bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix linear models for high-throughput chemical genetic screens
Authors: Liang Jane W. , Nichols Robert J. , Sen Śaunak 
Published: November 2018

AbstractWe develop a flexible and computationally efficient approach for analysing high throughput chemical genetic screens. In such screens, a library of genetic mutants is phenotyped in a large number of stresses. The goal is to detect interactions between genes and stresses. Typically, this is achieved by grouping the mutants and stresses into categories, and performing modified t-tests for each combination. This approach does not have a natural extension if mutants or stresses have quantitative or non-overlapping annotations (eg. if conditions have doses, or a mutant falls into more than one category simultaneously). We develop a matrix linear model framework that allows us to model relationships between mutants and conditions in a simple, yet flexible multivariate framework. It encodes both categorical and continuous relationships to enhance detection of associations. To handle large datasets, we develop a fast estimation approach that takes advantage of the structure of matrix linear models. We evaluate our method’s performance in simulations and in an E. coli chemical genetic screen, comparing it with an existing univariate approach based on modified t-tests. We show that matrix linear models perform slightly better than the univariate approach when mutants and conditions are classified in non-overlapping categories, and substantially better when conditions can be ordered in dosage categories. Our approach is much faster computationally and is scalable to larger datasets. It is an attractive alternative to current methods, and provides a natural framework extensible to larger, and more complex chemical genetic screens. A Julia implementation of matrix linear models and the code used for the analysis in this paper can be found at https://bitbucket.org/jwliang/mlm_packages and https://bitbucket.org/jwliang/mlm_gs_supplement, respectively.
Composition of the Survival Motor Neuron (SMN) complex in Drosophila melanogaster
Authors: Matera A. Gregory , Raimer Amanda C. , Schmidt Casey A. , Kelly Jo A. , Droby Gaith N. , Baillat David , ten Have Sara , Lamond Angus I. , Wagner Eric J. , Gray Kelsey M. 
Published: November 2018

AbstractSpinal Muscular Atrophy (SMA) is caused by homozygous mutations in the human survival motor neuron 1 (SMN1) gene. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. SMN is part of an oligomeric complex with core binding partners, collectively called Gemins. Biochemical and cell biological studies demonstrate that certain Gemins are required for proper snRNP assembly and transport. However, the precise functions of most Gemins are unknown. To gain a deeper understanding of the SMN complex in the context of metazoan evolution, we investigated the composition of the SMN complex in Drosophila melanogaster. Using a stable transgenic line that exclusively expresses Flag-tagged SMN from its native promoter, we previously found that Gemin2, Gemin3, Gemin5, and all nine classical Sm proteins, including Lsm10 and Lsm11, co-purify with SMN. Here, we show that CG2941 is also highly enriched in the pulldown. Reciprocal co-immunoprecipitation reveals that epitope-tagged CG2941 interacts with endogenous SMN in Schneider2 cells. Bioinformatic comparisons show that CG2941 shares sequence and structural similarity with metazoan Gemin4. Additional analysis shows that three other genes (CG14164, CG31950 and CG2371) are not orthologous to Gemins 6-7-8, respectively, as previously suggested. In D.melanogaster, CG2941 is located within an evolutionarily recent genomic triplication with two other nearly identical paralogous genes (CG32783 and CG32786). RNAi-mediated knockdown of CG2941 and its two close paralogs reveals that Gemin4 is essential for organismal viability.
Information sharing, operations capabilities, market intelligence responsiveness and firm performance
Authors: Song Moxi , Liao Yuanhong 
Published: November 2018

Purpose
The purpose of this paper is to offer an alternative explanation for inconclusive results in the existing literature on the information sharing-firm performance link by examining a moderated mediation model in which operations capabilities mediate the interactive effects of information sharing and market intelligence responsiveness on firm performance within a supply chain context. Drawing on the indirect view of dynamic capability theory, the authors propose that information sharing redeploys and reconfigures operations capabilities, thus leading to superior firm performance, even with a high level of market intelligence responsiveness.

Design/methodology/approach
The hypotheses were tested using hierarchical regression and bootstrapping methods with a sample of 154 Chinese manufacturing firms. A survey-based, two-informant design was used to collect data.

Findings
The results revealed that operations capabilities fully mediate the relationship between information sharing and firm performance. The information sharing-operations capabilities link is positively moderated by market intelligence responsiveness. Moreover, operations capabilities positively mediate the interactive effects of information sharing and responsiveness on performance.

Originality/value
The study shifts the research focus from the moderating effect of market intelligence responsiveness in the information sharing-performance link to the interactive effects between information sharing and responsiveness on performance via operations capabilities, thus offering a finer-grained picture of the essential information sharing-performance link. To the best of our knowledge, this study is among the first to advocate and substantiate the theoretical claim that even with a high level of responsiveness, a firm’s performance relies on its operations capabilities, which are renewed and enhanced by information sharing, rather than on information sharing itself.
Comparison of algorithms for road surface temperature prediction
Authors: Liu Bo , Shen Libin , You Huanling , Dong Yan , Li Jianqiang , Li Yong 
Published: November 2018

PurposeThe influence of road surface temperature (RST) on vehicles is becoming more and more obvious. Accurate predication of RST is distinctly meaningful. At present, however, the prediction accuracy of RST is not satisfied with physical methods or statistical learning methods. To find an effective prediction method, this paper selects five representative algorithms to predict the road surface temperature separately.Design/methodology/approachMultiple linear regressions, least absolute shrinkage and selection operator, random forest and gradient boosting regression tree (GBRT) and neural network are chosen to be representative predictors.FindingsThe experimental results show that for temperature data set of this experiment, the prediction effect of GBRT in the ensemble algorithm is the best compared with the other four algorithms.Originality/valueThis paper compares different kinds of machine learning algorithms, observes the road surface temperature data from different angles, and finds the most suitable prediction method.
Heart Valve Disease Predict Mortality in Hemodialysis Patients: A Single Center Experience
Authors: Ozelsancak Ruya , Tekkarismaz Nihan , Torun Dilek , Micozkadioglu Hasan 
Published: November 2018

AbstractOur aim is to investigate the clinical and laboratory findings affecting the mortality of the patients in 3 years follow‐up who underwent hemodialysis at our center. In this retrospective, observational cohort study, 432 patients who underwent hemodialysis at our center for at least 5 months were included. The first recorded data and subsequent clinical findings of patients who died and survived were compared. Two hundred and ninety patients survived, 142 patients died. The mean age of the patients who died was higher (63.4 ± 12.3 years, vs. 52 ± 16.1 years, P = 0.0001), 60.5% of them had coronary artery disease (P = 0.0001), 93.7% of them had a heart valve disease. Duration of hemodialysis (survived 57 [21–260] months; died 44 [5–183] months, P = 0.000) was lower in patients who died. Serum potassium level before dialysis (5.1 ± 0.6; 4.9 ± 0.7 mEq/L, P = 0.030), parathyroid hormone (435 [4–3054]; 304 [1–3145] pg/mL, P = 0.0001), albumin (3.9 ± 0.4; 3.8 ± 0.4 mg/dL, P = 0.0001) and Kt/V (1.48 ± 0.3; 1.40 ± 0.3, P = 0.019) levels were lower, C‐reactive protein (5[1–208]; 8.7[2–256] mg/L, P = 0.000) levels were higher in patients who died. Logistic regression analysis showed age (OR = 1.1), coronary artery disease (OR = 1.7) and more than one heart valve disease (OR = 2.4) are independent risk factors for mortality. Potassium level before dialysis (OR = 0.60), parathyroid hormone (OR = 0.99), and higher Kt/V (OR = 0.28) were found to be an advantage for survival. Age, coronary artery disease and especially pathology in more than one heart valve are risk factors for mortality. Heart valve problems might develop because of malnutrition and inflammation caused by the chronic renal failure.
Case–control study found that primary language disorders were associated with screen exposure
Authors: Collet M , Gagnière B , Rousseau C , Chapron A , Fiquet L , Certain C 
Published: November 2018

AbstractAimWe explored the associations between childhood exposure to screens, including televisions, computers, game consoles, tablets and smartphones and primary language disorders.MethodsThis multi‐centre case–control study comprised 167 children aged 3.5–6.5 years, who were born in 2010–2012 and diagnosed with primary language disorders, and 109 matched controls without language disorders. Questionnaires were completed by their parents who were recruited by 16 family doctors and 27 speech and language therapists in the Ille‐et‐Vilaine region of France. The data were analysed using a multivariate logistic regression model and presented as adjusted odds ratios (aOR) and 95% confidence intervals (95% CI).ResultsWe found that cases (44.3%) and controls (22.0%) exposed to screens in the morning before nursery or primary school were three times more likely to develop primary language disorders (aOR 3.40, 95% CI 1.60–7.23). When this risk was combined with rarely or never discussing screen content with their parents (aOR 2.14, 95% CI 1.01–4.54) they were six times more likely to have language problems (aOR 5.86, 95% CI 1.44–23.95).ConclusionBeing exposed to screens in the morning before school, and rarely or never discussing screen content with parents, meant children were six times more likely to develop primary language disorders.
Traffic‐related air pollution induces non‐allergic eosinophilic airway inflammation and cough hypersensitivity in guinea‐pigs
Authors: Fang Zhangfu , Huang Chuqin , Zhang Junfeng (Jim) , Xie Jiaxing , Dai Shouhui , Ge Erjia , Xiang Juan , Yao Hongmei , Huang Rongquan , Bi Xinhui , Wang Boguang , Zhong Nanshan , Lai Kefang 
Published: November 2018

AbstractBackgroundThe pathogenesis and pathophysiology of eosinophilia‐related chronic cough such as non‐asthmatic eosinophilic bronchitis and cough variant asthma are still not clear.ObjectiveThis study is to examine the potential role of traffic‐related air pollution (TRAP) in eosinophilic inflammation and cough responses.MethodsNon‐sensitized guinea‐pigs were exposed to TRAP in an urban traffic tunnel or kept in a filtered air environment for 7 or 14 days. Reflexive cough was measured using citric acid and allyl isothiocyanate (AITC) challenges, respectively. Spontaneous cough counting was determined using audio recording and a waveform analysis. Airway inflammation was evaluated using differential cells in bronchoalveolar lavage fluid (BALF) and lung histopathology. To further elucidate the relationship between airway inflammation and cough hypersensitivity, a subgroup of those exposed for 14 days received a dexamethasone treatment.ResultsCompared to reflexive cough count (mean (95% confidence interval) in 10 minutes) provoked by the AITC challenge for the unexposed animals (3.1 (1.7‐4.5)), those were increased significantly following both the 7‐day (12.0 (6.8‐17.2), P < 0.01) and the 14‐day (12.0 (6.4‐17.6), P < 0.01) TRAP exposure. The effect provoked by the citric acid challenge was more profound following the 14‐day exposure (26.0 (19.5‐32.5) vs 3.8 (1.5‐6.0) for the control, P < 0.001). TRAP exposures enhanced spontaneous cough events, caused a significant increase of eosinophils and neutrophils in BALF and resulted in a dramatic eosinophilic infiltration in submucosal layer of trachea and bronchus, which can be inhibited significantly by dexamethasone treatment.Conclusions & Clinical RelevanceTRAP exposures induced cough hypersensitivity and non‐allergic eosinophilic inflammation of airways in guinea‐pigs. This study highlights the potential mechanisms of eosinophilia‐related chronic cough that can be induced by traffic‐related air pollution.
Antihistamine‐resistant chronic spontaneous urticaria: 1‐year data from the AWARE study
Authors: Maurer Marcus , Raap Ulrike , Staubach Petra , Richter‐Huhn Grit , Bauer Andrea , Oppel Eva M. , Hillen Uwe , Baeumer Daniel , Reinhardt Maximilian , Chapman‐Rothe Nadine 
Published: November 2018

SummaryBackgroundPrevious reports indicate that patients with chronic spontaneous urticaria (CSU) are undertreated and that physicians show poor adherence to guideline recommendations. Awareness of CSU has improved in recent years, but it remains unclear if this has improved the management of these patients in clinical practice.ObjectiveTo describe disease burden, quality of life (QoL), and treatment patterns of patients with H1‐antihistamine‐refractory CSU in Germany.MethodA World‐wide Antihistamine‐Refractory chronic urticaria (CU) patient Evaluation (AWARE) is a global prospective, non‐interventional study of CU in the real‐world setting, supported by the manufacturer of omalizumab. Patients (18‐75 years) were included who had H1‐antihistamine‐refractory CSU for ≥2 months. Disease characteristics, pharmacological treatments, and QoL (dermatology life quality index [DLQI], CU‐QoL questionnaire, and angioedema QoL questionnaire) are reported for patients enrolled in Germany.ResultsAfter 1 year in AWARE, CSU remained uncontrolled (urticaria control test [UCT] score <12) in 432 of 1032 (42.2%) patients. QoL impairment remained high after 1 year, with 28.2% of patients reporting that CSU had a moderate/very large/extremely large effect on the DLQI. Most patients did not receive guideline‐recommended treatments at the end of the 1‐year observation period. Changes in treatments were most evident at the first patient visit, with an increase in patients receiving omalizumab vs prior therapy from 8.5% to 21.4%, and a decrease in those receiving no treatment from 29.9% to 12.8%. These changes were associated with reduced hives, angioedema, UCT scores, and QoL scores at Month 3, but only modest improvements thereafter. Of 528 patients with uncontrolled CSU and who were eligible for treatment escalation, only 3% received up‐dosing of H1‐antihistamines and only 5% were initiated on omalizumab during 1 year of treatment.Conclusions & Clinical RelevanceThis study highlights a significant discrepancy between recommendations for managing CSU in international guidelines, and in real‐world clinical practice in Germany.
Variability of blood eosinophils in patients in a clinic for severe asthma
Authors: Rakowski Ewa , Zhao Sibo , Liu Mengling , Ahuja Shilpi , Durmus Nedim , Grunig Gabriele , Curotto de Lafaille Maria , Wu Yinxiang , Reibman Joan 
Published: November 2018

SummaryBackgroundBlood eosinophils are used to determine eligibility for agents targeting IL‐5 in patients with uncontrolled asthma. However, little is known about the variability of blood eosinophil measures in these patients before treatment initiation.ObjectiveTo characterize variability and patterns of variability of blood eosinophil levels in a real‐world clinic for severe asthmatics.MethodsRetrospective review of blood eosinophils measured over a 5‐year period in patients enrolled in an urban clinic. Repeated measures of blood eosinophil levels in individuals were evaluated, and cluster analysis was performed to characterize patients by eosinophil patterns. Clinical characteristics associated with eosinophil levels and patterns of variability were analysed.ResultsPatients treated in the Bellevue Hospital Asthma Clinic within a 3‐month period were identified (n = 219). Blood eosinophil measures were obtained over the previous 5 years. Only 6% (n = 13) of patients had levels that were consistently above 300 cells/μL. Nearly 50% (n = 104) had eosinophil levels that traversed the threshold of 300 cells/μL. In contrast, 102 (46%) had levels that never reached the threshold of 300 cells/μL. Cluster analyses revealed three clusters with differing patterns of levels and variability. There was a suggestion of decreased clinical control and increased atopy in the cluster with the greatest variability in blood eosinophil measures.ConclusionIn an urban clinic for patients referred for uncontrolled asthma, blood measures of eosinophils were variable and showed differing patterns of variability. These data reinforce the need to perform repeated eosinophil blood measures for appropriate designation for therapeutic intervention.
Dividing neutrophils in subsets reveals a significant role for activated neutrophils in the development of airway hyperreactivity
Authors: Ekstedt Sandra , Säfholm Jesper , Georén Susanna Kumlien , Cardell Lars Olaf 
Published: November 2018

AbstractBackgroundPrevious research has emphasized the importance of eosinophils in allergic asthma, while paying less attention to neutrophils. The known functionality of neutrophils in the inflammatory process has recently changed and knowledge about subsets of neutrophils, as characterized by their expression of CD16 and CD62L, has surfaced. Their specific roles in asthma are still unknown.ObjectiveTo study the functional differences between subsets of neutrophils by characterizing the impact of individual subsets on airway smooth muscle reactivity.MethodsThe direct effect of neutrophils on airway hyperresponsiveness was assessed by co‐culturing different subsets of neutrophils (produced by LPS in vitro stimulation) with human isolated small airways or murine tracheae with subsequent evaluation of smooth muscle reactivity to bradykinin in myographs. Supernatants and tissue were saved for ELISA and immunohistochemistry.ResultsThe CD16high CD62Ldim neutrophils were found to enhance the response to bradykinin in both human isolated small airways and murine tracheae. No such effects were obtained for the other subsets. The response is due to an upregulation of bradykinin receptor 2 through release of TNFα from the neutrophil.Conclusions and Clinical RelevanceThe present study introduces a new concept regarding the role of neutrophils and defines a novel direct link between a specific activated neutrophil subset and airway smooth muscle, establishing neutrophils as important players in the development of asthmatic airway hyperactivity.
Individual shark profiling: An innovative and environmentally responsible approach for selectively managing human fatalities
Authors: Clua Eric E. G. , Linnell John D. C. 
Published: November 2018

AbstractMost shark‐induced human fatalities are followed by widespread and unselective culling campaigns that have limited effectiveness and may have high ecological costs for threatened species. The blanket culling strategy implicitly assumes that incident risk is directly correlated with shark density, an assumption that has yet to be demonstrated. We present the alternative hypothesis that incidents are more likely to be caused by behavioral variability among individual sharks than due to shark density. Throughout their ontogenetic development, large species of sharks opportunistically establish a diet that is rarely, if ever, inclusive of humans as a food source. We propose that, some animals with specific behaviors (including boldness) may potentially pose a higher risk than conspecifics. Under this scenario, the risk of a shark attack in a given area would relate to the presence of a limited number of high‐risk individuals rather than shark density.In terms of management of human fatalities, such a hypothesis would favor abandoning general culling campaigns and replacing them with approaches that profile and selectively remove the potential problem individuals, as is done in the terrestrial realm when managing predators that attack humans or livestock.
Lung cancer after lung transplantation: An analysis of 25 years of experience in a single institution
Authors: Chatron Eva , Dégot Tristan , Salvaterra Elena , Dumazet Antoine , Porzio Michele , Hirschi Sandrine , Schuller Armelle , Massard Gilbert , Renaud‐Picard Benjamin , Kessler Romain 
Published: November 2018

AbstractBackgroundThe aim of our study was to describe the lung cancer characteristics in lung transplant recipients at our institution.MethodsBetween January 1, 1992, and August 15, 2017, 463 patients underwent lung transplantation.ResultsWe found a total of 19 lung cancers (4.10%). Eight patients had lung cancer in the explanted lung, 8 in the native remaining lung, and 3 in the transplanted lung. Histopathological findings were: adenocarcinoma in 10, SCC in 8 patients, and 1 was undetermined. Among lung cancers in the explanted lungs, there were 6 stage I, 1 stage III, 1 stage IV. Among patients with a lung cancer in the remaining native lung, 3 had early stage disease and 5 had stage IV disease. Among lung cancers in the transplanted lung, there were: 1 stage I, 1 stage II and 1 stage IV. Overall median survival in lung transplant recipients without lung cancer was 8.77 ± 0.74 years compared to 6.19 ± 1.4 years in recipients with lung cancer.ConclusionLung cancer following lung transplantation was uncommon. Early stage lung cancer discovered in the explanted lungs had no impact on survival. Lung cancer occurring in the transplanted or in the native remaining lung had a poor prognosis.
The role of sensorimotor experience in the development of mimicry in infancy
Authors: de Klerk Carina C. J. M. , Lamy‐Yang Iona , Southgate Victoria 
Published: November 2018

AbstractDuring social interactions we often have an automatic and unconscious tendency to copy or ‘mimic’ others’ actions. The dominant view on the neural basis of mimicry appeals to an automatic coupling between perception and action. It has been suggested that this coupling is formed through associative learning during correlated sensorimotor experience. Although studies with adult participants have provided support for this hypothesis, little is known about the role of sensorimotor experience in supporting the development of perceptual‐motor couplings, and consequently mimicry behaviour, in infancy. Here we investigated whether the extent to which an observed action elicits mimicry depends on the opportunity an infant has had to develop perceptual‐motor couplings for this action through correlated sensorimotor experience. We found that mothers’ tendency to imitate their 4‐month‐olds’ facial expressions during a parent‐child interaction session was related to infants’ facial mimicry as measured by electromyography. Maternal facial imitation was not related to infants’ mimicry of hand actions, and instead we found preliminary evidence that infants’ tendency to look at their own hands may be related to their tendency to mimic hand actions. These results are consistent with the idea that mimicry is supported by perceptual‐motor couplings that are formed through correlated sensorimotor experience obtained by observing one's own actions and imitative social partners.