bluuebunny/crossref_metadata_2025_split huggingface dataset:
PrePPI: A structure informed proteome-wide database of protein-protein interactions
Authors: Petrey Donald , Zhao Haiqing , Trudeau Stephen , Murray Diana , Honig Barry 
Published: February 2023

AbstractWe present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural clues within a Bayesian framework to compute a likelihood ratio (LR) for essentially every possible pair of proteins in a proteome; the current database is for the human interactome. The structural modeling (SM) clue is derived from templatebased modeling and its application on a proteome-wide scale is enabled by a unique scoring function used to evaluate a putative complex. The updated version of PrePPI leverages AlphaFold structures that are parsed into individual domains. As has been demonstrated in earlier applications, PrePPI performs extremely well as measured by receiver operating characteristic curves derived from testing onE. coliand human protein-protein interaction (PPI) databases. A PrePPI database of ~1.3 million human PPIs can be queried with a webserver application that comprises multiple functionalities for examining query proteins, template complexes, 3D models for predicted complexes, and related features (https://honiglab.c2b2.columbia.edu/PrePPI). PrePPI is a state-of- the-art resource that offers an unprecedented structure-informed view of the human interactome.Graphic Abstract
Integrated Stress Response signaling acts as a metabolic sensor in fat tissues to regulate oocyte maturation and ovulation
Authors: Grmai Lydia , Michaca Manuel , Lackner Emily , Nampoothiri V.P. Narayanan , Vasudevan Deepika 
Published: February 2023

AbstractReproduction is an energy-intensive process requiring systemic coordination. However, the inter-organ signaling mechanisms that relay nutrient status to modulate reproductive output are poorly understood. Here, we useDrosophila melanogasteras a model to establish the Integrated Stress response (ISR) transcription factor, Atf4, as a fat tissue metabolic sensor which instructs oogenesis. We demonstrate that Atf4 regulates the lipase Brummer to mediate yolk lipoprotein synthesis in the fat body. Depletion ofAtf4in the fat body also blunts oogenesis recovery after amino acid deprivation and re-feeding, suggestive of a nutrient sensing role for Atf4. We also discovered that Atf4 promotes secretion of a fat body-derived neuropeptide, CNMamide, which modulates neural circuits that promote egg-laying behavior (ovulation). Thus, we posit that ISR signaling in fat tissue acts as a “metabolic sensor” that instructs female reproduction: directly, by impacting yolk lipoprotein production and follicle maturation, and systemically, by regulating ovulation.
luxAgene fromEnhygromyxa salinaencodes a functional homodimeric luciferase
Authors: Yudenko Anna , Bazhenov Sergey V. , Aleksenko Vladimir A. , Goncharov Ivan M. , Semenov Oleg , Remeeva Alina , Nazarenko Vera V. , Kuznetsova Elizaveta , Fomin Vadim V. , Konopleva Maria N. , Al Ebrahim Rahaf , Sluchanko Nikolai N. , Ryzhykau Yury , Semenov Yury S. , Kuklin Alexander , Manukhov Ilya V. , Gushchin Ivan 
Published: February 2023

AbstractSeveral clades of luminescent bacteria are known currently. They all contain similarluxoperons, which include the genesluxAandluxBencoding a heterodimeric luciferase. The aldehyde oxygenation reaction is catalyzed by the subunit LuxA, while LuxB is inactive. Recently, genomic analysis identified a subset of bacterial species with rearrangedluxoperons lackingluxB. Here, we show that the product of theluxAgene from the reducedluxACDEoperon ofEnhygromyxa salinais luminescent upon addition of aldehydes bothin vivoinEscherichia coliandin vitro. Overall,EsLuxA is less bright compared with luciferases fromAliivibrio fischeri(AfLuxAB) andPhotorhabdus luminescens(PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure ofEsLuxA determined at the resolution of 2.71 Å reveals a classical monooxygenase fold, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil inVibrio harveyiLuxA, form α-helices inEsLuxA. Phylogenetic analysis showsEsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of theluxAgene and its speciation toluxAandluxBin the previously described luminescent bacteria. Our work paves the way for discovery of new luciferases that have an advantage of being encoded by a single gene.
Syndapin Regulates the RAP-1 GTPase to Control Endocytic Recycling via RHO-1 and Non-Muscle Myosin II
Authors: Rodriguez-Polanco Wilmer R. , Norris Anne , Velasco Agustin B. , Gleason Adenrele M. , Grant Barth D. 
Published: February 2023

AbstractAfter endocytosis, many plasma membrane components are recycled via narrow-diameter membrane tubules that emerge from early endosomes to form recycling endosomes, eventually leading to their return to the plasma membrane. We previously showed that the F-BAR and SH3 domain Syndapin/PACSIN-family protein SDPN-1 is requiredin vivofor basolateral endocytic recycling in theC. elegansintestine. Here we sought to determine the significance of a predicted interaction between the SDPN-1 SH3 domain and a target sequence in PXF-1/PDZ-GEF1/RAPGEF2, a known exchange factor for Rap-GTPases. We found that endogenous mutations we engineered into the SDPN-1 SH3 domain, or its binding site in the PXF-1 protein, interfere with recyclingin vivo, as does loss of the PXF-1 target RAP-1. Rap-GTPases have been shown in several contexts to negatively regulate RhoA activity. Our results show that RHO-1/RhoA is enriched on SDPN-1 and RAP-1 positive endosomes in theC. elegansintestine, and loss of SDPN-1 or RAP-1 elevates RHO-1(GTP) levels on intestinal endosomes. Furthermore, we found that depletion of RHO-1 suppressedsdpn-1mutant recycling defects, indicating that control of RHO-1 activity is a key mechanism by which SDPN-1 acts to promote endocytic recycling. RHO-1/RhoA is well-known for controlling actomyosin contraction cycles, although little is known of non-muscle myosin II on endosomes. Our analysis found that non-muscle myosin II is enriched on SDPN-1 positive endosomes, with two non-muscle myosin II heavy chain isoforms acting in apparent opposition. Depletion ofnmy-2inhibited recycling likesdpn-1mutants, while depletion ofnmy-1suppressedsdpn-1mutant recycling defects, indicating actomyosin contractility in controlling recycling endosome function.
CRISPR/Cas9-Based Edition of Frataxin Gene inDictyostelium discoideumfor Friedreich’s Ataxia Disease Modeling
Authors: Gentili Hernan G. , Pignataro María Florencia , Olmos Justo , Pavan Florencia , Ibáñez Itati , Santos Javier , Velázquez Duarte Francisco 
Published: February 2023

AbstractIn this paper we describe the development of a new model system for Friedreich’s Atax- ia (FA) usingDictyostelium discoideum. We investigated the conservation of function between humans andD. discoideumand showed that DdFXN can substitute the human version in the interaction and activation of the Fe-S assembly supercomplex. We edited thefxnlocus and isolated a defective mutant, clone 8, which presents landmarks of frataxin deficiency, such as a decrease in Fe-S cluster-dependent enzymatic functions, growth rate reduction, and increased sensitivity to oxidative stress. In addition multicellular development is affected as well as grow on bacterial lawn.We also assessed the rescuing capacity of DdFXN-G122V, a version that mimics a human variant present in some FA patients. While the expression of DdFXN-G122V rescues growth and enzymatic activity defects, as DdFXN does, multicellular development defects were only partially rescuedThe results of the study suggest that this new model system offers a wide range of pos- sibilities to easily explore diverse phenotypes in FA and develop drug or treatment screenings for designing and evaluating therapeutic strategies.
The function of ER-phagy receptors is regulated through phosphorylation-dependent ubiquitination pathways
Authors: Berkane Rayene , Ho-Xuan Hung , Glogger Marius , Sanz-Martinez Pablo , Brunello Lorène , Glaesner Tristan , Kuncha Santosh Kumar , Holzhüter Katharina , Cano-Franco Sara , Buonomo Viviana , Cabrerizo-Poveda Paloma , Balakrishnan Ashwin , Tascher Georg , Husnjak Koraljka , Juretschke Thomas , Misra Mohit , González Alexis , Dötsch Volker , Grumati Paolo , Heilemann Mike , Stolz Alexandra 
Published: February 2023

AbstractSelective autophagy of the endoplasmic reticulum (ER), known as ER-phagy, is an important regulator of ER remodeling and essential to maintain cellular homeostasis during environmental changes. We recently showed that members of the FAM134 family play a critical role during stress-induced ER-phagy. However, the mechanisms on how they are activated remain largely unknown. In this study, we analyzed phosphorylation of FAM134 as a trigger of FAM134-driven ER-phagy upon mTOR (mechanistic target of rapamycin) inhibition. An unbiased screen of kinase inhibitors revealed that CK2 is essential for FAM134B- and FAM134C-driven ER-phagy after mTOR inhibition. Furthermore, we provide evidence that ER-phagy receptors are regulated by ubiquitination events and that treatment with E1 inhibitor suppresses Torin1-induced ER-phagy flux. Using super-resolution microscopy, we show that CK2 activity is essential for the formation of high-density FAM134B and FAM134C clusters. In addition, dense clustering of FAM134B and FAM134C requires phosphorylation-dependent ubiquitination of FAM134B and FAM134C. Treatment with the CK2 inhibitor SGC-CK2-1 or mutation of FAM134B and FAM134C phosphosites prevents ubiquitination of FAM134 proteins, formation of high-density clusters, as well as Torin1-induced ER-phagy flux. Therefore, we propose that CK2-dependent phosphorylation of ER-phagy receptors precedes ubiquitin-dependent activation of ER-phagy flux.
Sing to me, baby: Infants show neural tracking and rhythmic movements to live and dynamic maternal singing
Authors: Nguyen Trinh , Reisner Susanne , Lueger Anja , Wass Samuel V. , Hoehl Stefanie , Markova Gabriela 
Published: February 2023

AbstractInfant-directed singing has unique acoustic characteristics that may allow even very young infants to respond to the rhythms carried through the caregiver’s voice. The goal of this study was to examine neural and movement responses to live and dynamic maternal singing in 7-month-old infants and their relation to linguistic development. In total, 60 mother-infant dyads were observed during two singing conditions (playsong and lullaby). In Study 1 (n= 30), we measured infant EEG and used an encoding approach utilizing ridge regressions to measure neural tracking. In Study 2 (n= 40), we coded infant rhythmic movements. In both studies, we assessed children’s vocabulary when they were 20 months old. In Study 1, we found above-threshold neural tracking of maternal singing, with superior tracking of lullabies than playsongs. We also found that the acoustic features of infant-directed singing modulated tracking. In Study 2, infants showed more rhythmic movement to playsongs than lullabies. Importantly, neural coordination (Study 1) and rhythmic movement (Study 2) to playsongs were positively related to infants’ expressive vocabulary at 20 months. These results highlight the importance of infants’ brain and movement coordination to their caregiver’s musical presentations, potentially as a function of musical variability.
Compressive sensing-based de-aliasing method for array electrostatic signal
Authors: Zhong Zhirong , Jiang Heng , Guo Jiachen , Zuo Hongfu 
Published: February 2023

PurposeThe aero-engine array electrostatic monitoring technology (AEMT) can provide more and more accurate information about the direct product of the fault, and it is a novel condition monitoring technology that is expected to solve the problem of high false alarm rate of traditional electrostatic monitoring technology. However, aliasing of the array electrostatic signals often occurs, which will greatly affect the accuracy of the information identified by using the electrostatic sensor array. The purpose of this paper is to propose special solutions to the above problems.Design/methodology/approachIn this paper, a method for de-aliasing of array electrostatic signals based on compressive sensing principle is proposed by taking advantage of the sparsity of the distribution of multiple pulse signals that originally constitute aliased signals in the time domain.FindingsThe proposed method is verified by finite element simulation experiments. The simulation experiments show that the proposed method can recover the original pulse signal with an accuracy of 96.0%; when the number of pulse signals does not exceed 5, the proposed method can recover the pulse peak with an average absolute error of less than 5.5%; and the recovered aliased signal time-domain waveform is very similar to the original aliased signal time-domain waveform, indicating that the proposed method is accurate.Originality/valueThe proposed method is one of the key technologies of AEMT.
Employee engagement and performance of MSMEs during COVID-19: the moderating effect of job demands and job resources
Authors: Coffie Rosemary Boateng , Gyimah Raymond , Boateng Kofi Agyenim , Sardiya Alimatu 
Published: February 2023

PurposeThis study explores how employee engagement (EE) influences employee performance and how this relationship is moderated by job demands and job resources among micro, small and medium enterprises (MSMEs) in an emerging economy context during the COVID-19 pandemic.Design/methodology/approachThe study adopts the survey and quantitative approach to gathering data from 395 MSMEs operating in an emerging economy in sub-Saharan Africa. Data were analyzed using Partial Least Squares, version 3.0.FindingsThe results reveal that EE significantly influences employee performance among MSMEs during the pandemic. Also, job resources were found to be significant predictors of EE in the MSME sector. In contrast, job demands did not have a significant effect on EE during the pandemic. Finally, job resources but not job demand moderate the relationship between EE and employee performance.Originality/valueThis study is one of the earliest to explore the effects of EE on employee performance and how this relationship is moderated by job resources and job demands in sub-Saharan Africa's MSME sector since the influx of COVID-19.
Lessons learnt from COVID-19 vaccine operations and distribution performance: challenges and resilience strategies
Authors: Chowdhury Md. Maruf Hossan , Mahmud A.K.M. Shakil , Khan Eijaz , Hossain Mohammad , Barua Zapan 
Published: February 2023

PurposeGrounded in dynamic capability view, this research develops a decision support model, which enables determining consistent and sufficient configurations of resilience strategies to mitigate vaccine operations and distributions (O&D) challenges and thus improve O&D performance (i.e. O&DP).Design/methodology/approachThrough qualitative in-depth interviews, the authors first identified challenges and resilience strategies related to vaccine O&D. Next, using the quality function deployment technique, three quantitative case studies were performed to determine the most important challenges and resilience strategies. Finally, utilising fuzzy set qualitative comparative analysis, the authors determine sufficient conditions of challenges and strategies leading to improve vaccine O&DP.FindingsThe findings reveal that strategies alone are not effective instead a combination of strategies and nullification of challenges is needed to enhance vaccine O&DP. Further, the findings revealed that not only the presence of challenges, but also the lack of strategies reduces the vaccine O&DP.Practical implicationsThe authors' findings will assist the health service decision-makers for strategizing an effective and efficient vaccination program by selecting the right combination of challenges and resilience strategies.Originality/valueThe authors' study develops a novel decision support model and offers significant learning for the future vaccine O&DP.
A meta-analysis of social commerce adoption and the moderating effect of culture
Authors: Wang Ning , Zhao Yang , Zhou Ruoxin 
Published: February 2023

PurposeAs a derivative model of e-commerce, social commerce has received increasing attention in recent years. Empirical studies on social commerce have examined the key factors that influence users' attitudes or adoption intentions, but their conclusions are context-based and are not entirely consistent. This study aims to draw a general conclusion by systematically synthesizing the findings of previous studies and examine whether cultural differences play a moderating role in users' social commerce adoption.Design/methodology/approachA meta-analysis based on 11,786 independent samples from 39 empirical studies was conducted to integrate their results and develop a comprehensive conceptual model. A moderator analysis was carried out to investigate the moderating effect of culture by dividing the context into subgroups of individualistic and collectivistic cultures.FindingsThe results show that this comprehensive conceptual model can help better understand the adoption of social commerce. Meanwhile, the moderator analysis indicates that cultural differences have a significant moderating effect on the relationship between the determinants and the adoption of social commerce.Originality/valueThe findings of this paper have theoretical implications and make managerial contributions.
Organizational readiness for building information modeling
Authors: Magalhães Rachel Madeira , Mello Luiz Carlos Brasil de Brito , Hippert Maria Aparecida Steinherz 
Published: February 2023

PurposeThe main factor that leads organizations to implement Building Information Modeling (BIM) is customer demand. While this is a frequent topic in the BIM literature, few studies address BIM organizational readiness. Due to this gap in BIM implementation literature, this paper aims to understand what affects organizational BIM readiness and how the BIM readiness process occurs.Design/methodology/approachThe present paper adopts design science research as a methodological approach. A literature review examined 69 journal articles. The analysis focused on multiple theories, such as organizational readiness for change, adoption and diffusion of innovations and project management.FindingsBy investigating BIM organizational readiness, this study presents a construct and a conceptual model for driving BIM readiness.Originality/valueThis study can benefit researchers and organizations. The results presented may drive further research and discussions on the topic. But it is important to state that these results must be tested on real situations.
The Indian contribution to organizational institutionalism: implications for organizational theorizing
Authors: Shekhar Sudhanshu 
Published: February 2023

Purpose
Organization studies in India has largely remained insular to the writings of Indian scholars in parent disciplines such as sociology. The lack of engagement with Indian sociological works has promoted excessive dependence on Euro–American theory. It has further hindered the development of indigenous theories. This paper aims to argue that engagement with the writings of classical and contemporary Indian sociologists can resolve this issue.

Design/methodology/approach
The paper delineates the contribution of Indian sociologists to organizational or sociological institutionalism. It focuses specifically on the contribution of these scholars concerning two subtopics: conceptualization of institutions and fields, and the dynamics of institutional change.

Findings
The paper draws upon the work of Indian sociologists to develop a concept of ecological field. It further delves into the dynamic interplay between ideas and institutional change. More precisely, it draws attention to the role of actors and mechanisms that produce ideas.

Originality/value
Future studies can leverage the contribution of Indian scholars to explicate, elaborate and develop creative theories of organizational institutionalism. Such cumulative efforts can help in building an Indian tradition of organizational institutionalism.
Nash equilibrium in emerging partnership-based Islamic banking industry with a Bayesian game-theoretic approach
Authors: Ghaemi Asl Mahdi , Ghasemoghli Ali , Khalfaoui Rabeh 
Published: February 2023

PurposeA hypothesis developed in this paper models the relationship between the borrower and the bank as a dynamic game based on incomplete information (business game) and seeks an equilibrium point at which the facilitated applicant can act according to the terms of the loan agreement once the contract is signed and meet the requirements of the contract.Design/methodology/approachThe primary assumption in the formation of the Islamic bank in Islamic society is that the members of the society are Muslims and act according to religious orders. However, the non-fulfillment of divine principles and orders is always possible. In partnership agreements, the risk of infringement is reduced and corrupt contracts are prevented in some circumstances. Our basic model was constructed using the Beer-Quiche classic game, which has been modified dynamically along with a generalization of complexity terms. The information asymmetry led us to use a heterogeneous belief system to evaluate the probability of the customer transmitting a low credit risk signal to the bank and the probability of the customer transmitting a high credit risk signal to the bank. There are several assumptions of the basic model that are released in the extended model by the presence of a social inspector, by exploring credit risk signals in the generalized model and by considering various commitment levels in the comprehensive model.FindingsAs a result, it is observed that there is no Nash equilibrium in cases where the customer applies separation strategies. But if the pulling strategies are applied, the Nash equilibrium can be achieved under certain conditions, including inspection bodies in the banking system, the creation of necessary transparency and the proper treatment of criminals by government and regulatory bodies. So, by using alternative belief systems, applying different filters and paying attention to all sectors of the economy, new Nash equilibrium points can be achieved. Moreover, multi-stage facilities payment reduces the risk of corrupt contracts.Originality/valueThis paper sets out to analyze Nash Equilibrium and its possible encounter in Islamic Banking for the first time, utilizing a Bayesian Game-Theoretic framework. A major aspect of the research is the contribution to a better understanding of the role of transparency and government oversight in the implementation of Islamic banking regulatory standards.