bluuebunny/crossref_metadata_2025_split huggingface dataset:
How a highly acidic SH3 domain folds in the absence of its charged peptide target
Authors: Jaramillo-Martinez Valeria , Dominguez Matthew J. , Bell Gemma M , Souness Megan E , Carhart Anna H. , Cuibus M. Adriana , Masoumzadeh Elahe , Lantz Benjamin J , Adkins Aaron J , Latham Michael P , Ball K. Aurelia , Stollar Elliott J 
Published: March 2023

AbstractCharged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years.Statement for broader audienceSome protein domains are highly charged because they are adapted to bind oppositely charged proteins and nucleic acids. However, it is unknown how these highly charged domains fold as during folding there will be significant repulsion between like-charges. We investigate how one of these highly charged domains folds in the presence of salt, which can screen the charge repulsion and make folding easier, allowing us to understand how folding occurs despite the protein’s high charge.Supplementary materialSupplementary material document containing additional details on protein expression methods, thermodynamics and kinetics equations, and the effect of urea on electrostatic interactions, as well as 4 supplemental figures and 4 supplemental data tables. (Supplementary_Material.docx), 15 pagesSupplemental excel file containing covariation data across AbpSH3 orthologs (FileS1.xlsx)
WITHDRAWN: The influence of the bullseye versus standard fixation cross on eye movements and classifying natural images from EEG
Authors: Häberle Greta , Çelikkol Aynur Pelin , Cichy Radoslaw M. 
Published: March 2023

Withdrawn StatementThe authors have withdrawn this manuscript because we detected fundamental errors in the formula we used to convert eye tracking data (x and y coordinates) from pixels to degrees. After addressing these errors, the results changed considerably. On the one hand, the behavioral results point towards differences for the bullseye versus the standard fixation cross different and larger than originally reported. However, the eyetracking decoding difference between standard and bullseye fixation cross is no longer significant. Therefore, the main claim of the paper – that bullseye fixation cross leads to lower eye movements compared to standard fixation cross, in turn resulting in lower decoding performance of object identity for eyetracking and EEG data – no longer stands. Given this change in the main results, we therefore withdraw the preprint.. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
MIL Cell – A tool for multi-scale simulation of yeast replication and prion transmission
Authors: Hall Damien 
Published: March 2023

AbstractThe single celled baker’s yeast,Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, with the three most prominent examples being [URE3] formed from the Ure2 protein (a regulator of nitrogen catabolism), [PSI+] formed from the Sup35 protein (a yeast translation termination release factor) and [PIN+] formed from the Rnq1 protein (of as yet unknown function). In a laboratory environment, haploidS. cerevisiaecells of a single mating type can acquire an amyloid prion in one of two ways (i.) Spontaneous nucleation of the prion within the yeast cell, and (ii.) Receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost from a yeast due to (i) Dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) Preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool, called MIL-CELL, for modelling these four general processes using a multiscale approach that is able to describe both spatial and kinetic aspects of the yeast life cycle and the amyloid- prion behavior. The yeast growth cycle is considered in two stages, a mature yeast that is competent to bud (M), and a daughter yeast (D) defined as a fully grown and detached bud. In the virtual plate experiment each transition in yeast growth is stochastically regulated, according to temporal and spatial characteristics, in a manner able to incorporate concepts of confluent growth. Between the relatively coarse time-points used for the particle level description, a set of differential equations, describing the nucleation, growth, fragmentation and clumping of amyloid fibrils, is solved numerically, for each individual yeast cell. Distribution of amyloid between the mother and the daughter is carried out by solving a set of kinetic partition equations between mother and the newly forming (and still attached) daughter during the yeast budding stage. In this paper we describe the workings of the model, the assumptions upon which it is based and some interesting simulation results that pertain to wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL (MonitoringInduction andLoss of prions inCells) is provided as a stand-alone graphical user interface-based executable program for free download with the paper (supplementary section).MIL-CELL download:https://drive.google.com/drive/folders/1xNBSL_2sGNkyXfYLYUyXjyM9ibGAcQUL?usp=sharing
Age differences in neural distinctiveness during memory retrieval versus reinstatement
Authors: Pauley Claire , Kobelt Malte , Werkle-Bergner Markus , Sander Myriam C. 
Published: March 2023

AbstractRobust evidence points to mnemonic deficits in older adults related to dedifferentiated, i.e., less distinct, neural responses during memory encoding. However, less is known about retrieval-related dedifferentiation and its role in age-related memory decline. In this study, younger and older adults were scanned both while incidentally learning face and house stimuli and while completing a surprise recognition memory test. Using pattern similarity searchlight analyses, we looked for indicators of neural dedifferentiation during retrieval and asked whether this might explain interindividual differences in memory performance. Our findings revealed age-related reductions in neural distinctiveness during memory retrieval as well as in encoding-retrieval reinstatement in visual processing regions. We further demonstrated that the degree to which patterns elicited during encoding were reinstated during retrieval tracked variability in memory performance better than retrieval-related distinctiveness only. All in all, we contribute to meager existing evidence for age-related neural dedifferentiation during memory retrieval. We propose that the recognition task (as opposed to a cued recall task) may have revealed impairment in perceptual processing in older adults, leading to particularly widespread age differences in neural distinctiveness. We additionally provide support for the idea that well-defined reactivation of encoding patterns plays a major role in successful memory retrieval.
A novel miR-99b-5p-Zbp1pathway in microglia contributes to the pathogenesis of schizophrenia
Authors: Kaurani Lalit , Islam Md Rezaul , Heilbronner Urs , Krüger Dennis M. , Zhou Jiayin , Methi Aditi , Strauss Judith , Pradhan Ranjit , Burkhardt Susanne , Pena Tonatiuh , Erlebach Lena , Bühler Anika , Budde Monika , Senner Fanny , Kohshour Mojtaba Oraki , Schulte Eva C. , Schmauß Max , Reininghaus Eva Z. , Juckel Georg , Kronenberg-Versteeg Deborah , Delalle Ivana , Odoardi Francesca , Flügel Alexander , Schulze Thomas G. , Falkai Peter , Sananbenesi Farahnaz , Fischer Andre 
Published: March 2023

AbstractSchizophrenia is a psychiatric disorder that is still not readily treatable. Pharmaceutical advances in the treatment of schizophrenia have mainly focused on the protein coding part of the human genome. However, the vast majority of the human transcriptome consists of non-coding RNAs. MicroRNAs are small non-coding RNAs that control the transcriptome at the systems level. In the present study we analyzed the microRNAome in blood and postmortem brains of controls and schizophrenia patients and found that miR-99b-5p was downregulated in both the prefrontal cortex and blood of patients. At the mechanistic level we show that inhibition of miR-99b-5p leads to schizophrenia-like phenotypes in mice and induced inflammatory processes in microglia linked to synaptic pruning. The miR-99b-5p-mediated inflammatory response in microglia depended onZ-DNA binding protein 1(Zbp1) which we identified as a novel miR-99b-5p target. Antisense oligos (ASOs) againstZbp1ameliorated the pathological phenotypes caused by miR-99b-5p inhibition. In conclusion, we report a novel miR-99b-5p-Zbp1pathway in microglia that contributes to the pathogenesis of schizophrenia. Our data suggest that strategies to increase the levels of miR-99b-5p or inhibitZbp1could become a novel therapeutic strategy.
A spinal synergy of excitatory and inhibitory neurons coordinates ipsilateral body movements
Authors: Hayashi Marito , Gullo Miriam , Senturk Gokhan , Di Costanzo Stefania , Nagasaki Shinji C. , Kageyama Ryoichiro , Imayoshi Itaru , Goulding Martyn , Pfaff Samuel L. , Gatto Graziana 
Published: March 2023

AbstractInnate and goal-directed movements require a high-degree of trunk and appendicular muscle coordination to preserve body stability while ensuring the correct execution of the motor action. The spinal neural circuits underlying motor execution and postural stability are finely modulated by propriospinal, sensory and descending feedback, yet how distinct spinal neuron populations cooperate to control body stability and limb coordination remains unclear. Here, we identified a spinal microcircuit composed of V2 lineage-derived excitatory (V2a) and inhibitory (V2b) neurons that together coordinate ipsilateral body movements during locomotion. Inactivation of the entire V2 neuron lineage does not impair intralimb coordination but destabilizes body balance and ipsilateral limb coupling, causing mice to adopt a compensatory festinating gait and be unable to execute skilled locomotor tasks. Taken together our data suggest that during locomotion the excitatory V2a and inhibitory V2b neurons act antagonistically to control intralimb coordination, and synergistically to coordinate forelimb and hindlimb movements. Thus, we suggest a new circuit architecture, by which neurons with distinct neurotransmitter identities employ a dual-mode of operation, exerting either synergistic or opposing functions to control different facets of the same motor behavior.
Politics of accounting evidence in privatising telecommunications in Sri Lanka
Authors: Gunatilake Gayathri , Lord Beverley , Dixon Keith 
Published: March 2023

PurposeThis paper illustrates the socio-political nature of accountings, referring to the partial privatisation of the monopoly telecommunications organisation in a lower-middle-income country.Design/methodology/approachActor-network theory and an ANTi-history approach are used to trace circumstances and occurrences. Empirical materials include official documents, print media and retrospective interviews with organisation employees ten years on from the privatisation.FindingsProponents of privatisation used retrospectively constructed historical accounts to problematise the natural monopoly of telecommunications and the government organisation administering it. A restructuring programme followed. Proponents addressed controversies pertaining to the programme thus garnering widespread support for complex and controversial changes. Proponents produced and reproduced accounting artefacts as evidence in these processes of history reconstruction, consequent changes and restoring stability to telecommunications in its reconfigured commercial domain. The proponents used selective, controversial accounting evidence to problematise the government organisation's existence, then to mobilise various actors to reduce and close the controversies previously aroused and reinstate stability in a partially privatised telecommunications company. Although no longer having a monopoly this company still dominates. Dissenters did the same but with little success.Research limitations/implicationsThe findings demonstrate the importance of tracing the socio-political process of arriving at the dominant outcome about the past. This assists in making sense of present circumstances and re-imagining the future.Originality/valueThe study demonstrates that, during controversial circumstances, taken-for-granted history, as well as what is thought to have not existed in the past, support the dominant network in gaining advantage over their opponents and black-boxing their perspectives of how things should be.
The impact of self-efficacy beliefs of employees on contextual issues of online learning: with reference to the banking sector in Sri Lanka
Authors: Rathnasekara Kushan , Suraweera Namali , Yatigammana Kaushalya 
Published: March 2023

PurposeThe paper aims to clarify the relationship between perceived contextual issues and the self-efficacy beliefs of the employees with e-learning engagement for their competency development. It proposes a model for the banks to utilize their e-learning interventions more effectively by managing the identified contextual issues. Simultaneously, this study aims to expand the domain of self-efficacy beliefs and apply its principles to dilute the impact of the negative contextual issues which were not addressed through similar research.Design/methodology/approachThe paper focuses on an exploratory study using a deductive approach grounded on self-efficacy – one of the main dimensions of Bandura's social cognitive theory. It adopted a mixed methodology, and primary data were collected through an online survey (792 responses analyzed through Statistical Package Social Science [SPSS]) and semi-structured interviews (20 respondents analyzed through thematic analysis). The population comprises employees of private commercial banks who have recently introduced e-learning.FindingsThe paper provides empirical insights into the contextual issues influencing e-learning and how self-efficacy beliefs can be utilized to enhance the effective engagement of employees. Contextual issues related to technological, organizational, personal and time-intensive factors influence e-learning engagement. The strengthening of self-efficacy beliefs (learners' enthusiasm and gaining) can be utilized to manage personal and time-intensive factors. However, technological and organizational factors cannot be managed through a similar approach as they did not report a significant relationship with self-efficacy.Originality/valueThis paper fulfills an identified need to study how e-learning can be utilized as an effective competency development tool in the banking sector.
Does “low-carbon pilot policy” affect the carbon intensity of construction industry? Exploring the implementation mechanism and effectiveness in China
Authors: Wang Qi , Appolloni Andrea , Liu Junqi 
Published: March 2023

PurposeCarbon reduction in the construction industry is related to the achievement of carbon emission peaks and carbon neutrality targets. Therefore, exploring the influence of current carbon reduction policies on the construction industry is necessary. China’s low-carbon pilot (LCP) policy has been extensively studied, while LCPs mechanism and effectiveness on carbon reduction in the construction industry remain to be explored.Design/methodology/approachThis study selected four provincial LCP regions as case studies and adopted the grounded theory method for case studies to analyze the implementation mechanism of the LCP policy on carbon reduction in the construction industry. Then, this study adopted the propensity score matching and difference-in-differences regression (PSM-DID) approach to evaluate the influence of the LCP policy on carbon intensity (CI) in the construction industry by using panel data taken from 30 provinces in China between 2008 and 2017.FindingsThe authors found that (1) the LCP policy promotes carbon reduction in the construction industry through the crossing implementation mechanism of five vertical support approaches and five horizontal support approaches. (2). The LCP policy can significantly reduce CI in the construction industry.Originality/valueThe study not only explored how is the LCP policy implemented, but also examined the effectiveness of the LCP policy in the construction industry. The policy implications of this study can help policy-makers better achieve low-carbon development targets in the construction industry.
The consumer–activity relationship and separation distress
Authors: Hawkins Matthew A. , Thyroff Anastasia 
Published: March 2023

Purpose
Despite the rich history of examining the connections between symbolic consumption and identity formation, nearly all the research has focused on brands and possessions; the role of activities has been critically overlooked. This study aims to expand marketing’s understanding of identity formation by examining it in conjunction with attribution theory, exploring the relationship between activity engagement and separation distress.

Design/methodology/approach
A pilot study (n = 90) using a thematic content analysis reveals six themes (i.e. separation distress, negative emotions, indifference, adapting, positive decision and acceptance), providing support for the conceptual model. The main study (n = 347) tests the conceptual model via five hypotheses.

Findings
Self-worth match with an activity predicts the perceived separation distress of stopping the activity. Furthermore, self-activity connection mediates this relationship, but only if consumers believe they are in control of or the cause for stopping the activity.

Research limitations/implications
This research provides critical baseline understanding of activity consumption. Yet, future research on the topic of activities is needed to advance activity engagement as a unique category of consumer behavior.

Practical implications
To craft effective messaging and strategies, marketers should consider the meaning and value embedded in consumer activities (not just possessions and brands).

Originality/value
This research reveals that consumers use activities to construct their identity and manage their self-worth. It also demonstrates that stopping an activity may lead to separation distress.
Trust-in-government and social economic norms: assessing the heterogeneity of consumers in the USA and Mexico using the VBN theory
Authors: Robles-Avila Sergio Enrique , Sakib Md Nazmus 
Published: March 2023

PurposeThe improper disposal of potentially harmful products is a problem that affects both developed and emerging countries. Using the Values-Beliefs-Norms (VBN) theory, this research attempts to uncover the key differences and similarities between both contexts and to extend the theory to include trust-in-government (TIG) as a moderating variable.Design/methodology/approachThe data used in this study were drawn from two samples: Mexicans and Americans by administering a paper and pencil survey. To test the conceptual model and to contrast the results, partial least squares (PLS-SEM) and multigroup analysis were used.FindingsThis research finds that consumers in emerging countries like Mexico are less likely to act on their beliefs to engage in protesting behaviors when confronted with an environmental problem such as the improper disposal of potentially harmful products. Consumers on both sides of the border are more likely to engage in consumer activism behaviors if social economic norms (SEN) are considered. Furthermore, the multi-group analysis revealed that US consumers' TIG moderates the relationship between awareness of consequences (AC) and consumer activism intention (CAI) contrasting with Mexican consumers where such moderating relationship does not exist.Originality/valueThis research makes a significant contribution to the literature by evaluating TIG as an important predictor of consumer activism behaviors. TIG can significantly affect consumer activism behaviors in the United States, but not in Mexico. It also demonstrates that SEN rather than social benefit norms (SBN) can trigger CAI in both samples.
What is a retail brand - a systematic review of terms and definitions
Authors: Chen Shaoyuan , Wang Pengji , Wood Jacob 
Published: March 2023

PurposeAlthough many scholars have acknowledged inconsistencies in the use of the retail brand term within the existing empirical literature, no one has conducted a systematic study to clarify the confusion of terms. Aiming at unifying the use of terms, this study aims to explore the terms that best express each retail brand concept, and discusses the definitions of proposed terms that can distinguish the connotation of different retail brand concepts.Design/methodology/approachThrough a systematic review, 463 articles were obtained, from which retail brand terms and their definitions were further extracted. Semantic analysis and content analysis were adopted to analyze terms and definitions, respectively.FindingsSemantically, the terms that best express four levels of retail brand concepts are own product brand, store brand, platform brand and retailer brand. Six key elements to distinguish different levels of a retail brand are identified through the content analysis of definitions, and on this basis, four proposed terms are defined.Originality/valueNoting that no study focuses on the conceptual confusion of retail brands in recent decades, the findings are expected to clarify the confusion of terms and unify the use of terms, hence facilitating the communication between scholars and the sharing of research results.