bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework
Authors: Hall E.K. , Bernhardt E.S , Bier R.L. , Bradford M.A. , Boot C.M. , Cotner J.B. , del Giorgio P.A. , Evans S.E. , Graham E.B. , Jones S.E. , Lennon J.T. , Locey K.J. , Nemergut D. , Osborne B.B. , Rocca J.D. , Schimel J.S. , Waldrop M.P. , Wallenstein M.W. 
Published: July 2016

AbstractTranslating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.
Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis
Authors: Haider Muhammad Salman , Zhang Cheng , Kurjogi Tariq Pervaiz Mahantesh M. , Zheng Ting , Zhang Chao bo , Lide Chen , Shangguan Lingfie , Fang Jinggui 
Published: July 2016

AbstractGrapevine is economically important and widely cultivated fruit crop, which is seriously hampered by drought worldwide. It is necessary to understand the impact of glitches incurred by the drought on grapevine genetic resources. Therefore, in the present study RNA-sequencing analysis was performed using cDNA libraries constructed from both drought-stress and control plants. Results yielded, a total of 12,451 differentially expressed genes (DEGs) out of which 8,022 genes were up-regulated and 4,430 were down-regulated. Further physiological and biochemical analyses were carried out to validate the various biological processes involved in the development of grapevine in response to drought stress. Results also showed that decrease in rate of stomatal conductance in-turn decrease the photosynthetic activity and CO2assimilation rate in the grapevine leaves and most ROS detoxification systems, including stress enzymes, stress related proteins and secondary metabolites were strongly induced. Moreover, various hormones were known to be induced in the present study in response to drought. Overall the present study concludes that these DEGs play both positive and negative role in drought tolerance by regulating different biological pathways of grapevine. However our findings have provided valuable gene information for future studies of abiotic stress in grapevine and other fruit crops.
Population and individual effects of non-coding variants inform genetic risk factors
Authors: M. Pala , Zappala Z. , Marongiu M. , Li X. , Davis J.R. , Cusano R. , Crobu F. , Kukurba K.R. , Reiner F. , Berutti R. , Piras M.G. , Mulas A. , Zoledziewska M. , Marongiu M. , Busonero F. , Maschio A. , Steri M. , Sidore C. , Sanna S. , Fiorillo E. , Battle A. , Novembre J. , Jones C. , Angius A. , Abecasis G.R. , Schlessinger D. , Cucca F. , Montgomery S.B. 
Published: July 2016

ABSTRACTIdentifying functional non-coding variants can enhance genome interpretation and inform novel genetic risk factors. We used whole genomes and peripheral white blood cell transcriptomes from 624 Sardinian individuals to identify non-coding variants that contribute to population, family, and individual differences in transcript abundance. We identified 21,183 independent expression quantitative trait loci (eQTLs) and 6,768 independent splicing quantitative trait loci (sQTLs) influencing 73 and 41% of all tested genes. When we compared Sardinian eQTLs to those previously identified in Europe, we identified differentiated eQTLs at genes involved in malarial resistance and multiple sclerosis, reflecting the long-term epidemiological history of the island’s population. Taking advantage of pedigree data for the population sample, we identify segregating patterns of outlier gene expression and allelic imbalance in 61 Sardinian trios. We identified 809 expression outliers (median z-score of 2.97) averaging 13.3 genes with outlier expression per individual. We then connected these outlier expression events to rare non-coding variants. Our results provide new insight into the effects of non-coding variants and their relationship to population history, traits and individual genetic risk.
Introducing py_emra: the Python module for Ensemble Modeling Robustness Analysis
Authors: Theisen Matthew K 
Published: July 2016

AbstractThe py_emra module implements the Ensemble Modeling Robustness Analysis (EMRA) algorithm in Python. Previous implementations in MATLAB have been used to gain useful insights into metabolic dynamics and metabolic engineering strategies. The py_emra package performs favorably in comparison to MATLAB. Potential extensions and improvements are discussed.
The Secondary Market Impact of Quality and Pricing Decisions for New Product Generations
Authors: Ding Yifei , Hicks Daniel , Ju Jiandong 
Published: July 2016

AbstractWe develop a two‐period model of firm choice with a used good market in which a monopolist producer of durable goods selects quality and price in each period. Our model allows for endogenous quality improvements and demonstrates the importance of analysing the impact of pricing decisions and quality improvements on the secondary market jointly, as under reasonable circumstances, quality improvements can lead to the appearance of a spurious inverse relationship between the price for a new product and the secondary market price. Examined jointly, quality improvements in the new product are shown to lower used good prices, while higher new good prices have the opposite effect. An empirical investigation using a newly compiled data set of the US video game market supports our theoretical analysis.
Surgical lymph node assessment in mucinous ovarian carcinoma staging: a systematic review and meta‐analysis
Authors: Hoogendam JP , Vlek CA , Witteveen PO , Verheijen RHM , Zweemer RP 
Published: July 2016

BackgroundThe proportion of women with mucinous ovarian carcinoma in whom nodal metastases are identified during staging remains unclear.ObjectivesTo review the literature on surgical lymph node assessment during staging of women diagnosed with mucinous ovarian carcinoma.Search strategyA systematic search using synonyms of ‘mucinous ovarian carcinoma’ and ‘lymph node assessment’ was conducted in PubMed, Scopus, Embase and the Cochrane Library.Selection criteriaWhen they covered ten or more mucinous ovarian carcinoma cases, staging surgery and minimally one of the following outcomes: prevalence of metastases, stage shift or survival data.Data collection and analysisStudies were quality evaluated with the Cochrane risk‐of‐bias assessment tool for non‐randomised studies of interventions. Outcomes were pooled using an inverse variance weighted random effects model.Main resultsSixteen studies were included. In 278 women with mucinous ovarian cancer suspected to be stage I–II, a pooled proportion of 0.8% (95% CI <0.1–2.9%) had lymph node metastases and were upstaged. In those suspected of stage I (n = 184), this proportion was 0.7% (95% CI <0.1–3.8%). No difference (P = 0.287) was found in metastases between sampling at 0.0% (95% CI 0.0–3.3%) and complete pelvic and/or para‐aortic lymph node dissection at 1.2% (95% CI <0.1–4.2%). One study directly compared the survival of patients staged with and without lymph node dissection and reported no significant difference.ConclusionsSurgical lymph node assessment in women suspected of stage I–II mucinous ovarian carcinoma rarely identifies nodal metastases and consequently has no significant impact on staging.Tweetable abstractSurgical lymph node assessment in women with stage I–II mucinous ovarian cancer rarely has staging consequences.
Are We Moving Towards Functioning Agricultural Markets and Trade Relations?
Authors: Brosig Stephan , Glauben Thomas , Levkovych Inna , Prehn Sören , Teuber Ramona 
Published: July 2016

AbstractWe introduce a special feature on the functioning of international agricultural markets. This feature is motivated by the increased interest in the functioning of commodity markets raised by unprecedented price turbulences since 2008, major structural changes through changed roles of emerging economies and related concerns regarding food security. We argue that the delineation of non‐functioning markets from markets that adequately adjusted to adverse framework conditions lacks theoretical foundation. We discuss the relevance of some results on institutions for agricultural markets in emerging and transition countries. A synthesis of the articles included in the special feature is provided by highlighting the selection of topics that span a topical range covering price formation on world and domestic markets, market power and trade policy modelling.
On the Radicalization Process
Authors: Leistedt Samuel J. 
Published: July 2016

AbstractThis study aimed to provide an in‐depth description of the radicalization process, which is a very important step in terrorist activities. The author proposes a translational analysis that is first based on the author's experience in the psychological evaluation of terrorist behavior and second on an exhaustive review of the current literature. The search terms “terrorism,” “radicalization,” “social psychology,” and “psychopathology” were used to identify relevant studies in the following databases: Scopus, Medline, PubCentral, and Science Direct. Because of its importance, understanding radicalization process should be one of the priorities of behavioral scientists. International studies should be performed with a focus on several aspects, such as radicalization risk factors, brainwashing, the role of the media, and finally, in de‐radicalization programs.
Natural vegetation cover in the landscape and edge effects: differential responses of insect orders in a fragmented forest
Authors: González Ezequiel , Salvo Adriana , Valladares Graciela 
Published: July 2016

AbstractHuman activities have led to global simplification of ecosystems, among which Neotropical dry forests are some of the most threatened. Habitat loss as well as edge effects may affect insect communities. Here, we analyzed insects sampled with pan traps in 9 landscapes (at 5 scales, in 100–500 m diameter circles) comprising cultivated fields and Chaco Serrano forests, at overall community and taxonomic order level. In total 7043 specimens and 456 species of hexapods were captured, with abundance and richness being directly related to forest cover at 500 m and higher at edges in comparison with forest interior. Community composition also varied with forest cover and edge/interior location. Different responses were detected among the 8 dominant orders. Collembola, Hemiptera, and Orthoptera richness and/or abundance were positively related to forest cover at the larger scale, while Thysanoptera abundance increased with forest cover only at the edge. Hymenoptera abundance and richness were negatively related to forest cover at 100 m. Coleoptera, Diptera, and Hymenoptera were more diverse and abundant at the forest edge. The generally negative influence of forest loss on insect communities could have functional consequences for both natural and cultivated systems, and highlights the relevance of forest conservation. Higher diversity at the edges could result from the simultaneous presence of forest and matrix species, although “resource mapping” might be involved for orders that were richer and more abundant at edges. Adjacent crops could benefit from forest proximity since natural enemies and pollinators are well represented in the orders showing positive edge effects.
The Influence of the Pacific Decadal Oscillation on Annual Floods in the Rivers of Western Canada
Authors: Gurrapu Sunil , St‐Jacques Jeannine‐Marie , Sauchyn David J. , Hodder Kyle R. 
Published: July 2016

AbstractWe analyzed annual peak flow series from 127 naturally flowing or naturalized streamflow gauges across western Canada to examine the impact of the Pacific Decadal Oscillation (PDO) on annual flood risk, which has been previously unexamined in detail. Using Spearman's rank correlation ρ and permutation tests on quantile‐quantile plots, we show that higher magnitude floods are more likely during the negative phase of the PDO than during the positive phase (shown at 38% of the stations by Spearman's rank correlations and at 51% of the stations according to the permutation tests). Flood frequency analysis (FFA) stratified according to PDO phase suggests that higher magnitude floods may also occur more frequently during the negative PDO phase than during the positive phase. Our results hold throughout much of this region, with the upper Fraser River Basin, the Columbia River Basin, and the North Saskatchewan River Basin particularly subject to this effect. Our results add to other researchers' work questioning the wholesale validity of the key assumption in FFA that the annual peak flow series at a site is independently and identically distributed. Hence, knowledge of large‐scale climate state should be considered prior to the design and construction of infrastructure.
Long‐term effectiveness of a combined student—parent and a student‐only smoking prevention intervention among 7th grade school children in Berlin, Germany
Authors: Krist Lilian , Lotz Fabian , Bürger Christin , Ströbele‐Benschop Nanette , Roll Stephanie , Rieckmann Nina , Müller‐Nordhorn Jacqueline , Willich Stefan N. , Müller‐Riemenschneider Falk 
Published: July 2016

AbstractBackground and aimsIn Germany, the smoking prevalence among adolescents is among the highest in Europe. Our aim was to evaluate the long‐term effectiveness of a combined student–parent and a student‐only smoking prevention programme to reduce the smoking prevalence among 7th grade students in Berlin.DesignThree‐armed cluster‐randomized controlled trial (RCT). Schools as cluster units were randomized into (i) student intervention, (ii) combined student–parent intervention or (iii) control group, with follow‐up after 12 and 24 months.SettingHigh schools and integrated secondary schools in Berlin, Germany.ParticipantsSeventh grade students aged 11–16 years. We included 47 schools, 161 classes and 2801 students [50.1% girls, mean age ± standard deviation (SD) = 13.0 ± 0.6 years].MeasurementsThe primary outcome was self‐reported regular smoking (at least one cigarette per day) after 24 months (point prevalence). Further self‐reported outcomes were other smoking behaviours as well as parental rules and attitudes towards smoking. Comparisons were calculated as odds ratios (OR) with 95% confidence intervals (CI).FindingsAt baseline, 2.3% of the students reported that they smoked regularly. After 24 months, 7.8% and 7.0% were regular smokers in the student–only intervention and the student–parent intervention, respectively, compared with 10.1% in the control group. The OR for being a regular smoker was 0.81 (0.34–1.92) for the student–parent intervention versus control, 0.95 (CI = 0.41–2.22) for the student‐only intervention versus control and 0.85 (0.38–1.89) for student–parent intervention versus student‐only intervention.ConclusionA combined student–parent smoking prevention intervention delivered via secondary schools in Berlin, Germany did not result in a statistically significant reduction in regular smoking compared with a control group or a student‐only intervention. The student‐only intervention did not result in a significant reduction in regular smoking compared with the control group.
Alcohol‐induced place conditioning in moderate social drinkers
Authors: Childs Emma , de Wit Harriet 
Published: July 2016

AbstractAimsTo test whether non‐dependent drinkers show place preference for a location paired with alcohol, and to test if the amount of time spent in the alcohol‐paired location is related to self‐reported subjective alcohol effects experienced in that environment.DesignTwo groups of subjects completed six conditioning sessions: three with alcohol (0.8 g/kg) and three without alcohol. Individuals were assigned randomly to two groups, paired and unpaired, in a 2 : 1 ratio. The paired group (n = 78) received alcohol in one testing room and no‐alcohol in another testing room (biased assignment). The unpaired group (n = 30) received alcohol and no‐alcohol in each testing room.SettingHuman Behavioral Pharmacology Laboratory, University of Chicago, Chicago, IL, USA (single site).ParticipantsHealthy male and female social drinkers (n = 108) aged 21–40 years participated in the study (consisting of 10 separate laboratory visits) between March 2012 and August 2014 (an average of 36 separate subject visits per month).MeasurementsThe primary outcome measure was the pre‐ to post‐conditioning change in the percentage of time spent in the least preferred room (obtained during drug‐free exploration tests conducted at separate visits before and after the six conditioning sessions were completed). Secondary measures included self‐reported subjective mood and drug effects obtained during the conditioning sessions.FindingsThe groups differed in the change in the percentage of time spent in the initially least preferred room, from pre‐ to post‐conditioning; paired group = 11.0%, unpaired group = −1.4%, mean difference = 12.4%, 95% confidence interval = 1.9–23.0, P = 0.02. The change in the percentage of time spent in the least‐preferred room was related to the self‐reported sedative effects of alcohol during conditioning sessions among paired group participants only.ConclusionsNon‐dependent consumers of alcohol appear to develop a behavioral preference for locations paired with alcohol consumption, more so for those who experience sedative effects from alcohol in those locations.
A dual CysLT1/2 antagonist attenuates allergen‐induced airway responses in subjects with mild allergic asthma
Authors: Gauvreau G. M. , Boulet L.‐P. , FitzGerald J. M. , Cockcroft D. W. , Davis B. E. , Leigh R. , Tanaka M. , Fourre J. A. , Tanaka M. , Nabata T. , O'Byrne P. M. 
Published: July 2016

AbstractBackgroundThe cysteinyl leukotrienes (cysLTs) play a key role in the pathophysiology of asthma. In addition to functioning as potent bronchoconstrictors, cysLTs contribute to airway inflammation through eosinophil and neutrophil chemotaxis, plasma exudation, and mucus secretion. We tested the activity of the dual cysLT1/2 antagonist, ONO‐6950, against allergen‐induced airway responses.MethodsSubjects with documented allergen‐induced early (EAR) and late asthmatic response (LAR) were randomized in a three‐way crossover study to receive ONO‐6950 (200 mg) or montelukast (10 mg) or placebo q.d. on days 1–8 of the three treatment periods. Allergen was inhaled on day 7 two hours postdose, and forced expiratory volume in 1 s (FEV1) was measured for 7 h following challenge. Sputum eosinophils and airway hyperresponsiveness were measured before and after allergen challenge. The primary outcome was the effect of ONO‐6950 vs placebo on the EAR and LAR.ResultsTwenty‐five nonsmoking subjects with mild allergic asthma were enrolled and 20 subjects completed all three treatment periods per protocol. ONO‐6950 was well tolerated. Compared to placebo, ONO‐6950 significantly attenuated the maximum % fall in FEV1 and area under the %FEV1/time curve during the EAR and LAR asthmatic responses (P < 0.05) and allergen‐induced sputum eosinophils. There were no significant differences between ONO‐6950 and montelukast.ConclusionsAttenuation of EAR, LAR, and airway inflammation is consistent with cysLT1 blockade. Whether dual cysLT1/2 antagonism offers additional benefit for treatment of asthma requires further study.
Symptomatic suspected gluten exposure is common among patients with coeliac disease on a gluten‐free diet
Authors: Silvester J. A. , Graff L. A. , Rigaux L. , Walker J. R. , Duerksen D. R. 
Published: July 2016

SummaryBackgroundA gluten‐free diet is the only recommended treatment for coeliac disease.AimTo determine the prevalence and characteristics of reactions to gluten among persons with coeliac disease on a gluten‐free diet.MethodsAdults with biopsy proven, newly diagnosed coeliac disease were prospectively enrolled. A survey related to diet adherence and reactions to gluten was completed at study entry and 6 months. The Coeliac Symptom Index, Coeliac Diet Assessment Tool (CDAT) and Gluten‐Free Eating Assessment Tool (GF‐EAT) were used to measure coeliac disease symptoms and gluten‐free diet adherence.ResultsOf the 105 participants, 91% reported gluten exposure <1 per month and median CDAT score was 9 (IQR 8–11), consistent with adequate adherence. A suspected symptomatic reaction to gluten was reported by 66%. Gluten consumption was unsuspected until a reaction occurred (63%) or resulted from problems ordering in a restaurant (29%). The amount of gluten consumed ranged from cross‐contact (30%) to a major ingredient (10%). Median time to symptom onset was 1 h (range 10 min to 48 h), and median symptom duration was 24 h (range 1 h to 8 days). Common symptoms included abdominal pain (80%), diarrhoea (52%), fatigue (33%), headache (30%) and irritability (29%).ConclusionsReactions to suspected gluten exposure are common among patients with coeliac disease on a gluten‐free diet. Eating at restaurants and other peoples’ homes remain a risk for unintentional gluten exposure. When following individuals with coeliac disease, clinicians should include questions regarding reactions to gluten as part of their assessment of gluten‐free diet adherence.