bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oryza CLIMtools: A Genome-Environment Association Resource Reveals Adaptive Roles for Heterotrimeric G Proteins in the Regulation of Rice Agronomic Traits
Authors: Ferrero-Serrano Ángel , Chakravorty David , Kirven Kobie J. , Assmann Sarah M. 
Published: May 2023

AbstractModern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To this end, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that allow the user to: i) explore the local environments of traditional rice varieties (landraces) in South-Eastern Asia, and; ii) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We exemplify the value of these resources, identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation inOsHD2and disrupted by a natural variant inOsSOC1. Prior QTL analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing Potential Evapotranspiration gradient and their regulation of key agronomic traits including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce crops that are climate resilient.
Exposing the molecular heterogeneity of glycosylated biotherapeutics
Authors: Schachner Luis F. , Mullen Christopher , Phung Wilson , Hinkle Joshua D. , Beardsley Michelle Irwin , Bentley Tracy , Day Peter , Tsai Christina , Sukumaran Siddharth , Baginski Tomasz , DiCara Danielle , Agard Nicholas , Masureel Matthieu , Gober Joshua , ElSohly Adel , Syka John E. P. , Huguet Romain , Marty Michael T. , Sandoval Wendy 
Published: May 2023

AbstractGlycosylated biotherapeutics are an emerging class of drugs with high molecular heterogeneity, which can affect their safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins. Here, we present a new approach to glycoform fingerprinting that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact glycoproteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment and offers insights into glycoform composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug’s pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.
Discrimination of Vocal Folds Lesions by Multiclass Classification using Autofluorescence Spectroscopy
Authors: Gaiffe Olivier , Mahdjoub Joackim , Ramasso Emmanuel , Mauvais Olivier , Lihoreau Thomas , Pazart Lionel , Wacogne Bruno , Tavernier Laurent 
Published: May 2023

AbstractObjectivesThe diagnosis of vocal fold cancer currently relies on invasive surgical biopsies, which can compromise laryngeal function. Distinguishing between different types of laryngeal lesions without invasive tissue sampling is therefore crucial. Autofluorescence spectroscopy (AFS) has proved to be efficient as a non-invasive detection technique but has yet to be fully exploited in the context of a multi-class tissue analysis. This study evaluates whether AFS can be used to discriminate between different types of laryngeal lesions in view of assisting in vocal fold surgery and preoperative investigations.Materials and methodsEx vivospectral autofluorescence scans were recorded for each sample using a 405-nm laser excitation. A total of 1308 spectra were recorded from 29 vocal fold samples obtained from 23 patients. Multiclass analysis was conducted on the spectral data, classifying lesions either as normal, benign, dysplastic, or carcinoma. The results were compared to histopathological diagnosis.ResultsThrough an appropriate selection of spectral components and a cascading classification approach based on artificial neural networks (ANN), a classification rate of 97% was achieved for each lesion class, compared to 52% using autofluorescence intensity.ConclusionThe study demonstrates the effectiveness of AFS combined with multivariate analysis for accurate classification of vocal fold lesions. Comprehensive spectral data analysis significantly improves classification accuracy, even in challenging situations such as distinguishing between malignant and premalignant or benign lesions. This method could provide a way to performin situmapping of tissue states for minimally-invasive biopsy and surgical resection margins.
Attention drives visual processing and audiovisual integration during multimodal communication
Authors: Seijdel Noor , Schoffelen Jan-Mathijs , Hagoort Peter , Drijvers Linda 
Published: May 2023

AbstractDuring communication in real-life settings, our brain often needs to integrate auditory and visual information, and at the same time actively focus on the relevant sources of information, while ignoring interference from irrelevant events. The interaction between integration and attention processes remains poorly understood. Here, we use rapid invisible frequency tagging (RIFT) and magnetoencephalography (MEG) to investigate how attention affects auditory and visual information processing and integration, during multimodal communication. We presented human participants (male and female) with videos of an actress uttering action verbs (auditory; tagged at 58 Hz) accompanied by two movie clips of hand gestures on both sides of fixation (attended stimulus tagged at 65 Hz; unattended stimulus tagged at 63 Hz). Integration difficulty was manipulated by a lower-order auditory factor (clear/degraded speech) and a higher-order visual semantic factor (matching/mismatching gesture). We observed an enhanced neural response to the attended visual information during degraded speech compared to clear speech. For the unattended information, the neural response to mismatching gestures was enhanced compared to matching gestures. Furthermore, signal power at the intermodulation frequencies of the frequency tags, indexing non-linear signal interactions, was enhanced in left frontotemporal and frontal regions. Focusing on LIFG, this enhancement was specific for the attended information, for those trials that benefitted from integration with a matching gesture. Higher power at this intermodulation frequency was related to faster reaction times. Together, our results suggest that attention modulates the strength and speed of audiovisual processing and interaction, depending on the congruence and quality of the sensory input.
Development and Biophysical Characterization of a Humanized FSH–Blocking Monoclonal Antibody Therapeutic Formulated at an Ultra–High Concentration
Authors: Rojekar Satish , Pallapati Anusha R. , Gimenez–Roig Judit , Korkmaz Funda , Sultana Farhath , Sant Damini , Haeck Clement , Macdonald Anne , Kim Se-Min , Rosen Clifford J. , Barak Orly , Meseck Marcia , Caminis John , Lizneva Daria , Yuen Tony , Zaidi Mone 
Published: May 2023

ABSTRACTHighly concentrated antibody formulations are oftentimes required for subcutaneous, self-administered biologics. Here, we report the creation of a unique formulation for our first–in– class FSH–blocking humanized antibody, MS-Hu6, which we propose to move to the clinic for osteoporosis, obesity, and Alzheimer’s disease. The studies were carried out using our Good Laboratory Practice (GLP) platform, compliant with the Code of Federal Regulations (Title 21, Part 58). We first used protein thermal shift, size exclusion chromatography, and dynamic light scattering to examine MS-Hu6 concentrations between 1 and 100 mg/mL. We found that thermal, monomeric, and colloidal stability of formulated MS-Hu6 was maintained at a concentration of 100 mg/mL. The addition of the antioxidant L–methionine and chelating agent disodium EDTA improved the formulation’s long–term colloidal and thermal stability. Thermal stability was further confirmed by Nano differential scanning calorimetry (DSC). Physiochemical properties of formulated MS-Hu6, including viscosity, turbidity, and clarity, conformed with acceptable industry standards. That the structural integrity of MS-Hu6 in formulation was maintained was proven through Circular Dichroism (CD) and Fourier Transform Infrared (FTIR) spectroscopy. Three rapid freeze–thaw cycles at –80°C/25°C or –80°C/37°C further revealed excellent thermal and colloidal stability. Furthermore, formulated MS-Hu6, particularly its Fab domain, displayed thermal and monomeric storage stability for more than 90 days at 4°C and 25°C. Finally, the unfolding temperature (Tm) for formulated MS-Hu6 increased by >4.80°C upon binding to recombinant FSH, indicating highly specific ligand binding. Overall, we document the feasibility of developing a stable, manufacturable and transportable MS-Hu6 formulation at a ultra–high concentration at industry standards. The study should become a resource for developing biologic formulations in academic medical centers.
Circadian PERIOD proteins regulate TC-DSB repair through anchoring to the nuclear envelope
Authors: Le Bozec Benjamin , Guitton-Sert Laure , Collins Sarah , Finoux Anne-Laure , Payrault Charlotte , Frison Jessica , Carette Romane , Rocher Vincent , Guillou Emmanuelle , Arnould Coline , Guénolé Aude , Aguirrebengoa Marion , Lazar Ikrame , Marnef Aline , Frit Philippe , Calsou Patrick , Mangeat Thomas , Puget Nadine , Legube Gaëlle 
Published: May 2023

AbstractRepair of DNA Double-Strand Breaks (DSBs) produced in transcriptionally active chromatin occurs through a poorly characterized pathway called Transcription-Coupled DSB repair (TC-DSBR). Here, using a screening approach scoring multiple outputs in human cells, we identified proteins from the PERIOD complex, a key module ensuring circadian oscillations, as novel TC-DSBR players. We show that the core PER complex protein PER2 is recruited at TC-DSBs and that it contributes to the targeting of TC-DSBs at the nuclear envelope (NE). At the NE, SUN1 and the Nuclear Pore Complex (NPC) act as docking sites for TC-DSBs and TC-DSB anchoring fosters RAD51 assembly. Impaired DSB localization at the NE results in elevated DSB clustering and translocation rate. In agreement, the circadian clock regulates TC-DSB anchoring to the NE, RAD51 assembly, and DSB clustering. Our study shows that DSB localization to the NPC is a conserved molecular pathway that also occurs in human cells and provides a direct link between the circadian rhythm and the response to DSBs occurring in active genes. This opens new therapeutic strategies for chemotherapies based on drugs that are inducing DSBs in active loci such as topoisomerase poisons.
Enhlink infers distal and context-specific enhancer-promoter linkages
Authors: Poirion Olivier B. , Zuo Wulin , Spruce Catrina , Daigle Sandra L. , Olson Ashley , Skelly Daniel A. , Chesler Elissa J. , Baker Christopher L. , White Brian S. 
Published: May 2023

AbstractEnhancers play a crucial role in regulating gene expression and their functional status can be queried with cell type precision using using single-cell (sc)ATAC-seq. To facilitate analysis of such data, we developed Enhlink, a novel computational approach that leverages single -cell signals to infer linkages between regulatory DNA sequences, such as enhancers and promoters. Enhlink uses an ensemble strategy that integrates cell-level technical covariates to control for batch effects and biological covariates to infer robust condition-specific links and their associatedp-values. It can integrate simultaneous gene expression and chromatin accessibility measurements of individual cells profiled by multi-omic experiments for increased specificity. We evaluated Enhlink using simulated and real scATAC-seq data, including those paired with physical enhancer-promoter links enumerated by promoter capture Hi-C and with multi-omic scATAC-/RNA-seq data we generated from the mouse striatum. These examples demonstrated that our method outperforms popular alternative strategies. In conjunction with eQTL analysis, Enhlink revealed a putative super-enhancer regulating key cell type-specific markers of striatal neurons. Taken together, our analyses demonstrate that Enhlink is accurate, powerful, and provides features that can lead to novel biological insights.
Phase transition of maternal RNAs during vertebrate oocyte-to-embryo transition
Authors: Hwang Hyojeong , Chen Sijie , Ma Meng , Divyanshi  , Fan Hao-Chun , Borwick Elizabeth , Böke Elvan , Mei Wenyan , Yang Jing 
Published: May 2023

SummaryThe oocyte-to-embryo transition (OET) is regulated by maternal products stored in the oocyte cytoplasm, independent of transcription. How maternal products are precisely remodeled to dictate the OET remains an open question. In this work, we discover the dynamic phase transition of maternal RNAs duringXenopusOET. We have identified 863 maternal transcripts that transition from a soluble state to a detergent-insoluble one after oocyte maturation. These RNAs are enriched in the animal hemisphere and many of them encode key cell cycle regulators. In contrast, 165 transcripts, including nearly allXenopusgermline RNAs and some vegetally localized somatic RNAs, undergo an insoluble-to-soluble phase transition. This phenomenon is conserved in zebrafish. Our results demonstrate that the phase transition of germline RNAs influences their susceptibility to RNA degradation machinery and is mediated by the remodeling of germ plasm. This work thus uncovers novel remodeling mechanisms that act on RNAs to regulate vertebrate OET.
An SMR cell-cycle inhibitor inducible by a carotenoid metabolite resets root development and drought tolerance in Arabidopsis
Authors: Braat Jeanne , Jaonina Meryl , David Pascale , Leschevin Maïté , Légeret Bertrand , D’Alessandro Stefano , Beisson Frédéric , Havaux Michel 
Published: May 2023

AbstractNew regulatory functions in plant development and environmental stress responses have recently emerged for a number of apocarotenoids produced by enzymatic or non-enzymatic oxidation of carotenoids. β-cyclocitric acid (β-CCA) is one such compound derived from β-carotene which triggers defense mechanisms leading to a marked enhancement of plant tolerance to drought stress. We show here that this response is associated with an inhibition of root growth affecting both root cell elongation and division. Remarkably, β-CCA selectively induced cell cycle inhibitors of the SIAMESE-RELATED (SMR) family, especially SMR5, in root tip cells. Overexpression of theSMR5gene in Arabidopsis induced molecular and physiological changes that mimicked in large part the effects of β-CCA. In particular, theSMR5overexpressors exhibited an inhibition of root development and a marked increase in drought tolerance which is not related to stomatal closure.SMR5up-regulation induced changes in gene expression that strongly overlapped with the β-CCA-induced transcriptomic changes. Both β-CCA and SMR5 led to a down-regulation of many cell cycle activators (cyclins, cyclin-dependent kinases) and a concomitant up-regulation of genes related to water deprivation, cellular detoxification and biosynthesis of lipid biopolymers such as suberin and lignin. This was correlated with an accumulation of suberin lipid polyesters in the roots and a decrease in non-stomatal leaf transpiration. Taken together, our results identify the β-CCA-and drought-inducibleSMR5gene as a key component of a stress signaling pathway that reorients root metabolism from growth to multiple defense mechanisms leading to drought tolerance.
Platform ecosystem research in the technology and innovation management discipline: a multi-method literature review
Authors: Mukhopadhyay Sandip , Whalley Jason , Pandey Ritesh , Ranganathan Vinodhini 
Published: May 2023

PurposeIn parallel with the rising importance of innovation and digital technologies, research on platform ecosystems is rapidly accumulating. This study aims to summarize the current research published in leading technical and innovation management (TIM) journals and provide recommendation for future research.Design/methodology/approachIn this paper, the authors combine multiple quantitative literature review methods (social network analysis, citation analysis and co-citation analysis) with a systematic literature review of articles published in the 13 most influential TIM journals over a 15-year period.FindingsThe citation network of 168 selected papers is sparse, with low network density indicating the emerging nature of the field. Using network centrality values, the authors identified the 33 most influential articles. The review of methodologies in these articles found that conceptual and case study research dominate, suggesting the need for additional confirmatory and quantitative analysis. Co-citation analysis of the references identified six research clusters: foundation, network-centric innovation, complementor management, platform competition, ecosystemsand product platforms.Originality/valueThis analysis is among the first to examine the knowledge structure of platform ecosystem research in the TIM domain by using multiple evidence-based analysis methods. The authors also apply the theory, context, characteristics and methodology framework to suggest areas for future research.
Longitudinal effects of high-performance work practices on job performance via person–job fit
Authors: Kaur Harleen , Kaur Rajpreet 
Published: May 2023

Purpose
This present three-wave longitudinal study aims to elucidate underlying mechanism in high-performance work practices (HPWPs) and job performance relationship by examining the role of person–job as a potential mediator.

Design/methodology/approach
Data were collected from 357 faculty members of universities in Punjab (India) using a well-structured questionnaire for four consecutive months. Hypotheses were tested using PLS-SEM software.

Findings
This study results substantiated HPWPs have a direct favorable impact on the person–job fit because their extensive engagement policies, such as employee empowerment and rewards, help employees to perceive their jobs as being a good fit. Furthermore, these practices fulfil employment expectations for employees, resulting in job fit and boosting the employee’s performance; highlighting person–job fit as potential mediator.

Research limitations/implications
Grounding on the person–environment congruence theory, this study shed light on the relationship between HPWPs and job performance via person–job fit in the Indian higher education sector. This develops a unique management philosophy and strategies for long-term sustainable growth of organizations to give proper concrete evidence for the significance of human resource management (HRM).

Practical implications
This study findings persuade HR professionals in higher education institutions to actively engage in reconsidering and implementing their current HPWPs efficaciously to ensure that the employees are well-suited to their roles, i.e. increased person–job fit and perform at a higher level. Furthermore, considering the favorable impact of HPWPs on job fit and performance, it is pertinent to extensively use these practices in organizations all over the world especially across developing nations as a successful HRM solution.

Originality/value
This longitudinal study provides first-hand information on person–job fit intervening as a mediator in HPWPs and job performance relationship thereby contributing to the current corpus of HPWPs work. This fills the gap in HPWPs and job performance literature by identifying a novel concept of person–job fit that is mostly unexplored in developing countries like India.
Unlocking employees resilience in turbulent times: the role of spiritual leadership and meaning
Authors: Ahmed Syed Saad , Khan Muhammad Mumtaz , ur Rahman Mustaghis 
Published: May 2023

Purpose The aim of this research is to examine the relationship between spiritual leadership and employee resilience. Specifically, this research explores how meaning mediates the relationship between spiritual leadership and employee resilience.Design/methodology/approach This quantitative study collected data from the 439 respondents using a seven-point Likert scale. Structural equation modeling was employed to test the relationship among spiritual leadership, meaning and employee resilience.Findings The results shows that spiritual leadership, directly and indirectly, influences employee resilience. Spiritual leadership also instills meaning among employees through exhibiting genuine concern and communicating a shared vision. This research also demonstrates that meaning cultivates employee resilience to survive and thrive in a challenging business environment.Practical implications First, organizations should assess, incorporate and promote altruistic values and shared vision in their leadership program and staffing process. Second, this study urges leaders and managers to create meaning in the workplace. Lastly, the COVID-19 pandemic has disrupted the daily routines and order that humans are accustomed to, causing distressing circumstances for many people. This research calls for spiritual leadership to respond proactively by providing employees with support, appreciation and direction in those times.Originality/value This research moves forward the extant academic discussion on spiritual leadership, meaning and employee resilience in two ways. First, this study adds empirical evidence to the relationship between spiritual leadership and employee resilience, which has drawn scant attention from scholars. Second, this research buttresses the proposed framework from the perspective of positive psychology and broaden-and-build theory.