bluuebunny/crossref_metadata_2025_split huggingface dataset:
S1 hydrophobic residues modulate voltage sensing phosphatase enzymatic function and voltage sensing
Authors: Rayaprolu Vamseedhar , Miettinen Heini M. , Baker William , Young Victoria C. , Fisher Matthew , Mueller Gwendolyn , Rankin William O. , Kelly J. Jack , Ratzan William J. , Leong Lee Min , Davisson Joshua A. , Baker Bradley J. , Kohout Susy C. 
Published: December 2023

AbstractThe voltage sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage sensing proteins, the VSDs do not interact with one another and the S1-S3 helices are considered mainly as scaffolding. The two exceptions are the voltage sensing phosphatase (VSP) and the proton channel (Hv). VSP is a voltage-regulated enzyme and Hv’s are channels that only have VSDs. To investigate the S1 contribution to VSP function, we individually mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134 and L137). We also combined these mutations to generate quadruple mutation designated S1-Q. Most of these mutations shifted the voltage dependence of activity to higher voltages though interestingly, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions were consistently shifted to lower voltages and indicated a second voltage dependent motion. Co-immunoprecipitation demonstrated that none of the mutations broke the VSP dimer indicating that the S1 impact could stem from intrasubunit and/or intersubunit interactions. Lastly, when the same alanine mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzyme’s conformational response to membrane potential transients and influencing the function of the VSD.
ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations
Authors: Ovek Damla , Keskin Ozlem , Gursoy Attila 
Published: December 2023

AbstractProteins are vital components of the biological world, serving a multitude of functions. They interact with other molecules through their interfaces and participate in crucial cellular processes. Disruptions to these interactions can have negative effects on the organism, highlighting the importance of studying protein-protein interfaces for developing targeted therapies for diseases. Therefore, the development of a reliable method for investigating protein-protein interactions is of paramount importance. In this research, we present an approach for validating protein-protein interfaces using learned interface representations. The approach involves using a graph-based contrastive autoencoder architecture and a transformer to learn representations of proteinprotein interaction interfaces from unlabeled data, then validating them through learned representations with a graph neural network. Our method achieves an accuracy of 0.91 for the test set, outperforming existing GNN-based methods. We demonstrate the effectiveness of our approach on a benchmark dataset and show that it provides a promising solution for validating protein-protein interfaces.
Ventral Pallidum and Amygdala Cooperate to Restrain Reward Approach from Overriding Defensive Behaviors
Authors: Hernández-Jaramillo Alejandra , Illescas-Huerta Elizabeth , Sotres-Bayón Francisco 
Published: December 2023

SummaryForaging decisions involve assessing potential risks and prioritizing food sources, which can be challenging when confronted with changing and conflicting circumstances. A crucial aspect of this decision-making process is the ability to actively suppress defensive reactions to threats (fear) and focus on achieving specific goals. The ventral pallidum (VP) and basolateral amygdala (BLA) are two brain regions that play key roles in regulating behavior motivated by either rewards or threats. However, it is unclear whether these regions are necessary in decision-making processes involving competing motivational drives during conflict. Our aim was to investigate the requirements of the VP and BLA for foraging choices in conflicts involving fear suppression. Here, we used a novel foraging task and pharmacological techniques to inactivate either the VP or BLA, or to disconnect these brain regions before conducting a conflict test. Our findings showed that BLA is necessary for making calculated risky choices during conflicts, whereas VP is necessary for invigorating the drive to obtain food, regardless of the presence of conflict. Importantly, our research revealed that the connection between VP and BLA is critical in limiting risk behaviors when searching for food that requires effort in conflict situations. This study provides a new perspective on the collaborative function of VP and BLA in driving behavior, aimed at achieving goals in the face of danger.
Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression
Authors: Bhat Aditi , Sharma Reena , Lucas M. Mercedes , Desigan Kumaran , Clear Michael , Mishra Ankita , Bowers Robert , Woyke Tanja , Epstein Brendan , Tiffin Peter , Pueyo José J. , Paape Tim 
Published: December 2023

AbstractMercury (Hg) is highly toxic and has the potential to cause severe health problems for foraging animals and humans when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Using long-read sequencing, we assembled the genomes ofSinorhizobium medicaeandRhizobium leguminosarumfrom the Almadén mercury mine in Spain with high variation in Hg-tolerance to identify structural and transcriptomic differences between low and high Hg-tolerant strains. While independent mercury reductase A (merA) genes are prevalent in α-proteobacteria, Mer operons are rare and often vary in their gene organization. Our analyses identified multiple structurally conserved merA homologs in the genomes ofS. medicae, including a dihydrolipoamide 2-oxoglutarate dehydrogenase (D2OD), but only the strains that possessed a Mer operon exhibited hypertolerance to Hg. Using RNAseq reads mapped to the unique genome assemblies, we found the Hg-tolerant strains which possessed a Mer operon, that nearly all genes within the operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of DEGs in the genome, indicating a rapid and efficient detoxification of Hg2+from the cells that reduced general stress responses to the Hg-treatment. Expression changes inS. medicaewhile inside of nodules showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes,nifgenes which are involved in nitrogenase activity inS. medicaeshowed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant, indicating a genotype-by-genotype interaction that influences nitrogen-fixation under stress conditions. Transfer of the Mer operon to non-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the operon is solely necessary to confer hypertolerance to Hg, despite paralogous merA genes present elsewhere in the genome. This study demonstrated that the Mer operon can be exchanged via horizontal gene transfer into non-tolerant rhizobia strains naturally and experimentally.
Direct Male Development in Chromosomally ZZ Zebrafish
Authors: Wilson Catherine A. , Batzel Peter , Postlethwait John H. 
Published: December 2023

AbstractThe genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish (Danio rerio), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB strain fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome or fewer than two Z chromosomes is essential to initiate oocyte development; and without the W factor or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.
Abscisic acid signaling gates salt-specific responses of plant roots
Authors: Lamers Jasper , Zhang Yanxia , van Zelm Eva , Meyer A. Jessica , de Zeeuw Thijs , Verstappen Francel , Veen Mark , Deolu-Ajayi Ayodeji O. , Gommers Charlotte M.M. , Testerink Christa 
Published: December 2023

AbstractSoil salinity presents a dual challenge for plants, involving both osmotic and ionic stress. In response, plants deploy distinct yet interconnected mechanisms to cope with these facets of salinity stress. In this investigation, we observed a substantial overlap in the salt (NaCl)-induced transcriptional responses of Arabidopsis roots with those triggered by osmotic stress or the plant stress hormone abscisic acid (ABA), as anticipated. Notably, a specific cluster of genes responded uniquely to sodium (Na+) ions. Surprisingly, expression of sodium-induced genes exhibited a negative correlation with the ABA response and preceded the activation of genes induced by the osmotic stress component of salt. Elevated exogenous ABA levels resulted in the complete abolition of sodium-induced responses. Consistently, ABA signalling mutants displayed prolonged sodium-induced gene expression, coupled with increased root cell damage under high salinity conditions. Moreover, ABA signalling mutants were unable to redirect root growth to avoid high sodium concentrations and failed to contain their root cell swelling in the presence of elevated salt levels.In summary, our findings unveil an unexpected and pivotal role for ABA signaling in mitigating cellular damage induced by salinity stress and modulating sodium-specific responses in plant roots.
Longitudinal conditional probability of symmetric DNA methylation inArabidopsisplants
Authors: Fernandes Humberto 
Published: December 2023

AbstractDNA replication in high eukaryotes requires the faithful transmission of both the sequence and its methylation status. DNA methyltransferases are not consistently reliable enzymes for accurately restoring methylation in newly synthesised DNA strands when working in isolation. In this study, we evaluated some of the factors that enhance the fidelity of DNA methyltransferases and measure their local and distant impacts on the neighbouring methylation status. A clear understanding of DNA methylation fidelity during replication is important for advances in epigenetic knowledge in general and the potential development of new diagnostics and therapies for epigenetic diseases. We used theArabidopsismodel system because it is moderately methylated, which is an important advantage over animal models since it reduces the chance of a fully-methylated symmetric methylation to virtually nil while providing sufficient occupancy to ensure reliable interpretations. In this study, we employed hairpin bisulfite and nanopore sequencing (1D and 1D2) to test the inter- and intra-strand relationships among the neighbouring 5-methylcytosines (5mC) and evaluate the distribution of hemimethylated sites, as well as the correlations to other cues such as DNA methylation and histone marks. We observed that the presence of a CpG methylation site can predict the occurrence of neighbouring CpG methylation sites, but not necessarily CWG sites, whereas CWG methylation can predict both neighbouring CWG and CpG methylation locations. These predictabilities extend far beyond the size of a nucleosome, and sites 4 kb away still show higher probabilities of methylation compared to the global average.Graphic abstractGraphic abstractFidelity and longitudinal conditional methylation probability of CpG and CWG DNA methylation inArabidopsisplants
The potential for community-driven ecosystem-based disaster risk reduction in South Asia: a literature review
Authors: Lansakara Damithri Chathumani , Le De Loic , Petterson Michael , Wickramasinghe Deepthi 
Published: December 2023

PurposeThe paper reviews existing literature on South Asian ecosystem-based disaster risk reduction (DRR) and identifies how community participation can be used to plan and implement ecosystem-based DRR approaches.Design/methodology/approachThe literature review methodology involved several stages. Firstly, the research objective was determined. Secondly keywords for the literature search were determined. Scopus, Google Scholar, JSTOR and AUT online library were utilized for the literature search. After the search, the literature was screened. The study design, methodology, results and limitations were identified and documented. After data extraction, the literature was analyzed. The patterns, trends and inconsistencies in the literature were identified based on the research question. Later the gaps, controversies and future research needs were identified. Then, a comprehensive and structured literature review that summarizes the relevant literature, synthesizes the findings and provides a critical evaluation of the literature was documented. After writing the document, it was reviewed and edited to ensure its clarity, accuracy and coherence.FindingsThe paper identifies four different themes recurrently emerging in literature on the importance of community participation in ecosystem-based DRR in South Asia. The themes are local community participation in ecosystem-based DRR governance, knowledge production, livelihood enhancement and increased public acceptance.Originality/valueThe paper also illustrates the challenges in integrating community participation with the dominant physical scientific approaches ecosystem-based DRR and proposes a five-element framework to facilitate the integration.
The reward crowdfunding campaign management process: an engagement perspective
Authors: Arshad Nadia , Shneor Rotem , Berndt Adele 
Published: December 2023

PurposeCrowdfunding is an increasingly popular channel for project fundraising for entrepreneurial ventures. Such efforts require fundraisers to develop and manage a crowdfunding campaign over a period of time and several stages. Thus, the authors aim to identify the stages fundraisers go through in their crowdfunding campaign process and how their engagement evolves throughout this process.Design/methodology/approachFollowing a multiple case study research design analysing six successful campaigns, the current study suggests a taxonomy of stages the fundraisers go through in their crowdfunding campaign management process while identifying the types of engagement displayed and their relative intensity at each of these stages.FindingsThe study proposes a five-stage process framework (pre-launch, launch, mid-campaign, conclusion and post-campaign), accompanied by a series of propositions outlining the relative intensity of different types of engagement throughout this process. The authors show that engagement levels appear with high intensity at pre-launch, and to a lesser degree also at the post-launch stage while showing low intensity at the stages in between them. More specifically, cognitive and behavioural engagement are most prominent at the pre- and post-launch stages. Emotional engagement is highest during the launch, mid-launch and conclusion stages. And social engagement maintains moderate levels of intensity throughout the process.Originality/valueThis study focuses on the campaign process using engagement theory, thus identifying the differing engagement patterns throughout the dynamic crowdfunding campaign management process, not just in one part.
ImageNet classification with Raspberry Pis: federated learning algorithms of local classifiers
Authors: Do Thanh-Nghi , Tran-Nguyen Minh-Thu 
Published: December 2023

PurposeThis study aims to propose novel edge device-tailored federated learning algorithms of local classifiers (stochastic gradient descent, support vector machines), namely, FL-lSGD and FL-lSVM. These algorithms are designed to address the challenge of large-scale ImageNet classification.Design/methodology/approachThe authors’ FL-lSGD and FL-lSVM trains in a parallel and incremental manner to build an ensemble local classifier on Raspberry Pis without requiring data exchange. The algorithms load small data blocks of the local training subset stored on the Raspberry Pi sequentially to train the local classifiers. The data block is split intokpartitions using thek-means algorithm, and models are trained in parallel on each data partition to enable local data classification.FindingsEmpirical test results on the ImageNet data set show that the authors’ FL-lSGD and FL-lSVM algorithms with 4 Raspberry Pis (Quad core Cortex-A72, ARM v8, 64-bit SoC @ 1.5GHz, 4GB RAM) are faster than the state-of-the-art LIBLINEAR algorithm run on a PC (Intel(R) Core i7-4790 CPU, 3.6 GHz, 4 cores, 32GB RAM).Originality/valueEfficiently addressing the challenge of large-scale ImageNet classification, the authors’ novel federated learning algorithms of local classifiers have been tailored to work on the Raspberry Pi. These algorithms can handle 1,281,167 images and 1,000 classes effectively.
Influence of manufacturing surface topography on torque and load bearing capacity of hydro-viscous drive clutch under mixed lubrication stage
Authors: Chen Shi , Han Zhiyong , Zeng Qiang , Wang Bing , Wang Liming , Guo Liuyang , Shao Yimin 
Published: December 2023

PurposeHydro-viscous drive (HVD) clutches are widely used in equipment requiring soft start, such as fans and pumps, to transmit torque and adjust speed by changing the gap distance between friction pairs. This paper aims to propose a novel two-parameter evaluation method for HVD during the mixed lubrication stage. The objective is to develop an effective model that establishes the relationship between these parameters and the actual surface topography.Design/methodology/approachIn the presented methods, the fractal features of the real manufacturing surface are calculated based on the power spectrum function by the ultra-depth three-dimensional microscope. After that, the hybrid friction model of the friction plate is established based on mixed elasto-hydrodynamic lubrication theory, boundary friction model and fractal theory. Then the torque and load bearing characteristics of the clutch are obtained, and the influences of the surface fractal features are investigated and discussed. Finally, the Weierstrass–Mandelbrot function is adopted for the surface topography characterization and evaluation.FindingsThe results indicate that the proposed method exhibits good accuracy, while the speed difference between the friction pair exceeds 2,500 rpm. It is concluded that this paper proposed a way to evaluate the torque and loading capacity of HVD considering the real manufacturing surface topography and is helpful for surface optimization.Originality/valueThe originality and value of this study lie in its development of a novel torque and load bearing capacity evaluation method for HVD in mixed lubrication stage, considering manufacturing surface topography and describing the real manufacturing surface.
Transparency and trust in cargo claims: microenterprises selling internationally on a peer-to-peer platform
Authors: Caliskan Ferhat , Idug Yavuz , Gligor David M. , Uvet Hasan , Adana Saban , Celik Hasan , Cevikparmak Sedat 
Published: December 2023

PurposeThe purpose of this study is to determine the factors that impact the trust of microenterprises in online selling platforms and cargo carriers and examine the consequences of a lack of trust.Design/methodology/approachThis study adopts a qualitative exploratory approach and uses grounded theory to generate insights based on interviews with 27 microenterprise owners selling internationally on an online selling platform.FindingsThe results show that a lack of competence, an absence of an integrated claim system and a lack of transparency are the main factors affecting sellers’ trust in online selling platforms. The relationship between the sellers’ intention to continue to use the online selling platform and their trust in the platform was found to be moderated by switching costs.Research limitations/implicationsThis study is limited in that the results were mainly based on the sellers’ perspectives although the phenomenon of interest involves various actors. To mitigate this limitation and cross-check the data, the customer reviews and some of the sellers’ account statistics were also analyzed.Practical implicationsThis study introduces the sellers’ perspectives on the dynamics of supply chain management in international micro trade. These dynamics provide a guideline for how to build and manage an online selling platform targeting microenterprises.Originality/valueUnlike previous studies, this study examines online transaction behaviors from the standpoint of sellers, not buyers. Moreover, it is the first study examining the damaged or lost shipments within the context of online transactions in international micro trade.