bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of neonatal brain functional centrality and alterations associated with preterm birth
Authors: Fenn-Moltu Sunniva , Fitzgibbon Sean P , Ciarrusta Judit , Eyre Michael , Cordero-Grande Lucilio , Chew Andrew , Falconer Shona , Gale-Grant Oliver , Harper Nicholas , Dimitrova Ralica , Vecchiato Katy , Fenchel Daphna , Javed Ayesha , Earl Megan , Price Anthony N , Hughes Emer , Duff Eugene P , O’Muircheartaigh Jonathan , Nosarti Chiara , Arichi Tomoki , Rueckert Daniel , Counsell Serena , Hajnal Joseph V , Edwards A David , McAlonan Grainne , Batalle Dafnis 
Published: June 2022

AbstractFormation of the functional connectome in early life underpins future learning and behaviour. However, our understanding of how the functional organisation of brain regions into interconnected hubs (centrality) matures in the early postnatal period is limited, especially in response to factors associated with adverse neurodevelopmental outcomes such as preterm birth. We characterised voxel-wise functional centrality (weighted degree) in 366 neonates from the Developing Human Connectome Project. We tested the hypothesis that functional centrality matures with age at scan in term-born babies and is disrupted by preterm birth. Finally, we asked whether neonatal functional centrality predicts general neurodevelopmental outcomes at 18 months. We report an age-related increase in functional centrality predominantly within visual regions and decrease within motor and auditory regions in term-born infants. Preterm-born infants scanned at term equivalent age had higher functional centrality predominantly within visual regions and lower measures in motor regions. Functional centrality was not related to outcome at 18 months old. Thus, preterm birth appears to affect functional centrality in regions undergoing substantial development during the perinatal period. Our work raises the question of whether these alterations are adaptive or disruptive, and whether they predict neurodevelopmental characteristics that are more subtle or emerge later in life.
Proactive inhibition of goal-directed movements involves explicit changes to movement planning
Authors: Pickavance John P. , Mon-Williams M. , Mushtaq Faisal , Morehead J. Ryan 
Published: June 2022

ABSTRACTInhibition can be implemented reactively, withholding movement in response to a stop-signal, or by proactive changes to movement planning when a stop-signal is expected. Previous studies have typically employed simple button presses, finding proactive delays to movement onset when a stop-signal might appear. Here, we consider inhibition in the context of more complex, goal-directed movements, such as the swing of a bat. Thus, we observe two additional dimensions of movement planning under proactive control, movement duration and end-point error. We found, in addition to onset delay, movements were briefer and arrived later when a stop-signal might appear. This challenges a classical theoretical dichotomy, suggesting proactive inhibition is underlay by both response suppression and delayed facilitation. Moreover, participants were aware of delays to onset and arrival, but reported magnitudes were smaller than observed. This suggests proactive inhibition operates as an explicitly retrievable compensatory strategy whose finer details are implicitly tuned.
Dissociation of CED-4 from CED-9 upon EGL-1 binding: Molecular mechanism of linear apoptotic pathway inCaenorhabditis elegans
Authors: Reddy C. Narendra , Sankararamakrishnan Ramasubbu 
Published: June 2022

AbstractMany steps in programmed cell death are evolutionarily conserved across different species. TheCaenorhabditis elegansproteins CED-9, CED-4 and EGL-1 involved in apoptosis are respectively homologous to anti-apoptotic Bcl-2 proteins, Apaf-1 and the “BH3-only” pro- apototic proteins in mammals. In the linear apoptotic pathway ofC.elegans, EGL-1 binding to CED-9 leads to the release of CED-4 from CED-9/CED-4 complex. The molecular events leading to this process are not clearly elucidated. While the structures of CED-9 apo, CED- 9/EGL-1 and CED-9/CED-4 complexes are known, the CED-9/CED-4/EGL-1 ternary complex structure is not yet determined. In this work, we modeled this ternary complex and performed molecular dynamics simulations of six different systems involving CED-9. CED-9 displays differential dynamics depending upon whether it is bound to CED-4 and/or EGL-1. CED-4 exists as an asymmetric dimer (CED4a and CED4b) in CED-9/CED-4 complex. CED-4a exhibits higher conformational flexibility when simulated without CED-4b. Principal Component Analysis revealed that the direction of CED-4a’s winged-helix domain motion differs in the ternary complex. Upon EGL-1 binding, majority of non-covalent interactions involving CARD domain in the CED-4a-CED-9 interface have weakened and only half of the contacts found in the crystal structure between α/β domain of CED4a and CED-9 are found to be stable. Additional stable contacts in the ternary complex and differential dynamics indicate that winged-helix domain may play a role in CED-4a’s dissociation from CED-9. This study has provided a molecular level understanding of potential intermediate states that are likely to occur at the time of CED-4a’s release from CED-9.
In-text citation error rate as a scientometric tool for evaluating accuracy and weighing evidence
Authors: Lee Derek E. 
Published: June 2022

AbstractScientists are fallable and biased, but accuracy can be assessed through empirical analysis of published work that quantifies in-text citation (or quotation) errors. In scientific conflicts, it can be difficult for outsiders to know whose evidence or interpretation to trust. In-text citation error rate can assist decision- and policy-making bodies, as well as the courts when conflicts reach the judicial branch of government, by quantifying absolute and relative accuracy of scientists presenting scientific evidence. I propose the use of in-text citation error rates as a scientometric tool to quantify the accuracy of an author’s work. In-text citation error rates in excess of an established overall mean (e.g., 11% for minor errors and 7% for major errors in ecology), or differences in in-text citation error rates between opposing groups of scientists could be used to reveal excessive inaccuracies in an author or group. The spotted owl (Strix occidentalis) has been at the center of a multi-decadal conflict caused by competition among people over forest resources, with scientific experts representing opposing stakeholders often presenting conflicting evidence. I applied the in-text citation error rate tool to important papers in the spotted owl and forest fire debate and found evidence of greater error rates in works on one side of this debate. In-text citation error rate can be an effective tool for quantifying accuracy among scientists.
Immune-mediated Tubule Atrophy Promotes Acute Kidney Injury to Chronic Kidney Disease Transition
Authors: Xu Leyuan , Guo Jiankan , Moledina Dennis G. , Cantley Lloyd G. 
Published: June 2022

ABSTRACTIncomplete repair after acute kidney injury (AKI) is associated with progressive loss of tubular cell function and development of chronic kidney disease (CKD). Here, we compared mice subjected to either unilateral ischemia-reperfusion kidney injury with contralateral nephrectomy (IRI/CL-NX, in which tubule repair predominates) or unilateral IRI with contralateral kidney intact (U-IRI, in which fibrosis and atrophy predominates) to investigate the mechanism(s) underlying transition to CKD following AKI. The initial injury and early recruitment and activation of macrophages, dendritic cells (DCs), neutrophils, and T cells were similar through day 7 but markedly diverged afterwards between the two models. By day 14, kidneys subjected to U-IRI had greater numbers of macrophages with higher expression of Ccl2, Ccl7, Ccl8, Ccl12, and Cxcl16. These chemokines correlated with a second wave of Ccr1-positive neutrophils and Cxcr6-positive T cells, resulting in a proinflammatory milieu, accompanied by increased expression of tubular cell injury, oxidative stress and major histocompatibility complex genes. This second wave of immune dysfunction led to a distinct profile of tubule injury with morphologic kidney atrophy and a decreased proportion of differentiated tubule cells. Combined depletion of neutrophils and T cells beginning on day 5 after U-IRI was found to reduce tubular cell loss and the associated kidney atrophy. In kidney biopsy samples from patients with AKI, the number of interstitial T cells and neutrophils negatively correlated with 6-month recovery of GFR. Together, our findings demonstrate that macrophage persistence after AKI promotes a T cell- and neutrophil-mediated proinflammatory milieu that leads to progressive tubule damage.
Automated protein-protein structure prediction of the T cell receptor-peptide major histocompatibility complex
Authors: Rollins Zachary A. , Curtis Matthew B. , Faller Roland , George Steven C. 
Published: June 2022

ABSTRACTT Cell Receptor (TCR) recognition of a peptide-major histocompatibility complex (pMHC) is a crucial component of the adaptive immune response. The identification of therapeutically relevant TCR-pMHC pairs is a significant bottleneck in the implementation of TCR-based immunotherapies but may be augmented by computational methodologies. The ability to computationally design TCRs to target a specific pMHC will require an automated integration of next-generation sequencing, protein-protein structure prediction, molecular dynamics (MD), and TCR ranking. We present a generic pipeline to evaluate patient-specific, sequence-based TCRs to a target pMHC. Using the three most frequently expressed TCRs from 16 colorectal cancer patients, we predicted the protein-protein structure of the TCRs to the target CEA peptide-MHC using Modeller and ColabFold. Then, these TCR-pMHC structures were compared by performing an automated molecular dynamics equilibration. ColabFold generates starting configurations that require, on average, a ~2.5X reduction in simulation time to equilibrate TCR-pMHC structures compared to Modeller. In addition, the structural differences between Modeller and ColabFold are demonstrated by an increase in root mean square deviation (~0.20 nm) between clusters of equilibrated configurations, which can impact the number of hydrogen bonds and Lennard-Jones contacts between the TCR and pMHC. Finally, we identify a TCR ranking criteria that may be used to prioritize TCRs for evaluation of in vitro immunogenicity.
Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD+ regeneration in KRas-mutant lung adenocarcinoma
Authors: Sessions Dane T. , Kim Kee-Beom , Kashatus Jennifer A. , Churchill Nikolas , Park Kwon-Sik , Mayo Marty W. , Sesaki Hiromi , Kashatus David F. 
Published: June 2022

SummaryOncogenic KRas activates mitochondrial fission through Erk-mediated phosphorylation of the mitochondrial fission GTPase Drp1. Drp1 deletion inhibits tumorigenesis of KRas-driven pancreatic cancer, but the role of mitochondrial dynamics in other Ras-driven malignancies is poorly defined. Here we demonstrate that in vitro and in vivo growth of KRas-driven lung adenocarcinoma is unaffected by deletion of Drp1, but inhibited by deletion of Opa1, the GTPase that regulates inner membrane fusion and promotes proper cristae morphology. Mechanistically, Opa1 knockout induces loss of electron transport chain (ETC) complex I assembly and activity that inhibits tumor cell proliferation through loss of NAD+ regeneration. Simultaneous inactivation of Drp1 and Opa1 restores cristae morphology, complex I activity and cell proliferation indicating that mitochondrial fission activity drives ETC dysfunction induced by Opa1 knockout. Our results support a model in which mitochondrial fission events disrupt cristae structure and tumor cells with hyperactive fission activity require Opa1 activity to maintain ETC function.
SVDquintets: a New Tool for Species Tree Inference
Authors: Richards A. 
Published: June 2022

1AbstractSpecies tree inference is complicated by the fact that different segments have the genome can have evolutionary histories that differ from each other and from the evolutionary history of the species as a whole. One source of this mismatch is incomplete lineage sorting (ILS), which is commonly modeled by the multispecies coalescent process. Here we derive site pattern probabilities under the multispecies coalescent model, the Jukes-Cantor substitution model, and a relaxed molecular clock for five species at a time. As a result, we can demonstrate that the rank results that form the theoretical basis for SVDQuartets also appear to hold for sets of five species. Based on this, we have developed a new species tree inference algorithm: SVDquintets. Comparison with SVDQuartets shows improved species tree inference under a variety of simulated data settings.
Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs
Authors: Han Seong Kyu , McNulty Michelle T. , Benway Christopher J. , Wen Pei , Greenberg Anya , Onuchic-Whitford Ana C. ,   NEPTUNE, Wilson Parker C. , Humphreys Benjamin D. , Wen Xiaoquan , Han Zhe , Lee Dongwon , Sampson Matthew G. 
Published: June 2022

AbstractExpression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5,371 GLOM and 9,787 TUBE eQTLs by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an “integrative prior” for Bayesian statistical fine mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses.
Abdominal movements in insect flight reshape the role of non-aerodynamic structures for flight maneuverability I: Model predictive control for flower tracking
Authors: Bustamante Jorge , Ahmed Mahad , Deora Tanvi , Fabien Brian , Daniel Thomas L. 
Published: June 2022

AbstractResearch on insect flight control has focused primarily on the role of wings. Yet abdominal deflections during flight can potentially influence the dynamics of flight. This paper assesses the role of airframe deformations in flight, and asks to what extent the abdomen contributes to flight maneuverability. To address this, we use a combination of both a Model Predictive Control (MPC)-inspired computational inertial dynamics model, and free flight experiments in the hawkmoth, Manduca sexta. We explored both underactuated (i.e. number of outputs are greater than the number of inputs) and fully actuated (equal number of outputs and inputs) systems. Using metrics such as the non-dimensionalized tracking error and cost of transport to evaluate flight performance of the inertial dynamics model, we show that fully actuated simulations minimized the tracking error and cost of transport. Additionally, we tested the effect of restricted abdomen movement on free flight in live hawkmoths by fixing a carbon fiber rod over the thoracic-abdomen joint. Moths with a restricted abdomen performed worse than sham treatment moths. This study finds that abdominal motions contribute to flight control and maneuverability. Such motions of non-aerodynamic structures, found in all flying taxa, can inform the development of multi-actuated micro air vehicles.
Evaluation of folliculin detection by immunohistochemistry in Birt-Hogg-Dubé associated kidney tumors
Authors: Glykofridis Iris E. , van de Beek Irma , Vos Wim , Kortman Pim C. , van de Valk Paul , Freire Raimundo , Houweling Arjan C. , Wolthuis Rob M.F. 
Published: June 2022

AbstractGermline inactivating mutations in folliculin (FLCN) cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing to kidney tumors. Kidney tumors associated with BHD typically lack FLCN expression due to loss of heterozygosity. In this study we assessed the potential of four commercial anti-FLCN antibodies for immunohistochemistry, as currently no routine diagnostic FLCN stainings are performed in the clinic. Despite comprehensive testing, we could not identify a commercial anti-FLCN antibody that is reproducibly effective in immunohistochemical analyses of formalin-fixed paraffin-embedded tissue material. We propose that dedicated future efforts are required to develop a suitable antibody for diagnostic immunohistochemical stainings. The inclusion of FLCN expression status as part of standard renal tumor pathology may contribute to better analyses of the molecular pathology of BHD tumors and facilitate identification of BHD patients, improve their (genetic and clinical) counseling, and enable genetic testing of at risk relatives.
The interplay of IPD and BIM: a systematic literature review
Authors: Karasu Taha , Aaltonen Kirsi , Haapasalo Harri 
Published: June 2022

Purpose
Integrated project delivery (IPD) and building information modeling (BIM) have been discussed as prominent collaborative concepts in recent architecture, engineering and construction (AEC) literature, thus recommended for more advanced value creation. However, they have been studied predominantly as discrete even though they are typically highly interrelated. This study aims to enhance collaboration in AEC projects by tracing recent trends in IPD and BIM literature by making sense of trends and by exploring how their interplay has been discussed and conceptualized.

Design/methodology/approach
This systematic literature review draws on Scopus and Web of Science as the primary databases. In total, 120 academic papers and review articles were sourced. Yet, the final sample includes 71 sources from the past decade (2011–2020), focusing on both IPD and BIM.

Findings
This study identifies 11 interrelated and overlapping themes that are indicative of trends in the recent IPD and BIM literature. This research found that among the identified themes, the clusters of sustainability, transformation and increasing the competence level of staff in the AEC industry, in addition to the concept of quality, require more extensive research in the context of IPD and BIM. Additionally, this study identifies four different approaches to the interplay of IPD and BIM, indicating an absence of scholarly consistency.

Originality/value
Based on the systematic analysis of the recent literature, this study indicates that IPD and BIM have several joint fundamental cornerstones. It is evident that both concepts support the implementation of each other. The success of implementing either one is strongly related to the other. Additionally, we have not found earlier systematic literature reviews that examine the interplay between IPD and BIM in the recent AEC literature.
Generation Z domestic food tourists’ experienced restaurant innovativeness toward destination cognitive food image and revisit intention
Authors: Ding Li , Jiang Caifen , Qu Hailin 
Published: June 2022

Purpose
This study aims to investigate the impacts of Generation Z (Gen Z) domestic food tourists’ perceived restaurant innovativeness on destination cognitive food image and examine the impacts of destination cognitive food image on destination brand image and tourists’ revisit intention.

Design/methodology/approach
Data were collected through an online survey, and 337 Gen Z domestic food tourists in Guangzhou participated. Partial least squares structural equation modeling was used for the data analysis.

Findings
This study found that tourists’ perceptions of restaurant menu, technology-based service and experiential innovativeness played essential roles in enhancing destination cognitive food image. In addition, the destination cognitive food image strengthened the destination brand image and increased tourists’ revisit intentions for the future.

Practical implications
The destination cognitive food image perceived by Gen Z domestic food tourists is affected by the restaurant menu, technology-based service and experiential innovativeness. To build a solid destination food image, restaurant operators and decision-makers should prioritize the allocation of resources to develop their innovation capacity. This study also suggests a path of food tourism destination branding from stakeholders’ perspectives and encourages collaboration with stakeholders. Enhanced food tourism destination competitiveness toward the young tourists’ market will generate an overall win for stakeholders

Originality/value
Food providers’ innovativeness, an important factor attracting young tourists’ attention, has been neglected in the discussion of the food tourism experience. This study fills the research gap, investigates the importance of restaurant innovativeness in building food tourism destination competitiveness and provides valuable suggestions to destination restaurant operators and decision-makers.
Conflict in virtual teams: a bibliometric analysis, systematic review, and research agenda
Authors: Caputo Andrea , Kargina Mariya , Pellegrini Massimiliano Matteo 
Published: June 2022

PurposeThe purpose of this study is to map the intellectual structure of the research concerning conflict and conflict management in virtual teams (VT), to contribute to the further integration of knowledge among different streams of research and to develop an interpretative framework to stimulate future research.Design/methodology/approachA data set of 107 relevant papers on the topic was retrieved using the Web of Science Core Collection database covering a period ranging from 2001 to 2019. A comparative bibliometric analysis consisting of the integration of results from the citation, co-citation and bibliographic coupling was performed to identify the most influential papers. The systematic literature review complemented the bibliometric results by clustering the most influential papers.FindingsThe results revealed different intellectual structures across several types of analyses. Despite such differences, 41 papers resulted as the most impactful and provided evidence of the emergence of five thematic clusters: trust, performance, cultural diversity, knowledge management and team management.Research limitations/implicationsBased on the bibliometric analyses an interpretative research agenda has been developed that unveils the main future research avenues. The paper also offers important theoretical contributions by systematizing knowledge on conflict in identifying VTs. Managerial contributions in the form of the identification of best practices are also developed to guide conflict management in VTs.Originality/valueThe uniqueness of this paper is related to its effort in studying, mapping and systematizing the knowledge concerning the topic of handling conflicts in VTs. Considering the current contingencies, this research is particularly timely.