bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decontextualized learning for interpretable hierarchical representations of visual patterns
Authors: Etheredge R. Ian , Schartl Manfred , Jordan Alex 
Published: August 2020

SummaryApart from discriminative models for classification and object detection tasks, the application of deep convolutional neural networks to basic research utilizing natural imaging data has been somewhat limited; particularly in cases where a set of interpretable features for downstream analysis is needed, a key requirement for many scientific investigations. We present an algorithm and training paradigm designed specifically to address this: decontextualized hierarchical representation learning (DHRL). By combining a generative model chaining procedure with a ladder network architecture and latent space regularization for inference, DHRL address the limitations of small datasets and encourages a disentangled set of hierarchically organized features. In addition to providing a tractable path for analyzing complex hierarchal patterns using variation inference, this approach is generative and can be directly combined with empirical and theoretical approaches. To highlight the extensibility and usefulness of DHRL, we demonstrate this method in application to a question from evolutionary biology.
Individual bitter-sensing neurons inDrosophilaexhibit both ON and OFF responses that influence synaptic plasticity
Authors: Devineni Anita V. , Deere Julia U. , Sun Bei , Axel Richard 
Published: August 2020

ABSTRACTThe brain creates internal representations that translate sensory stimuli into appropriate behavior. Most studies of sensory processing focus on which subsets of neurons are activated by a stimulus, but the temporal features of the neural response are also important for behavior. In the taste system, the timing of peripheral sensory responses has rarely been examined. We investigated the temporal properties of taste responses inDrosophila melanogasterand discovered that different types of taste sensory neurons show striking differences in their response dynamics. Strong responses to stimulus onset (ON responses) and offset (OFF responses) were observed in bitter-sensing neurons in the labellum, whereas bitter neurons in the leg and other classes of labellar taste neurons showed only an ON response. Individual bitter labellar neurons generate both the ON and OFF responses through a cell-intrinsic mechanism that requires canonical bitter receptors. The bitter ON and OFF responses at the periphery are propagated to dopaminergic neurons that innervate the mushroom body and mediate aversive learning. When bitter is used as a reinforcement cue, the bitter ON and OFF responses can drive opposing types of synaptic plasticity and the effect of the OFF response dominates, likely due to the rapid and preferential habituation of the ON response. Together, these studies characterize novel features of neural responses in the taste system and reveal their importance for neural circuit function.
Transport Mechanism of Class-3 P4 ATPase Lipid Flippases
Authors: Bai Lin , You Qinglong , Jain Bhawik K. , Kovach Amanda , Graham Todd R. , Li Huilin 
Published: August 2020

ABSTRACTThe P4 ATPases are a large family of membrane-embedded enzymes that use ATP hydrolysis to transport large lipid substrates across lipid bilayers. P4 ATPases differ in their cellular membrane location and their substrates. The structures of the endosome- and Golgi-localized class-1 phosphatidylserine flippases—such as the yeast Drs2 and human ATP8A1—have recently been reported, revealing a substrate binding site on the lumenal side and several transport states. However, a substrate binding site on the cytosolic side has not been found, and the transport mechanisms of P4 ATPases in other classes are still unknown. Here we report a systematic structural and functional study on two plasma-membrane localized, class-3 P4 ATPases that have broader substrate specificity, theS. cerevisiaeDnf1–Lem3 and Dnf2–Lem3 complexes. We have captured substrate lipids on both the exoplasmic and cytosolic sides, and we found that these two enzymes have very similar structures, consistent with their high sequence identity and redundant function. Unexpectedly, Lem3 contributes to substrate binding near the cytosolic surface. We found that the conformational transitions through the substrate transport cycle of these two class-3 enzymes match those of the class-1 enzymes, suggesting a conserved lipid-flipping mechanism among all classes of the P4 ATPases. Our study also revealed a helix-turn-helix insertion in the cytosolic P domain that is unique to the class-3 enzymes and plays a crucial role in their function. Therefore, the P4 ATPases may have retained an overall transport mechanism while evolving distinct features for cellular membrane localization, regulatory mechanisms, and transporting different lipid substrates.
Distributed Visual Category Processing Across Medial Superior Temporal and Lateral Intraparietal Cortices
Authors: Zhou Yang , Mohan Krithika , Freedman David J. 
Published: August 2020

AbstractCategorization is an essential cognitive and perceptual process for recognition and decision making. The posterior parietal cortex (PPC), particularly the lateral intraparietal (LIP) area has been suggested to transform visual feature encoding into cognitive or abstract category representations. By contrast, areas closer to sensory input, such as the middle temporal (MT) area, encode stimulus features but not more abstract categorical information during categorization tasks. Here, we compare the contributions of PPC subregions in category computation by recording neuronal activity in the medial superior temporal (MST) and LIP areas during a categorization task. MST is a core motion processing area interconnected with MT, and often considered an intermediate processing stage between MT and LIP. Here we show that MST shows robust decision-correlated category encoding and working memory encoding similar to LIP, suggesting that MST plays a substantial role in cognitive computation, extending beyond its widely recognized role in visual motion processing.
Alcohol-induced Hsp90 acetylation is a novel driver of liver sinusoidal endothelial dysfunction and alcoholic liver disease
Authors: Yang Yilin , Sungwung Panjamaporn , Jung Yirang , Kondo Reiichiro , McConnell Matthew , Utsumi Teruo , Sessa William C. , Iwakiri Yasuko 
Published: August 2020

AbstractBackgroundIt is unknown whether liver sinusoidal endothelial cells (LSECs) metabolize alcohol. Chronic alcohol consumption decreases endothelial nitric oxide synthase (eNOS)-derived NO production typical of LSEC dysfunction. Heat shock protein 90 (Hsp90) interacts with eNOS to increase its activity. Cytochrome P450 2E1 (CYP2E1) is a key enzyme in alcohol metabolism and facilitates protein acetylation via acetyl-CoA, but its expression in LSECs is unknown. This study investigates alcohol metabolism by LSECs, the mechanism of alcohol-induced LSEC dysfunction and a potential therapeutic approach for alcohol-induced liver injury.MethodsPrimary human, rat and mouse LSECs were used. Histone deacetylase 6 (HDAC6) was overexpressed specifically in liver ECs using an adeno-associated virus (AAV)-mediated gene delivery system to decrease Hsp90 acetylation in ethanol fed mice.ResultsLSECs expressed CYP2E1 and alcohol dehydrogenase 1 (ADH1) and metabolized alcohol. Ethanol induced CYP2E1 in LSECs, but not ADH1. Alcohol metabolism by CYP2E1 increased Hsp90 acetylation and decreased its interaction with eNOS along with a decrease in NO production. A non-acetylation mutant of Hsp90 increased its interaction with eNOS and NO production, whereas a hyper-acetylation mutant decreased NO production, compared with wildtype Hsp90. These results indicate that Hsp90 acetylation is responsible for decreases in its interaction with eNOS and eNOS-derived NO production. Adeno-associated virus 8 (AAV8)-driven HDAC6 overexpression specifically in liver ECs deacetylated Hsp90, restored Hsp90’s interaction with eNOS and ameliorated alcohol-induced liver injury in mice.ConclusionRestoring LSEC function is important for ameliorating alcohol-induced liver injury. To this end, blocking acetylation of Hsp90 specifically in LSECs via AAV-mediated gene delivery has the potential to be a new therapeutic strategy.
Single nucleus analysis of Arabidopsis seeds reveals new cell types and imprinting dynamics
Authors: Picard Colette L. , Povilus Rebecca A. , Williams Ben P. , Gehring Mary 
Published: August 2020

AbstractSeeds are the basis of agriculture, yet their full transcriptional complexity has remained unknown. Here, we employ single-nucleus RNA-sequencing to characterize developingArabidopsis thalianaseeds, with a focus on endosperm. Endosperm, the site of gene imprinting in plants, mediates the relationship between the maternal parent and embryo. We identify new cell types in the chalazal endosperm region, which interfaces with maternal tissue for nutrient unloading. We further demonstrate that the extent of parental bias of maternally expressed imprinted genes varies with cell cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. These data indicate imprinting in endosperm is heterogeneous and suggest that parental conflict, which is proposed to drive the evolution of imprinting, is fiercest at the boundary between filial and maternal tissues.
The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation
Authors: Sharma Tapan , Witwicka Hanna , Imbalzano Anthony N. 
Published: August 2020

ABSTRACTSkeletal muscle differentiation induces changes in the epigenome of myoblasts as they proceed towards a myogenic phenotype. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors and are key regulators of differentiation. Three mSWI/SNF proteins, the mutually exclusive ATPases, BRG1 and BRM, and the BAF180 protein (Polybromo1, PBRM1) contain bromodomains belonging to the same structural subfamily. Bromodomains bind to acetylated lysines on histone N-terminal tails and on other proteins. Pharmacological inhibition of mSWI/SNF bromodomain function using the selective inhibitor PFI-3 reduced differentiation, decreased expression of myogenic genes, and increased the expression of cell cycle-related genes, and the number of cells that remained in the cell cycle. Knockdown of BAF180 had no effect on differentiation, suggesting that only the BRG1 and BRM bromodomains contributed to differentiation. Comparison with existing gene expression data from myoblasts subjected to knockdown of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. ChIP analysis revealed decreased BRG1 and BRM binding to target gene promoters, indicating that the BRG1 and BRM bromodomains promote chromatin binding. Thus mSWI/SNF ATPase bromodomains contribute to cell cycle exit, to skeletal muscle-specific gene expression, and to stable promoter binding by the mSWI/SNF ATPases.
Auxin Regulates Sucrose Transport to Repress Petal Abscission in Rose (Rosa hybrida)
Authors: Liang Yue , Jiang Chuyan , Liu Yang , Gao Yuerong , Lu Jingyun , Aiwaili Palinuer , Fei Zhangjun , Jiang Cai-Zhong , Hong Bo , Ma Chao , Gao Junping 
Published: August 2020

Abstract
Developmental transitions in plants require adequate carbon resources, and organ abscission often occurs due to competition for carbohydrates/assimilates. Physiological studies have indicated that organ abscission may be activated by Suc deprivation; however, an underlying regulatory mechanism that links Suc transport to organ shedding has yet to be identified. Here, we report that transport of Suc and the phytohormone auxin to petals through the phloem of the abscission zone (AZ) decreases during petal abscission in rose (Rosa hybrida), and that auxin regulates Suc transport into the petals. Expression of the Suc transporter RhSUC2 decreased in the AZ during rose petal abscission. Similarly, silencing of RhSUC2 reduced the Suc content in the petals and promotes petal abscission. We established that the auxin signaling protein RhARF7 binds to the promoter of RhSUC2, and that silencing of RhARF7 reduces petal Suc contents and promotes petal abscission. Overexpression of RhSUC2 in the petal AZ restored accelerated petal abscission caused by RhARF7 silencing. Moreover, treatment of rose petals with auxin and Suc delayed ethylene-induced abscission, whereas silencing of RhARF7 and RhSUC2 accelerated ethylene-induced petal abscission. Our results demonstrate that auxin modulates Suc transport during petal abscission, and that this process is regulated by a RhARF7-RhSUC2 module in the AZ.
Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems
Authors: Arora Deepanksha , Abel Nikolaj B. , Liu Chen , Van Damme Petra , Yperman Klaas , Eeckhout Dominique , Vu Lam Dai , Wang Jie , Tornkvist Anna , Impens Francis , Korbei Barbara , Van Leene Jelle , Goossens Alain , De Jaeger Geert , Ott Thomas , Moschou Panagiotis Nikolaou , Van Damme Daniël 
Published: August 2020

AbstractProximity labeling is a powerful approach for detecting protein-protein interactions. Most proximity labeling techniques use a promiscuous biotin ligase or a peroxidase fused to a protein of interest, enabling the covalent biotin labeling of proteins and subsequent capture and identification of interacting and neighboring proteins without the need for the protein complex to remain intact. To date, only a few studies have reported on the use of proximity labeling in plants. Here, we present the results of a systematic study applying a variety of biotin-based proximity labeling approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols that combine mass spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as a test case. We further benchmark the efficiency of various promiscuous biotin ligases in comparison with one-step affinity purification approaches. We identified both known and novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both nonbiotinylated and biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to suggest structural information of protein complexes.
Study on micro-arc oxidation coating of magnetic metal powder composite magnesium alloy
Authors: Su Zhaowei , Mu Rui , Cui Yonghui , Zhu Hongda , Li Xuetian , Shao Zhongcai 
Published: August 2020

Purpose
The purpose of this paper is to prepare composite micro-arc oxide coatings with better wear resistance and corrosion resistance.

Design/methodology/approach
A nickel powder composite micro-arc oxide film was prepared on the surface of the magnesium alloy by the method of organically combining ultra-fine Ni powder with micro arc oxidation film layer. In this experiment, the changes in the corrosion resistance and microstructure of the composite film layer after adding Ni powder were studied, and the effect of the addition of glycerin on the corrosion resistance of the film layer was analyzed.

Findings
The results show that the ultra-fine nickel powder was successfully prepared by the liquid phase reduction method, and the micro-arc oxidation process was modified under the optimal addition amount. The surface of the micro-arc oxide film made of ultra-fine nickel powder was found by SEM to have smooth surfaces and few holes. According to X-ray diffraction analysis, the phase composition of the micro-arc oxide film layer was Mg, Ni, NiSiO4, MgNi (SiO4) and Mg2SiO4. According to the results of electrochemical tests, the corrosion resistance of the micro-arc oxidation composite film layer was improved after the addition of ultra-fine Ni powder, the corrosion current was greatly reduced and the impedance has been improved. And after adding glycerin, the surface of the film layer becomes denser, and the corrosion resistance of the micro-arc oxide film is significantly improved.

Originality/value
Through this experimental research, a micro-arc oxide coating of powder composite magnesium alloy was successfully prepared. The corrosion resistance of the micro-arc oxidation film layer has been improved, and certain functions had been given to the micro-arc oxidation composite film, which has increased the application field of magnesium alloys.
Effect of managerial ownership on bank value: insights of an emerging economy
Authors: Moudud-Ul-Huq Syed , Biswas Tanmay , Proshad Dola Shukla 
Published: August 2020

PurposeThis study aims to empirically investigate the effect of managerial ownership on bank value concerning conventional and Islamic bank. The analysis uses a balanced panel data set based on a sample consisting of 480 bank-year observations between 2003 and 2017.Design/methodology/approachOrdinary least squares, fixed effect and random effect have been used primarily to examine the relationship between managerial ownership and banks' value. Later, the authors validate the core results by using the generalized linear model.FindingsThis study provides general support for the claim of interest alignment that encourages bank standards with a high level of managerial ownership and partly opposes the view of the entrenchment effects.In addition, the study finds a U-shaped and insignificant relation between managerial ownership and bank value. This indicates that initially, managerial ownership is a blessing, and later, it becomes a curse in considering bank value. Moreover, bank value affects managerial ownership positively both for conventional and Islamic banks.Originality/valueA good number of studies are available in the current literature, which examine the impact of managerial ownership on either bank performance or risk-taking. However, very few studies are found that examine the bidirectional relationship between managerial ownership and banks' value. Moreover, to the best of authors’ knowledge, there is a dearth of literature on this topic that is built on the comparative analysis between conventional and Islamic banks.
Sustainable architectural design: towards climate change mitigation
Authors: Sijakovic Milan , Peric Ana 
Published: August 2020

PurposeExcessive amounts of carbon dioxide (CO2) undoubtedly lead to climate change, which directly affects both the natural and the built environment. Observing the impact of climate change on the construction industry, this paper examines sustainable architectural design as a tool to mitigate climate change.Design/methodology/approachTo achieve the previous goal, the authors conduct a comprehensive documentary analysis of three types of sources: (1) scholarly articles in the fields of climate research, sustainable construction, green buildings and sustainable architecture; (2) contemporary global reports on climate change and its impact on the built environment and (3) practitioners' guides explaining practical architectural solutions to the climate crisis.FindingsThe systematic analysis provides three types of results: objectives, strategies and principles of sustainable architectural design aimed at mitigating the effects of climate change. On the one hand, the research results provide a solid basis for further conceptual research into architectural design responsive to the effects of changing climate. On the other hand, the detailed strategies and principles are relevant for urban designers and architects.Originality/valueAmong a range of literature in the field of climate change and its effects on the built environment, a particular value of the paper is in addressing a very local level, i.e. the level of individual building and its immediate surroundings. More specifically, this paper provides concrete design components that help reduce CO2 emissions, finally decreasing the vulnerability index of urban systems.
Development of a conceptual life cycle performance measurement system for build–operate–transfer (BOT) projects
Authors: Okudan Ozan , Budayan Cenk , Dikmen Irem 
Published: August 2020

PurposeThe purpose of this paper is to develop a new conceptual life cycle performance measurement system (PMS) based on stage level key performance indicators (KPIs) to measure the performance of build–operate–transfer (BOT) projects.Design/methodology/approachThis study uses a literature review to reveal the deficiencies of existing PMSs for public–private partnership (PPP) projects. Based on these deficiencies, four recommendations were proposed for developing a PMS. The validation of these recommendations was performed via focus group discussion sessions conducted with 12 experts. Then, a conceptual framework was developed based on the validated recommendations and the additional recommendations emerged during focus group discussions. Finally, the recommendations proposed by the focus group were tested by a questionnaire survey, the findings of the Friedman test and descriptive analysis validated these recommendations.FindingsFindings of the focus group discussion, Friedman test and descriptive analysis indicated that the PMS should have four crucial features to develop an efficient, effective and comprehensible PMS for the BOT project. Firstly, non-financial and financial KPIs should be integrated. Secondly, the PMS should be developed as a process-based system with stage level KPIs. The performance of the BOT projects should be monitored and reviewed continuously, however the most important KPIs should be used for continuous performance measurement to increase the applicability of the system and allocate the resources more efficiently.Research limitations/implicationsThis survey was conducted on experts who have experience with BOT projects located in Turkey, therefore, judgments of experts might be affected by external factors specific to Turkey such as geopolitical situations, investment environment. However, due to the nature of BOT projects, the experience of experts can also be utilized at the international level.Originality/valueThis is the first time a PMS has been developed to measure the performance of a BOT project. In addition, this system has unique features when compared with the PMS proposed in the literature. Especially, the stage level KPIs and continuous performance measurement with the most important KPIs throughout each stage has never been used. This research provides both public sector and private entities with an insight into effectively measure, control and manage their BOT infrastructure projects' performances throughout their life cycles.