bluuebunny/crossref_metadata_2025_split huggingface dataset:
An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing
Authors: Zhang Jie , Wei Zhi 
Published: February 2016

AbstractMotivation: Next-generation RNA sequencing (RNA-seq) has been widely used to investigate alternative isoform regulations. Among them, alternative 3′ splice site (SS) and 5′ SS account for more than 30% of all alternative splicing (AS) events in higher eukaryotes. Recent studies have revealed that they play important roles in building complex organisms and have a critical impact on biological functions which could cause disease. Quite a few analytical methods have been developed to facilitate alternative 3′ SS and 5′ SS studies using RNA-seq data. However, these methods have various limitations and their performances may be further improved.Results: We propose an empirical Bayes change-point model to identify alternative 3′ SS and 5′ SS. Compared with previous methods, our approach has several unique merits. First of all, our model does not rely on annotation information. Instead, it provides for the first time a systematic framework to integrate various information when available, in particular the useful junction read information, in order to obtain better performance. Second, we utilize an empirical Bayes model to efficiently pool information across genes to improve detection efficiency. Third, we provide a flexible testing framework in which the user can choose to address different levels of questions, namely, whether alternative 3′ SS or 5′ SS happens, and/or where it happens. Simulation studies and real data application have demonstrated that our method is powerful and accurate.Availability and implementation: The software is implemented in Java and can be freely downloaded from http://ebchangepoint.sourceforge.net/.Contact: zhiwei@njit.edu
The application of a resilience assessment approach to promote campus environmental management
Authors: Muller Irene , Tempelhoff Johann 
Published: February 2016

Purpose– This paper aims to outline the benefits of using resilience assessment instead of command and control mechanisms to evaluate sustainable campus environments.Design/methodology/approach– An exploratory mixed-method design was followed for the purposes of the project. During the first qualitative phase, a historical timeline of the focal system was created. In the quantitative phase, the resilience assessment guided the investigation. To collect data, the case study research strategy included a heuristic process of collecting and reviewing documents, semi-structured interviews, observations and the systematic implementation of the resilience assessment approach.Findings– Based on the resilience assessment approach, it is argued that the environmental status of university campuses can be considered relevant to the local community and immediate environment. Knowledge of the finite resources and their capacity in the context of the social-ecological system may increase the resilience of a campus.Originality/value– This research study explores the use of an alternative approach to environmental practices at university campuses. The resilience assessment is usually performed on large ecosystems. By applying this approach to a small ecosystem, the study fills a gap in the applicability of the resilience approach.
Too many compromises: survey research and the spectre of communism
Authors: Schwarzkopf Stefan 
Published: February 2016

Purpose– This paper aims to chart the influence of McCarthyism and of FBI surveillance practices on a number of prominent American social scientists, market researchers, opinion pollsters and survey research practitioners during the post-war years. Hitherto disparate sets of historical evidence on how Red Scare tactics influenced social researchers and marketing scientists are brought together and updated with evidence from original archival research.Design/methodology/approach– The paper draws on the existing secondary literature on how social research practitioners and social scientists reacted to the unusually high pressures on academic freedom during the McCarthy era. It supplements this review with evidence obtained from archival research, including declassified FBI files. The focus of this paper is set on prominent individuals, mainly Bernard Berelson, Samuel Stouffer, Hadley Cantril, Robert S. Lynd, Paul F. Lazarsfeld, Herta Herzog, Ernest Dichter, but also the Frankfurt School in exile.Findings– Although some of the historiography presents American social scientists and practitioners in the marketing research sector as victims of McCarthyism and FBI surveillance, it can also be shown that virtually all individuals in focus here also developed strategies of accommodation, compromise and even opportunism to benefit from the climate of suspicion brought about by the prevailing anti-Communism.Social implications– Anyone interested in questions about the morality of marketing, market research and opinion polling as part of the social sciences practicedin vivowill need to pay attention to the way these social-scientific practices became tarnished by the way prominent researchers accommodated and at times even abetted McCarthyism.Originality/value– Against the view of social scientists as harassed academic minority, evidence is presented in this paper which shows American social scientists who researched market-related phenomena, like media, voters choices and consumer behaviour, in a different light. Most importantly, this paper for the first time presents archival evidence on the scale of Paul F. Lazarsfeld’s surveillance by the FBI.
Marketing and the Cold War: an overview
Authors: Tadajewski Mark , Stole Inger L. 
Published: February 2016

Purpose
– This paper aims to examine the contents of the special issue, situating the material in appropriate historical context.

Design/methodology/approach
– The account is based on a close reading of each manuscript. Links to the wider academic literature are created, and a narrative thread is provided to introduce readers to the imbrication of marketing with the Cold War geopolitical climate.

Originality/value
– The debates surrounding the Cold War, marketing theory and marketing practice have been reviewed.
Association of anti‐RNA polymerase III antibody and silicone breast implants in patients with systemic sclerosis
Authors: Saigusa Ryosuke , Asano Yoshihide , Nakamura Kouki , Yamashita Takashi , Ichimura Yohei , Takahashi Takehiro , Toyama Tetsuo , Taniguchi Takashi , Yoshizaki Ayumi , Miyazaki Miki , Tamaki Zenshiro , Sato Shinichi 
Published: February 2016

AbstractSystemic sclerosis (SSc) is believed to be caused by a complex interplay between genetic factors and environmental influences. Although silicone has been considered to be a candidate of environmental agents, clinical data presented so far fail to show a significant association between silicone breast implant (SBI) and the development of SSc. Because we recently experienced two consecutive SSc patients with anti‐RNA polymerase III (RNAP III) antibody who underwent SBI, we here investigated the association of SBI history with the development of SSc positive for anti‐RNAP III antibody. Among 262 Japanese SSc patients, of note, the frequency of SBI history was significantly higher in the anti‐RNAP III antibody group (16.0% [4/25]) than in the anti‐topoisomerase I antibody group (0% [0/87], P < 0.005) and in the anticentromere antibody group (1.2% [2/150], P < 0.005). These results suggest that SBI could influence the development of SSc in a certain subset of patients with anti‐RNAP III antibody.
Suppression of Mcl‐1 induces apoptosis in mouse peritoneal macrophages infected with Mycobacterium tuberculosis
Authors: Wang Fei‐yu , Wang Xin‐min , Wang Chan , Wang Xiao‐fang , Zhang Yu‐qing , Wu Jiang‐dong , Wu Fang , Zhang Wan‐jiang , Zhang Le 
Published: February 2016

ABSTRACTThe effect of myeloid cell leukemia‐1 (Mcl‐1) inhibition on apoptosis of peritoneal macrophages in mice infected with Mycobacterium tuberculosis was investigated and the primary signaling pathway associated with the transcriptional regulation of Mcl‐1 was identified. Real‐time PCR and western blotting indicated that Mcl‐1 transcript and protein expression are upregulated during infection with virulent M. tuberculosis H37Rv and Xinjiang strains but not with attenuated M. tuberculosis strain H37Ra or Bacillus Calmette–Guérin. Mcl‐1 transcript and protein expression were downregulated by specific inhibitors of the Janus kinase/signal transducer and activator of transcription (JAK/STAT), mitogen‐activated protein kinase (MAPK) and phosphoinositol 3‐kinase (PI3K) pathways (AG490, PD98059 and LY294002, respectively). The strongest inhibitor of Mcl‐1 expression was PD98059, the MAPK inhibitor. Flow cytometry demonstrated that the rate of apoptosis in peritoneal macrophages is significantly higher in mice infected with M. tuberculosis and the rate of apoptosis is correlated with the virulence of the strain of M. tuberculosis. Apoptosis was found to be upregulated by AG490, PD98059 and LY294002, whereas inhibition of the MAPK pathway sensitized the infected macrophages to apoptosis. Taken together, these results suggest that specific downregulation of Mcl‐1 significantly increases apoptosis of peritoneal macrophages and that the MAPK signaling pathway is the primary mediator of Mcl‐1 expression.
Self‐weighing and simple dietary advice for overweight and obese pregnant women to reduce obstetric complications without impact on quality of life: a randomised controlled trial
Authors: McCarthy EA , Walker SP , Ugoni A , Lappas M , Leong O , Shub A 
Published: February 2016

ObjectiveTo determine the effect of serial weighing and dietary advice compared with standard antenatal care on obstetric outcomes.DesignRandomised controlled clinical trial.SettingAustralian tertiary obstetric hospital.PopulationThree hundred and eighty‐two overweight or obese non‐diabetic pregnant women at less than 20 weeks gestation with a singleton pregnancy.MethodsWomen were randomised to targeted, serial self‐weighing and simple dietary advice, (intervention), or standard antenatal care (control).Main outcomes measuresThe primary outcome was a reduction in a composite of obstetric complications: gestational hypertension, pre‐eclampsia, diabetes, assisted or caesarean birth, shoulder dystocia, severe perineal trauma, postpartum haemorrhage and maternal high dependency care. Secondary outcomes were gestational weight gain at 36 weeks' gestation, quality of life (QOL) and maternal serum levels of 28‐week leptin, adiponectin and C‐reactive protein (CRP).ResultsThere was no difference in the rate of the primary composite outcome of obstetric complications: 124/184 (67% control), 124/187 (66% intervention) [relative risk 0.98 (95% confidence interval (CI) 0.85–1.14)]. There was no difference in mean gestational weight gain [−0.9 kg (95% CI −2.0, 0.25)], QOL or leptin, adiponectin or CRP levels between intervention and control groups.ConclusionsThis low‐cost, pragmatic intervention failed to prevent obstetric complications or modify maternal biochemistry or gestational weight gain in overweight or obese pregnant women. Participation in the study did not impair participants' QOL.Tweetable abstractSerial self‐weighing and dietary advice failed to reduce obstetric complications in overweight pregnant women.
Characterization of Antibodies for Grain‐Specific Gluten Detection
Authors: Sharma Girdhari M. , Rallabhandi Prasad , Williams Kristina M. , Pahlavan Autusa 
Published: February 2016

AbstractGluten ingestion causes immunoglobulin E (IgE)‐mediated allergy or celiac disease in sensitive individuals, and a strict gluten‐free diet greatly limits food choices. Immunoassays such as enzyme‐linked immunosorbent assay (ELISA) are used to quantify gluten to ensure labeling compliance of gluten‐free foods. Anti‐gluten antibodies may not exhibit equal affinity to gluten from wheat, rye, and barley. Moreover, because wheat gluten is commonly used as a calibrator in ELISA, accurate gluten quantitation from rye and barley contaminated foods may be compromised. Immunoassays utilizing grain‐specific antibodies and calibrators may help improve gluten quantitation. In this study, polyclonal antibodies raised against gluten‐containing grain‐specific peptides were characterized for their immunoreactivity to gluten from different grain sources. Strong immunoreactivity to multiple gluten polypeptides from wheat, rye, and barley was observed in the range 34 to 43 kDa with anti‐gliadin, 11 to 15 and 72 to 95 kDa with anti‐secalin, and 30 to 43 kDa with anti‐hordein peptide antibodies, respectively. Minimal or no cross‐reactivity with gluten from other grains was observed among these antibodies. The anti‐consensus peptide antibody raised against a repetitive amino acid sequence of proline and glutamine exhibited immunoreactivity to gluten from wheat, rye, barley, and oat. The antibodies exhibited similar immunoreactivity with most of the corresponding grain cultivars by ELISA. The high specificity and minimal cross‐reactivity of grain‐specific antibodies suggest their potential use in immunoassays for accurate gluten quantitation.
The righteous and the rightful: The technomoral politics of NGOs, social movements, and the state in India
Authors: BORNSTEIN ERICA , SHARMA ARADHANA 
Published: February 2016

ABSTRACTCivil society groups today are honored and relied on by governments, as well as tightly regulated and scrutinized for challenging state policies and agencies. In contemporary India, political dynamics of collaboration and confrontation between state and nonstate actors increasingly unfold in legal‐social fields, taking “technomoral” forms. Mixing technocratic languages of law and policy with moral pronouncements, these actors assert themselves as virtuous agents, marking their political legitimacy as keepers of the public interest. Using ethnographic research with Indian NGOs, social movements, and a political party, we show that as civil society groups interact with state bodies, they redefine institutional boundaries and claim moral authority over public stewardship. Technomoral strategies are neither depoliticized nor antipolitical, but constitute a righteous and rightful form of politics. [NGOs, state, India, morality, activist politics, neoliberalism, law]
Rituals of care for the elderly in northern Thailand: Merit, morality, and the everyday of long‐term care
Authors: AULINO FELICITY 
Published: February 2016

ABSTRACTCaregivers’ quotidian actions challenge prevailing views of care that rely on the emotional or attentive orientation of the caregiver. The routinized care tasks provided by two middle‐aged women for their bedridden mother in northern Thailand reveal the realities of long‐term caregiving. For these sisters, care transforms “merit” and “karma” without reliance on internal conviction. This context in turn reflects how people enact values and maintain social worlds through habituated physical practices of providing for others. Ordinary care in practice—termed “rituals of care”—dislodges fixation on particular personal sentiments and affirms the study of care as a powerful tool for assessing enduring modes of moral experience as well as subtle forms of social change. [care,ritual,phenomenology,Buddhism,Thailand,embodiment,morality]
Strategies for Using Plagiarism Software in the Screening of Incoming Journal Manuscripts: Recommendations Based on a Recent Literature Survey
Authors: Lykkesfeldt Jens 
Published: February 2016

AbstractIn recent years, several online tools have appeared capable of identifying potential plagiarism in science. While such tools may help to maintain or even increase the originality and ethical quality of the scientific literature, no apparent consensus exists among editors on the degree of plagiarism or self‐plagiarism necessary to reject or retract manuscripts. In this study, two entire volumes of published original papers and reviews from Basic & Clinical Pharmacology & Toxicology were retrospectively scanned for similarity in anonymized form using iThenticate software to explore measures to predictively identify true plagiarism and self‐plagiarism and to potentially provide guidelines for future screening of incoming manuscripts. Several filters were applied, all of which appeared to lower the noise from irrelevant hits. The main conclusions were that plagiarism software offers a unique opportunity to screen for plagiarism easily but also that it has to be employed with caution as automated or uncritical use is far too unreliable to allow a fair basis for judging the degree of plagiarism in a manuscript. This remains the job of senior editors. Whereas a few cases of self‐plagiarism that would not likely have been accepted with today's guidelines were indeed identified, no cases of fraud or serious plagiarism were found. Potential guidelines are discussed.
Apolipoprotein E genotype is not associated with cognitive impairment in older adults with bipolar disorder
Authors: Kerr Daniel Shikanai , Stella Florindo , Radanovic Márcia , Aprahamian Ivan , Bertollucci Paulo Henrique Ferreira , Forlenza Orestes Vicente 
Published: February 2016

ObjectivesCognitive decline is part of the long‐term outcome for many individuals with bipolar disorder (BD). The ε4 allele (APOE*4) of apolipoprotein E (APOE) is a well‐established risk factor for dementia in Alzheimer's disease (AD). However, its contribution to the risk of cognitive deterioration in BD has not yet been determined. Our aim was to analyze the APOE genotype association with cognitive status in a sample of older adults with BD and compare this to the association in individuals with AD, individuals with mild cognitive impairment (MCI), and healthy controls.MethodsParticipants (n = 475) were allocated to four groups: individuals with BD (n = 77), those with AD (n = 211), those with MCI (n = 43), and healthy controls (n = 144) according to clinical and neuropsychological assessment. APOE was genotyped by real‐time polymerase chain reaction. Tukey's honest significant difference test and Pearson's chi‐squared test were used to compare diagnostic groups.ResultsSubjects with BD were similar to controls with respect to the distribution of the APOE genotype (p = 0.636) and allele frequencies (p = 0.481). Significant differences were found when comparing the AD group to the BD group or to controls (APOE genotype: p < 0.0002; allele frequencies: p < 0.001). APOE*4 was significantly increased in the AD group when compared to the BD group (p = 0.031) and controls (p < 0.0001). The cognitively impaired BD subgroup (Mini‐Mental State Examination below the cutoff score and/or neuropsychological assessment compatible with MCI) had a statistically significant higher frequency of APOE*2 compared to the AD group (p = 0.003).ConclusionsAPOE*4 is not associated with the diagnosis of BD and does not impact the occurrence of dementia in BD. Given the distinct clinical and biological features of cognitive impairment in BD, we hypothesized that dementia in BD is unrelated to AD pathological mechanisms.
The role of the antioxidant ascorbic acid in the elicitation of contact allergic reactions to p‐phenylenediamine
Authors: Coenraads Pieter‐Jan , Vogel Tatiana A. , Blömeke Brunhilde , Goebel Carsten , Roggeband Robert , Schuttelaar M.L.A. 
Published: February 2016

SummaryBackgroundAn allergic contact reaction is accompanied by high oxidative stress in the skin. Pretreatment of the skin with antioxidative substances could reduce the elicitation reaction.ObjectivesTo investigate, in a proof‐of‐principle study, whether pretreatment of the skin with the antioxidant ascorbic acid reduces the elicitation reaction to a p‐phenylenediamine (PPD)‐containing hair dye in sensitized subjects.MethodsTwelve subjects with contact allergy to PPD, a documented skin reaction to a hair dye simulation exposure model and a history of hair dye‐related skin complaints were included in this study. Skin areas on the forearms were, in a left versus right design, exposed to an emulsion with ascorbic acid and an emulsion without ascorbic acid, and then to a 2% PPD‐containing hair dye testing formulation. In addition, control areas were exposed to the emulsions and to the PPD‐containing hair dye formulation without pretreatment. Skin reactions were graded on day (D)2 and D3.ResultsPretreatment with ascorbic acid emulsion resulted in a reduction in the elicitation reaction in 7 of 12 subjects at D3 (p = 0.046). No statistically significant difference was observed at D2.ConclusionsPretreatment of the skin with the antioxidant ascorbic acid had an attenuating effect on the elicitation reaction to PPD in sensitized individuals.
The Image of theBedouin in Travel Literature and Western Researchers Who Visited Palestine in the Nineteenth Century
Authors: Suwaed Muhammad 
Published: February 2016

AbstractWith the weakening of the Ottoman government from the end of the sixteenth century onwards, the Bedouin took over the control of the entire Country of Palestine. As the Bedouin were present across the country, western travelers and researches visiting the Holy Land as tourists, visitors, and investigators often met the Bedouin, especially during the robbery and plunder executed by the Bedouin upon travelers, and when hiring them as tour guides, renting their camels, or employing them as guards. On their return to their countries, these travelers reported on their experiences in the East in the form of books. These western travelers and researchers, in their writings, dealt with the Bedouin. They described them as providers of services to caravans, transporters of luggage, tour guides, and robbers. The writers and researchers explicitly described the traits, characters, food habits, clothing, residences, and occupations of the Bedouin.
Social Media and Social Change
Authors: Miladi Noureddine 
Published: February 2016

AbstractThe growing impact of new media around the world has been the subject of study by scores of scientists in multidisciplinary fields. Satellite TV and the Internet have been viewed as instruments of social and political change — connecting communities, educating the youth, and creating social networks previously unaccounted for, like virtual groups. However, in the Arab World and the Middle East, such technological developments have been hailed as tools for the empowerment of marginalized communities such as women and the youth, also brought new opportunities that have resulted in the breaking of the communication monopoly by those in power and the creation of a new communication environment. Such environment has — as part of its manifestations — the current social transformations that the region is witnessing. Drawing on examples from social media networks used in Tunisia and Egypt, this article analyzes the extent to which new technologies have changed the rules of the game regarding public opinion construction and the communication flow traditionally monopolized by the hegemonic power structures in Arab society. This study not only reveals the decisiveness of platforms like Facebook, Twitter, and YouTube in the Arab Spring countries’ revolutions, but also the extent to which their availability served in a complex manner the democratic transition that Tunisia have been undergoing and the political turmoil that Egypt is witnessing. Furthermore this study argues that such online spheres of communication mark the emergence of the virtual yet vibrant space of political campaigning and social empowerment, especially for the youth and marginalized communities.