bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse cell death signature based subtypes predict the prognosis and immune characteristics within glioma
Authors: Wang Lin , Song Jia , Xu Jing , Qin Yidan , Li Jia , Sun Yajuan , Jin Hui , Chen Jiajun , Wang Ziqian 
Published: March 2024

AbstractBackgroundCell death plays an essential role in the pathogenesis, progression, drug resistance and recurrence of glioma. Although multiple cell death pathways are involved in glioma development, there is lack of a stratification and prognostic modelling for glioma based on the integration of diverse genes for cell deaths.MethodsIn this study, 1254 diverse cell death (DCD)-related genes were assessed using the ConsensusClusterPlus assessment to identify DCD patterns in glioma. CIBERSORT, ssGSEA, and ESTIMATE algorithms were applied to evaluate immune microenvironment differences between subtypes. LASSO Cox regression was used to screen prognosis-related DCD genes, and a risk score model was constructed. TMB, TIDE, immune infiltration, and immunotherapy response was analyzed to evaluate the immune characteristics.ResultsTwo DCD-related subgroups named Clusters 1 and 2, with distinct DCD levels, immune characteristics, and prognoses, were determined from glioma samples. A DCD-based risk score model was developed to assess DCD levels in glioma patients and divide patients into high- and low-risk groups. We found this risk model can be used as an independent prognostic factor for glioma patients. Notably, glioma patients with low risk scores exhibited subdued DCD activity, prolonged survival, and a favorable disposition towards benefiting from immune checkpoint blockade therapies.ConclusionsThis study established a novel signature classification and a risk model by comprehensively analyzing patterns of various DCDs to stratify glioma patients and to predict the prognosis and immune characteristics of glioma. We provided a theoretical basis for the clinical application of DCD-related genes in glioma prognosis and immunotherapy.
Limited Cell-Autonomous Anticancer Mechanisms in Long-Lived Bats
Authors: Athar Fathima , Zheng Zhizhong , Riquier Sebastien , Zacher Max , Alcock Dominic , Galazyuk Alex , Cooper Lisa Noelle , Schountz Tony , Wang Lin-Fa , Teeling Emma C. , Seluanov Andrei , Gorbunova Vera 
Published: March 2024

ABSTRACTBats are remarkably long-lived for their size with many species living more than 20-40 years, suggesting that they possess efficient anti-aging and anti-cancer defenses. Here we investigated requirements for malignant transformation in primary bat fibroblasts in four bat species - little brown bat (Myotis lucifugus), big brown bat (Eptesicus fuscus), cave nectar bat (Eonycteris spelaea) and Jamaican fruit bat (Artibeus jamaicensis) – spanning the bat evolutionary tree and including the longest-lived genera. We show that bat fibroblasts do not undergo replicative senescence and express active telomerase. Bat cells displayed attenuated stress induced premature senescence with a dampened secretory phenotype. Unexpectedly, we discovered that bat cells could be readily transformed by only two oncogenic perturbations or “hits”: inactivation of either p53 or pRb and activation of oncogenic RASV12. This was surprising because other long-lived mammalian species require up to five hits for malignant transformation. Additionally, bat fibroblasts exhibited increased p53 and MDM2 transcript levels, and elevated p53-dependent apoptosis. The little brown bat showed a genomic duplication of the p53 gene. We hypothesize that bats evolved enhanced p53 activity through gene duplications and transcriptional upregulation as an additional anti-cancer strategy, similar to elephants. In summary, active telomerase and the small number of oncogenic hits sufficient to malignantly transform bat cells suggest thatin vivobats rely heavily on non-cell autonomous mechanisms of tumor suppression.
Enzymatic Assembly for CRISPR Split-Cas9 System: The Emergence of a Sortase-based Split-Cas9 Technology
Authors: Helalat Seyed Hossein , Kristinsdóttir Helga Thora , Petersen Astrid Dolinger , Téllez Rodrigo Coronel , Boye Mads Nordlund , Sun Yi 
Published: March 2024

SummaryCRISPR-Cas9 has been widely used in scientific research and medical investigations as a pioneering technology. However, challenges such as the large size of the Cas9 sequence and potential off-target effects have impeded its widespread adoption. In response, various alternatives, such as split-Cas9 technology, have emerged. Split-Cas9 systems allow the large Cas9 sequence to be divided into two segments to aid in the delivery of the enzyme. Nevertheless, challenges persist in achieving precise control over the timing and location of Cas9 reassembly and activity to minimize off-target effects. This study presents an enzymatic-based split-Cas9 system, introducing a new approach utilizing the Sortase enzyme for the reconstitution of the full Cas9 protein. The developed method eliminates the need for chemical or physical induction and allows for precise genome editing in specific cells through the utilization of various specific promoters or targeted drug delivery. Experimental validation of the enzymatic system was conducted inE. coli, HEK cells, and Jurkat cells, demonstrating successful assembly and activity of the assembled Cas9 enzyme. In addition, this study explored the incorporation of nuclear localization signals, the evaluation of inducible promoters, and the delivery of the system’s components in mRNA or protein form. Furthermore, we investigated the potential of S/MAR minicircle technology instead of viral vectors within the system. Overall, we highlighted the feasibility and utility of the Sortase-based split-Cas9 system to enhance control and efficiency compared to traditional CRISPR-Cas9 approaches. Additionally, this study revealed the potential of using the Sortase enzyme for posttranslational modifications and protein assembly in human cells.
DistinctEscherichia colitranscriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection
Authors: Young Mark G. , Straub Timothy J. , Worby Colin J. , Metsky Hayden C. , Gnirke Andreas , Bronson Ryan A. , van Dijk Lucas R. , Desjardins Christopher A. , Matranga Christian , Qu James , Villicana Jesús Bazan , Azimzadeh Philippe , Kau Andrew , Dodson Karen W. , Schreiber Henry L. , Manson Abigail L. , Hultgren Scott J. , Earl Ashlee M. 
Published: March 2024

AbstractLow-abundance members of microbial communities are difficult to study in their native habitats. This includesEscherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenicEscherichia coli(UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverseE. coliin gastrointestinal communities, we developedE. coliPanSelect which uses a set of probes designed to specifically recognize and captureE. coli’s broad pangenome from sequencing libraries. We demonstrated the ability ofE. coliPanSelect to enrich, by orders of magnitude, sequencing data from diverseE. coliusing a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes betweenE. coliresiding in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gutE. coliare responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease.E. coliPanSelect is well suited for investigations of nativein vivobiology ofE. coliin other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
Conserved helical motifs in the Ikaros IDR mediate NuRD interaction and transcriptional repression
Authors: Zhang Tianyi , Wang Yi-Fang , Montoya Alex , Nebioglu Nehir , Pallikonda Husayn A. , Georgieva Radina , Patrascan Ilinca , King James WD , Kramer Holger B. , Shliaha Pavel V. , Rueda David S. , Merkenschlager Matthias 
Published: March 2024

AbstractThe transcription factor IKZF1/Ikaros is essential for B cell development, and recurrently mutated in human B-ALL. Ikaros has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of Ikaros-associated coregulatory complexes and their contribution to Ikaros-mediated gene regulation are not well understood. To address this issue, we performed an unbiased identification of Ikaros-interacting proteins in pre-B cells, and found that Ikaros interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to Ikaros induction. Transcriptional repression preceded transcriptional activation by several hours, and was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. Functional characterisation of intrinsically disordered regions in the Ikaros protein identified highly conserved helical motifs that mediate Ikaros association with the NuRD corepressor complex and contribute to the silencing of target genes in pre-B cells and antiproliferative functions of Ikaros in human B-ALL.
Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
Authors: Liu Yang , Botelho João , Iranzo Jaime 
Published: March 2024

AbstractProkaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms. By combining comparative genomics and phylogeny-aware statistical methods, we quantified the association between the presence of 7 widespread defense systems and the abundance of MGE in the genomes of 196 bacterial and 1 archaeal species. We also calculated the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon- and system-dependent. CRISPR-Cas stands out as the defense system that most often associates with a decrease in the number of MGE and reduced gene acquisition. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, at short evolutionary times, defense systems, MGE, and gene gain rates tend to be positively correlated. Based on these results and given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by recent co-transfer events involving MGE.
FHOD-1/profilin-mediated actin assembly protects sarcomeres against contraction-induced deformation inC. elegans
Authors: Kimmich Michael J. , Sundaramurthy Sumana , Geary Meaghan A. , Lesanpezeshki Leila , Yingling Curtis V. , Vanapalli Siva A. , Littlefield Ryan S. , Pruyne David 
Published: March 2024

ABSTRACTFormin HOmology Domain 2-containing (FHOD) proteins are a subfamily of actin-organizing formins important for striated muscle development in many animals. We showed previously that absence of the sole FHOD protein, FHOD-1, fromC. elegansresults in thin body-wall muscles with misshapen dense bodies that serve as sarcomere Z-lines. We demonstrate here that actin polymerization by FHOD-1 is required for its function in muscle development, and that FHOD-1 cooperates with profilin PFN-3 for dense body morphogenesis, and profilins PFN-2 and PFN-3 to promote body-wall muscle growth. We further demonstrate dense bodies infhod-1andpfn-3mutants are less stable than in wild type animals, having a higher proportion of dynamic protein, and becoming distorted by prolonged muscle contraction. We also observe accumulation of actin depolymerization factor/cofilin homolog UNC-60B in body-wall muscle of these mutants. Such accumulations may indicate targeted disassembly of thin filaments dislodged from unstable dense bodies, and may account for the abnormally slow growth and reduced strength of body-wall muscle infhod-1mutants. Overall, these results show the importance of FHOD protein-mediated actin assembly to forming stable sarcomere Z-lines, and identify profilin as a new contributor to FHOD activity in striated muscle development.
High resolution live cell imaging to define ultrastructural and dynamic features of the halotolerant yeastDebaryomyces hansenii
Authors: Xelhuantzi Martha S.C. , Ghete Daniel , Milburn Amy , Ioannou Savvas , Mudd Phoebe , Calder Grant , Ramos José , O’Toole Peter J. , Genever Paul G. , MacDonald Chris 
Published: March 2024

ABSTRACTAlthough some budding yeasts have proved tractable and intensely studied models, others are more recalcitrant.Debaryomyces hansenii, an important yeast species in food and biotechnological industries with curious physiological characteristics, has proved difficult to manipulate genetically and remains poorly defined. To remedy this, we have combined live cell fluorescent dyes with high resolution imaging techniques to define the sub-cellular features ofD. hansenii, such as the mitochondria, nuclei, vacuoles and the cell wall. Using these tools, we define biological processes like the cell cycle, organelle inheritance and different membrane trafficking pathways ofD. hanseniifor the first time. Beyond this, reagents designed to studySaccharomyces cerevisiaeproteins were used to access proteomic information aboutD. hansenii. Finally, we optimised the use of label free holotomography to image yeast, defining the physical parameters and visualising sub-cellular features like membranes and vacuoles. Not only does this work shed light onD. hanseniibut this combinatorial approach serves as a template for how other cell biological systems, which are not amenable to standard genetic procedures, can be studied.
Measurement of the neutron capture cross sections of rhenium up to stellar
s
- and
r
-process temperatures at the China Spallation Neutron Source Back-n facility
Authors: Yang Gaole , An Zhendong , Jiang Wei , Li Xiankai , Qiu Weiwei , Liao Zhengfa , Zhuang Ziyue , Zhang Xiaoping , Chen Shengli , Guo Chenchen , Xiao Erxi , Fang Xiao , Li Xinxiang , Wang Hongwei , Hu Xinrong , Jiang Bing , Shen Wenqing , Wang Jincheng , Ren Jie , Ruan Xichao , Wang Dexin , Zhang Su-Yalatu , Luo Wen , Zhu Zhichao , Lan Haoyang , Cao Zongwei , Ma Xu , Liu Yingdu , Wang Pusen , Yang Yi , Su Ping , Deng Xiangai , He Wanbing , Ma Yugang , Ma Chunwang , Wang Yuting , Dai Zhitao , Li Ertao , He Pengqin , Tang RenGuang , Zhou Tao , Wang Jing , Yi Han , Zhang Yue , Chen Yonghao , Fan Ruirui , Gao Keqing , Li Qiang , Sun Kang , Tan Zhixin , Gu Minhao , Jing Hantao , Tang Jingyu ,   The CSNS Back-n Collaboration
Published: March 2024

The neutron capture measurement of natural rhenium was performed with the time-of-flight technique at the Back-n facility of the China Spallation Neutron Source in the energy range from 1 to 500 eV of the resolved resonance region (RRR) and from 5 to 400 keV in the unresolved resonance region (URR). Prompt γ-rays originating from neutron-induced capture events were detected by four C6D6 detectors. The pulse height weighting technique and the double-bunch unfolding method based on the Bayesian theory were used in the data analysis. To obtain reliable measurement results, background subtraction, normalization, and corrections were carefully considered. The multilevel R-matrix Bayesian code was used to extract the resonance parameters in the RRR. An absence of resonance near 392 eV is observed in our measurement, which has been observed in previous works. The average cross sections in the URR of natural rhenium relative to Au197 were obtained in logarithmical equidistant energy bins with 20 bins per energy decade. The code was used to describe the average cross sections in the URR; the Maxwellian-averaged cross sections (MACSs) of Re185 and Re187 are given from kT=5 to 100 keV. At a thermal energy of kT=30 keV, the MACS value for Re185 (1469±127 mb) is in good agreement with the Karlsruhe Astrophysical Database of Nucleosynthesis in Stars (KADoNIS) recommended value (1535±62 mb) within the error bars. By contrast, the value of 1361±118 mb for Re187 shows a discrepancy with the recommended value (1160±57 mb).

Published by the American Physical Society
2024
Can you resist the virtual temptations? Unveiling impulsive buying in metaverse retail
Authors: Dang Quan Tri , Wei-Han Tan Garry , Aw Eugene Cheng-Xi , Cham Tat-Huei , Basu Sriparna , Ooi Keng-Boon 
Published: March 2024

PurposeThe main aim of this study is to examine the effect of virtual store atmospheric factors on impulsive purchasing in the metaverse context.Design/methodology/approachGrounded in purposive sampling, 451 individuals with previous metaverse experience were recruited to accomplish the objectives of this research. Next, to identify both linear and nonlinear relationships, the data were analyzed using partial least squares structural equation modeling (PLS-SEM) and artificial neural network (ANN) approaches.FindingsThe findings underscore the significance of the virtual store environment and online trust in shaping impulsive buying behaviors within the metaverse retailing setting. Theoretically, this study elucidates the impact of virtual store atmosphere and trust on impulsive buying within a metaverse retail setting.Practical implicationsFrom the findings of the study, because of the importance of virtual shop content, practitioners must address its role in impulse purchases via affective online trust. The study’s findings are likely to help retailers strategize and improve their virtual store presentations in the metaverse.Originality/valueThe discovery adds to the understanding of consumer behavior in the metaverse by probing the roles of virtual store atmosphere, online trust and impulsive buying.
Contextualising employee engagement in crisis: a protective caring approach to employee engagement in the banking sector in Bosnia and Herzegovina
Authors: Bešić Almina , Hirt Christian , Rahimić Zijada 
Published: March 2024

PurposeThis study focuses on HR practices that foster employee engagement during Covid-19. Companies in transition economies are particularly vulnerable to crisis and downsizing and other recessionary practices are frequently used.Design/methodology/approachDrawing on the model of caring human resource management, we utilise interviews with human resource representatives of 10 banks in the transition economy of Bosnia and Herzegovina. We analyse the banks at two different times to demonstrate how and why companies adapt their HR practices.FindingsOur findings show a changing mindset in the deployment of highly context-specific HR practices. Strengthening company culture through a sense of community and communication ensure stability and continuity in work. Rather than layoffs, flexible work has become standard.Practical implicationsBy highlighting the interplay between HR practices and employee engagement, we contribute to the discussion on engagement in exceptional circumstances and challenging settings and demonstrate how caring responsibilities “migrate” into HR practices in the professional context of a transition economy.Originality/valueWe propose a context-specific “protective caring approach” to foster employee engagement during crises.
Mental health and well-being in tourism scholarship: a Horizon 2050 paper
Authors: Gedecho Ermias Kifle , Kim Seongseop (Sam) 
Published: March 2024

Purpose
This study aims to assess extant research streams to delineate new research directions for tourism stakeholders’ mental health and well-being.

Design/methodology/approach
A comprehensive review of the literature on various topics related to mental health, well-being, memorable experiences, emotions, community well-being, wellness tourism and sustainable development was conducted.

Findings
Several research directions for different research subjects were identified: tourists employees, and the community. For tourists, the research topics included mental health, well-being, memorable experiences and wellness tourism. For research on employees, the focus included their mental health, psychological well-being and negative emotions. In studying the role of tourism in community mental health and well-being, research has explored community well-being and emotional solidarity and used a capital approach. This study discusses several new research directions based on past research trends, global trends and other relevant factors.

Originality/value
This conceptual study can help understand the new holistic research landscape of mental health and well-being.
Risk factors for violence in an emergency department: Nurses' perspectives
Authors: Ilarda Elisa , Senz Ainslie , Tynan Anna , McIlveen Peter 
Published: March 2024

AbstractObjectiveWork‐related violence remains a significant problem in healthcare settings, including EDs. Violence risk assessment tools have been developed to improve risk mitigation in this setting; however, incorporation of these tools into standard hospital processes remains scarce. This research aimed to explore nurses' perspectives on the Bröset Violence Checklist used in routine violence risk assessment and their recommendations for additional items.MethodsThirty nursing staff who used the Bröset Violence Checklist (BVC) as standard practice for 5 years participated in two focus groups where 23 violence risk factors were presented. Using multiple methods, participants were asked to select and elaborate from a pre‐determined list what they considered most useful in violence risk assessment in respect to descriptors and terminology.ResultsQuantitative data showed most risk factors presented to the group were considered to be predictive of violence. Ten were regarded as associated with risk, and overt behaviours received the highest votes. The terms ‘shouting and demanding’ was preferred over ‘boisterous’, and ‘cognitive impairment’ over ‘confusion’. Patient clinical characteristics and staff perceptions of harm, inability to observe subtle behaviour, imposed restrictions and interventions and environmental conditions and impact were also important considerations.ConclusionsWe recommend that violence risk assessment include: history of violence, cognitive impairment, psychotic symptoms, drug and alcohol influence, shouting and demanding, verbal abuse/hostility, impulsivity, agitation, irritability and imposed restrictions and interventions. These violence risk factors fit within the four categories of historical, clinical, behavioural and situational.