bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation ofAsian honeybees
Authors: Li Yancan , Yao Jun , Sang Huiling , Wang Quangui , Su Long , Zhao Xiaomeng , Xia Zhenyu , Wang Feiran , Wang Kai , Lou Delong , Wang Guizhi , Waterhouse Robert M. , Wang Huihua , Luo Shudong , Sun Cheng 
Published: June 2023

AbstractThe Asian honeybee,Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group ofA. cerana. Integrating this with 525 resequencing datasets, we constructed the first pan-genome ofA. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novelA. ceranaecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in theAtpalphagene, indicated that this SV may promote the cold adaptation ofA. ceranaby altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation ofA. cerana.
Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles
Authors: Gu Andre A. , Uçar Mehmet Can , Tran Peter , Prindle Arthur , Kamat Neha P. , Steinkühler Jan 
Published: June 2023

AbstractRecent advances in the field of bottom-up synthetic biology have led to the development of synthetic cells that mimic some features of real cells, such as division, protein synthesis, or DNA replication. Larger assemblies of synthetic cells may be used to form prototissues. However, existing prototissues are limited by their relatively small lateral dimensions or their lack of remodeling ability. In this study, we introduce a lipid-based tissue mimetic that can be easily prepared and functionalized, consisting of a millimeter-sized “lipid-foam” with individual micrometer-sized compartments bound by lipid bilayers. We characterize the structural and mechanical properties of the lipid-foam tissue mimetic. We demonstrate self-healing capabilities enabled by the fluidity of the lipid bilayers. Upon inclusion of bacteria in the tissue compartments, we observe that the tissue mimetic exhibits network-wide tension fluctuations driven by membrane tension generation by the swimming bacteria. Active tension fluctuations facilitate the fluidization and reorganization of the lipid-foam tissue mimetic, providing a versatile platform for understanding and mimicking biological tissues.
HCCDB v2.0: Decompose the Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC
Authors: Jiang Ziming , Wu Yanhong , Miao Yuxin , Deng Kaige , Yang Fan , Xu Shuhuan , Wang Yupeng , You Renke , Zhang Lei , Fan Yuhan , Guo Wenbo , Lian Qiuyu , Chen Lei , Zhang Xuegong , Zheng Yongchang , Gu Jin 
Published: June 2023

AbstractLarge-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). By integrating 15 transcriptomic datasets of HCC clinical samples, the first version of HCCDB was released in 2018. The meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. After four years, the database needs to integrate recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics provided a great opportunity to decipher the complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size, adding 1656 new samples of 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric was proposed to summarize the cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available athttp://lifeome.net/database/hccdb2.
Global transcriptome analysis revealsSalmonellaTyphimurium employs the nitrate-dependent anaerobic pathway to combat bile stress
Authors: Singh Madhulika , Chandra Deepti , Jagdish Sirisha , Nandi Dipankar 
Published: June 2023

AbstractSalmonellaTyphimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyse the stress and adaptive responses ofS. Typhimurium to bile. We identified the cellular pathways affected during bile stress in wild type (WT) and a mutant lackingcspE (ΔcspE), which plays an essential role in protection from bile stress. We observed transcriptional upregulation of several genes involved in nitrate metabolism, in response to bile stress. These genes were also differentially expressed between the bile-resilient WT and the bile-sensitive ΔcspE strain. To understand the role of nitrate metabolism in bile stress response, we generated a strain lackingfnr(Δfnr), which is the global regulator of nitrate metabolism inS. Typhimurium.fnrwas highly induced in the bile treated WT strain but not in the ΔcspE strain. Notably, the Δfnrstrain was susceptible to bile-mediated killing. Our studies revealed a new role forfnrin mediating the bile stress response. In addition, a strain lackingarcA (ΔarcA), a two-component system response regulator involved in anaerobic metabolism, also showed a marked reduction in growth in presence of bile. This corroborated the significance of anaerobic metabolism inS. Typhimurium bile tolerance. Importantly, overexpression offnrandarcA lowered reactive oxygen species and significantly enhanced the survival of the bile-sensitive ΔcspE strain. We also observed thatS. Typhimurium pre-treated with nitrate displayed better growth in the presence of bile. Together, these results demonstrate that nitrate-dependent anaerobic metabolism promotes adaptation ofS. Typhimurium to bile.ImportanceSalmonellaTyphimurium, as an enteric pathogen, manifests an extreme example of bile tolerance. This study describes the diverse metabolic changes at the level of transcriptome inS. Typhimurium exposed to bile. We identified the differential expression of several genes involved in anaerobic metabolism between bile-tolerant WT and bile-sensitive ΔcspE strains. Two major regulators of anaerobic metabolism,fnrandarcA, support the growth ofS. Typhimurium in bile. Our results highlight that, in presence of bile,S. Typhimurium activates genes involved in anaerobic metabolism, specifically nitrate metabolism, that improves survival of bacteria during bile stress.
Targeting BTN2A1 enhances Vγ9Vδ2 T cell effector functions and triggers tumor cells pyroptosis
Authors: le Floch Anne Charlotte , Imbert Caroline , Boucherit Nicolas , Gorvel Laurent , Fattori Stéphane , Orlanducci Florence , Le Roy Aude , Archetti Lorenzo , Crescence Lydie , Panicot-Dubois Laurence , Dubois Christophe , Vey Norbert , Briantais Antoine , Anastasio Amandine , Cano Carla E. , Guittard Geoffrey , Frechin Mathieu , Olive Daniel 
Published: June 2023

AbstractVγ9Vδ2 T cells are potent but elusive cytotoxic effectors. Means to stimulate their function could lead to powerful new cancer immunotherapies. BTN2A1, a surface protein has recently been shown to bind the Vγ9 chain of the γδ TCR but its precise role in modulating Vγ9Vδ2 T cells functions remains unknown.Here we show that 107G3B5, a monoclonal anti-BTN2A1 agonist antibody, significantly enhances Vγ9Vδ2 T cell functions against hematological or solid cell lines and against primary cells from adult acute lymphoblastic leukemia patients. New computer vision strategies applied to holotomographic microscopy videos show that 107G3B5 enhances the interaction between Vγ9Vδ2 T cells and target cells in a quantitative and qualitative manner. In addition, we provide evidence that Vγ9Vδ2 T cells activated by 107G3B5 induce caspase 3/7 activation in tumor cells, thereby triggering their death by pyroptosis.We thus demonstrate that targeting BTN2A1 with 107G3B5 enhances the Vγ9Vδ2 T cell antitumor response by triggering the pyroptosis-induced immunogenic cell death.
Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution
Authors: Adupa Vasista , Ustyantseva Elizaveta , Kampinga Harm H. , Onck Patrick R. 
Published: June 2023

AbstractDNAJB6b is a molecular chaperone of the heat shock protein network, shown to play a crucial role in preventing aggregation of several disease-related intrinsically disordered proteins. Despite its importance in maintaining cellular homeostasis, the structure-functional relationship of DNAJB6b is not yet known. Using homology modeling and microsecond-long all-atom molecular dynamics (MD) simulations, we show that monomeric DNAJB6b is a transiently interconverting protein cycling between three states: a closed state, an open state (both abundant), and a novel, less abundant extended state. Interestingly, the reported regulatory autoinhibitory anchor between helix V in the G/F1region and helices II/III of the J-domain, which obstructs the access of Hsp70 to the J-domain remains present in all three states. This possibly suggests a mechanistically intriguing regulation in which DNAJB6b only becomes exposed when loaded with substrates that require Hsp70 processing. Our MD results of DNAJB6b carrying mutations in the G/F1region that are linked to limb-girdle muscular dystrophy type D1 (LGMDD1) show that this G/F1region becomes highly dynamic, pointing towards a spontaneous release of the autoinhibitory helix V from helices II/III. This would increase the probability of non-functional Hsp70 interactions to DNAJB6b without substrates. Our cellular data indeed confirm that non-substrate loaded LGMDD1 mutants have aberrant interactions with Hsp70.
Dopamine D1-like receptors modulate synchronized oscillations in the hippocampal-prefrontal-amygdala circuit in contextual fear
Authors: Stubbendorff Christine , Hale Ed , Bast Tobias , Cassaday Helen J , Martin Stephen J , Suwansawang Sopapun , Halliday David M , Stevenson Carl W 
Published: June 2023

AbstractContextual fear conditioning (CFC) is mediated by a neural circuit that includes the hippocampus, prefrontal cortex, and amygdala, but the neurophysiological mechanisms underlying the regulation of CFC by neuromodulators remain unclear. Dopamine D1-like receptors (D1Rs) in this circuit regulate CFC and local synaptic plasticity, which is facilitated by synchronized oscillations between these areas. In rats, we determined the effects of systemic D1R blockade on CFC and oscillatory synchrony between dorsal hippocampus (DH), prelimbic (PL) cortex, basolateral amygdala (BLA), and ventral hippocampus (VH), which sends hippocampal projections to PL and BLA. D1R blockade altered DH-VH and reduced VH-PL and VH-BLA synchrony during CFC, as inferred from theta and gamma coherence and theta-gamma coupling. D1R blockade also impaired CFC, as indicated by decreased freezing at retrieval, which was characterized by altered DH-VH and reduced VH-PL, VH-BLA, and PL-BLA synchrony. This reduction in VH-PL-BLA synchrony was not fully accounted for by non-specific locomotor effects, as revealed by comparing between epochs of movement and freezing in the controls. These results suggest that D1Rs regulate CFC by modulating synchronized oscillations within the hippocampus-prefrontal-amygdala circuit. They also add to growing evidence indicating that this circuit synchrony at retrieval reflects a neural signature of learned fear.
Financial inclusion based on financial technology and risky behaviour of micro-finance institutes: evidence from South Asian micro-finance banks
Authors: Hussain Shahid , Rasheed Abdul 
Published: June 2023

PurposeThe purpose of this paper financial technology (FinTech) revolutions are promptly remodelling the worldwide financial industry and facilitating financial inclusion initiatives with the aid of micro-finance institutions. Such hi-tech modifications are anticipated to sell the stableness of the financial system and lessen its predominant actors’ risk-taking behaviour. However, there needs to be more practical proof to guide the effect of financial inclusion based on financial technology on the risky behaviour of South Asia micro-finance institutes.Design/methodology/approachTherefore, the authors industrialised a fresh index to calculate financial inclusion based on financial technology and empirically measure its position in decreasing the risk-taking approach of micro-finance institutes. The use of numerous robustness examinations endorsed the rationality of the authors’ outcomes.FindingsZ-scoring or standard scoring outcomes of FinInc support the extant studies displaying its incredible connection with economic stability, which interprets as a terrible courting with risky behaviour of micro-finance institutes. Consequently, the authors highlighted the significance of the universality and openness of financial technology solutions in minimising risk of micro-finance institutes. Moreover, the authors concluded that financial technology is greater related to small-size micro-finance institutes.Originality/valueThis study currently focusing South Asia, which has not been explored before, and it is the first time to research financial inclusion with Fintech in this area.
Fostering the sustainability of organizational learning: reviewing the role of Gen-Z employees
Authors: Pandita Deepika , Agarwal Yash , Vapiwala Fatima 
Published: June 2023

Purpose
Organizations must be resilient to be agile and sensitive to numerous shifting situations due to the pandemic. There is limited research on how to bring the disparate perspectives and requirements of different generational cohorts in companies together to achieve outcomes that encourage organizational development and sustainability. Therefore, the purpose of the present study is to explore how Gen Z’s competencies can be banked upon to foster organizational learning to sustain.

Design/methodology/approach
Considering the constantly changing scenario in business organizations and the growing need for organizational learning to sustain, the authors have conducted an extensive review of the literature to understand how to sustain organizational learning for and through Gen Z. An integrative secondary search was carried out for specific and relevant work on the topic. The authors have considered both empirical and qualitative studies in their review to highlight the various themes that emerge from the extant literature.

Findings
The study indicates that much of the knowledge and experience is filtered through a generational lens, and organizations must encourage the development of Gen Z employees through e-learning, psychological contract, intrapreneurship and reverse mentoring. Based on the findings, the authors have proposed an ICES model which unifies the above four factors. The proposed ICES model encompasses specific interventions of having an Integrated 360 degrees learning experience (I), Coaching leadership for enabling intrapreneurship (C), revamping EVP for Gen Z-specific psychological contract (E) and building a Skill-will inventory for reverse mentoring (S).

Practical implications
There is limited research on how to bring the disparate perspectives and requirements of different generational cohorts in companies together to achieve outcomes that encourage organizational development and sustainability. This study will enable organizations to break down generational barriers, enhance organizational harmony, foster initiative and innovation and boost organizational performance through sustained organizational learning.

Originality/value
In view of the pandemic situation, organizations need to adapt not just their systems and processes but also to look for ways to engage their talent. The proposed ICES model will enable the sustainability of organizational learning for and through the Gen Z workforce by fostering individual development and organizational performance.
Last train timetable optimization for metro network to maximize the passenger accessibility over the end-of-service period
Authors: Wen Fang , Bai Yun , Zhang Xin , Chen Yao , Li Ninghai 
Published: June 2023

PurposeThis study aims to improve the passenger accessibility of passenger demands in the end-of-operation period.Design/methodology/approachA mixed integer nonlinear programming model for last train timetable optimization of the metro was proposed considering the constraints such as the maximum headway, the minimum headway and the latest end-of-operation time. The objective of the model is to maximize the number of reachable passengers in the end-of-operation period. A solution method based on a preset train service is proposed, which significantly reduces the variables of deciding train services in the original model and reformulates it into a mixed integer linear programming model.FindingsThe results of the case study of Wuhan Metro show that the solution method can obtain high-quality solutions in a shorter time; and the shorter the time interval of passenger flow data, the more obvious the advantage of solution speed; after optimization, the number of passengers reaching the destination among the passengers who need to take the last train during the end-of-operation period can be increased by 10%.Originality/valueExisting research results only consider the passengers who take the last train. Compared with previous research, considering the overall passenger demand during the end-of-operation period can make more passengers arrive at their destination. Appropriately delaying the end-of-operation time can increase the proportion of passengers who can reach the destination in the metro network, but due to the decrease in passenger demand, postponing the end-of-operation time has a bottleneck in increasing the proportion of passengers who can reach the destination.
Looking similar but all different: Phylogenetic signature of Brazilian rocky outcrops and the influence of temperature variability on their phylogenetic structure
Authors: Massante Jhonny Capichoni , Neri Andreza Viana , Villa Pedro Manuel , Fialho Izabela Ferreira , Pontara Vanessa , Bueno Marcelo , Gastauer Markus 
Published: June 2023

Abstract

Old, climatically buffered, infertile landscapes (OCBILs) have a disjunct yet wide distribution worldwide. Old lineages, rare and geographically restricted species, generally characterise these landscapes. Although the last decade provided evidence supporting the OCBIL theory, many studies are biased towards local scales, woody plants and specific OCBILs. Therefore, broad‐scale investigations across different types of OCBILs are needed.

We used 5186 flowering plant species (woody and herbaceous) distributed across 129 rocky outcrop sites in Brazil to investigate (1) the relative influence of climate on the phylogenetic diversity and structure of OCBILs; (2) their phylogenetic signature; (3) whether vegetation type influences phylogenetic diversity and structure of OCBILs after controlling for climate; and (4) the OCBILs' evolutionary median community age.

We found that rocky outcrops exhibit lower than expected phylogenetic diversity and are home to plant communities composed of closely related species (i.e. phylogenetic clustering) relative to the reference species pool, primarily due to temperature seasonality. Each rocky outcrop shows a distinct phylogenetic signature, indicated by plant families with more descendant species than expected by chance. Even after controlling for climate, phylogenetic diversity and structure remain low and clustered in most rocky outcrops. The median community age estimated at the species level is lower in campos de altitude than in other rocky outcrops.

Synthesis. We show that the influence of climate seasonality is pervasive in the phylogenetic diversity and structure of Brazilian rocky outcrops at different taxonomic levels. We also show that the phylogenetic signature of rocky outcrops comprises a mix of relatively old and young overrepresented plant families whose descendants contribute to their low phylogenetic diversity and phylogenetic clustering. Overall, the combination of low phylogenetic diversity, phylogenetic clustering and comparably low median community age across Brazilian rocky outcrops indicates that, on average, these OCBILs are subjected to strong environmental constraints and serve as arenas of recent diversification rather than a steady accumulation of taxa. Therefore, these findings indicate different OCBILs as hotspots for various plant lineages and species.