bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants
Authors: Assis Braulio A. , Sullivan Alexis P. , Marciniak Stephanie , Bergey Christina M. , Garcia Vanessa , Szpiech Zachary A. , Langkilde Tracy , Perry George H. 
Published: September 2023

AbstractUnderstanding the process of genetic adaptation in response to human-mediated ecological change will help elucidate the eco-evolutionary impacts of human activity. Red fire ants (Solenopsis invicta) spread across Southeastern USA since their accidental introduction via Port Mobile, Alabama in the 1930s, serving today as both novel venomous predator and novel toxic prey to native eastern fence lizards (Sceloporus undulatus). To identify potential signatures of genetic adaptation in lizards to invasive fire ants, we generated whole genome sequencing data from 420 native fence lizards sampled across three populations, two of which had not been invaded by fire ants (in Tennessee and Arkansas) and one which had been invaded for ∼70 years (Alabama). We detected signatures of positive selection exclusive to the exposed Alabama population for genetic variants overlapping genes related to the membrane attack complex of the complement immune system, growth factor pathways, and morphological development. Prior work identified a relationship between increased lizard survival of fire ant attack and longer hind limbs, which lizards use to remove ants from their bodies. Furthermore, we conducted a genome-wide association study with 381 Alabama lizards to identify 24 hind limb length-associated genetic loci. For two loci, positive-effect alleles occur in high frequency and overlap genomic regions that are highly differentiated from the populations naïve to fire ants. Collectively, these findings represent plausible genetic adaptations in response to fire ant invasion, whereby morphological differentiation may increase survival against swarming ants and altered immune responses may allow the exploitation of a novel, toxic food resource.Significance statementHuman activity can force interactions between species from distinct ecological backgrounds. These interactions can consequently impose novel selective pressures on endemic populations via predation or disruption of ecological niches through community-wide effects. While some endemic taxa have been able to adapt biologically to these disruptions, we do not have a full understanding of the underlying genetic processes that may allow it. Here we identify genomic signatures of recent adaptation nearby genes involved in morphological and immunological processes in native fence lizards that are consistent with pressures imposed by the venomous, predatory fire ants introduced by humans. These signatures are largely absent from lizard populations that are naïve to fire ants.
Spotted fever grouprickettsiaewere the dominant pathogens in parasiticRhipicephalus microplusin Yunnan Province, China
Authors: Lin Zhang , GuangQing Miao , XueXia Hou , Peng Wang , Ying Guo , CunJuan Duan , XiaoNa Yang , Qin Hao 
Published: September 2023

AbstractObjectiveTicks as ectoparasites might carry many pathogens and transmitted to their hosts through blood feeding. Human might have the opportunity to be bite by ticks, therefore getting various tick-borne pathogens. Distribution of bacterium flora in ticks plays an essential role in mapping and preventing local tick-borne diseases. Our aim is to map the distribution of bacterium flora and identify the main tick-borne pathogens in dominant tick species in grazing areas of Yunnan province.MethodsV3-V4 region of 16S rRNA amplifier sequencing was used to analyze and study the tick-borne pathogens inRh. Microplus. The prevalence survey onB.burgdorferi s.l.,B. miyamotoi, E. chaffeensis, A. phagocytophilum, Coxiella burnetiiand Spotted fever grouprickettsiaewas carried out via PCR.ResultsThe results showed 105 genus and 117 species were detected in 50 (24 in Yunpan, 26 in Menghun) ticks. Pathogen prevalence testing showed the ticks were positive forB.burgdorferis.l.(9/50, 18%), Spotted fever grouprickettsiae(35/50, 70%), andA.phagocytophilum(1/50, 2%).ConclusionIn our analysis, Spotted fever grouprickettsiaewere the dominant pathogens in these areas. At the same time, we found that v3-v4 high-throughput sequencing of 16S rRNA gene is not sensitive to identify species for certain bacteria(such asB. burgdorferis.l.). More accurate and comprehensive analysis would be necessary for detecting tick bacterium flora.
Adaptive immunity: from CRISPR to CRIHSP?
Authors: Niu Zhiyuan , Wang Yanfeng , Xu Bingqian , Jin Xinru , Ning Linwei , Hao Yuekai , Yan Yangchun , Wang Mengjun , Zhu Wuling , Zhi Lingtong , Guo Changjiang 
Published: September 2023

AbstractClustered regularly interspaced short palindromic repeats (CRISPR) confer adaptive immunity in prokaryotes against viral infection and plasmid transformation. Here, we identified abundant clustered regularly interspaced homologous stem-loop pairs (CRIHSP) within human adaptive immunity-related genes, such as antigen receptor germline genes. By examining genomic stability under activation-induced cytidine deaminase (AID) overexpression, we found that CRIHSP structures are preferred targets for AID. Through collecting and analyzing cancer cell genomic mutation databases, we discovered that these mutation sites tend to cluster toward stem-loop structures. Importantly, the frequency of stem-loop sequences within immunoglobulin heavy chain variable (IGHV) gene segments was over 3-fold higher compared to that within other regions. We concurrently observed stem-loop structures frequently flanking RSS motifs. Conservative estimates indicate a 74.07% probability of immunoglobulin heavy chain diversity (IGHD) gene segment enclosure within stem-loop. These RSS-proximal stem-loops may assemble into homologous stem-loop pair (HSP)-like intermediates and subsequent CRIHSP arrays. Our results implicate CRIHSP architectures as critical enhancer of antigen receptor gene recombination and diversification. Further molecular dissection of these processes could potentially elucidate mechanisms underlying cancer cell genomic instability, chromatin folding and dynamic regulation, gene expression control, etc.
Structure prediction of alternative protein conformations
Authors: Bryant Patrick 
Published: September 2023

AbstractProteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins in the conformations most likely to exist in the PDB. However, almost all conformations in the PDB are seen during training. Therefore, it is not possible to assess whether alternative protein conformations can be predicted or if these are reproduced from memory. Here, we train a new structure prediction network on a conformational split of the PDB to generate alternative conformations. Our network, Cfold, enables efficient exploration of the conformational landscape of monomeric protein structures. 52% (81) of the nonredundant alternative protein conformations evaluated here are predicted with high accuracy (TM-score>0.8). Cfold is freely available at:https://github.com/patrickbryant1/Cfold
A Comparison of Embedding Aggregation Strategies in Drug-Target Interaction Prediction
Authors: Iliadis Dimitrios , De Baets Bernard , Pahikkala Tapio , Waegeman Willem 
Published: September 2023

AbstractThe prediction of interactions between novel drugs and biological targets is a vital step in the early stage of the drug discovery pipeline. Many deep learning approaches have been proposed over the last decade, with a substantial fraction of them sharing the same underlying two-branch architecture. Their distinction is limited to the use of different types of feature representations and branches (multi-layer perceptrons, convolutional neural networks, graph neural networks and transformers). In contrast, the strategy used to combine the outputs (embeddings) of the branches has remained mostly the same. The same general architecture has also been used extensively in the area of recommender systems, where the choice of an aggregation strategy is still an open question. In this work, we investigate the effectiveness of three different embedding aggregation strategies in the area of drug-target interaction (DTI) prediction. We formally define these strategies and prove their universal approximator capabilities. We then present experiments that compare the different strategies on benchmark datasets from the area of DTI prediction, showcasing conditions under which specific strategies could be the obvious choice.
Frontal midline theta power during the cue-target-interval reflects increased cognitive effort in rewarded task-switching
Authors: Arnau Stefan , Liegel Nathalie , Wascher Edmund 
Published: September 2023

AbstractCognitive performance largely depends on how much effort is invested during task-execution. This also means that we rarely perform as good as we could. Cognitive effort is adjusted to the expected outcome of performance, meaning that it is driven by motivation. The results from recent studies investigating the effects manipulations of motivation clearly suggest that it is the expenditure of cognitive control that is particularly prone to being affected by modulations of cognitive effort. Although recent EEG studies investigated the neural underpinnings of the interaction of effort and control, reports on how cognitive effort is reflected by oscillatory activity of the EEG are quite sparse. It is the goal of the present study to bridge this gap by performing an exploratory analysis of high-density EEG data from a switching-task using manipulations of monetary incentives. A beamformer approach is used to localize the sensor-level effects in source-space. The results indicate that the manipulation of cognitive effort was successful. The participants reported significantly higher motivation and cognitive effort in high versus low reward trials. Performance was also significantly increased. The analysis of the EEG data revealed that the increase of cognitive effort was reflected by an increased mid-frontal theta activity during the cue-target interval, suggesting an increased use of proactive control. Alpha-desynchronization throughout the trial was also more pronounced in high reward trials, signaling a bias of attention towards the processing of external stimuli. Source reconstruction suggests that these effects are located in areas related to cognitive control, and visual processing.
Tissue-specific knockout inDrosophilaneuromuscular system reveals ESCRT’s role in formation of synapse-derived extracellular vesicles
Authors: Chen Xinchen , Perry Sarah , Wang Bei , Wang Shuran , Hu Jiayi , Loxterkamp Elizabeth , Dickman Dion , Han Chun 
Published: September 2023

ABSTRACTTissue-specific gene knockout by CRISPR/Cas9 is a powerful approach for characterizing gene functions in animal development. However, this approach has been successfully applied in only a small number ofDrosophilatissues. TheDrosophilamotor nervous system is an excellent model system for studying the biology of neuromuscular junction (NMJ). To expand tissue-specific CRISPR to theDrosophilamotor system, here we present a CRISPR-mediated tissue-restricted mutagenesis (CRISPR-TRiM) toolkit for knocking out genes in motoneurons, muscles, and glial cells. We validated the efficacy of this toolkit by knocking out known genes in each tissue, demonstrated its orthogonal use with the Gal4/UAS binary expression system, and showed simultaneous knockout of multiple redundant genes. Using these tools, we discovered an essential role for SNARE pathways in NMJ maintenance. Furthermore, we demonstrate that the canonical ESCRT pathway suppresses NMJ bouton growth by downregulating the retrograde Gbb signaling. Lastly, we found that axon termini of motoneurons rely on ESCRT-mediated intra-axonal membrane trafficking to lease extracellular vesicles at the NMJ.SIGNIFICANCE STATEMENTIn this study, we developed a tissue-specific Cas9 toolkit that enables gene knockout specifically in motor neurons, glial cells, and muscle cells, the three cell types of theDrosophilaperipheral motor system. Complementary to existing RNAi methods, this versatile tissue-specific knockout system offers unique advantages for dissecting gene functions at the neuromuscular junction (NMJ). Using these tools, we discovered that SNARE-mediated secretory pathways are required to maintain the integrity of the NMJ and that ESCRT components play critical yet differential roles in the biogenesis of extracellular vesicles, bouton growth, and membrane turnover at the NMJ. This CRISPR toolkit can be applied to study many biological questions in the neuromuscular system.
ARID3A coordinates the proliferation-differentiation switch of transit-amplifying cells in the intestine
Authors: Angelis Nikolaos , Baulies Anna , Kucharska Anna , Kelly Gavin , Sopena Miriam L , Boeing Stefan , Li Vivian S.W. 
Published: September 2023

SummaryIntestinal stem cells (ISCs) at the crypt base divide and give rise to progenitor cells that have the capacity to proliferate and differentiate into various mature epithelial cell types in the transit-amplifying (TA) zone. Here, we identified the transcription factor ARID3A as a novel regulator of intestinal epithelial cell proliferation and differentiation at the TA compartment. We show that ARID3A forms an expression gradient from villus tip to the early progenitors at the crypts mediated by TGF-β and WNT signalling. Intestinal epithelial-specific deletion ofArid3areduces proliferation of TA cells. Bulk and single cell transcriptomic analysis shows increased enterocyte differentiation and reduced secretory cells in theArid3acKO intestine. Interestingly, upper-villus gene signatures of both enterocytes and secretory cells are enriched in the mutant intestine. We find that the enhanced enterocyte differentiation in theArid3acKO intestine is caused by increased binding of HNF1 and HNF4. Finally, we show that loss ofArid3aimpairs irradiation-induced regenerative process by altering the dynamics of proliferation and apoptosis. Our findings imply that ARID3A may play a gatekeeping role in the TA compartment to maintain the “just-right” proliferation-to-differentiation ratio for tissue homeostasis and plasticity.
The NS1 protein of influenza B virus binds 5’-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response
Authors: Woltz Ryan , Schweibenz Brandon , Tsutakawa Susan E. , Zhao Chen , Ma LiChung , Shurina Ben , Hura Gregory L. , John Rachael , Vorobiev Sergey , Swapna GVT , Solotchi Mihai , Tainer John A. , Krug Robert M. , Patel Smita S. , Montelione Gaetano T. 
Published: September 2023

SUMMARYInfluenza A and B viruses overcome the host antiviral response to cause a contagious and often severe human respiratory disease. Here, integrative structural biology and biochemistry studies on non- structural protein 1 of influenza B virus (NS1B) reveal a previously unrecognized viral mechanism for innate immune evasion. Conserved basic groups of its C-terminal domain (NS1B-CTD) bind 5’- triphosphorylated double-stranded RNA (5’ppp-dsRNA), the primary pathogen-associated feature that activates the host retinoic acid-inducible gene I protein (RIG-I) to initiate interferon synthesis and the cellular antiviral response. Like RIG-I, NS1B-CTD preferentially binds blunt-end 5’ppp-dsRNA. NS1B-CTD also competes with RIG-I for binding 5’ppp-dsRNA, and thus suppresses activation of RIG-I’s ATPase activity. Although the NS1B N-terminal domain also binds dsRNA, it utilizes a different binding mode and lacks 5’ppp-dsRNA end preferences. In cells infected with wild-type influenza B virus, RIG-I activation is inhibited. In contrast, RIG-I activation and the resulting phosphorylation of transcription factor IRF-3 are not inhibited in cells infected with a mutant virus encoding NS1B with a R208A substitution it its CTD that eliminates its 5’ppp-dsRNA binding activity. These results reveal a novel mechanism in which NS1B binds 5’ppp-dsRNA to inhibit the RIG-I antiviral response during influenza B virus infection, and open the door to new avenues for antiviral drug discovery.
The nudge effect to change the previous users' misbehaviors to stewardship behavior in personal mobility platforms
Authors: Bae Sung Hun , Bae Joonheui , Jo Seonggeun 
Published: September 2023

PurposeThis research aims to examine some nudges for creating psychological ownership in order to reduce misbehaviors, consequently encouraging subsequent users to demonstrate stewardship behaviors.Design/methodology/approachThis research examined the sentiment of tweets (Study 1) to explore user experience and conducted two experiments (Studies 2 and 3) to test the hypotheses.FindingsThe misbehavior of the previous user in relation to the subsequent user's stewardship behavior was moderated by nudges based on self-investment and local identity. Perceived responsibility mediated the relationship between misbehavior and stewardship behavior as a result of nudges.Originality/valueThe findings of this study provide a framework for the transition from misbehavior to stewardship behavior in PMVs.
Exploring factors influencing knowledge sharing in mobile social media groups within construction project teams
Authors: Jia Jianyao , Wu Ming , Hwang Bon-Gang 
Published: September 2023

PurposeAlthough previous research has recognized the pivotal role of mobile social media in knowledge sharing among project members, little is known about what factors affect knowledge sharing in mobile social media groups (MSMGs). Against this background, using normative social influence theory, this study attempts to explore factors influencing knowledge sharing in MSMGs.Design/methodology/approachData from 205 Chinese construction project members are collected and used for analysis. Ordinary least squares regression by Stata 16 is used to test the proposed hypotheses.FindingsConcerning role norms, gender difference in knowledge sharing behavior (KSB) is found, while it is not the case for knowledge quality (KQ). Work experience is found to positively affect KQ, but shows no influence on KSB. As for group norms, the inverted-U relationship between number of members and KSB is partially supported. In addition, organizational norms generally exhibit the greatest influence on both KSB and KQ among the three forms of norms.Originality/valueThis study deepens the understanding of knowledge sharing factors in mobile social media environments and affords practical implications for how to make full use of social media for knowledge management within construction project teams.
Blood is thicker than water: an analysis of women’s presence on Pakistani boards
Authors: Wagner Eva , Pernsteiner Helmut , Riaz Aisha 
Published: September 2023

Purpose
This study aims to provide insights into gender diversity in Pakistani boardrooms, particularly for the dominant family business type, which is strongly guided by (non-financial) family-related objectives when making business decisions, such as the appointment of board members. Pakistani companies operate within the framework of weak legal institutions and a traditionally highly patriarchal environment. This study examines how corporate decisions regarding the appointment of female board members play out in this socio-political and cultural environment.

Design/methodology/approach
Board composition and board characteristics were examined using hand-collected data from 213 listed family firms and non-family firms on the Pakistan Stock Exchange from 2003 to 2017. Univariate analyses, probit regressions and robustness tests were performed.

Findings
Pakistani family firms have a significantly higher proportion of women on their boards than do non-family firms. They are also significantly more likely to appoint women to top positions, such as CEO or chairs.

Practical implications
Evidently, women are allowed to enter boards through family affiliations. Gender quotas appear an ineffective instrument for breaking through the “glass ceiling” in this socio-cultural environment. Thus, gender parity must entail the comprehensive promotion of women and the enforcement of legal reforms for structural and cultural change.

Originality/value
The analysis focuses on a Muslim-majority emerging Asian market that has been scarcely researched, thus offering new perspectives and insights into board composition and corporate governance that go beyond the well-studied Western countries.
Using immersive technologies to enhance the student learning experience
Authors: Baxter Gavin , Hainey Thomas 
Published: September 2023

Purpose
The purpose of this paper is to evaluate undergraduate student perceptions about the application of immersive technologies for enhancing the student learning experience. This study assesses the viewpoints of students from varying multidisciplinary backgrounds about whether immersive technologies can enhance their learning experience and increase their level of engagement in the context of higher educational delivery.

Design/methodology/approach
The research used a case study methodology adopting a questionnaire-based research mixed methods approach. In total, 83 participants completed the questionnaire. The purpose of the research was to evaluate and interpret students’ perspectives at higher educational level about the use of immersive technologies towards enhancing their learning experience. There was also a focus on remote educational delivery due to the legacy of COVID-19.

Findings
The findings suggest that there is still more empirical work to be undertaken regarding the application of immersive technologies in higher education. The study revealed that there are immersive benefits though preference for face-to-face teaching remains popular. The negative connotations associated with immersive technology use in higher education, (e.g. virtual reality), such as cost of equipment and motion sickness, substantiates the themes identified in the academic literature.

Originality/value
The study explores a diversity of immersive technologies and their application in higher education (HE) contexts. Findings indicate that although there are acknowledged pedagogical benefits of immersive technology use in HE prevalent barriers remain that require further empirical research if immersive technology use is to be universally used in the sector.
Analytical modeling and optimal design of clamped sandwich beams with cellular cores subjected to shock loading
Authors: Li Lang , Li Jiahui , Zhang Fan , Jia Fusen , Li Lei 
Published: September 2023

PurposeSandwich structures with well-designed cellular cores exhibit superior shock resistance compared to monolithic structures of equal mass. This study aims to develop a comprehensive analytical model for predicting the dynamic response of cellular-core sandwich structures subjected to shock loading and investigate their application in protective design.Design/methodology/approachFirst, an analytical model of a clamped sandwich beam for over-span shock loading was developed. In this model, the incident shock-wave reflection was considered, the clamped face sheets were simplified using two single-degree-of-freedom (SDOF) systems, the core was idealized using the rigid-perfectly-plastic-locking (RPPL) model in the thickness direction and simplified as an SDOF system in the span direction. The model was then evaluated using existing analytical models before being employed to design the sandwich-beam configurations for two typical engineering applications.FindingsThe model effectively predicted the dynamic response of sandwich panels, especially when the shock-loading pulse shape was considered. The optimal compressive cellular-core strength increased with increasing peak pressure and shock-loading impulse. Neglecting the core tensile strength could result in an overestimation of the optimal compressive cellular-core strength.Originality/valueA new model was proposed and employed to optimally design clamped cellular-core sandwich-beam configurations subjected to shock loading.