bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unified VCF data set from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize
Authors: Andorf Carson M. , Ross-Ibarra Jeffrey , Seetharam Arun S. , Hufford Matthew B. , Woodhouse Margaret R. 
Published: May 2024

ABSTRACTEfforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison. To address these continuity issues, The Maize Genetics and Genomics Database has collaborated with researchers in the maize community to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, coverage, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool to filter, visualize, and download genotype sets based on genomic locations and accessions of interest. MaizeGDB plans to host regular updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.
ERK hyperactivation in epidermal keratinocytes impairs intercellular adhesion and drives Grover disease pathology
Authors: Simpson Cory L. , Tiwaa Afua , Zaver Shivam A. , Johnson Christopher J. , Chu Emily Y. , Harms Paul W. , Gudjonsson Johann E. 
Published: May 2024

ABSTRACTGrover disease is an acquired dermatologic disorder characterized by pruritic vesicular and eroded skin lesions. While its pathologic features are well-defined, including impaired cohesion of epidermal keratinocytes, the etiology of Grover disease remains unclear and it lacks any FDA-approved therapy. Interestingly, drug-induced Grover disease occurs in patients treated with B-RAF inhibitors that can paradoxically activate C-RAF and the downstream kinase MEK. We recently identified hyperactivation of MEK and ERK as key drivers of Darier disease, which is histologically identical to Grover disease, supporting our hypothesis that they share a pathogenic mechanism. To model drug-induced Grover disease, we treated human keratinocytes with clinically utilized B-RAF inhibitors dabrafenib or vemurafenib and leveraged a fluorescent biosensor to confirm they activated ERK, which disrupted intercellular junctions and compromised keratinocyte sheet integrity. Consistent with clinical data showing concomitant MEK blockade prevents Grover disease in patients receiving B-RAF inhibitors, we found that MEK inhibition suppressed excess ERK activity to rescue cohesion of B-RAF-inhibited keratinocytes. Validating these results, we demonstrated ERK hyperactivation in skin biopsies of vemurafenib-induced Grover disease, but also in spontaneous Grover disease. In sum, our data define a pathogenic role for ERK hyperactivation in Grover disease and support MEK inhibition as a therapeutic strategy.GRAPHICAL ABSTRACT
Ancient cyanobacterial proto-circadian clock adapted to short day-night cycles ∼ 0.95 billion years ago
Authors: Li Silin , Zhou Zengxuan , Wan Yufeng , Jia Xudong , Wang Peiliang , Wang Yu , Dong Shuqi , He Jun , Wang Xujing , Qin Ximing , Xie Qiguang , Xu Xiaodong , Zhao Yuwei , Liang Dan , Zhang Peng , Zhang Qinfen , Guo Jinhu 
Published: May 2024

SUMMARYIn the early history, the Earth rotation was much faster; however, how ancient organisms adapted to the day-night cycles of that time remains unclear. We resurrected the ancestor KaiABC (anKaiABC) genes circa 0.95 billion years (Ga) ago when the daily-night cycling period was ∼ 18 h. Compared with its contemporary counterpart KaiC, the anKaiC protein shows subtle structural differences, and the activities of kinase, phosphatase activities, and adenosine triphosphatase (ATPase) of anKaiC are lower. The anKaiAB proteins are less effective in regulating KaiC/anKaiC phosphorylation status. The anKaiABC system does not sustain an endogenous oscillation but it can be entrained by an 18-h light/dark cycle. The strain expressinganKaiABCshows better adaptation under 9-h light/9-h dark cycles (LD9:9) which mimic the 18-h day-night cycles. These findings suggest that the ancient cyanobacterial proto-circadian system may not be endogenous, but it conferred the capability to adapt to daily cycles ∼ 0.95 Ga ago.
Temperature influences immune cell development and body length in purple sea urchin larvae
Authors: Wilkins Emily M. , Anderson Audrey M. , Buckley Katherine M. , Strader Marie E. 
Published: May 2024

AbstractAnthropogenic climate change has increased the frequency and intensity of marine heatwaves that may broadly impact the health of marine invertebrates. Rising ocean temperatures lead to increases in disease prevalence in marine organisms; it is therefore critical to understand how marine heatwaves impact immune system development. The purple sea urchin (Strongylocentrotus purpuratus)is an ecologically important, broadcast-spawning, omnivore that primarily inhabits kelp forests in the northeastern Pacific Ocean. TheS. purputatuslifecycle includes a relatively long-lived (∼2 months) planktotrophic larval stage. Larvae have a well-characterized cellular immune system that is mediated, in part, by a subset of mesenchymal cells known as pigment cells. To assess the role of environmental temperature on the development of larval immune cells, embryos were generated from adult sea urchins conditioned at 14 °C. Embryos were then cultured in either ambient (14 °C) or elevated (18 °C) seawater. Results indicate find that larvae raised in an elevated temperature were slightly larger and had more pigment cells than those raised at ambient temperature. Further, the larval phenotypes varied significantly among genetic crosses, which highlights the importance of genotype in structuring how the immune system develops in the context of the environment. Overall, these results suggest that developmental temperature shapes the larval immune system and may adversely affect survival long-term.
Model-based prediction and ascription of deforestation risk within commodity sourcing domains: Improving traceability in the palm oil supply chain
Authors: Glick Henry B. , Ament Judith M. , Dallinga Jorn S. , Torres-Batlló Juan , Verma Megha , Clinton Nicholas , Wilcox Andrew 
Published: May 2024

AbstractPalm oil accounts for approximately 50% of global vegetable oil production, and trends in consumption have driven large-scale expansion of oil palm (Elaeis guineensis) plantations in Southeast Asia. This expansion has led to deforestation and other socio-environmental concerns that challenge consumer goods companies to meet no deforestation and sustainability commitments. In support of these commitments and supply chain traceability, we seek to improve on the current industry standard sourcing model for ascribing social and environmental risks to particular actors. Using passive geolocational traceability data (n= 3,355,437 cellular pings) and machine learning models, we evaluate the industry standard sourcing model, and we predict with high accuracy the undisclosed sourcing domains for 1,570 Indonesian and Malaysian palm oil mills on the Universal Mill List (as of November 2021). In combination with the World Wide Fund for Nature – Netherlands’ Forest Fore-sight, we use our predicted sourcing domains to provide an illustrative example of the proportional allocation of future deforestation, carbon loss, and biodiversity risk to relevant actors, permitting targeted outreach, contract negotiation, and mitigation of large-scale resource degradation. This example depends on a subset of model predictions in the absence of disclosed traceability data. The utilization of additional predictions or disclosed traceability data would influence and improve the results.
Monitoring biodiversity in the global change era: The importance of herbaria and genetic diversity
Authors: Viveiros-Moniz Melissa , García-Muñoz Ana , Matias Luis , Abdelaziz Mohamed , Muñoz-Pajares A. Jesús 
Published: May 2024

ABSTRACTClimate change is having far-reaching consequences on all living beings, altering ecosystems, habitats, and biodiversity worldwide. Species distributions are shifting or decreasing, with alpine plant species being particularly threatened. Natural population monitoring allows the assessment of the impact of human-induced global changes. However, traditional monitoring strategies based on individual counts may produce delayed signals of biodiversity loss. These approaches overlook the fact that genetic diversity is the fundamental basis for evolutionary processes, as it enables populations to adapt to environmental changes, including those caused by climate change. Here, we draw attention to the use of genetic diversity in monitoring schemes to anticipate negative trends in biodiversity and propose two fundamental methodologies: genomics and the use of herbarium specimens. Firstly, in contrast to genetic markers conventionally used to quantify genetic diversity, such as microsatellite markers, genomic approaches provide a vast amount of data that does not require previous knowledge of the studied organism, making them suitable for the study of non-model species. Secondly, herbaria worldwide serve as excellent sources of plant material for comparative studies across time with their precise chronologically recorded collection data. The accuracy of genetic diversity estimates increases with sample size, therefore a large number of vouchers is ideally required. However, the availability of specimens from the same species and populations in public herbaria is limited. Different strategies to quantify genetic diversity are proposed depending on the number of specimens available and their geographic distribution. Finally, we illustrate the potential of this approach in the most restrictive scenario, where only a few individuals are available, and there is no conspecific reference genome. Even in this restrictive scenario, there are signs of genetic depauperation in an alpine species with a narrow distribution, but not in a widely distributed congeneric.
Dynamic Electrical Stimulation Promotes hiPSC-CM Differentiation and Functionality
Authors: Kalkunte Nikhith , Sohn Sogu , Delambre Talia , Meng Sarah , Brock Amy , Zoldan Janet 
Published: May 2024

AbstractHuman induced pluripotent stem cell differentiated cardiomyocytes (hiPSC-CMs) hold great potential to resolve cardiovascular disease but are stymied by their functional immaturity. The complex electric potentials measured during cardiogenesis point to the potential of exogenous electrical stimulation in improving cardiac differentiation and functionality. Herein, we create, validate, and implement a low-cost electrical stimulation device to stimulate hiPSCs during cardiac differentiation. Notably, our open-source device enables the generation of complex electrical stimulation regimes that may vary in frequency and pulse duration over time. Our results demonstrate that dynamic stimulation during differentiation improves cardiac differentiation efficiency, calcium handling, and flow velocity, and promotes significant transcriptomic pathway enrichment compared to static stimulation or no stimulation controls. Moreover, dynamic stimulation enhances electrochemical coupling and promotes the expression of cardiogenic pathways, potentially via sarcomere development. We anticipate that more complex dynamic electrical stimulation regimens may be generated to further optimize hiPSC-CM functionality and maturity.
The opposite aging effect to single cell transcriptome profile among cell subsets
Authors: Okada Daigo 
Published: May 2024

AbstractComparing transcriptome profiling between younger and older samples reveals genes related to aging and provides insight into the biological functions affected by aging. Recent research has identified sex, tissue, and cell type-specific age-related changes in gene expression. This study reports the overall picture of the opposite aging effect, in which aging increases gene expression in one cell subset and decreases it in another cell subset. Using the Tabula Muris Senes dataset, a large public single-cell RNA sequencing dataset from mice, we compared the effects of aging in different cell subsets. As a result, the opposite aging effect was observed widely in genome-wide genes, particularly enriched in genes related to ribosomal function and translation. The opposite aging effect was observed in the known aging-related genes. Furthermore, the opposite aging effect was observed in the transcriptome diversity quantified by the number of expressed genes and the Shannon entropy. This study highlights the importance of considering the cell subset when intervening with aging-related genes.
Adapting C4photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in Sorghum and Sugarcane
Authors: Salesse-Smith Coralie E. , Adar Noga , Kannan Baskaran , Nguyen Thaibinhduong , Wei Wei , Guo Ming , Ge Zhengxiang , Altpeter Fredy , Clemente Tom E. , Long Stephen P. 
Published: May 2024

AbstractMeta-analyses and theory show that with rising atmospheric [CO2], Rubisco has become the greatest limitation to light-saturated leaf CO2assimilation rates (Asat) in C4crops. So would transgenically increasing Rubisco increaseAsatand result in increased productivity in the field? Here, we successfully overexpressed the Rubisco small subunit (RbcS) with Rubisco accumulation factor 1 (Raf1) in both sorghum and sugarcane, resulting in significant increases in Rubisco content of 13-25% and up to 90% respectively.Asatincreased 12-15% and Rubisco enzyme activity ∼40% in three independent transgenic events of both species. Sorghum plants also showed increased speeds of photosynthetic induction and decreased bundle sheath leakiness. These improvements translated into average increases of 15.5% in biomass in field-grown sorghum and a 37-81% increase in greenhouse-grown sugarcane. This suggests a potential opportunity to achieve substantial increases in productivity of this key economically important clade of C4crops, future proofing their value under global atmospheric change.Significance StatementThe world is projected to need a 60% increase in food supply by 2050 (UN), and this must be achieved under conditions of global change without expanding onto yet more land. C4crops, while few in number, account for a large proportion of agricultural productivity. We reason that rising atmospheric [CO2] has very recently made Rubisco, the enzyme used for all carbon fixation in plants, the greatest limitation to light saturated photosynthesis in C4crops. We demonstrate that transgenically increasing Rubisco content in sorghum and sugarcane, increases their photosynthetic efficiency and productivity, including in a field trial of sorghum. This shows a means to sustainably increase the productivity of this key group of crops.
Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures
Authors: Popp Joshua M. , Rhodes Katherine , Jangi Radhika , Li Mingyuan , Barr Kenneth , Tayeb Karl , Battle Alexis , Gilad Yoav 
Published: May 2024

AbstractIdentifying the molecular effects of human genetic variation across cellular contexts is crucial for understanding the mechanisms underlying disease-associated loci, yet many cell-types and developmental stages remain underexplored. Here we harnessed the potential of heterogeneous differentiating cultures (HDCs), anin vitrosystem in which pluripotent cells asynchronously differentiate into a broad spectrum of cell-types. We generated HDCs for 53 human donors and collected single-cell RNA-sequencing data from over 900,000 cells. We identified expression quantitative trait loci in 29 cell-types and characterized regulatory dynamics across diverse differentiation trajectories. This revealed novel regulatory variants for genes involved in key developmental and disease-related processes while replicating known effects from primary tissues, and dynamic regulatory effects associated with a range of complex traits.
A high-resolution characterization of surface film formed on alloys 800 and 690 exposed to chloride and thiosulfate-containing solution at 300°C
Authors: Gao Shan , Wang Bin , Yao Xinjie , Yuan Quan 
Published: May 2024

Purpose
This paper aims to characterize the surface film formed on Alloys 800 and 690 in chloride and thiosulfate-containing solution at 300°C.

Design/methodology/approach
Alloy 800 and 690 were immersed in chloride and thiosulfate-containing solution at 300°C up to five days, and then the surface film was analyzed by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and energy dispersive X-ray spectrometers (EDX).

Findings
Through static immersion experiments in a high-temperature and high-pressure water environment, the alloy samples covered by surface film after five days of immersion were obtained. The morphology of the surface film was characterized at both horizontal and cross-sectional scales using SEM and focused ion beam-TEM techniques. It was observed that due to the influence of the quartz lining, the surface film primarily exhibited a bilayered structure. The first layer contained a significant amount of SiO2, with a higher content of metal hydroxides compared to metal oxides. The second layer was predominantly composed of Fe, Ni and Cr, with a higher content of metal oxides compared to metal hydroxides.

Originality/value
The results showed that the materials of the lining of the autoclave could significantly influence the film composition of the tested material, which should be paid attention when analyzing the corrosion mechanism at high temperature.
Like minds think alike: impacts of cultural and trust congruences on joint innovation
Authors: Fang Mingjie , Wang Mengmeng 
Published: May 2024

PurposeEngaging suppliers in joint innovation can be an effective means for buyer firms to overcome internal resource/capability limitations. The purpose of this research is to investigate the impacts of cultural and trust congruences between the supplier and buyer firms on joint innovation. In addition, we examine the relationship commitment as an antecedent of cultural and trust congruences.Design/methodology/approachThe study constructs a theoretical model based on social exchange theory (SET) and examines it using data from Chinese manufacturing firms.FindingsThe results suggest that cultural and trust congruences between suppliers and buyers positively influence joint processes and product innovations. Furthermore, we find that while normative relationship commitments of supplier firms promote cultural and trust congruences with buyers, instrumental relationship commitments only positively affect trust congruence.Originality/valueThis study enhances our understanding of social exchanges by adopting a dyadic view to examine the interconnectedness between relationship commitment, cultural and trust congruences, and joint innovation. These findings also offer practical managerial implications for managing collaborative innovation projects.
Enabling near-real-time safety glove detection through edge computing and transfer learning: comparative analysis of edge and cloud computing-based methods
Authors: Gugssa Mikias , Li Long , Pu Lina , Gurbuz Ali , Luo Yu , Wang Jun 
Published: May 2024

PurposeComputer vision and deep learning (DL) methods have been investigated for personal protective equipment (PPE) monitoring and detection for construction workers’ safety. However, it is still challenging to implement automated safety monitoring methods in near real time or in a time-efficient manner in real construction practices. Therefore, this study developed a novel solution to enhance the time efficiency to achieve near-real-time safety glove detection and meanwhile preserve data privacy.Design/methodology/approachThe developed method comprises two primary components: (1) transfer learning methods to detect safety gloves and (2) edge computing to improve time efficiency and data privacy. To compare the developed edge computing-based method with the currently widely used cloud computing-based methods, a comprehensive comparative analysis was conducted from both the implementation and theory perspectives, providing insights into the developed approach’s performance.FindingsThree DL models achieved mean average precision (mAP) scores ranging from 74.92% to 84.31% for safety glove detection. The other two methods by combining object detection and classification achieved mAP as 89.91% for hand detection and 100% for glove classification. From both implementation and theory perspectives, the edge computing-based method detected gloves faster than the cloud computing-based method. The edge computing-based method achieved a detection latency of 36%–68% shorter than the cloud computing-based method in the implementation perspective. The findings highlight edge computing’s potential for near-real-time detection with improved data privacy.Originality/valueThis study implemented and evaluated DL-based safety monitoring methods on different computing infrastructures to investigate their time efficiency. This study contributes to existing knowledge by demonstrating how edge computing can be used with DL models (without sacrificing their performance) to improve PPE-glove monitoring in a time-efficient manner as well as maintain data privacy.
Does transparency facilitate the fundraising capacity of public welfare crowdfunding? An empirical examination on Weibo
Authors: Liang Ling , Xie Jiqing , Ren Jie , Wang Jialiang , Wang Chang 
Published: May 2024

PurposeInformation opacity in donation crowdfunding activities has constrained the healthy development of China’s public welfare activities. Addressing the trust crisis and enhancing public engagement warrants further investigation. This study aims to uncover the moderating effect of activity transparency by utilizing data from 1,029 donation crowdfunding projects on the Sina Weibo Public Welfare Social Platform. In this way, we seek to elucidate the impact of donation crowdfunding events on fundraising ability.Design/methodology/approachThis study selects text complexity, number of supporters, creator experience, and social capital as explanatory variables; innovatively selects the number of updates of online crowdfunding activities and total reading volume as moderating variables; selects the number of shares of crowdfunding activities as a mediating variable; and constructs a moderated mediation multiple regression model for fundraising ability.FindingsOur findings indicate that independent variables, such as text complexity, number of supporters, and social capital, can significantly affect the dependent variable, fundraising ability. However, creator experience does not influence fundraising ability. Furthermore, social interaction has a mediating effect, whereas activity transparency has a reverse moderating effect. These results indicate that social interaction can enhance the fundraising ability of donation crowdfunding events. However, with an increase in information transparency, the fundraising ability of social media decreases.Originality/valueThe originality of this research is in clarifying the internal factors affecting fundraising ability through induction, making bold assumptions, and focusing on how social media’s effective interaction and activity transparency will affect public welfare crowdfunding fundraising ability.