bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological classification with RNA-Seq data: Can alternative splicing enhance machine learning classifier?
Authors: Johnson Nathan T. , Dhroso Andi , Hughes Katelyn J. , Korkin Dmitry 
Published: June 2017

AbstractThe extent to which the genes are expressed in the cell can be simplistically defined as a function of one or more factors of the environment, lifestyle, and genetics. RNA sequencing (RNA-Seq) is becoming a prevalent approach to quantify gene expression, and is expected to gain better insights to a number of biological and biomedical questions, compared to the DNA microarrays. Most importantly, RNA-Seq allows to quantify expression at the gene and alternative splicing isoform levels. However, leveraging the RNA-Seq data requires development of new data mining and analytics methods. Supervised machine learning methods are commonly used approaches for biological data analysis, and have recently gained attention for their applications to the RNA-Seq data.In this work, we assess the utility of supervised learning methods trained on RNA-Seq data for a diverse range of biological classification tasks. We hypothesize that the isoform-level expression data is more informative for biological classification tasks than the gene-level expression data. Our large-scale assessment is done through utilizing multiple datasets, organisms, lab groups, and RNA-Seq analysis pipelines. Overall, we performed and assessed 61 biological classification problems that leverage three independent RNA-Seq datasets and include over 2,000 samples that come from multiple organisms, lab groups, and RNA-Seq analyses. These 61 problems include predictions of the tissue type, sex, or age of the sample, healthy or cancerous phenotypes and, the pathological tumor stage for the samples from the cancerous tissue. For each classification problem, the performance of three normalization techniques and six machine learning classifiers was explored. We find that for every single classification problem, the isoform-based classifiers outperform or are comparable with gene expression based methods. The top-performing supervised learning techniques reached a near perfect classification accuracy, demonstrating the utility of supervised learning for RNA-Seq based data analysis.
Punctuated evolution shaped modern vertebrate diversity
Authors: Landis Michael J. , Schraiber Joshua G. 
Published: June 2017

AbstractThe relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest very fast rates of evolution. One way to reconcile these observations is to imagine that evolution is punctuated, rather than gradual, on geological time scales. To test this hypothesis, we developed a novel maximum likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both a gradual and punctuated component. We found that a plurality of modern vertebrate clades examined are best fit by punctuated processes over models of gradual change, gradual stasis, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and with observations from the fossil record.
Genome Architecture Leads a Bifurcation in Cell Identity
Authors: Liu Sijia , Chen Haiming , Ronquist Scott , Seaman Laura , Ceglia Nicholas , Muir Lindsey A. , Meixner Walter , Chen Pin-Yu , Higgins Gerald , Baldi Pierre , Smale Steve , Hero Alfred , Rajapakse Indika 
Published: June 2017

SUMMARYGenome architecture is important in transcriptional regulation and study of its features is a critical part of fully understanding cell identity. Altering cell identity is possible through overexpression of transcription factors (TFs); for example, fibroblasts can be reprogrammed into muscle cells by introducing MYOD1. How TFs dynamically orchestrate genome architecture and transcription as a cell adopts a new identity during reprogramming is not well understood. Here we show that MYOD1-mediated reprogramming of human fibroblasts into the myogenic lineage undergoes a critical transition, which we refer to as a bifurcation point, where cell identity definitively changes. By integrating knowledge of genome-wide dynamical architecture and transcription, we found significant chromatin reorganization prior to transcriptional changes that marked activation of the myogenic program. We also found that the local architectural and transcriptional dynamics of endogenous MYOD1 and MYOG reflected the global genomic bifurcation event. These TFs additionally participate in entrainment of biological rhythms. Understanding the system-level genome dynamics underlying a cell fate decision is a step toward devising more sophisticated reprogramming strategies that could be used in cell therapies.
Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast
Authors: Masgrau Aina , Battola Andrea , Sanmartin Trinidad , Pryszcz Leszek P. , Gabaldón Toni , Mendoza Manuel 
Published: June 2017

AbstractBoi1 and Boi2 (Boi1/2) are budding yeast plasma membrane proteins that function in polarized growth, and in cytokinesis inhibition in response to chromosome bridges via the NoCut abscission checkpoint. How Boi1/2 act in these two distinct processes is not understood. We demonstrate that Boi1/2 are required for a late step in the fusion of secretory vesicles with the plasma membrane of the growing bud. Cells lacking Boi1/2 accumulate secretory vesicles and are defective in bud growth. In contrast, Boi2 is specifically required for abscission inhibition in cells with chromatin bridges. The SH3 domain of Boi2, which is dispensable for bud growth and targets Boi2 to the site of abscission, is essential for abscission inhibition. Gain of function of the exocyst, a conserved protein complex involved in tethering of exocytic vesicles to the plasma membrane, rescued secretion and bud growth defects in boi mutant cells, and abrogated NoCut checkpoint function. Thus, Boi2 functions redundantly with Boi1 to promote the fusion of secretory vesicles with the plasma membrane at sites of polarized growth, and acts as an abscission inhibitor during cytokinesis in response to chromatin bridges.
The effect of the CEO’s characteristics on EM: evidence from Jordan
Authors: Alqatamin Rateb Mohammmad , Aribi Zakaria Ali , Arun Thankom 
Published: June 2017

PurposeThis study aims to examine the effect of CEO’s personal characteristics on earnings management (EM) practices.Design/methodology/approachThe authors use panel data for 201 non-financial companies listed on the Amman Stock Exchange (ASE) for the period 2008-2013. The authors use random effect models to test the hypothesis of this study and extent the analysis to family versus non-family.FindingsThe study finds a positive relation between CEO’s overconfidence and EM practices in Jordan. Moreover, the findings reveal that managers in family companies are more likely to engage in EM practices than non-family companies. The findings shed more light on the intricate relationship between CEO’s characteristics, the decision-making process and financial reporting.Practical implicationsResults of this study could be beneficial for a number of users of financial information such as investors, auditors, regulators, lenders, as well other players in the capital market to make right decisions.Originality/valueA literature review finds that much less studies have investigated the relationship between EM practices and personal CEO characteristics (gender and overconfidence) in developing countries such as Jordan. Furthermore, no study yet has examined the influence of CEO age on EM practices. The authors extend previous literature by providing empirical evidence about effect of some personal CEO’s characteristics on EM practices.
Size, trading volume, and the profitability of technical trading
Authors: Chang Yung-Ho , Jong Chia-Ching , Wang Sin-Chong 
Published: June 2017

PurposeThe purpose of this paper is to evaluate the profitability of technical trading relative to buy-and-hold (BH) strategy at firm level, controlling for firm size and trading volume.Design/methodology/approachThis paper applies variable-length moving averages (VMAs) thoroughly to each and every stock listed on Taiwan Stock Exchange (TWSE) and computes the excess returns of technical trading relative to BH strategy. The samples are further grouped by firm size and trading volume. Furthermore, possible data snooping bias is investigated by employing Hansen’s (2005) Superior Predictive Ability tests.FindingsThe result shows that VMAs outperform the BH strategy. The profitability of VMAs, remarkably, is positively associated with size and trading volume. After correcting for data snooping bias, VMAs with longer moving averages outperform VMAs with shorter moving averages. The evidence suggests that size and volume information is accountable for trend projection.Originality/valueUnlike past studies simply applying technical trading rules to market indices, portfolios, or selected stocks, this paper evaluates the profitability of technical trading by applying VMAs comprehensively to each and every individual stock listed on TWSE controlling for the effect of firm size and trading volume, providing more practical insights for trading individual stocks.
What motivates social entrepreneurs to start social ventures?
Authors: Ghalwash Seham , Tolba Ahmed , Ismail Ayman 
Published: June 2017

PurposeThis study aims to explore the characteristics and backgrounds of social entrepreneurs, particularly in relation to what motivates them to start new social ventures, through an empirical examination of the phenomenon of social entrepreneurship in the specific context of Egypt.Design/methodology/approachThe study adopts a qualitative methodological approach based on a triangulation of data sources, including extensive interviews from five social entrepreneurs, interviews with senior executives in their organisations and industry experts, as well as secondary data.FindingsThe paper proposes a model that integrates common characteristics and motivations among individuals who start social ventures. Findings confirm the characteristics of social entrepreneurs as compassionate risk-takers with entrepreneurial mindsets who seek to address social issues in innovative ways. They also have the perseverance to face the inefficient institutional frameworks prevalent in developing economies. Social entrepreneurs are motivated by social problems and challenges, inspiration, and previous personal experiences, as well as their social networks.Research limitations/implicationsThere are limitations pertaining to the limited sample size and single country focus.Practical implicationsThis research offers useful and practical insights for current and future social entrepreneurs, particularly in developing economies. Moreover, the study contributes to expanding future research on social entrepreneurship in similar contexts.Originality/valueThis study makes several contributions to the literature on social entrepreneurship. First, by presenting an integrated model for the characteristics/traits and motivations of social entrepreneur. Second, it provides deeper understanding of social entrepreneurship in emerging economies. Third, it highlights the importance of personal inspiration and informal social networks as two sources of motivation for social entrepreneurs, in emerging countries.
The role of livestock intensification and landscape structure in maintaining tropical biodiversity
Authors: Alvarado Fredy , Escobar Federico , Williams David R. , Arroyo‐Rodríguez Víctor , Escobar‐Hernández Fernando 
Published: June 2017

Abstract

As tropical cattle ranching continues to expand, successful conservation will require an improved understanding of the relative impacts of different livestock systems and landscape structure on biodiversity. Here, we provide the first empirical and multi‐scale assessment of the relative effects of livestock intensification and landscape structure on biodiversity in the threatened tropical dry forests of Mesoamerica.

We used a dataset of dung beetles (169,372 individuals from 33 species) collected from 20 1‐km2 landscapes, ranging from zero‐yielding forest sites to high‐yield cattle ranches and maize farms, to investigate the relative effect of livestock intensification (net cattle production; macrocyclic lactone use; annual dung production) and landscape structure (landscape composition and configuration) at multiple spatial scales on different attributes of dung beetle communities using a multi‐model averaging approach.

Dung beetle species richness, biomass and composition were more strongly related to landscape structure than to livestock intensification.

Forest cover was the best predictor of dung beetle assemblages, being positively related to species diversity and biomass across multiple spatial scales. The use of macrocyclic lactones was strong and negatively related to dung beetle communities at the local scale.

Synthesis and applications: Maximising forest protection through a “land sparing” strategy is likely to be the best strategy for reducing negative impacts of cattle farming on Neotropical dung beetle communities. However, increasing or maintaining yields while reducing agrochemical inputs will be important for conserving on‐farm biodiversity and the ecosystem services that dung beetles provide in livestock‐dominated landscapes.
Biodiversity change is uncoupled from species richness trends: Consequences for conservation and monitoring
Authors: Hillebrand Helmut , Blasius Bernd , Borer Elizabeth T. , Chase Jonathan M. , Downing John A. , Eriksson Britas Klemens , Filstrup Christopher T. , Harpole W. Stanley , Hodapp Dorothee , Larsen Stefano , Lewandowska Aleksandra M. , Seabloom Eric W. , Van de Waal Dedmer B. , Ryabov Alexey B. 
Published: June 2017

Abstract

Global concern about human impact on biological diversity has triggered an intense research agenda on drivers and consequences of biodiversity change in parallel with international policy seeking to conserve biodiversity and associated ecosystem functions. Quantifying the trends in biodiversity is far from trivial, however, as recently documented by meta‐analyses, which report little if any net change in local species richness through time.

Here, we summarise several limitations of species richness as a metric of biodiversity change and show that the expectation of directional species richness trends under changing conditions is invalid. Instead, we illustrate how a set of species turnover indices provide more information content regarding temporal trends in biodiversity, as they reflect how dominance and identity shift in communities over time.

We apply these metrics to three monitoring datasets representing different ecosystem types. In all datasets, nearly complete species turnover occurred, but this was disconnected from any species richness trends. Instead, turnover was strongly influenced by changes in species presence (identities) and dominance (abundances). We further show that these metrics can detect phases of strong compositional shifts in monitoring data and thus identify a different aspect of biodiversity change decoupled from species richness.

Synthesis and applications: Temporal trends in species richness are insufficient to capture key changes in biodiversity in changing environments. In fact, reductions in environmental quality can lead to transient increases in species richness if immigration or extinction has different temporal dynamics. Thus, biodiversity monitoring programmes need to go beyond analyses of trends in richness in favour of more meaningful assessments of biodiversity change.
A dual role for farmlands: food security and pollinator conservation
Authors: Burkle Laura A. , Delphia Casey M. , O'Neill Kevin M. 
Published: June 2017

Summary

We briefly review current understanding of wild pollinators and pollination services on farmlands.

We consider how concepts in plant ecology – community assembly and functional trait diversity ‐ may be applied to create diverse, wild pollinator communities across scales in agroecosystems.

We also make recommendations for best practices to enhance pollination services and create more sustainable food production systems under changing environmental conditions, including creating greater landscape connectivity, embracing pollinator dynamics, and providing incentives and other motivations to support these practices.

Synthesis. We highlight the opportunity for agricultural lands to serve a dual role for both food production and pollinator conservation, and conclude by posing unanswered questions and top priorities for future studies.
Conditions on Iterative Rounding Harmony in Oroqen
Authors: Dresher B. Elan , Nevins Andrew 
Published: June 2017

AbstractIn this paper, we re‐examine the claim that Baiyinna Oroqen, a language of the Tungusic family with a largely predictable distribution of non‐high round vowels, requires a non‐iterative type of rounding harmony, by demonstrating instead the need for a clear distinction between stem‐internal morpheme structure constraints and suffixal vowel harmony. We also propose to revise what was thought to be a requirement that harmony donors must be anchored in two successive syllables; it is instead a restriction that copying of the harmonic feature must be from the closest non‐initial vowel.
ROMAN LAW AND THE TWO LANGUAGES IN JUSTINIAN'S EMPIRE
Authors: CORCORAN SIMON 
Published: June 2017

Abstract
This paper, reflecting Fergus Millar's work on linguistic and cultural diversity in the Roman empire, surveys the evolving relationship of Latin and Greek as languages for Roman law. Normative texts remained predominantly Latin until the completion of Justinian's codification (534), even though that was a genuinely bilingual product. However, following the already existing pattern in the Greek east, a vast corpus of Greek materials was then quickly created to teach the codification in the official law schools. Designed to aid engagement with the source-texts, these ended up superseding them. Roman legal Greek, a mixture of Latin terminology plus standardized Greek vocabulary, became stabilized. After 534, new legislation was most often in Greek, necessitating parallel Latin materials to help Latin-speaking students, although sixth-century collections of Novels (‘new laws’) were still bilingual. In practice, however, in most of Justinian's empire, a lawyer (such as Dioscorus of Aphrodito) could function with limited Latin. Soon Roman law would bifurcate into two monolingual traditions, Greek in the east, Latin in the west.
Intrathecal dexamethasone vs. meperidine for prevention of shivering during transurethral prostatectomy: a randomized controlled trial
Authors: Moeen S. M. , Moeen A. M. 
Published: June 2017

BackgroundShivering is a common complication after spinal anesthesia. Also, during transurethral prostatectomy a large amount of irrigating fluids is used which may cause hypothermia and shivering. We hypothesized that intrathecal dexamethasone could effectively attenuate post‐spinal shivering following transurethral prostatectomy as intrathecal meperidine.MethodsNinety male patients, ASA II‐III, 50–75 years old were included in this prospective and randomized double‐blind study. Patients were divided into three equal groups; Group D received 8 mg dexamethasone, Group M received 0.2 mg/kg meperidine, and Group C received 2 ml of normal saline, each in addition to intrathecal hyperbaric bupivacaine 0.5%. Shivering incidence, intensity and recurrence, dose of IV meperidine required to treat shivering, and adverse events were recorded for 150 min after the start of spinal anesthesia.ResultsThe number of patients with shivering was higher in Group C (13) than in Group D (2) and Group M (3) with no differences between Group D and M; P = 0.001. Intensity and recurrence of shivering and dose of IV meperidine used to treat shivering were higher in Group C compared to Group D and Group M; P = 0.01, P = 0.064, and P = 0.004, respectively. Adverse events were not different between groups except sedation and pruritus which occurred only in Group M compared to Group D and Group C; P = 0.005 and P = 0.001, respectively.ConclusionIntrathecal dexamethasone was as effective as intrathecal meperidine in attenuation of shivering compared to placebo in patients scheduled for prostate surgery under spinal anesthesia with less adverse events.
Delivery parameters, neonatal parameters and incidence of urinary incontinence six months postpartum: a cohort study
Authors: Wesnes Stian Langeland , Hannestad Yngvild , Rortveit Guri 
Published: June 2017

AbstractIntroductionContradictory results have been reported regarding most delivery parameters as risk factors for urinary incontinence. We investigated the association between the incidence of urinary incontinence six months postpartum and single obstetric risk factors as well as combinations of risk factors.Material and methodsThis study was based on the Norwegian Mother and Child Cohort Study, conducted by the Norwegian Institute of Public Health during 1998–2008. This substudy was based on 7561 primiparous women who were continent before and during pregnancy. Data were obtained from questionnaires answered at weeks 15 and 30 of pregnancy and six months postpartum. Data were linked to the Medical Birth Registry of Norway. Single and combined delivery‐ and neonatal parameters were analyzed by logistic regression analyses.ResultsBirthweight was associated with significantly higher risk of urinary incontinence six months postpartum [3541–4180 g: odds ratio (OR) 1.4, 95% confidence interval (CI) 1.2–1.6; >4180 g: OR 1.6, 95% CI 1.2–2.0]. Fetal presentation, obstetric anal sphincter injuries, episiotomy and epidural analgesia were not significantly associated with increased risk of urinary incontinence. The following combinations of risk factors among women delivering by spontaneous vaginal delivery increased the risk of urinary incontinence six months postpartum; birthweight ≥3540 g and ≥36 cm head circumference; birthweight ≥3540 g and forceps, birthweight ≥3540 g and episiotomy; and ≥36 cm head circumference and episiotomy.ConclusionSome combinations of delivery parameters and neonatal parameters seem to act together and may increase the risk of incidence of urinary incontinence six months postpartum in a synergetic way.