indicate a similar DO threshold–growth relationship, suggesting the observed effect of density on growth may have been at least partially due to minimum DO levels being below that needed for optimal growth at 27,225 fish/ha.
NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
Authors: Gaudreault Francis , Morency Louis-Philippe , Najmanovich Rafael J. 
Published: August 2015

AbstractLigand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS.Availability and implementation: http://bcb.med.usherbrooke.ca/flexaid.Contact: rafael.najmanovich@usherbroke.caSupplementary information: Supplementary data are available at Bioinformatics online.
Landscape and dynamics of transcription initiation in the malaria parasitePlasmodium falciparum
Authors: Adjalley Sophie H. , Chabbert Christophe D. , Klaus Bernd , Pelechano Vicent , Steinmetz Lars M. 
Published: August 2015

AbstractThe lack of a comprehensive map of transcription start sites (TSS) across the highly AT-rich genome ofP. falciparumhas hindered progress towards deciphering the molecular mechanisms that underly the timely regulation of gene expression in this malaria parasite. Using high-throughput sequencing technologies, we generated a comprehensive atlas of transcription initiation events at single nucleotide-resolution during the parasite intra-erythrocytic developmental cycle. This detailed analysis of TSS usage enabled us to define architectural features of plasmodial promoters. We demonstrate that TSS selection and strength are constrained by local nucleotide composition. Furthermore, we provide evidence for coordinate and stage-specific TSS usage from distinct sites within the same transcriptional unit, thereby producing transcript isoforms, a subset of which are developmentally regulated. This work offers a framework for further investigations into the interactions between genomic sequences and regulatory factors governing the complex transcriptional program of this major human pathogen.
The relationship between international trade openness and economic growth in the developing economies
Authors: Tahir Muhammad , Azid Toseef 
Published: August 2015

Purpose
– This paper aims to establish a relationship between trade openness and economic growth in the context of the developing countries. This study has proposed a new measure of trade openness to the literature, as the available measures are flawed.

Design/methodology/approach
– Empirical analyses are carried out with the help of panel econometric techniques.

Findings
– The main finding of the paper is that the relationship between trade openness and economic growth is positive and statistically significant for developing countries. Besides trade openness, other determinants of economic growth such as investment and labour force are also significantly related with economic growth and carry expected coefficients. Further, it is found that frequent fluctuations in prices are detrimental to long-run economic growth.

Practical implications
– Therefore, the developing countries are suggested to speed up the process of trade liberalization and also pay favourable attention to other determinants of economic growth to achieve high economic growth.

Originality/value
– The authors have used a new measure of trade openness apart from the conventional trade volume measure of trade openness.
SMEs, environmental management and global warming: a fusion of influencing factors?
Authors: Raar Jean 
Published: August 2015

Purpose– Stakeholder theory provided the broad theoretical lens to explore environmental issues in small and medium enterprises (SMEs). The diversity in issues examined ranged from concern for immediate stakeholders, their industry group and the influence of global warming on their business activities, to the type of environmental information included within their internal information systems. The paper aims to discuss these issues.Design/methodology/approach– A mailed survey was used to obtain data from SMEs operating in Australia. The focus was primarily directed to medium size firms.Findings– The findings indicate that SMEs were aware that their stakeholders, particularly their employees and customers were concerned with environmental issues. The respondent SMEs were also aware that global warming would influence their activities, for example, the design of their projects, occupational, health and safety, labour contracts and customer relations. Overall, the findings suggest that any tailored approach to regulate or self-regulate environmental management in SMEs, be industry and stakeholder driven.Research limitations/implications– The limitations of this research are primarily those applicable to the survey method, SME response rates, and the geographical location covered by the survey. The focus of this study is primarily medium size firms, rather than micro small business.Originality/value– This study gains insights into some of the practical aspects of environmental management in SMEs and in so doing adds to the growing body of literature in this under researched area.
The discursive construction of the recent European economic crisis in two political magazines
Authors: Mitsikopoulou Bessie , Lykou Christina 
Published: August 2015

Purpose
– Acknowledging the important role of the media in shaping a European public sphere, the purpose of this paper is to explore how the recent economic crisis is discursively construed in the context of the British media discourse. It investigates discursive constructions of the economic crisis in two political magazines of different ideological positioning by placing emphasis on the economic crisis in Greece, the “weak link” of the Eurozone.

Design/methodology/approach
– The study draws on systemic functional linguistics which views language as social semiotic and conducts a transitivity analysis of a corpus consisting of 59 articles (a total of 61,820 words) from two weekly British political magazines, one of conservative and one of centre-left political position. The analysis is assisted by Wordsmith 6.0 concordance corpus tool.

Findings
– It is argued that the articles of the conservative magazine construe the crisis as primarily local and financial, discussing its effects on the British economy. On the other hand, the articles of the centre-left magazine view the crisis as a systemic one derived from and, at the same time, affecting European Union policies and stress its political and economic implications in all of Eurozone.

Originality/value
– The findings of the study contribute to the body of studies which investigate the role of language in the construction of the economic crisis and also adds to the on-going discussion regarding the development of a European public sphere as part of the wider European Project and the process of European integration.
Economic thought in the 17th and 18th centuries: a linguistic approach
Authors: Lima Iara Vigo de 
Published: August 2015

Purpose
– The purpose of this paper is to analyse Michel Foucault’s new epistemological model regarding an analogy between the theory of language and economic thought in the seventeenth and eighteenth centuries.

Design/methodology/approach
– Through the scrutiny of language, Foucault intended to demonstrate that some analogies, among different branches of knowledge (interdiscursive practice), allow us to apprehend the underlying configuration of thought regarding ontological and epistemological conditions that have historically determined knowledge. He draws a parallel between four theoretical segments borrowed from general grammar (Attribution, Articulation, Designation and Derivation) and economic thought on wealth.

Findings
– One of the most remarkable propositions of this approach is that the theory of language and economic thought were epistemologically isomorphic in that context. What the theory of language stated in relation to “attribution” and “articulation” corresponded to the “theory of value” in economic thought. What grammar investigated regarding “designation” and “derivation” was analogous to the “theory of money and trade” in economic thought. The relationships that were – directly and diagonally – identified between and among them led to the conclusion that there was ‘a circular and surface causality’ in economic thought insofar as “circulation” preceded “production”. It was “superficial” because it could not find an explanation for the cause of “wealth”, which was only possible when “production” was placed in the front position of theories.

Practical implications
– Such an epistemological point of view can inspire other studies in the history of economic thought.

Originality/value
– This paper offers a perspective on how to think about the history of ontological and epistemological conditions of economic thought.
Agency culture and the banality of risk
Authors: Wehr Kevin 
Published: August 2015

Purpose– The purpose of this paper is to investigate the role that agency culture, training, and supervision play in the rates of on-the-job seatbelt use among peace officers, as well as other officer safety-related driving concerns such as cell phone use, Mobile Data Terminal use, and other sources of distraction.Design/methodology/approach– Based on semi-structured interviews with California peace officers.Findings– This study found an array of agency culture issues related to on-duty collisions, including distraction, failure to follow policy or procedure, fatigue, self-selection processes among officers and agencies, supervision and field training processes, morale issues, and family/lifestyle issues.Originality/value– To explain these agency culture findings, this paper introduces the concept of the “banality of risk” to understand why many officers choose not to use risk-attenuating equipment. The findings are suggestive of a set of best practices that agencies could consider regarding in-vehicle officer safety.
Police drowsy driving: predicting fatigue-related performance decay
Authors: James Stephen M. , Vila Bryan 
Published: August 2015

Purpose
– Fatigue associated with shift work is a well-established and pervasive problem in policing that affects officer performance, safety, and health. It is critical to understand the extent to which fatigue degrades officer driving performance. Drowsy driving among post-shift workers is a well-established risk factor yet no data are available about officer injuries and deaths due to drowsy driving. The purpose of this paper is to assess the impact of fatigue associated with work shift and prior sleep on officers’ non-operational driving using laboratory experiments to assess post-shift drowsy driving risks and the ability of a well-validated vigilance and reaction-time task to assess these risks.

Design/methodology/approach
– Experienced police patrol officer volunteers (n=78) from all four shifts of a medium-sized city’s police department were tested using a within- and between-subjects design to assess the impact of fatigue on individual officers, as well as the impact of different work shifts, on post-shift driving performance. Controlled laboratory experiments were conducted during which participants drove high-fidelity driving training simulators on two occasions: immediately following five consecutive 10:40-hour patrol shifts (fatigued condition) and again 72 hours after completing the last shift in a work cycle (rested condition).

Findings
– Generalized linear mixed-model analyses of driving performance showed that officers working night shifts had significantly greater lane deviation during post-shift, non-operational driving than those working day shifts (F=4.40, df=1, 150, p=0.038). The same method also showed that easy to measure psychomotor vigilance test scores for reaction time predicted both lane deviation (F=31.48, df=1, 151, p
<
0.001) and collisions (F=14.10, df=1, 151, p
<
0.001) during the simulated drives.

Research limitations/implications
– Simulated driving tasks done by participants were generally less challenging than patrol or off-duty driving and likely underestimate the impact of fatigue on police driving post-shift or during extended shifts.

Originality/value
– This is the first experimental research to assess the impact of shiftwork, fatigue, and extended shifts on police post-shift drowsy driving, a known risk factor for shift workers in general.
Prevalence of β‐Lactamase Producing Escherichia coli from Retail Meat in Turkey
Authors: Pehlivanlar Önen Sevda , Aslantaş Özkan , Şebnem Yılmaz Ebru , Kürekci Cemil 
Published: August 2015

AbstractExtended spectrum β‐lactamase (ESBL) and plasmid‐mediated AmpC β‐lactamase (pAmpC) producing Escherichia coli have been shown to be present in humans and animals representing a significant problem worldwide. This study aimed to search the presence of ESBL and/or AmpC‐producing E. coli in retail meats (chicken and beef) in Turkey. A total of 88 β‐lactamase‐producing E. coli were isolated from chicken (n = 81/100) and beef meat (n = 7/100) samples and their susceptibility to several antimicrobials were tested using disc diffusion method. E. coli isolates were further characterized for their phylogenetic groups. β‐Lactamase encoding (blaTEM, blaSHV, blaOXA, blaCTX‐M, and blaAmpC) and quinolone resistance genes (qnrA, qnrB, qnrS, qepA, and acc(6′)‐Ib‐cr) were also secreened by polymerase chain reaction (PCR). However, in regard to β‐lactamase genes, 84 of 88 isolates were positive for blaCTX‐M‐1 (n = 39), blaCTX‐M‐3 (n = 5), blaCTX‐M‐15 (n = 4), blaTEM‐1b (n = 2), blaSHV‐12 (n = 1), blaCTX‐M‐1/blaTEM‐1b (n = 10), blaCTX‐M‐1/blaTEM‐1b/blaSHV‐5 (n = 1), blaCTX‐M‐1/blaCMY‐2 (n = 1) and blaTEM‐1b/blaCMY‐2 (n = 6), blaCTX‐M‐15/blaSHV‐12 (n = 1), blaCTX‐M‐15/blaTEM‐1b (n = 1), blaTEM‐1b/blaSHV‐12 (n = 1), and blaCMY‐2 (n = 12) genes. Resistance to cefuroxime (75.6% and 85.7%), nalidixic acid (89% and 85.7%), tetracycline (91.4% and 100%), streptomycin (40.2% and 100%), and trimethoprim‐sulfamethoxazole (36.6% and 85.7%) was observed among strains isolated from chicken and beef, respectively. However, all isolates were found to be susceptible to amikacin, imipenem, and cefepime. Resistance to ampicillin and cefoxitin was significantly linked to blaCMY‐2 gene, while there was a significant correlation between CTX‐M type ESBL and antimicrobial resistance to cefuroxime and streptomycin (P < 0.05). The results of this study suggest that raw chicken retail meats are highly contaminated with ESBL‐producing E. coli implementing a great risk to human health in Turkey.
rApi m 3 and rApi m 10 improve detection of honey bee sensitization in Hymenoptera venom‐allergic patients with double sensitization to honey bee and yellow jacket venom
Authors: Frick M. , Müller S. , Bantleon F. , Huss‐Marp J. , Lidholm J. , Spillner E. , Jakob T. 
Published: August 2015

AbstractRecombinant allergens improve the diagnostic precision in Hymenoptera venom allergy (HVA), in particular in patients with double sensitization to both honey bee (HBV) and yellow jacket venom (YJV). While currently available vespid allergens allow the detection of >95% of YJV‐allergic patients, the sensitization frequency to the only available HBV marker allergen rApi m 1 in HBV‐allergic patients is lower. Here, we demonstrate that sIgE to additional HBV marker allergens rApi m 3 and rApi m 10 allows the detection of genuine HBV sensitization in 46–65% of Api m 1 negative sera. This is of particular relevance in patients with double sensitization to HBV and YJV that did not identify the culprit insect. Addition of sIgE to rApi m 3 and rApi m 10 provides evidence of HBV sensitization in a large proportion of rApi m 1‐negative patients and thus provides a diagnostic marker and rationale for VIT treatment with HBV, which otherwise would have been missing.
Influence of co‐culture with denuded oocytes during in vitro maturation on fertilization and developmental competence of cumulus‐enclosed porcine oocytes in a defined system
Authors: Appeltant Ruth , Somfai Tamás , Kikuchi Kazuhiro , Maes Dominiek , Van Soom Ann 
Published: August 2015

AbstractCo‐culture of cumulus‐oocyte complexes (COCs) with denuded oocytes (DOs) during in vitro maturation (IVM) was reported to improve the developmental competence of oocytes via oocyte‐secreted factors in cattle. The aim of the present study was to investigate if addition of DOs during IVM can improve in vitro fertilization (IVF) and in vitro culture (IVC) results for oocytes in a defined in vitro production system in pigs. The maturation medium was porcine oocyte medium supplemented with gonadotropins, dbcAMP and β‐mercaptoethanol. Cumulus‐oocyte complexes were matured without DOs or with DOs in different ratios (9 COC, 9 COC+16 DO and 9 COC+36 DO). Consequently; oocytes were subjected to IVF as intact COCs or after denudation to examine if DO addition during IVM would affect cumulus or oocyte properties. After fertilization, penetration and normal fertilization rates of zygotes were not different between all tested groups irrespective of denudation before IVF. When zygotes were cultured for 6 days, no difference could be observed between all treatment groups in cleavage rate, blastocyst rate and cell number per blastocyst. In conclusion, irrespective of the ratio, co‐culture with DOs during IVM did not improve fertilization parameters and embryo development of cumulus‐enclosed porcine oocytes in a defined system.
A systematic review of the emerging definition of ‘deprescribing’ with network analysis: implications for future research and clinical practice.
Authors: Reeve Emily , Gnjidic Danijela , Long Janet , Hilmer Sarah 
Published: August 2015

AimsThe aim of this study was to identify what definitions have been published for the term ‘deprescribing’, and determine whether a unifying definition could be reached. A secondary aim was to uncover patterns between the published definitions which could explain any variation.MethodsSystematic literature searches were performed (earliest records to February 2014) in MEDLINE, Embase, CINAHL, Informit, Scopus and Google Scholar. The terms deprescrib* or de‐prescrib* were employed as a keyword search in all fields. Conventional content analysis and word frequencies were used to identify characteristics of the definitions. Network analysis was conducted to visualize characteristic distribution across authors and articles.ResultsFollowing removal of duplicates, 231 articles were retrieved, 37 of which included a definition. Eight characteristics of the definitions were identified: use of the term stop/withdraw/cease/discontinue (35 articles), aspect of prescribing included e.g. long term therapy/inappropriate medications (n = 18), use of the term ‘process’ or ‘structured’ (n = 13), withdrawal is planned/supervised/judicious (n = 11), involving multiple steps (n = 7), includes dose reduction/substitution (n = 7), desired goals/outcomes described (n = 5) and involves tapering (n = 4). Network analysis did not reveal patterns responsible for variations in previously used definitions.ConclusionsThese findings show that there is lack of consensus on the definition of deprescribing. This article proposes the following definition: ‘Deprescribing is the process of withdrawal of an inappropriate medication, supervised by a health care professional with the goal of managing polypharmacy and improving outcomes’. This definition has not yet been externally validated and further work is required to develop an internationally accepted and appropriate definition.