bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative substitutions of N332 in HIV-1AD8gp120 differentially affect envelope glycoprotein function and viral sensitivity to broadly neutralizing antibodies targeting the V3-glycan
Authors: Jeffy Jeffy , Parthasarathy Durgadevi , Ahmed Shamim , Cervera-Benet Héctor , Xiong Ulahn , Harris Miranda , Mazurov Dmitriy , Pickthorn Stephanie , Herschhorn Alon 
Published: November 2023

ABSTRACTThe envelope glycoprotein (Env) trimer on the surface of human immunodeficiency virus type I (HIV-1) mediates viral entry into host CD4+ T cells and is the sole target of neutralizing antibodies. Broadly neutralizing antibodies (bnAbs) that target gp120 V3-glycan of HIV-1 Env trimer are potent and block the entry of diverse HIV-1 strains. Most V3-glycan bnAbs interact, to a different extent, with a glycan attached to N332 but Asn at this position is not absolutely conserved or required for HIV-1 entry based on prevalence of N332 in different circulating HIV-1 strains from diverse clades. Here, we studied the effects of amino acid changes at position 332 of HIV-1AD8Envs on HIV-1 sensitivity to antibodies, cold exposure, and soluble CD4. We further investigated how these changes affect Env function and HIV-1 infectivityin vitro. Our results suggest robust tolerability of HIV-1AD8Env N332 to changes with specific changes that resulted in extended exposure of gp120 V3 loop, which is typically concealed in most primary HIV-1 isolates. Viral evolution leading to Asn at position 332 of HIVAD8Envs is supported by the selection advantage of high levels of cell-cell fusion, transmission, and infectivity even though cell surface expression levels are lower than most N332 variants. Thus, tolerance of HIV-1AD8Envs to different amino acids at position 332 provides increased flexibility to respond to changing conditions/environments and to evade the immune system. Modeling studies of the distance between N332 glycan and specific bnAbs was in agreement with N332 glycan dependency on bnAb neutralization. Overall, our studies provide insights into the contribution of specific amino acids at position 332 to Env antigenicity, stability on ice, and conformational states.
vmrseq: probabilistic modeling of single-cell methylation heterogeneity
Authors: Shen Ning , Korthauer Keegan 
Published: November 2023

AbstractSingle-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated regions (VMRs) have relied on predefined regions or sliding windows, and report regions insensitive to heterogeneity level present in input. We present vmrseq, a statistical method that overcomes these challenges to detect VMRs with increased accuracy in synthetic benchmarks and improved feature selection in case studies. vmrseq also highlights context-dependent correlations between methylation and gene expression, supporting previous findings and facilitating novel hypotheses on epigenetic regulation. vmrseq is available athttps://github.com/nshen7/vmrseq.
Structure of the γ-tubulin ring complex-capped microtubule
Authors: Aher Amol , Urnavicius Linas , Xue Allen , Neselu Kasahun , Kapoor Tarun M. 
Published: November 2023

AbstractMicrotubules are composed of α/β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the filament’s long-axis. We report that the human ∼2.3MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryo-EM reconstructions of γ-TuRC-capped microtubule minus-ends reveal the extensive intra- and inter-domain motions of γ-TuRC subunits that accommodate its actin-containing luminal bridge and establish lateral and longitudinal interactions between γ- and α-tubulins. Our structures reveal how free γ-TuRC, an inefficient nucleation template due to its splayed conformation, transforms into a stable cap that blocks addition or loss of α/β-tubulins from minus-ends and sets the lattice architecture of cellular microtubules.One Sentence SummaryStructural insights into how the γ-tubulin ring complex nucleates and caps a 13-protofilament microtubule.
XCP-D: A Robust Pipeline for the post-processing of fMRI data
Authors: Mehta Kahini , Salo Taylor , Madison Thomas , Adebimpe Azeez , Bassett Danielle S. , Bertolero Max , Cieslak Matthew , Covitz Sydney , Houghton Audrey , Keller Arielle S. , Luo Audrey , Miranda-Dominguez Oscar , Nelson Steve M. , Shafiei Golia , Shanmugan Sheila , Shinohara Russell T. , Sydnor Valerie J. , Feczko Eric , Fair Damien A. , Satterthwaite Theodore D. 
Published: November 2023

ABSTRACTFunctional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.
Nonlinear readout of spatial cues underlies robustness of asymmetric cell division
Authors: Rodrigues Nelio T.L. , Bland Tom , Ng KangBo , Hirani Nisha , Goehring Nathan W. 
Published: November 2023

AbstractA key challenge in the development of an organism is to maintain robust phenotypic outcomes in the face of perturbation. Yet, how such robust outcomes are encoded by developmental networks remains poorly explored. Here we use theC. eleganszygote as a model to understand sources of developmental robustness during PAR polarity-dependent asymmetric cell division. By quantitatively linking alterations in protein dosage to phenotype in individual embryos, we show that spatial information in the zygote is read out in a highly nonlinear fashion and, as a result, phenotypes are highly canalized against substantial variation in input signals. Specifically, our data point towards an intrinsic robustness of the conserved PAR polarity network that renders polarity axis specification resistant to variations in both the strength of upstream symmetry-breaking cues and PAR protein dosage. At the same time, we find that downstream pathways involved in cell size and fate asymmetry are similarly robust to dosage-dependent changes in the local concentrations of PAR proteins, implying non-trivial complexity in translating PAR signals into pathway outputs. We propose that “quantitative decoupling” of symmetry-breaking, polarity, and asymmetric division modules acts to suppress the accumulation of error as embryos move along this developmental trajectory, thereby ensuring that asymmetric division is robust to perturbation. Such modular organization of developmental networks is likely to be a general mechanism to achieve robust developmental outcomes.
Theoretical exploration of executive compensation in state-owned enterprises
Authors: Zhang Chi 
Published: November 2023

PurposeThis paper aims to establish a theoretical framework that can comprehensively explain the executive compensation in state-owned enterprises (SOEs) within the context of socialism with Chinese characteristics.Design/methodology/approachThe author develops a theoretical framework for executive compensation in SOEs from the perspective of Marxist economics and points out that the executives in SOEs are engaged in management labor, and their compensation should adhere to the principle of distribution according to labor contribution.FindingsBased on this theory, the author posits that the continuous upward trend of executive compensation in SOEs, is consistent with the trend of SOEs' ongoing expansion, which reflects a continuous improvement of SOE executives' management labor in both quality and quantity.Originality/valueIt is necessary to start with Marxist economic theory and scientifically study the issue of SOE executive compensation, adhere to the principle of distribution according to work in the context of a socialist market economy and implement the specific guideline of the Party Central Committee; only in this way can the long-term healthy development of SOEs be promoted continuously.
Using mixed methods in logistics and supply chain management research: current state and future directions
Authors: Grant David B. , Shaw Sarah , Sweeney Edward , Bahr Witold , Chaisurayakarn Siriwan , Evangelista Pietro 
Published: November 2023

PurposeMixed methods research is useful to enhance theoretical and practical research contributions. However, single methods have predominated much logistics and supply chain management (LSCM) research. This paper presents a review of mixed methods research across ten years in LSCM to determine their usage, identify benefits and inhibitors, and provide suggestions for LSCM researchers to realise the benefits from using mixed methods.Design/methodology/approachThis paper adopts a mixed methods approach through a quantitative analysis of methods used in six leading LSCM journals, an e-mail survey of mixed methods article authors during the review period, and four published case studies that used mixed methods.FindingsOnly 144 (ten percent) of all empirical articles were published using mixed methods during the review period. A range of benefits and inhibitors regarding mixed methods adoption were found. Suggestions for LSCM authors include research training in mixed methods use and developing a project-specific research design due to the specificity and complexity associated with mixed methods research.Originality/valueLSCM is at a critical juncture, shaped by new contexts, themes and challenges, and would benefit from different research approaches and methods. This paper contributes to the LSCM domain through analysing the current state, benefits and inhibitors of mixed methods research in LSCM journals to provide a renewed call to action and guidelines for mixed methods LSCM research, and suggesting research design adaptation to enable agile and resilient research when investigating rapidly changing and complex phenomena.
Increasing plant species diversity suppresses free‐living N2 fixation in litter and soil of a subtropical karst forest
Authors: Fang Yuantian , He Xunyang , Gao Kun , Zhu Zihong , Wang Kelin , Li Dejun 
Published: November 2023

Abstract

Free‐living N2 fixation (FNF) is an important source of bioavailable nitrogen for forests. Though increasing plant species diversity (PSD) benefits soil nitrogen accumulation, how it impacts FNF rate has not been explored.

Forty‐five plots covering a PSD gradient were selected in a subtropical karst forest, southwest China. FNF rates in leaf litter and soil were measured using acetylene reduction assay calibrated with a 15N2 fixation method. Diazotrophic community, litter and soil properties were determined as well.

The nifH gene abundance was not significantly altered in litter but was significantly decreased in soil by higher PSD. Diazotrophic community's Shannon diversity was significantly increased by higher PSD in both litter and soil. Increasing PSD inhibited litter FNF rate via aggravating phosphorus limitation and decreasing the relative abundance of Betaproteobacteria and Deltaproteobacteria. For the mineral soil horizon, increasing PSD suppressed FNF rate via decreasing nifH gene abundance caused by elevated N availability and lowered phosphorus and iron availability or through decreasing the relative abundance of Deltaproteobacteria but increasing that of Betaproteobacteria.

Our findings, for the first time, reveal the microbial and abiotic controls on FNF in litter and soil in response to PSD, and hence benefit the prediction of nitrogen input via biological N2 fixation under changes in PSD.

Read the free Plain Language Summary for this article on the Journal blog.
Gravity and magnetic exploration applied to iron ore deposits in the Sierra Grande area, Río Negro Province, Argentina
Authors: Bahía Marcos E. , Strazzere Leonardo , Benedini Leonardo , Gregori Daniel A. , Kostadinoff José 
Published: November 2023

AbstractThe Ordovician–Devonian Sierra Grande Formation, Río Negro Province, Argentina contains three quarzitic members with two iron horizons. Its South Deposit includes both iron horizons. However, the East Deposit is relatively unknown, lacking information about geometry, depth and reserves. To answer these questions, we apply geophysical methods for the rapid evaluation of the East Deposit, using gravity and magnetic measures. The processing of these data allows the suggestion of two 2D models for calculating thicknesses, angles and depth of the iron horizons. The adjustments between the calculated and the observed curve are less than 6%. One model proposes the existence of the Alfaro iron horizon, and the other one proposes the presence of the Rosales iron horizon at depth. The Bouguer anomaly gravimetric maps allow us to calculate the mineral mass, resulting in 125 million iron tons. Thus, this study allowed us to calculate the thicknesses, angles and depth of both iron horizons, and to adjust and evaluate the mineral reserves with the maximum reliability that potential methods allow when applied to mineral prospecting. These results provide new and valuable information for future mining prospects.
Transcriptomic analysis of the effect of shaking and tumbling degree on quality formation of Wuyi rock tea
Authors: Chen Meihui , Zhang Ying , Wang Yuhua , Cheng Pengyuan , Zhang Qi , Li Mingzhe , Jia Xiaoli , Pan Yibin , Lin Shaoxiong , Luo Zhengwei , Wang Haibin , Ye Jianghua 
Published: November 2023

AbstractShaking and tumbling are extremely important for the formation of the special flavor of Wuyi rock tea. In this study, we analyzed the effects of different shaking and tumbling degrees on the quality index content of tea leaves and determined changes in gene expression in tea leaves using RNA sequencing technology. On this basis, the correlation between gene expression intensities in tea leaves and tea quality index content was analyzed. The results showed that heavy shaking and tumbling (MW3) increased gene expression of metabolic pathways, biosynthesis of secondary metabolites, starch and sucrose metabolism, biosynthesis of amino acids, glycine, serine, and threonine metabolism, alpha‐linolenic acid metabolism pathways and decreased gene expression of flavonoid biosynthesis, carbon fixation in photosynthetic organisms, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways in tea leaves, which in turn increased the content of caffeine, soluble sugar, amino acid and decreased the content of flavone, tea polyphenol, catechin component in tea leaves; the opposite was true for light shaking and tumbling. Second, this study found that MW3 was more beneficial in improving the mellowness, sweetness, and fresh and brisk taste of tea leaves and reducing the bitterness of tea leaves. This study provides some references to guide the processing of Wuyi rock tea with different flavors.Practical ApplicationHeavy shaking and tumbling was more beneficial in improving the mellowness, sweetness, and fresh and brisk taste of tea leaves and reducing the bitterness of tea leaves. Therefore, the degree of shaking and tumbling in Wuyi production can be appropriately improved to produce high‐quality tea and improve the economic benefits of tea.
Temporal associations of diabetes‐related complications with health‐related quality of life decrements in Chinese patients with type 2 diabetes: A prospective study among 19 322 adults—Joint Asia Diabetes Evaluation (JADE) register (2007–2018)
Authors: Lui Juliana N. M. , Lau Eric S. H. , Yang Aimin , Wu Hongjiang , Fu Amy , Lau Vanessa , Loo Kitman , Yeung Theresa , Yue Rebecca , Ma Ronald C. W. , Kong Alice P. S. , Ozaki Risa , Luk Andrea O. Y. , Chow Elaine Y. K. , Chan Juliana C. N. 
Published: November 2023

AbstractBackgroundPatients with type 2 diabetes (T2D) are at high risk of developing multiple complications, affecting their health‐related quality of life (HRQoL). Existing studies only considered impact of complication on HRQoL in the year of occurrence but not its residual impacts in subsequent years. We investigated temporal impacts of diabetes‐related complications on HRQoL in a 12‐year prospective cohort of ambulatory Chinese patients with T2D enrolled in the clinic‐based Joint Asia Diabetes Evaluation (JADE) Register.MethodsHRQoL utility measures were derived from EuroQol five‐dimensional three‐level questionnaire (EQ‐5D‐3L) questionnaires completed by 19 322 patients with T2D in Hong Kong (2007–2018). Temporal EQ‐5D utility decrements associated with subtypes of cardiovascular‐renal events were estimated using generalized linear regression model after stepwise selection of covariates with p < .01 as cutoff.ResultsIn this cohort (mean ± SD age:61.2 ± 11.5 years, 55.3% men, median [interquartile range] duration of diabetes:10.1 [3.0–15.0] years, glycated hemoglobin [HbA1C] 7.5 ± 1.5%), EQ‐5D utility was 0.860 ± 0.163. The largest HRQoL decrements were observed in year of occurrence of hemorrhagic stroke (−0.230), followed by ischemic stroke (−0.165), peripheral vascular disease (−0.117), lower extremity amputation (−0.093), chronic kidney disease (CKD) G5 without renal replacement therapy (RRT) (−0.079), congestive heart failure (CHF) (−0.061), and CKD G3–G4 without RRT (−0.042). Residual impacts on HRQoL persisted for 2 years after occurrence of CHF or ischemic stroke and 1 year after hemorrhagic stroke or CKD G3–G4 without RRT.ConclusionThis is the first comprehensive report on temporal associations of HRQoL decrements with subtypes of diabetes‐related complications in ambulatory Asian patients with T2D. These data will improve the accuracy of cost‐effectiveness analysis of diabetes interventions at an individual level in an Asian setting.image
Parkinson's disease physical therapy services during COVID‐19: A phenomenological study
Authors: Tham Alexa Y. Z. , Harrison Eloise , Farlie Melanie K. 
Published: November 2023

AbstractObjectivesParkinson's disease (PD) is the most rapidly increasing movement disorder globally. Physical therapies improve the motor and non‐motor symptoms of PD. During the COVID‐19 pandemic, telehealth was the primary method of physical therapy service adaptation in response to restrictions preventing in‐person therapy attendance. This study explores the perspectives of people with PD and their therapists who experienced physical therapy service delivery before and during the COVID‐19 pandemic in Melbourne, Australia.MethodsA phenomenological study that purposively recruited patients and therapists from a movement disorders service at an outer metropolitan rehabilitation hospital. Participants completed in‐depth interviews, and data were analysed using reflexive thematic analysis.ResultsTen people with PD and five therapists completed interviews. Six themes were identified: patients value access to therapy, a key mechanism is trust, an opportunity to empower patients, ticking boxes for telehealth, contrasting experiences of telehealth and something is better than nothing.ConclusionsThis study explored the experiences of people with PD and their therapists by contrasting their prepandemic and in‐pandemic experiences. People with PD valued telehealth access during the pandemic, but extra support was initially required to use telehealth successfully. Empowering aspects of telehealth included patients learning new skills and self‐management strategies from telehealth interactions with therapists. Therapists at this health service were motivated to continue with telehealth beyond the pandemic. Despite finding it challenging initially, they were surprised by how well people with PD managed telehealth using locally developed procedures based on clinical judgement and staff training that addressed patient safety while supporting people with PD to utilise telehealth.
Oral health promotion for rural adolescents: A process evaluation of a co‐designed pilot program
Authors: Tchaba Elsin , Satur Julie , Reid Carol , Burrows Jenny 
Published: November 2023

AbstractIntroductionAdolescents living in rural areas are more likely to have poorer oral health compared with their metropolitan counterparts. Co‐design is emerging as an effective method for developing health promotion programs that meets the needs of stakeholders; however, little evidence exists to inform successful co‐designed oral health promotion programs for rural adolescents.ObjectiveThe aim of this study is to understand the value of a co‐designed oral health promotion program undertaken with rural adolescents in northeast Victoria with objectives to:

Co‐design an oral health promotion program with rural adolescents.
Evaluate the program for appropriateness, acceptability, and feasibility.
Make recommendations for program refinement and scalability.
DesignStudy participants included year 11 and 12 students in a rural secondary school in Northern Victoria (n=2), who collaboratively along with schoolteachers, and the local health service staff led by an oral health therapist, co‐designed, and delivered an oral gealth promotion program in their schools. This qualitative study used semi‐structured group interviews (n = 8) to evaluate the co‐design process and impact. Audio‐recorded interviews were transcribed and thematically analysed using a co‐design evaluation toolkit as a framework for analysis.FindingsQualitative inductive analysis revealed three main thematic categories around participant benefits (intended and unintended learning outcomes; interpersonal skills), the quality of the process (value of co‐design, qualities of facilitators, and engagement); and scalability and replicability.ConclusionThe study indicates that co‐design was both acceptable and appropriate for designing an oral health promotion program for rural adolescents delivering unexpected benefits. Building the capacity of schoolteachers could offer sustainable and cost‐effective solutions for scalability.