bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precise tuning of cortical contractility regulates cell shape during cytokinesis
Authors: Taneja Nilay , Bersi Matthew R. , Baillargeon Sophie , Fenix Aidan M. , Cooper James A. , Ohi Ryoma , Gama Vivian , Merryman W. David , Burnette Dylan T. 
Published: May 2019

ABSTRACTThe mechanical properties of the cellular cortex regulate shape changes during cell division, cell migration and tissue morphogenesis. During cell division, contractile force generated by the molecular motor myosin II (MII) at the equatorial cortex drives cleavage furrow ingression. Cleavage furrow ingression in turn increases stresses at the polar cortex, where contractility must be regulated to maintain cell shape during cytokinesis. How polar cortex contractility controls cell shape is poorly understood. We show a balance between MII paralogs allows a fine-tuning of cortex tension at the polar cortex to maintain cell shape during cytokinesis, with MIIA driving cleavage furrow ingression and bleb formation, and MIIB serving as a stabilizing motor and mediating completion of cytokinesis. As the majority of non-muscle contractile systems are cortical, this tuning mechanism will likely be applicable to numerous processes driven by MII contractility.
Determining sufficient sequencing depth in RNA-Seq differential expression studies
Authors: Bass Andrew J. , Robinson David G. , Storey John D. 
Published: May 2019

AbstractRNA-Seq studies require a sufficient read depth to detect biologically important genes. Sequencing below this threshold will reduce statistical power while sequencing above will provide only marginal improvements in power and incur unnecessary sequencing costs. Although existing methodologies can help assess whether there is sufficient read depth, they are unable to guide how many additional reads should be sequenced to reach this threshold. We provide a new method called superSeq that models the relationship between statistical power and read depth. We apply the superSeq framework to 393 RNA-Seq experiments (1,021 total contrasts) in the Expression Atlas and find the model accurately predicts the increase in statistical power gained by increasing the read depth. Based on our analysis, we find that most published studies (> 70%) are undersequenced, i.e., their statistical power can be improved by increasing the sequencing read depth. In addition, the extent of saturation is highly dependent on statistical methodology: only 9.5%, 29.5%, and 26.6% of contrasts are saturated when using DESeq2, edgeR, and limma, respectively. Finally, we also find that there is no clear minimum per-transcript read depth to guarantee saturation for an entire technology. Therefore, our framework not only delineates key differences among methods and their impact on determining saturation, but will also be needed even as technology improves and the read depth of experiments increases. Researchers can thus use superSeq to calculate the read depth to achieve required statistical power while avoiding unnecessary sequencing costs.
Stable Species Boundaries Despite Ten Million Years of Hybridization in Tropical Eels
Authors: Barth Julia M. I. , Gubili Chrysoula , Matschiner Michael , Tørresen Ole K. , Watanabe Shun , Egger Bernd , Han Yu-San , Feunteun Eric , Sommaruga Ruben , Jehle Robert , Schabetsberger Robert 
Published: May 2019

AbstractGenomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genusAnguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.
An early phase of instructive plasticity in visual cortex before the typical onset of sensory experience
Authors: Roy Arani , Wang Shen , Meschede-Krasa Benyamin , Breffle Jordan , Van Hooser Stephen D. 
Published: May 2019

AbstractWhile early experience with moving stimuli is necessary for the development of direction selectivity in visual cortex of carnivores, it is unclear whether experience exerts a permissive or instructive influence. To test if the specific parameters of the experienced stimuli could instructively sculpt the emergent responses, visually naive ferrets were exposed to several hours of experience with unusual spatiotemporal patterns. In the most immature ferrets, cortical neurons developed selectivity to these patterns, indicating an instructive influence. In animals that were 1-10 days more mature, exposure to the same patterns led to a developmentally-typical increase in direction selectivity. We conclude that visual development progresses via an early phase of instructive plasticity, when the specific patterns of neural activity shape the specific parameters of the emerging response properties, followed by a late phase of permissive maturation, when sensory-driven activity merely serves to enhance the response properties already seeded in cortical circuits.
Electrocorticographic dissociation of alpha and beta rhythmic activity in the human sensorimotor system
Authors: Stolk Arjen , Brinkman Loek , Vansteensel Mariska J. , Aarnoutse Erik , Leijten Frans S. S. , Dijkerman Chris H. , Knight Robert T. , de Lange Floris P. , Toni Ivan 
Published: May 2019

AbstractThis study uses electrocorticography in humans to assess how alpha- and beta-band rhythms modulate excitability of the sensorimotor cortex during movement selection, as indexed through a psychophysically-controlled movement imagery task. Both rhythms displayed effector-specific modulations, tracked spectral markers of action potentials in the local neuronal population, and showed spatially systematic phase relationships (traveling waves). Yet, alpha- and beta-band rhythms differed in their anatomical and functional properties, were weakly correlated, and traveled along opposite directions across the sensorimotor cortex. Increased alpha-band power in the somatosensory cortex ipsilateral to the selected arm was associated with spatially-unspecific inhibition. Decreased beta-band power over contralateral motor cortex was associated with a focal shift from relative inhibition to excitation. These observations indicate the relevance of both inhibition and disinhibition mechanisms for precise spatiotemporal coordination of neuronal populations during movement selection. Those mechanisms are implemented through the substantially different neurophysiological properties of sensorimotor alpha- and beta-band rhythms.
A structural model of the human serotonin transporter in an outward-occluded state
Authors: Hellsberg Eva , Ecker Gerhard F. , Stary-Weinzinger Anna , Forrest Lucy R. 
Published: May 2019

AbstractThe human serotonin transporter hSERT facilitates the reuptake of its endogenous substrate serotonin from the synaptic cleft into presynaptic neurons after signaling. Reuptake regulates the availability of this neurotransmitter and therefore hSERT plays an important role in balancing human mood conditions. In 2016, the first 3D structures of this membrane transporter were reported in an inhibitor-bound, outward-open conformation. These structures revealed valuable information about interactions of hSERT with antidepressant drugs. Nevertheless, the question remains how serotonin facilitates the specific conformational changes that open and close pathways from the synapse and to the cytoplasm as required for transport. Here, we present a serotonin-bound homology model of hSERT in an outward-occluded state, a key intermediate in the physiological cycle, in which the interactions with the substrate are likely to be optimal. Our approach uses two template structures and includes careful refinement and comprehensive computational validation. According to microsecond-long molecular dynamics simulations, this model exhibits interactions between the gating residues in the extracellular pathway, and these interactions differ from those in an outward-open conformation of hSERT bound to serotonin. Moreover, we predict several features of this state by monitoring the intracellular gating residues, the extent of hydration, and, most importantly, protein-ligand interactions in the central binding site. The results illustrate common and distinct characteristics of these two transporter states and provide a starting point for future investigations of the transport mechanism in hSERT.
Simple methods to obtain a food listing and portion size distribution estimates for use in semi-quantitative dietary assessment methods
Authors: Hotz Christine , Abdelrahman Lubowa 
Published: May 2019

AbstractSemi-quantitative dietary assessment methods are frequently used in low income countries, and the use of photographic series for portion size estimation is gaining popularity. However, when adequate data on commonly consumed foods and portion sizes are not available to design these tools, alternative data sources are needed. This study aimed to develop and test methods to: (i) identify foods likely to be consumed in a study population in rural Uganda, and; (ii) to derive distributions of portion sizes for common foods and dishes. A process was designed to derive detailed food and recipe lists using guided group interviews with women from the survey population, including a ranking for the likelihood of foods being consumed. A rapid recall method to estimate portion sizes using direct weight by a representative sample of the survey population was designed and implemented. Results were compared to data from a 24 hour dietary recall. Of the 82 food items reported in the 24 hour recall survey, 87% were among those ranked with a high or medium likelihood of being consumed and accounted for 95% of kilocalories. Of the most frequently reported foods in the 24 hour recall, portion sizes for many (15/25), but not all foods did not differ significantly (p<0.05) from those in the portion size estimation method. The percent of portion sizes reported in the 24 hour recall between the 5th and 95th percentiles determined by the portion size distribution estimation method ranged from a low of 18% up to 100%. In conclusion, a simple food listing and ranking method effectively identified foods most likely to occur in a dietary survey. A simple method to obtain reliable portion size distributions was effective for many foods, while the approach for others should be modified. These methods are an improvement on those in current use.
Maternal Obesity-Induced Endoplasmic Reticulum Stress Causes Metabolic Alterations and Abnormal Hypothalamic Development in the Offspring
Authors: Park Soyoung , Jang Alice , Bouret Sebastien G. 
Published: May 2019

AbstractThe steady increase in the prevalence obesity and associated type II diabetes is a major health concern, particularly among children. Maternal obesity represents a risk factor that contributes to metabolic perturbations in the offspring. Endoplasmic reticulum (ER) stress has emerged as a critical mechanism involved in leptin resistance and type 2 diabetes in adult individuals. Here, we used a mouse model of maternal obesity to investigate the importance of early life ER stress in the nutritional programming of metabolic disease. Offspring of obese dams displayed increased body weight, adiposity, food intake and developed glucose intolerance. Moreover, maternal obesity disrupted the development of melanocortin circuits associated with neonatal hyperleptinemia and leptin resistance. ER stress-related genes were upregulated in the hypothalamus of neonates born to obese mothers and neonatal treatment with the ER stress-relieving drug tauroursodeoxycholic acid improved metabolic and neurodevelopmental deficits and reverses leptin resistance in neonates born to obese dams.
Topological data analysis of vascular disease: A theoretical framework
Authors: Nicponski John , Jung Jae-Hun 
Published: May 2019

AbstractVascular disease is a leading cause of death world wide and therefore the treatment thereof is critical. Understanding and classifying the types and levels of stenosis can lead to more accurate and better treatment of vascular disease. Some clinical techniques to measure stenosis from real patient data are invasive or of low accuracy.In this paper, we propose a new methodology, which can serve as a supplementary way of diagnosis to existing methods, to measure the degree of vascular disease using topological data analysis. We first proposed the critical failure value, which is an application of the 1-dimensional homology group to stenotic vessels as a generalization of the percent stenosis. We demonstrated that one can take important geometric data including size information from the persistent homology of a topological space. We conjecture that we may use persistent homology as a general tool to measure stenosis levels for many different types of stenotic vessels.We also proposed the spherical projection method, which is meant to allow for future classification of different types and levels of stenosis. We showed empirically using the spectral approximation of different vasculatures that this projection could provide a new medical index that measures the degree of vascular disease. Such a new index is obtained by calculating the persistence of the 2-dimensional homology of flows. We showed that the spherical projection method can differentiate between different cases of flows and reveal hidden patterns about the underlying blood flow characteristics, that is not apparent in the raw data. We showed that persistent homology can be used in conjunction with this technique to classify levels of stenosis.The main interest of this paper is to focus on the theoretical development of the framework for the proposed method using a simple set of vascular data.
Corporate misconduct, trade credit and charitable donations: evidence from Chinese listed companies
Authors: Liu Zheming , Zeng Saixing , Xu Xiaodong , Lin Han , Ma Hanyang 
Published: May 2019

PurposeThe purpose of this paper is to investigate how revelations of corporate misconduct are associated with trade credit. Specifically, it investigates how this association varies in different regions, in different types of industries and in response to companies’ subsequent charitable donations.Design/methodology/approachThe authors empirically tested various hypotheses using a sample of 2,725 Chinese A-share listed companies from 2009 to 2014 based on signaling theory. Fixed effect models underpinned the methods used.FindingsThe authors found that corporate misconduct has a significant negative impact on an irresponsible company’s trade credit received and granted, and the negative impact is heterogeneous for different regions and industries. There is no evidence that charitable donations mitigate the effect on the trade credit of irresponsible companies following revelations of corporate misconduct.Practical implicationsThe results suggest that listed companies in China should obey national and local laws and regulations if they wish to avoid the risk of significant trade credit loss. If a company’s violation of these laws and regulations is disclosed, making charitable donations is not an effective strategy for safeguarding trade credit.Originality/valueThis study enriches understanding on the consequences of corporate misconduct and extends the literature on trade credit. It fills a research gap by identifying the impact of corporate misconduct on trade credit.
Effect of partially wet-surface condition on the performance of fin-tube heat exchanger
Authors: Payambarpour Seyed Abdolkarim , Alhuyi Nazari Mohammad , Ahmadi Mohammad Hossein , Chamkha Ali J. 
Published: May 2019

Purpose
This study aims to investigate heat and mass transfer in a one-row heat exchanger. The required equations are obtained based on two-dimensional model analysis in a cell of the heat exchanger. By using finite difference approach, the obtained equations are solved to determine distribution of temperature and the efficiency of the heat exchanger in the case of partially wet surface. In this research, Lewis Number as unity and water vapor saturation as parabolic are assumed. Obtained results show that increase in thermal conductivity fin leads to decreasing thermal resistance; therefore, temperature changes in radial from center to out of fin are reduced and efficiency of fin increases.

Design/methodology/approach
In this regard, fin material plays a significant role in fin efficiency. Changes in airflow also result in an efficiency increase by temperature and relative humidity, and efficiency is decreased by airflow velocity increase, and these changes are almost linear. Moreover, the fins with more wet surface are more sensitive to changes in fin dimensions and air flow characteristics, and it is a result of conjugate heat transfer mechanism, in which latent heat transfer in the fins with more wet surface has a significant role.

Findings
Thermal property and geometry of the fin under wet conditions play a more important role than the fin under dry conditions. Changes in airflow result in an efficiency increase by temperature and relative humidity, and efficiency is decreased by airflow velocity increase, and these changes are almost linear. Fins with more wet surface are more sensitive to changes in fin dimensions and air flow characteristics.

Originality/value
Effects of the temperature of water supply and mass flow rate were considered in the study. The results had good agreement with actual data.
Redesigning initial teacher’s education practices with learning scenarios
Authors: Pedro Ana , Piedade João , Matos João Filipe , Pedro Neuza 
Published: May 2019

PurposeThe construction of learning scenarios is a way to plan for teaching activities, promoting the development of skills related to problem solving, collaboration, critical thinking and creativity. Using learning scenarios as a lesson planning strategy becomes a powerful tool in initial teacher education. On the one hand, it mobilizes teaching-related scientific concepts, and on the other hand, it offers opportunities to think on innovative pedagogic approaches involving strategies and capacities essential for the future teacher. Research shows that teacher education programs within real school contexts enriched with digital technologies represent an important factor in increasing the quality of teachers’ preparation and their future professional practice. The paper aims to discuss these issues.Design/methodology/approachThe authors present the analysis of practice of design and implementation of learning scenarios in teachers’ initial education courses developed with students of teaching master degrees. Activity theory is used in the analysis of a case study of a student-teacher in Computer Science.FindingsThe results have been analyzed, contributing to the specification of the principles underlying the learning scenarios in initial teacher education.Research limitations/implicationsResults show the affordances and possibilities of using learning scenarios as structuring resources for the initial teacher education practice.Originality/valueTherefore, the use of learning scenarios brings a set of potentialities to teacher training given its prospective nature.
Improving public works’ value for money: a new procurement strategy
Authors: Marinelli Marina , Antoniou Fani 
Published: May 2019

Purpose
The purpose of this paper is to propose a new procurement strategy with the aim to achieve higher value for money (VFM) in public works delivery. Its main innovation lies in the possibility of optional submission of cost-efficient design variants by any interested contractor within the context of an open procedure. The final scope of works incorporates the variants approved, and all contractors are invited to submit a bid for the revised scope and budget.

Design/methodology/approach
This paper is a piece of applied research presenting the development of a new, cost-effective procurement strategy for public works, geared at the European Union (EU) legal framework. The strategy’s feature compilation has been based on comprehensive literature review while numerical data from a real world project were used to demonstrate its financial advantages.

Findings
The proposed strategy enables the delivery of the best value project at the lowest cost possible. This is achieved through ensuring high competition among competent contractors, improving the cost efficiency of technical solutions, discouraging future scope changes and establishing objectivity, fairness and transparency in the process of contract award.

Practical implications
The use of the proposed strategy results in public projects of enhanced VFM, reduced constructability issues and less scope changes during the construction stage.

Originality/value
The proposed strategy marks a new approach in procurement which enables the delivery of best VFM in public works. Therefore, it makes a valuable contribution towards the achievement of the overarching EU target for efficient public spending.
Cost overruns of public sector construction projects: a developing country perspective
Authors: Asiedu Richard Ohene , Adaku Ebenezer 
Published: May 2019

Purpose
Cost overrun of construction projects has been a key concern for all stakeholders of projects for many decades now. Many studies have been done in the past and continue to be done currently to understand the underlying causes of construction project cost overruns. However, the empirical evidence of the causes seem not be clear due to the silo approach in understanding the causes of construction project cost overruns. The purpose of this paper is to take the debate a step forward by providing an understanding of the causes of project cost overrun from a system’s perspective, especially from a less researched environment.

Design/methodology/approach
Data were collected and analysed from 131 respondents who were mainly involved in construction works in public procurement entities in Ghana. A two-staged approach was employed in collecting data from the respondents. The first stage involved an interview session with key informants in the construction industry in Ghana to ascertain the detailed causes of cost overrun of construction projects. The second stage focussed on the validation of these detailed factors by a wider stakeholder group through questionnaires. Factor analysis was employed to consolidate these detailed factors into major causes of construction project cost overruns.

Findings
The results show that there are primarily four major causes of most public sector construction projects cost overruns. These four major causes of cost overruns are poor contract planning and supervision; change orders; weak institutional and economic environment of projects and lack of effective coordination among the contracting parties.

Originality/value
The study provides more insights as to the critical and major factors that underpin public sector construction projects cost overruns and more importantly provides a basis for common treatment of the multiple risk factors engendering public sector construction projects cost overruns.