bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free-ranging dogs understand human intentions and adjust their behavioral responses accordingly
Authors: Bhattacharjee Debottam , Sau Shubhra , Bhadra Anindita 
Published: July 2018

ABSTRACTDomestic dogs (Canis lupus familiaris) are remarkably sensitive and responsive while interacting with humans. Pet dogs are known to have social skills and abilities to display situation-specific responses, but there is lack of information regarding free-ranging dogs which constitute majority of the world’s dog population. Free-ranging dogs found in most of the developing countries interact constantly with familiar and unfamiliar humans receiving both positive and negative behavior. Thus, understanding human intentions and subsequent behavioral adjustments are crucial for dogs that share habitats with humans. Here we subjected free-ranging dogs to different human social communicative cues (friendly and threatening – low and high), followed by a food provisioning phase and tested their responsiveness. Dogs exhibited higher proximity seeking behavior as a reaction to friendly gesture whereas, they were prompted to maintain distance depending on the impact of the threatening cues. Interestingly, only the high-impact threatening showed to have a persistent effect which also remained during the subsequent food provisioning phase. An elevated approach in the food provisioning phase elicited the dependency of free-ranging dogs on humans for sustenance. Our findings suggest that free-ranging dogs demonstrate behavioral plasticity on interacting with humans; which provides significant insights into the establishment of the dog-human relationship on streets.
The wheatSr22,Sr33,Sr35andSr45genes confer resistance against stem rust in barley
Authors: Asyraf Md. Hatta M. , Johnson Ryan , Matny Oadi , Smedley Mark A. , Yu Guotai , Chakraborty Soma , Bhatt Dhara , Xia Xiaodi , Arora Sanu , Steuernagel Burkhard , Richardson Terese , Mago Rohit , Lagudah Evans S. , Patron Nicola , Ayliffe Mick , Rouse Matthew N. , Harwood Wendy A. , Periyannan Sambasivam K. , Steffenson Brian J. , Wulff Brande B. H. 
Published: July 2018

SummaryIn the last 20 years, stem rust caused by the fungusPuccinia graminisf. sp.tritici(Pgt), has re-emerged as a major threat to wheat and barley cultivation in Africa and Europe. In contrast to wheat with 82 designated stem rust (Sr) resistance genes, barley’s genetic variation for stem rust resistance is very narrow with only seven resistance genes genetically identified. Of these, only one locus consisting of two genes is effective against Ug99, a strain ofPgtwhich emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheatSrgenes effective against Ug99.Sr22,Sr33,Sr35andSr45were transformed into barley cv. Golden Promise usingAgrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogenPuccinia hordei, indicating that the resistance conferred by these wheatSrgenes was specific forPgt. ClonedSrgenes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
Highly efficient scarless knock-in of reporter genes into human and mouse pluripotent stem cells via transient antibiotic selection
Authors: Sluch Valentin M. , Chamling Xitiz , Wenger Claire , Duan Yukan , Rice Dennis S. , Zack Donald J. 
Published: July 2018

AbstractPluripotent stem cells (PSCs) edited with genetic reporters are useful tools for differentiation analysis and for isolation of specific cell populations for study. Reporter integration into the genome is now commonly achieved by targeted DNA nuclease-enhanced homology directed repair (HDR). However, human PSCs are known to have a low frequency of gene knock-in (KI) by HDR, making reporter line generation an arduous process. Here, we report a methodology for scarless KI of large fluorescent reporter genes into PSCs by transient selection with puromycin or zeocin. With this method, we can perform targeted KI of a single reporter gene with up to 65% efficiency, as well as simultaneous KI of two reporter genes into different loci with up to 11% efficiency. Additionally, we demonstrate that this method also works in mouse PSCs.
Sulci of the canine brain: a review of terminology
Authors: Czeibert Kálmán , Piotti Patrizia , Petneházy Örs , Kubinyi Enikő 
Published: July 2018

AbstractOver the last decades there have been several publications of anatomical and neurological textbooks, which include descriptions about the dogs’ brain. However, the terminology used is inconsistent, partly due to individual differences in neocortical gyration and partly due to the common practice of adapting terms from human and murine anatomy. In order to identify such incongruences, in Study 1, we reviewed the existing literature and identified the common terms used as well as any discrepancies between textbooks. Three main forms of inconsistencies were found; a) the use of terms that are not included in the Nomina Anatomica Veterinaria (NAV), b) the inclusion of structures that are listed as not canine-specific, and c) the use of similar names to identify potentially different anatomical structures. To address these issues, in Study 2 we investigated the consistency in appearance of the cerebral sulci, performing a macroscopical examination on 79 canine brains obtained through the Canine Brain and Tissue Bank (CBTB). We then evaluated whether sulci on the frontal regions of brachycephalic breeds differed from those of mesocephalic and dolichocephalic groups, as frontal and olfactory regions are subjected to the most extreme modifications following the shortening of the skull. The statistical analysis showed no difference across the skull length types regarding the occurrence of these sulci, although furrows on the lateral side of the brain proved to be more stable than those on the medial side. In Study 3, we summarized the findings in accordance with the NAV to produce a definitive index of the terms that we recommend be used for each identified sulci. Such an index is beneficial for educational, clinical use, and research (e.g. neuroscience) purposes. The dog is emerging as a pioneering and exceptional model in comparative neuroscience, and therefore the implications for canine neuroscience research should not be underestimated.
HOPS-dependent endosomal fusion required for efficient cytosolic delivery of therapeutic peptides and small proteins
Authors: Steinauer Angela , LaRochelle Jonathan R. , Wissner Rebecca , Berry Samuel , Schepartz Alanna 
Published: July 2018

AbstractProtein therapeutics represent a significant and growing component of the modern pharmacopeia, but their potential to treat human disease is limited because most proteins fail to traffic across biological membranes. Recently, we discovered that cell-permeant miniature proteins (CPMPs) containing a precisely defined, penta-arginine motif traffic readily to the cytosol and nucleus with efficiencies that rival those of hydrocarbon-stapled peptides active in animals and man. Like many cell-penetrating peptides (CPPs), CPMPs enter the endocytic pathway; the difference is that CPMPs are released efficiently from endosomes while other CPPs are not. Here, we seek to understand how CPMPs traffic from endosomes into the cytosol and what factors contribute to the efficiency of endosomal release. First, using two complementary cell-based assays, we exclude endosomal rupture as the primary means of endosomal escape. Next, using a broad spectrum of techniques, including an RNA interference (RNAi) screen, fluorescence correlation spectroscopy (FCS), and confocal imaging, we identify VPS39—a gene encoding a subunit of the homotypic fusion and protein sorting (HOPS) complex—as a critical determinant in the trafficking of CPMPs and hydrocarbon-stapled peptides to the cytosol. Although CPMPs neither inhibit nor activate HOPS function, HOPS activity is essential to efficiently deliver CPMPs to the cytosol. Subsequent multi-color confocal imaging studies identify CPMPs within the endosomal lumen, particularly within the intraluminal vesicles (ILVs) of Rab7+and Lamp1+endosomes that are the products of HOPS-mediated fusion. These results suggest that CPMPs require HOPS to reach ILVs—an environment that serves as a prerequisite for efficient endosomal escape.
FIFO ATP synthase responds to glycolysis inhibition by localization into the inner boundary membrane
Authors: Zalyevskiy K. , Hager F. , Richter C. P. , Psathaki K. , Appelhans T. , Busch K.B. 
Published: July 2018

ABSTRACTMitochondrial F1F0ATP synthase is the key enzyme to fuel the cell with essential ATP. Strong indications exist that the respiratory chain and the ATP synthase are physically separated within cristae. How static this organization is, is largely unknown. Here, we investigated the effect of substrate restriction on mitochondrial respiration and the spatio-temporal organization of ATP synthase. By superresolution microscopy, the localization and mobility of single labelled mitochondrial ATP synthase was determined in live cells. We found, that the ATP synthase under oxidative respiration displayed a clear localization and confined mobility in cristae. Trajectories of individual ATP synthase proteins show a perpendicular course to the longitudinal axis of the respective mitochondrion, exactly following the ultrastructure of cristae. When substrate for TCA cycle and respiration was limited, a significant proportion of ATP synthase localized from cristae to the inner boundary membrane, and only less mobile ATP synthase remained in cristae. These observations showing the plasticity of the spatio-temporal organisation of ATP synthase can explain why ATP synthase show interactions with proteins in distinct mitochondrial subcompartments such as inner boundary membrane, cristae junctions and cristae.
Modulating hinge flexibility in the APP transmembrane domain alters γ-secretase cleavage
Authors: Götz Alexander , Mylonas Nadine , Högel Philipp , Silber Mara , Heinel Hannes , Menig Simon , Vogel Alexander , Feyrer Hannes , Huster Daniel , Luy Burkhard , Langosch Dieter , Scharnagl Christina , Muhle-Goll Claudia , Kamp Frits , Steiner Harald 
Published: July 2018

ABSTRACTIntramembrane cleavage of the β-amyloid precursor protein C99 substrate by γ-secretase is implicated in Alzheimer’s disease pathogenesis. Since conformational flexibility of a di-glycine hinge in the C99 transmembrane domain (TMD) might be critical for γ-secretase cleavage, we mutated one of the glycine residues, G38, to a helix-stabilizing leucine and to a helix-distorting proline. CD, NMR and hydrogen/deuterium exchange measurements as well as MD simulations showed that the mutations distinctly altered the intrinsic structural and dynamical properties of the TMD. However, although helix destabilization/unfolding was not observed at the initial ε-cleavage sites of C99, both mutants impaired γ-secretase cleavage and altered its cleavage specificity. Moreover, helix flexibility enabled by the di-glycine hinge translated to motions of other helix parts. Our data suggest that both local helix stabilization and destabilization in the di-glycine hinge may decrease the occurrence of enzyme-substrate complex conformations required for normal catalysis and that hinge mobility can be conducive for productive substrate-enzyme interactions.
Improving Whole-Brain Neural Decoding of fMRI with Domain Adaptation
Authors: Zhou Shuo , Cox Christopher R. , Lu Haiping 
Published: July 2018

AbstractIn neural decoding, there has been a growing interest in machine learning on whole-brain functional magnetic resonance imaging (fMRI). However, the size discrepancy between the feature space and the training set poses serious challenges. Simply increasing the number of training examples is infeasible and costly. In this paper, we proposed a domain adaptation framework for whole-brain fMRI (DawfMRI) to improve whole-brain neural decoding on target data leveraging pre-existing source data. DawfMRI consists of three steps: 1) feature extraction from whole-brain fMRI, 2) source and target feature adaptation, and 3) source and target classifier adaptation. We evaluated its eight possible variations, including two non-adaptation and six adaptation algorithms, using a collection of seven task-based fMRI datasets (129 unique subjects and 11 cognitive tasks in total) from the OpenNeuro project. The results demonstrated that appropriate source domain can help improve neural decoding accuracy for challenging classification tasks. The best-case improvement is 8.94% (from 78.64% to 87.58%). Moreover, we discovered a plausible relationship between psychological similarity and adaptation effectiveness. Finally, visualizing and interpreting voxel weights showed that the adaptation can provide additional insights into neural decoding.
Perspective: Genomic inference using diffusion models and the allele frequency spectrum
Authors: Ragsdale Aaron P. , Moreau Claudia , Gravel Simon 
Published: July 2018

AbstractEvolutionary, biological, and demographic processes combine to shape the variation observed in populations. Understanding how these processes are expected to influence variation allows us to infer past demographic events and the nature of selection in human populations. Forward models such as the diffusion approximation provide a powerful tool for analyzing the distribution of allele frequencies in contemporary populations due to their computational tractability and model flexibility. Here, we discuss recent computational developments and their application to reconstructing human demographic history and patterns of selection at new mutations. We also reexamine how some classical assumptions that are still commonly used in inference studies fare when applied to modern data. We use whole-genome sequence data for 797 French Canadian individuals to examine the neutrality of synonymous sites. We find that selection can lead to strong biases in the inferred demography, mutation rate, and distributions of fitness effects. We use these distributions of fitness effects together with demographic and phenotype-fitness models to predict the relationship between effect size and allele frequency, and contrast those predictions to commonly used models in statistical genetics. Thus the simple evolutionary models investigated by Kimura and Ohta still provide important insight into modern genetic research.
Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF
Authors: Correia Kevin , Ho Hanchen , Mahadevan Radhakrishnan 
Published: July 2018

ABSTRACTBackgroundOrganohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremediation of industrial sites contaminated with chlorinated organics. One notable OHRB is Dehalobacter restrictus strain CF, which is capable of respiring chloroform to dichloromethane. Improved bioremediation strategies could be employed with a greater understanding of D. restrictus’ metabolism in isolate and community cultures. To this end, we reconstructed the genome-scale metabolic network of D. restrictus to study its metabolism in future studies using flux balance analysis.MethodThe RAST annotation server and Model SEED framework were used to obtain a draft metabolic network reconstruction. Additional curation was required for its acetyl-CoA sources, the Wood-Ljungdahl pathway, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes.ResultsiHH623 is the first curated genome-scale metabolic model in the Peptococcaceae family. It spans 1087 reactions and 983 metabolites, covering 623 genes (21% of all ORF’s). Its potential sources of acetyl-CoA are pyruvate ferredoxin oxidoreductase, pyruvate formate lyase, acetyl-CoA synthetase, phosphate acetyltransferase, and CO-methylating acetyl-CoA synthase. NADPH may be regenerated by isocitrate dehydrogenase, malic enzyme, NADP-reducing hydrogenase, cytosolic formate dehydrogenase, ferredoxin-dependent bifurcating transhydrogenase, 5-methyltetrahydrofolate dehydrogenase, and 5-10-methylenetetrahydrofolate. Additional reactions that were added or removed to the D. restrictus reconstruction are discussed.ConclusionsWe reconstructed the genome-scale metabolic network of D. restricus by obtaining an initial draft with the RAST server and Model SEED framework. Curation was required for D. restricus’ acetyl-CoA sources, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes. This metabolic model can be used to decipher D. restrictus’ metabolism in isolate and community cultures in future studies, or as a template to reconstruct the metabolic network of other Peptococcaceae species. The extensive curation of the draft metabolic network reconstruction highlights the need to be cautious of automated metabolic network reconstruction.
Thermal insulation and morphology of natural and synthetic filled outdoor sportswear by repeated water washing and dry cleaning
Authors: Kim Sunyoung , Kim Eunae , Park Youngmi 
Published: July 2018

PurposeThe purpose of this paper is to examine the thermal insulation and water vapor transmission rate (WVTR) according to the type of the filling material, and compared the thermal insulation in the dynamic state considering actual wearing conditions.Design/methodology/approachThe thermal insulation and WVTR were evaluated in a standard state depending on the type of filling material (goose down (GD), duck down (DD), Thinsulate700 (T700), Thinsulate600 (T600) and Polyester (PET)), and the changes in thermal insulation were examined by measuring the microclimate in the case of an environmental change from a high temperature to a low temperature. In addition, the clumping of filling material and the changes in the thickness/weight depending on the laundry process were observed, and the relationships with the thermal insulation were analyzed.FindingsThe results showed that for natural filling materials (GD and DD), the thermal insulation deteriorated significantly due to changes in the thickness/weight after laundering ten times, and water washing was more appropriate than the dry cleaning. On the other hand, the artificial filling materials (T700, T600 and PET) showed a relatively smaller difference, except for clumping, when they went through more dry cleaning or water washing cycles compared to the natural filling materials.Originality/valueThe results showed that the laundry methods have different effects on the damage to the filling material, the change in thermal insulation, and the change in the comfort-related physical property. Therefore, it is important to select the optimal laundry method depending on the filling material.
Dynamic thermal transfer of textiles in rotational motions
Authors: Li Wenbin , Xu Weilin , Wang Xin 
Published: July 2018

Purpose
Clothing is subject to a dynamic thermal transport process in its routine service in which the apparel and human body together with environment interact with each other. Understanding of the thermal transfer in this case should take the variations of human body and environment together with clothing attributes into consideration. The paper aims to discuss these issues.

Design/methodology/approach
Based on the purpose-built dynamic thermal and moisture tester, this study focuses on the thermal transfer of fabrics in different rotational motions. The energy consumption and power of the simulated human skin, the temperature and the thermal retention rate were monitored in the process of rotation of the testing platform with gradually increased rotating speed.

Findings
It has been found that the thermal transfer of a rotating fabric is greatly affected by the rotating speed, the angle of the fabric toward the moving direction and the attributes of the fabric such as its thickness, layers, structure and its fiber composition.

Practical implications
This study will benefit the understanding of the dynamic thermal interaction of human with the environment, and the designing of clothing with excellent thermal comfort.

Originality/value
This work reveals the dynamic thermal transfer of fabrics in rotational motions. It provides a platform to study the dynamic thermal behavior of clothing in daily use.
What made base erosion and profit shifting project possible?
Authors: Matsuoka Akira 
Published: July 2018

Purpose
The purpose of this paper is to unveil the true background of the Base Erosion and Profit Shifting (BEPS) Project and to suggest crucial indexes for bringing a movement into a future ceiling causing a struggle of the international tax system.

Design/methodology/approach
This paper looks into the historical context of this project before and after Starbucks’ scandal, comparing to other contexts of the international tax system. Also, this paper partially reviews BEPS from a legal perspective.

Findings
The key factors for building momentum of reform of international taxation are a country having a government willing to embrace the cause of reform, unfairness felt toward entities using tax avoidance schemes which other comparable entities could not be use, grass-roots pressure for the reform, effective places to negotiate cooperation among major countries for the reform, solid cooperation among many countries in the world to implement standards and rhetoric of slogan with less opposition.

Originality/value
The momentum of the reform of international taxation was analyzed before. But the BEPS Project has involved some unique events as compared with the Organization for Economic Cooperation and Development’s project on harmful tax practices, such as initiation of NGOs and boycott by consumers. Additionally, this paper will discuss insights, which the former research did not do.