bluuebunny/crossref_metadata_2025_split huggingface dataset:
QuicK-mer: A rapid paralog sensitive CNV detection pipeline
Authors: Shen Feichen , Kidd Jeffrey 
Published: October 2015

AbstractQuicK-mer is a unified pipeline for estimating genome copy-number from high-throughput Illumina sequencing data. QuicK-mer utilizes the Jellyfish application to efficiently tabulate counts of predefined sets of k-mers. The program performs GC-normalization using defined control regions and reports paralog-specific estimates of copy-number suitable for downstream analysis. The package is freely available athttps://github.com/KiddLab/QuicK-mer
Gene discovery for Mendelian conditions via social networking:de novovariants inKDM1Acause developmental delay and distinctive facial features
Authors: Chong Jessica X. , Yu Joon-Ho , Lorentzen Peter , Park Karen M. , Jamal Seema M. , Tabor Holly K. , Rauch Anita , Saenz Margarita Sifuentes , Boltshauser Eugen , Patterson Karynne E. , Nickerson Deborah A. ,   University of Washington Center for Mendelian Genomics, Bamshad Michael J. 
Published: October 2015

ABSTRACTPurpose:The pace of Mendelian gene discovery is slowed by the “n-of-1 problem” – the difficulty of establishing causality of a putatively pathogenic variant in a single person or family. Identification of an unrelated person with an overlapping phenotype and suspected pathogenic variant in the same gene can overcome this barrier but is often impeded by lack of a convenient or widely-available way to share data on candidate variants / genes among families, clinicians and researchers.Methods:Social networking among families, clinicians and researchers was used to identify three children with variants of unknown significance inKDM1Aand similar phenotypes.Results:De novo variants inKDM1Aunderlie a new syndrome characterized by developmental delay and distinctive facial features.Conclusion:Social networking is a potentially powerful strategy to discover genes for rare Mendelian conditions, particularly those with non-specific phenotypic features. To facilitate the efforts of families to share phenotypic and genomic information with each other, clinicians, and researchers, we developed the Repository for Mendelian Genomics Family Portal (RMD-FP). Design and development of a web-based tool, MyGene2, that enables families, clinicians and researchers to search for gene matches based on analysis of phenotype and exome data deposited into the RMD-FP is underway.
Inferred Model of the Prefrontal Cortex Activity Unveils Cell Assemblies and Memory Replay
Authors: Tavoni Gaia , Ferrari Ulisse , Battaglia Francesco P. , Cocco Simona , Monasson Rémi 
Published: October 2015

AbstractCell assemblies are thought to be the units of information representation in the brain, yet their detection from experimental data is arduous. Here, we propose to infer effective coupling networks and model distributions for the activity of simultaneously recorded neurons in prefrontal cortex, during the performance of a decision-making task, and during preceding and following sleep epochs. Our approach, inspired from statistical physics, allows us to define putative cell assemblies as the groups of co-activated neurons in the models of the three recorded epochs. It reveals the existence of task-related changes of the effective couplings between the sleep epochs. The assemblies which strongly coactivate during the task epoch are found to replay during subsequent sleep, in correspondence to the changes of the inferred network. Across sessions, a variety of different network scenarios is observed, providing insight in cell assembly formation and replay.Author SummaryMemories are thought to be represented in the brain through groups of coactivating neurons, the so-called cell assemblies. We propose an approach to identify cell assemblies from multi-electrode recordings of neural activityin vivo,and apply it to the prefrontal cortex activity of a behaving rat. Our statistical physics inspired approach consists in inferring effective interactions between the recorded cells, which reproduce the correlations in their spiking activities. The analysis of the effective interaction networks and of the model distributions allows us to identify cell assemblies, which strongly co-activate when the rat is learning, and also during subsequent sleep. Our approach is thus capable of providing detailed insights in cell-assembly formation and replay, crucial for memory consolidation.
The beginning of the end of Chinese Surrogate Manufacture? Cool-Comfort Shoes International Company Limited and its Ace-of-Biz
Authors: Zhuang Lee , Qiu Yi 
Published: October 2015

Subject area
Strategic management

Study Level/applicability
Undergraduate/postgraduate modules in strategic management.

Case overview
The case portrays a Chinese surrogate manufacturer – Cool-Comfort Shoes International Co. Ltd. (CCS) – which attempted to build its own brand, Ace-of-Biz (AoB). The surrogate manufacturing business had accumulated the funds needed to develop its AoB brand for sale in the domestic market. The 2007 world financial crisis and subsequent world recession caused exports and, thus, surrogate manufacturing to plummet. CCS was hoping that their loss in export of surrogate products would be more than compensated for by the gain in the domestic sales of AoB. However, despite 10 years of commitment, AoB's sales still had not grown sufficiently to counter the slowdown in exports, and the leaders at CCS were wondering what the future would hold for the company and its AoB brand.

Expected Learning Outcomes
This case study provides students with an ideal context to develop an appreciation of how changes in the domestic and international business environment affect the corporate and business strategies of a small- to medium-sized enterprise and the differences between corporate and business strategies, and to demonstrate their ability to apply a number of strategic management tools and techniques for the critical appraisal of a strategic situation and justify their recommended course of action.

Supplementary Materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
Universities’ contributions to social innovation: reflections in theory
&
practice
Authors: Benneworth Paul , Cunha Jorge 
Published: October 2015

Purpose
– The purpose of this paper is to resolve a tension in understanding how universities contribute to knowledge-based urban development (KBUD).

Design/methodology/approach
– The paper is a conceptual paper, which analyses the tension as emerging between the university and the wider societal activity. The paper creates a framework for combining insights from both those theoretical frameworks to better understand why universities might choose to contribute to KBUD.

Findings
– The paper argues that it is important to understand the benefits that the universities get from participating in the KBUD. This can be through the unique tacit knowledge that emerges in the social innovation process, but their might also be value for the university in terms of two other variables, material resources and symbolic legitimacy.

Research limitations/implications
– The paper is a literature review and therefore is limited to raising a series of future questions and directions for research in the field, as well as to providing a lens and context for existing work.

Practical implications
– There are clear implications for those seeking to improve universities contributions to KBUD. It is not merely enough for strategic leaders to come together and agree that promoting the university will promote KBUD: it is necessary to modify a range of processes within the university to ensure that a wide range of actors are able to benefit from participating in KBUD activities, and that it facilitates their own teaching and research activities.

Social implications
– For universities to make a substantive contribution to promoting KBUD, policy-makers must ensure that they do not create disincentives through universities’ teaching and research activities.

Originality/value
– This is the first time that a paper has sought to bridge between theories of urban development and social innovation, and universities’ internal institutional and organisational dynamics.
Robotic training for hand movements during manual welding with real-time alarm feedback
Authors: Erden Mustafa Suphi , Billard Aude 
Published: October 2015

Purpose– The purpose of this study is to develop a robotic training system for the hand movements during manual welding. The system provides real-time notice-feedback with sound or light alarms, whenever the welding hand vibrates beyond the nominal level observed with professional welders.Design/methodology/approach– The large variations of hand movements are detected by monitoring the deviation of the tool position from a smooth curve estimated in real time by a Kalman filter. An alarm is generated in the form of a flashing light or beep sound whenever the deviations exceed a predetermined threshold. The performance of hand movements is measured in terms of the variations of the position data. Twelve novice and five professional welders took part in the experiments and answered a questionnaire that assessed the usability and work load of the system.Findings– Compared to the sound alarms, the light alarms resulted in a larger and statistically significant decrease in the variation of hand movements of the novice welders and brought the level of variation close to that of the professional welders. The alarms did not result in a significant decrease in the variation of hand movements of the professional welders. The responses to the questionnaire indicated that both professional and novice welders found the system useful and they did not experience any significant work load.Social implications– The system developed in this study can ease the training of novice welders, by speeding up the learning and reducing the need for human tutors.Originality/value– This study is first to provide real-time notice-feedback for training while manual welding, based on a comparison of the performances of novice and professional welders.
Determining the necessity for right heart catheterization in pulmonary hypertension associated with connective tissue diseases assessed by echocardiography
Authors: Choi Joon Hyouk , Joo Seung‐Jae , Kim Jinseok 
Published: October 2015

AbstractAimThe prognosis of pulmonary hypertension (PH) in systemic sclerosis (SSC) and in systemic lupus erythematosus (SLE) is different. According to the guidelines, right heart catheterization (RHC) is necessary in pulmonary arterial hypertension (PAH) associated with connective tissue diseases (CTD). However, there is little supporting evidence. Therefore, we attempted to determine the necessity for RHC and the causes of differences in prognosis of PH by comparing SSC to SLE.MethodsThe inclusion criteria were all patients with SSC or SLE with exertional dyspnea. Echocardiography and carotid Doppler ultrasound were performed.ResultsTwenty‐three patients with SSC and 23 with SLE participated in this study. There was no difference in the right ventricular systolic pressure (RVSP) between SSC and SLE (33.0 mmHg, range 25.3–41.7 mmHg vs. 32.4 mmHg, range 27.0–37.7 mmHg; P = 0.835). In multiple linear regression analysis, the ratio of peak tricuspid regurgitant velocity to right ventricular outflow tract time‐velocity integral, which represents pulmonary vascular resistance (PVR), was correlated with RVSP in SSC (r2 = 0.928, β = 0.362, P = 0.003), and the independent predictor of increased RVSP was the ratio of early diastolic transmitral filling velocity to early diastolic septal mitral annular velocity, which represents diastolic dysfunction in SLE (R2 = 0.806, β = 0.803, P = 0.023).ConclusionsPVR was an important cause of PH in SSC. Left ventricular dysfunction was an important cause of PH in SLE. Thus, these findings demonstrate the necessity for RHC and differences in prognosis of PH in CTD.
Assessment of first‐trimester thymus size and correlation with maternal diseases and fetal outcome
Authors: Borgelt Judith M. A. , Möllers Mareike , Falkenberg Maria K. , Amler Susanne , Klockenbusch Walter , Schmitz Ralf 
Published: October 2015

AbstractIntroductionWe investigated the reliability of fetal thymus measurement during first‐trimester screening, and associated fetal thymus size with crown–rump length, maternal diseases and fetal outcome.Material and MethodsIn a retrospective cohort of 971 normal singleton first‐trimester fetuses, we measured the anterior–posterior diameter of the thymus in a midsagittal plane in 767 fetuses. The intra‐observer and inter‐observer reliabilities were tested by intra‐class correlation coefficient. We correlated thymus size with fetal crown–rump length, and investigated its association with maternal diseases (diabetes mellitus, rheumatic disorders, hypertension and coagulation disorders) and fetal outcome (small for gestational age, preterm birth and umbilical artery pH) using regression analyses.ResultsThe intra‐observer and inter‐observer reliabilities of fetal thymus measurement were excellent (intra‐class correlation coefficient 0.926, 95% CI 0.745–0.981 and 0.945, 95% CI 0.886–0.993, respectively). A linear relationship was found between crown–rump length and thymus size (β = 0.023, p = 0.001). Pregnancies affected by maternal diabetes had a decreased fetal thymus size (β = −0.209, p = 0.001), whereas in pregnancies affected by maternal rheumatic disease the thymus size was increased (β = 0.285, p < 0.001). Fetal thymus size was not associated with maternal hypertension or maternal coagulation disorders. There was a positive association between preterm birth and fetal thymus size (p < 0.001).ConclusionMeasurement of first‐trimester thymus size is reliable. Fetal thymus size has a linear correlation with crown–rump length. Maternal diabetes, rheumatic disease and preterm birth appear to have an association with fetal thymus size.
Estimating DNA Methylation Levels by Joint Modeling of Multiple Methylation Profiles From Microarray Data
Authors: Wang Tao , Chen Mengjie , Zhao Hongyu 
Published: October 2015

Summary
DNA methylation studies have been revolutionized by the recent development of high throughput array-based platforms. Most of the existing methods analyze microarray methylation data on a probe-by-probe basis, ignoring probe-specific effects and correlations among methylation levels at neighboring genomic locations. These methods can potentially miss functionally relevant findings associated with genomic regions. In this article, we propose a statistical model that allows us to pool information on the same probe across multiple samples to estimate the probe affinity effect, and to borrow strength from the neighboring probe sites to better estimate the methylation values. Using a simulation study, we demonstrate that our method can provide accurate model-based estimates. We further use the proposed method to develop a new procedure for detecting differentially methylated regions, and compare it with a state-of-the-art approach via a data application.
Revisiting Patterns of Tree Species Composition and their Driving Forces in the Atlantic Forests of Southeastern Brazil
Authors: Eisenlohr Pedro V. , de Oliveira‐Filho Ary Teixeira 
Published: October 2015

AbstractThe elucidation of phytogeographic patterns and their drivers in biodiversity hotspots is essential to the study of ecology and the conservation of these areas. In 2000, an important study by Oliveira‐Filho and Fontes led to changes in the paradigms that define our understanding of the Atlantic Forest (Brazil). Here, our aim was to revisit this study using a more comprehensive set of environmental predictors, an updated and much larger tree species dataset and checklist, and more refined data analyses. We performed exploratory and confirmatory analyses, including the modeling of the spatial components with Moran's Eigenvector Maps, using data from 483 sites in southeastern Brazil, which encompass a total of 3546 species and 33 geo‐climatic variables. We observed strong floristic similarities between rain‐ and seasonal forests and a species distribution continuum across the main gradients. The environmental and spatial variables were significantly correlated with floristic patterns, and we demonstrated that the tree flora of the seasonal forests should no longer be considered a simple subset of the rain forest flora. The findings of the original paper were not only confirmed but we also unveiled additional, important phytogeographic patterns. We also reinforced the main conclusion of the paper that the Atlantic Forest concept must encompass all of the forest types east of the dry corridor in South America, a designation of utmost importance for the conservation of this biodiversity hotspot.
A prospective randomized controlled study of a virtual clinic integrating primary and specialist care for patients with Type 2 diabetes mellitus
Authors: Basudev N. , Crosby‐Nwaobi R. , Thomas S. , Chamley M. , Murrells T. , Forbes A. 
Published: October 2015

AbstractAimsTo investigate the effectiveness of a diabetes virtual clinic to enhance diabetes in primary care by developing clinical management plans for patients with suboptimal metabolic control and/or case complexity.MethodsA prospective study with randomized allocation to virtual clinic or usual care. Patients with Type 2 diabetes (n = 208) were recruited from six general practices in South London. The primary outcome for the study was glycaemic control, secondary outcomes included: lipids, blood pressure, weight (kg and BMI) and renal function (eGFR). Data were collected from participants' records at baseline and 12 months. We also considered process measures including therapy optimization.ResultsThe 12‐month data show equivalence between the virtual clinic and control groups for glycaemic control with both achieving clinically significant reductions in HbA1c of 8 mmol/mol (0.6 ± 1.7%) and 10 mmol/mol (0.8 ± 1.9%), respectively (P = 0.4). The virtual clinic group showed superiority over the intervention group for blood pressure control with a mean reduction in systolic blood pressure of 6 ± 16 mmHg compared with an increased of 2 ± 18 mmHg in the control group (P = 0.008). There were no significant differences between the groups in terms of cholesterol, weight and renal function. Process measures showed an increased level of therapy adjustment in the virtual clinic group.ConclusionThe virtual clinic model explored in this study showed a clinically important improvement in glycaemic control. Although this improvement was not superior to that observed in the control participants, this might be attributable to the systemic impact of the virtual clinic on the practice as a whole.
Feeding preferences of Melanoplus femurrubrum grasshoppers on native and exotic grasses: behavioral and molecular approaches
Authors: Avanesyan Alina , Culley Theresa M. 
Published: October 2015

AbstractGeneralist insect herbivores, such as grasshoppers, may either avoid feeding on exotic plants, potentially enabling these plants to become invasive in the introduced range, or insects may incorporate exotic plants into their diet, contributing to the biotic resistance of native communities and potentially preventing plant invasions. Accurate determination of insect diet preferences with regard to native and exotic plants can be challenging, but this information is critical for understanding the interaction between native herbivores and exotic plants, and ultimately the mechanisms underlying plant invasions. To address this, we combined behavioral and molecular approaches to accurately compare food consumption of the polyphagous red‐legged grasshopper, Melanoplus femurrubrum (De Geer) (Orthoptera: Acrididae), on native [Andropogon gerardii Vitman and Bouteloua curtipendula (Michx.) Torr.] and exotic, potentially invasive grasses [Miscanthus sinensis Andersson and Bothriochloa ischaemum (L.) Keng] (all Poaceae). We found that M. femurrubrum grasshoppers demonstrated strong feeding preferences toward exotic grasses in experiments with intact plants under both field and greenhouse conditions, but they showed no preference in experiments with clipped leaves. Additionally, we sampled the gut contents of M. femurrubrum collected in the field and identified the ingested plant species based on DNA sequences for the non‐coding region of the chloroplast trnL (UAA) gene. We found that exotic plants were prevalent in the gut contents of grasshoppers collected at study sites in Ohio and Maryland, USA. These results suggest that the generalist herbivore M. femurrubrum does not avoid feeding on exotic grasses with which they do not share coevolutionary history. In addition, by demonstrating greater food consumption of exotic plants, these grasshoppers potentially provide biotic resistance should these grasses escape cultivation and become invasive in the introduced range.
Does climate directly influence NPP globally?
Authors: Chu Chengjin , Bartlett Megan , Wang Youshi , He Fangliang , Weiner Jacob , Chave Jérôme , Sack Lawren 
Published: October 2015

AbstractThe need for rigorous analyses of climate impacts has never been more crucial. Current textbooks state that climate directly influences ecosystem annual net primary productivity (NPP), emphasizing the urgent need to monitor the impacts of climate change. A recent paper challenged this consensus, arguing, based on an analysis of NPP for 1247 woody plant communities across global climate gradients, that temperature and precipitation have negligible direct effects on NPP and only perhaps have indirect effects by constraining total stand biomass (Mtot) and stand age (a). The authors of that study concluded that the length of the growing season (lgs) might have a minor influence on NPP, an effect they considered not to be directly related to climate. In this article, we describe flaws that affected that study's conclusions and present novel analyses to disentangle the effects of stand variables and climate in determining NPP. We re‐analyzed the same database to partition the direct and indirect effects of climate on NPP, using three approaches: maximum‐likelihood model selection, independent‐effects analysis, and structural equation modeling. These new analyses showed that about half of the global variation in NPP could be explained by Mtot combined with climate variables and supported strong and direct influences of climate independently of Mtot, both for NPP and for net biomass change averaged across the known lifetime of the stands (ABC = average biomass change). We show that lgs is an important climate variable, intrinsically correlated with, and contributing to mean annual temperature and precipitation (Tann and Pann), all important climatic drivers of NPP. Our analyses provide guidance for statistical and mechanistic analyses of climate drivers of ecosystem processes for predictive modeling and provide novel evidence supporting the strong, direct role of climate in determining vegetation productivity at the global scale.
Brief analysis of causes of sensitive skin and advances in evaluation of anti‐allergic activity of cosmetic products
Authors: Fan L. , He C. , Jiang L. , Bi Y. , Dong Y. , Jia Y. 
Published: October 2015

AbstractThis review focuses on the causes of sensitive skin and elaborates on the relationship between skin sensitivity and skin irritations and allergies, which has puzzled cosmetologists. Here, an overview is presented of the research on active ingredients in cosmetic products for sensitive skin (anti‐sensitive ingredients), which is followed by a discussion of their experimental efficacy. Moreover, several evaluation methods for the efficacy of anti‐sensitive ingredients are classified and summarized. Through this review, we aim to provide the cosmetic industry with a better understanding of sensitive skin, which could in turn provide some theoretical guidance to the research on targeted cosmetic products.