bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat-Net: Segmentation of habitat images using deep learning
Authors: Abrams Jesse F. , Vashishtha Anand , Wong Seth T. , Nguyen An , Mohamed Azlan , Wieser Sebastian , Kuijper Arjan , Wilting Andreas , Mukhopadhyay Anirban 
Published: November 2018

ABSTRACTUnderstanding environmental factors that influence forest health, as well as the occurrence and abundance of wildlife, is a central topic in forestry and ecology. However, the manual processing of field habitat data is time-consuming and months are often needed to progress from data collection to data interpretation. Computer-assisted tools, such as deep-learning applications can significantly shortening the time to process the data while maintaining a high level of accuracy. Here, we propose Habitat-Net: a novel method based on Convolutional Neural Networks (CNN) to segment habitat images of tropical rainforests. Habitat-Net takes color images as input and after multiple layers of convolution and deconvolution, produces a binary segmentation of the input image. We worked on two different types of habitat datasets that are widely used in ecological studies to characterize the forest conditions: canopy closure and understory vegetation. We trained the model with 800 canopy images and 700 understory images separately and then used 149 canopy and 172 understory images to test the performance of Habitat-Net. We compared the performance of Habitat-Net with a simple threshold based method, a manual processing by a second researcher and a CNN approach called U-Net upon which Habitat-Net is based. Habitat-Net, U-Net and simple thresholding reduced total processing time to milliseconds per image, compared to 45 seconds per image for manual processing. However, the higher mean Dice coefficient of Habitat-Net (0.94 for canopy and 0.95 for understory) indicates that accuracy of Habitat-Net is higher than that of both the simple thresholding (0.64, 0.83) and U-Net (0.89, 0.94). Habitat-Net will be of great relevance for ecologists and foresters, who need to monitor changes in their forest structures. The automated workflow not only reduces the time, it also standardizes the analytical pipeline and, thus, reduces the degree of uncertainty that would be introduced by manual processing of images by different people (either over time or between study sites). Furthermore, it provides the opportunity to collect and process more images from the field, which might increase the accuracy of the method. Although datasets from other habitats might need an annotated dataset to first train the model, the overall time required to process habitat photos will be reduced, particularly for large projects.
Anin vivoknockdown strategy reveals multiple functions for circMbl
Authors: Pamudurti Nagarjuna Reddy , Konakondla-Jacob Vinay Vikas , Krishnamoorthy Aishwarya , Ashwal-Fluss Reut , Bartok Osnat , Wüst Stas , Seitz Katerina , Maya Roni , Lerner Noam , Patop Ines Lucia , Rizzoli Silvio , Beautus Tsevi , Kadener Sebastian 
Published: November 2018

ABSTRACTCircular RNAs (circRNAs) are highly abundant and evolutionary conserved RNAs of mostly unknown functions. circRNAs are enriched in the brain and accumulate with age in flies, worms and mice. Despite their abundance, little is known about their functions, especially in the context of whole organisms. Here we report the development and use of shRNAs to knock down and study the function of circMbl, the most abundant circRNA inDrosophila.This circRNA is highly conserved through evolution and is generated from the locus of the essential splicing factormuscleblind(mbl). Briefly, we generated flies in which circMbl is reduced more than 90% without measurable off-target effects in the hosting gene as well as in other RNAs. These flies display specific defects that suggest roles of circMbl in muscle and neural tissues during development and in adult flies. More specifically, whole organism downregulation of circMbl leads to male developmental lethality, altered gene expression, behavioral defects, wing posture- and flight defects. Moreover, these phenotypes are recapitulated by a second shRNA targeting circMbl. Importantly, knockdown and overexpression of circMbl affect mostly the same genes but in the opposite direction. Last but not least, downregulation of circMbl in the fly central nervous system caused abnormal synaptic function. Together, our results demonstrate the functionality of circMbl at the organismal level likely by acting in multiple tissues. Moreover, here we provide the first proof of functionality of circRNAs inDrosophilaas well as a methodological approach that enables the comprehensive study of circRNAsin vivo.SIGNIFICANCE STATEMENTCircular RNAs (circRNAs) are highly abundant and evolutionary conserved RNAs of mostly unknown functions. Here we report the development and use of a shRNA-based system to knockdown specific circRNAsin vivo. We generated flies in which circMbl, the most abundant circRNA is reduced more than 90% without measurable off-target effects. These flies display male developmental lethality, altered gene expression, behavioral defects, wing posture- and flight defects. These phenotypes are recapitulated by a second shRNA targeting circMbl. Moreover, downregulation of circMbl in the fly central nervous system caused abnormal synaptic function. Together, our results demonstrate the functionality of circMbl at the organismal level and provide a methodological approach that enables the comprehensive study of circRNAsin vivo.
Self-agency built with sensorimotor processing: Decoding self-other action attribution in the human brain
Authors: Ohata Ryu , Asai Tomohisa , Kadota Hiroshi , Shigemasu Hiroaki , Ogawa Kenji , Imamizu Hiroshi 
Published: November 2018

AbstractA sense of agency can be defined as a subjective experience that I am the one who is causing or generating an action. Several brain regions have been proposed as neural substrates of the subjective experience; however, how the information is processed and organized by each region to achieve the sense of agency still remains unclear. In this study, we have clarified the neural representations corresponding to three processes namely, sensorimotor error, feeling of agency, and judgment of agency. Specifically, we found that the widespread sensorimotor areas represent sensorimotor error information. The right inferior parietal lobe represents the information solely on self-/other-attribution even during movements, which corresponds to the feeling of agency. Finally, the right inferior frontal gyrus shows a distinct representation between self- and other-attribution immediately before reporting the judgment on the movement attribution. These results suggest that the brain builds a sense of agency by developing distinct types of information each corresponding to the three processes with the passage of time.
A Toolbox of IgG Subclass-Switched Recombinant Monoclonal Antibodies for Enhanced Multiplex Immunolabeling of Brain
Authors: Andrews Nicolas P. , Boeckman Justin X. , Manning Colleen F. , Nguyen Joe T. , Bechtold Hannah , Dumitras Camelia , Gong Belvin , Nguyen Kimberly , List Deborah van der , Murray Karl D. , Engebrecht JoAnne , Trimmer James S. 
Published: November 2018

AbstractGenerating recombinant monoclonal antibodies (R-mAbs) from mAb-producing hybridomas offers numerous advantages that increase the effectiveness, reproducibility, and transparent reporting of research. We report here the generation of a novel resource in the form of a library of recombinant R-mAbs validated for neuroscience research. We cloned immunoglobulin G (IgG) variable domains from cryopreserved hybridoma cells and input them into an integrated pipeline for expression and validation of functional R-mAbs. To improve efficiency over standard protocols, we eliminated aberrant Sp2/0-Ag14 hybridoma-derived variable light transcripts using restriction enzyme trea™ent. Further, we engineered a plasmid backbone that allows for switching of the IgG subclasses without altering target binding specificity to generate R-mAbs useful in simultaneous multiplex labeling experiments not previously possible. The method was also employed to rescue IgG variable sequences and generate functional R-mAbs from a non-viable cryopreserved hybridoma. All R-mAb sequences and plasmids will be archived and disseminated from open source suppliers.
The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells
Authors: Ratzan Wil , Rayaprolu Vamseedhar , Killian Scott E. , Bradley Roger , Kohout Susy C. 
Published: November 2018

AbstractVoltage-sensing phosphatases (VSPs) are transmembrane proteins that couple changes in membrane potential to hydrolysis of inositol signaling lipids. VSPs catalyze the dephosphorylation of phosphatidylinositol phosphates (PIPs) that regulate diverse aspects of cell membrane physiology including cell division, growth and migration. VSPs are highly conserved among chordates, and their RNA transcripts have been detected in the adult and embryonic stages of frogs, fish, chickens, mice and humans. However, the subcellular localization and biological function of VSP remains unknown. Using reverse transcriptase-PCR (RT-PCR), we show that both Xenopus laevis VSP (Xl-VSP1 and Xl-VSP2) mRNAs are expressed in early embryos, suggesting that both Xl-VSPs are involved in early tadpole development. To understand which embryonic tissues express Xl-VSP mRNA, we used in situ hybridization (ISH) and found Xl-VSP mRNA in both the brain and kidney of NF stage 32-36 embryos. By Western blot analysis with a VSP antibody, we show increasing levels of Xl-VSP protein in the developing embryo, and by immunohistochemistry (IHC), we demonstrate that Xl-VSP protein is specifically localized to the apical membrane of both embryonic and adult kidney tubules. We further characterized the catalytic activity of both Xl-VSP homologs and found that while Xl-VSP1 catalyzes 3- and 5-phosphate removal, Xl-VSP2 is a less efficient 3-phosphatase with different substrate specificity. Our results suggest that Xl-VSP1 and Xl-VSP2 serve different functional roles and that VSPs are an integral component of voltage-dependent PIP signaling pathways during vertebrate kidney tubule development and function.
Trynity controls epidermal barrier function and respiratory tube maturation inDrosophilaby modulating apical extracellular matrix nano-patterning
Authors: Itakura Yuki , Inagaki Sachi , Wada Housei , Hayashi Shigeo 
Published: November 2018

AbstractThe outer surface of insects is covered by the cuticle, which is derived from the apical extracellular matrix (aECM). The aECM is secreted by epidermal cells during embryogenesis. The aECM exhibits large variations in structure, function, and constituent molecules, reflecting the enormous diversity in insect appearances. To investigate the molecular principles of aECM organization and function, here we studied the role of a conserved aECM protein, the ZP domain protein Trynity, inDrosophila melanogaster. We first identifiedtrynityas an essential gene for epidermal barrier function.trynitymutation caused disintegration of the outermost envelope layer of the cuticle, resulting in small- molecule leakage and in growth and molting defects. In addition, the tracheal tubules oftrynitymutants showed defects in pore-like structures of the cuticle, and the mutant tracheal cells failed to absorb luminal proteins and liquid. Our findings indicated thattrynityplays essential roles in organizing nano-level structures in the envelope layer of the cuticle that both restrict molecular trafficking through the epidermis and promote the massive absorption pulse in the trachea.Summary StatementThe zona pellucida domain protein Trynity controls the structural organization and function of the apical extracellular matrix in the epidermis and trachea ofDrosophila.
qRT-PCR/High Resolution Melting Analyses detected polymorphisms of HSP-70 gene in Zebu cattle
Authors: Onasanya G.O. , Okpeku M. , Thiruvekander K.A. , Sreekumar C. , Tirumurugaan G.K. , Msalya G.M. , anni T. M. S , Olowofeso O. , Fafiolu A.O. , deleke M.A. A , Ikeobi C.O.N. 
Published: November 2018

AbstractConcerns over environmental heat stress have increased in recent years with the realization of global warming effects on environment and subsequently on animal production. Heat stress indicators help to monitor adaptability and survivability of livestock to thermal assault; a consequent effect of global warming. Heat shock proteins (HSPs) are highly conserved and are classified into six groups. Heat shock protein (HSP) 70 gene is a member of molecular chaperone, known to be highly expressed under stressful environmental and physiological conditions. In this study, we used a one-step qReal-Time PCR, followed by high-resolution melting analyses (HRMA) for detection and identification of polymorphism of HSP-70 gene in four extant cattle breeds of (White Fulani, Sokoto Gudali, Red Bororo and Ambala). qRT-PCR/HRMA-based assay detected twelve (12) genetic variant groups of HSP-70 gene. Ambala breed of Nigerian Zebu cattle had the highest number (7) of genetic variants of HSP-70 gene followed by Red Bororo breed (6 genetic variants), Sokoto Gudali breed had 5 genetic variants while White Fulani breed had the least (4 genetic variants) number of genetic variants in the population of Nigerian Zebu cattle breeds examined. We therefore hypothesize that the detected variant groups can be interrogated for their possible effects on thermo-tolerance performance of zebu cattle bred under thermal assaults of tropical conditions.
Human online adaptation to changes in prior probability
Authors: Norton Elyse H. , Acerbi Luigi , Ma Wei Ji , Landy Michael S. 
Published: November 2018

AbstractOptimal sensory decision-making requires the combination of uncertain sensory signals with prior expectations. The effect of prior probability is often described as a shift in the decision criterion. Can observers track sudden changes in probability? To answer this question, we used a change-point detection paradigm that is frequently used to examine behavior in changing environments. In a pair of orientation-categorization tasks, we investigated the effects of changing probabilities on decision-making. In both tasks, category probability was updated using a sample-and-hold procedure. We developed an ideal Bayesian change-point detection model in which the observer marginalizes over both the current run length (i.e., time since last change) and the current category probability. We compared this model to various alternative models that correspond to different strategies – from approximately Bayesian to simple heuristics – that the observers may have adopted to update their beliefs about probabilities. We find that probability is estimated following an exponential averaging model with a bias towards equal priors, consistent with a conservative bias. The mechanism underlying change of decision criterion is a combination of on-line estimation of prior probability and a stable, long-term equal-probability prior, thus operating at two very different timescales.Author summaryWe demonstrate how people learn and adapt to changes to the probability of occurrence of one of two categories on decision-making under uncertainty. The study combined psychophysical behavioral tasks with computational modeling. We used two behavioral tasks: a typical forced-choice categorization task as well as one in which the observer specified the decision criterion to use on each trial before the stimulus was displayed. We formulated an ideal Bayesian change-point detection model and compared it to several alternative models. We found that the data are best fit by a model that estimates category probability based on recently observed exemplars with a bias towards equal probability. Our results suggest that the brain takes multiple relevant time scales into account when setting category expectations.
The impact of cultural values and economic constraints on tourism businesses’ ethical practices
Authors: Skinner Heather 
Published: November 2018

Purpose
Anecdotal evidence suggests that in times of economic constraints particularly in countries such as Greece that have long been stereotyped as corrupt, business practices amongst small- and medium-sized organisations that make up the majority of these nations’ tourism operators may become less than ethical or legal. The purpose of this paper is to explore these issues empirically in order to understand the impact of both cultural values and economic constraints on tourism businesses’ practices.

Design/methodology/approach
An exploratory case study using mixed methods has been adopted. Quantitative data were gathered from tourism business owners, managers and employees via questionnaires to establish the nature and scope of various unethical, illegal or immoral practices. Qualitative data were gathered to explore the ways these issues are considered and enacted.

Findings
Results show that there are many unethical and illegal practices that have been witnessed first-hand. Businesses’ attempts at acting in an ethical and socially responsible manner tend to be affected by not only cultural issues, but also economic constraints, yet there remains a desire to act in a way that does not impact negatively on tourists or on the local society and environment.

Originality/value
This research fills a gap in the literature relating to the ethical stance and practices of tourism entrepreneurs. It also presents an original conceptualisation of these issues in light of their location within the extant literature on ethics, corporate social responsibility and both sustainable and responsible tourism.
Simulation and measurement study of metro wheel wear based on the Archard model
Authors: Zhu AiHua , Yang Si , Li Qiang , Yang JianWei , Li Xi , Xie YiDong 
Published: November 2018

PurposeThe purpose of this paper is to study the wear evolution of metro wheels under the conditions of different track sequences, track composition and vehicle load and then to predict wheel wear and to guide its maintenance.MethodologyBy using the SIMPACK and MATLAB software, numerical simulation analysis of metro wheel wear is carried out based on Hertz theory, the FASTSIM algorithm and the Archard model. First of all, the vehicle dynamics model is established to calculate the motion relationship and external forces of wheel-rail in the SIMPACK software. Then, the normal force of wheel-rail is solved based on Hertz theory, and the tangential force of wheel-rail is calculated based on the FASTSIM algorithm through the MATLAB software. Next, in the MATLAB software, the wheel wear is calculated based on the Archard model, and a new wheel profile is obtained. Finally, the new wheel profile is re-input into the vehicle system dynamics model in the SIMPACK software to carry out cyclic calculation of wear.FindingsThe results show that the setting order of different curves has an obvious influence on wear when the proportion of the straight track and the curve is fixed. With the increase in running mileage, the severe wear zone is shifted from tread to flange root under the condition of the sequence-type track, but the wheel wear distribution is basically stable for the unit-type track, and their wear growth rates become closer. In the tracks with different straight-curved ratio, the more proportion the curved tracks occupy, the closer the severe wear zone is shifted to flange root. At the same time, an increase in weight of the vehicle load will aggravate the wheel wear, but it will not change the distribution of wheel wear. Compared with the measured data of one city B type metro in China, the numerical simulation results of wheel wear are nearly the same with the measured data.Practical implicationsThese results will be helpful for metro tracks planning and can predict the trend of wheel wear, which has significant importance for the vehicle to do the repair operation. At the same time, the security risks of the vehicle are decreased economically and effectively.Originality/valueAt present, many scholars have studied the influence of metro tracks on wheel wear, but mainly focused on a straight line or a certain radius curve and neglected the influence of track sequence and track composition. This study is the first to examine the influence of track sequence on metro wheel wear by comparing the sequence-type track and unit-type track. The results show that the track sequence has a great influence on the wear distribution. At the same time, the influence of track composition on wheel wear is studied by comparing different straight-curve ratio tracks; therefore, wheel wear can be predicted integrally under different track conditions.
Ownership feature and firm performance via corporate innovation performance
Authors: Nguyen Dung , Nguyen Hoai , Nguyen Kien S. 
Published: November 2018

PurposeThe purpose of this paper is to investigate the simultaneous relationship among ownership concentration, innovation and firm performance of the small- and medium-sized enterprises (SMEs) in Vietnam during the 2011–2015. By employing a Conditional Mixed Process (CMP) model, the findings show that: there is no impact of ownership concentration on innovation, but it has a positive impact on sales growth; innovation positively affects firm performance; and there exists a positively reverse causality from sales growth to innovation.Design/methodology/approachIn this study, the authors propose the adaption of CMP model (Roodman, 2011). The nature of the first stage dependent variable – Innovation – is a binary one while the dependent variable Performance is continuous. Therefore, a model that can adapt the binary nature of the dependent variable and perform the estimation of a system of equations such as CMP model is preferred. The CMP framework is substantially that of seemingly unrelated regression, but with application in a larger scope. This approach is based on a “simulated maximum likelihood method” suggested by Geweke–Hajivassiliou–Keane algorithm.FindingsBy applying CMP method, this study examines the simultaneous relationship among ownership concentration, innovation and firm performance of the SMEs in Vietnam from 2011 to 2015. The findings indicate that: there is no impact of ownership concentration on innovation, but it has a positive impact on sales growth; innovation positively affects firm performance; and there exists a positively reverse causality from sales growth to innovation.Research limitations/implicationsIn spite of the efforts to explore the simultaneous relationship among ownership concentration, innovation and firm performance of the SMEs in Vietnam, the study still has some limitations which are promising further research directions. First, the SME surveys by Central Institute for Economic Management do not have much information about other types of ownership including state-owned and foreign ownership. Therefore, possible further studies with richer data sets may explore the impacts of different types of ownership on firm innovation and performance. Second, other types of innovation such as organizational innovation, marketing innovation can also be investigated in further studies in a richer data set for the case of Vietnam SMEs.Originality/valueThe findings show that: there is no impact of ownership concentration on innovation, but it has a positive impact on sales growth; innovation positively affects firm performance; and there exists a positively reverse causality from sales growth to innovation. The policy implications insist on facilitating SMEs with easier access to capital via loans with preferred interest or trust loans without collateral, training programs for the labor force and SME leaders, and reduction of unnecessary administrative procedure.