bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying TYMP as an Immune Prognostic Marker in Clear Cell Renal Cell Carcinoma
Authors: Chen Shao-An , Zhang Jun-Peng , Wang Ning , Chen Ji 
Published: December 2023

Background In clear cell renal cell carcinoma (ccRCC), only some patients can benefit from immunotherapy therapy, and it is urgent to find immune-related molecular markers and targets. Methods Thymidine phosphorylase (TYMP) expression level and predictive value in pan-cancers were analyzed using TIMER, GEPIA2, and The Human Protein Atlas. We obtained ccRCC tissues to verify the differential expression of TYMP and confirmed the biological function in vitro. Subsequently, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) are used to explore the potential mechanism of TYMP. Finally, TIMER was used to analyze the infiltration levels and prognostic value of different immune cells. Results TYMP is upregulated in various cancers, including ccRCC, and there is a certain degree of causality between high expression and poor prognosis in ccRCC. It was confirmed that TYMP knockdown could suppress cell aggressiveness, and cause cell death. Differential analysis showed that 55 differential genes were upregulated in the high-expression groups of TYMP. KEGG and GSEA analyses suggested that TYMP was linked to immune cell invasion, fatty acid metabolism, and P53 signaling pathway. Further investigation revealed that the expression level of TYMP linked positively to T-cell follicular helper and Tregs, but negatively with mast cell activation. Finally, a Nomogram was established on the base of expression level of TYMP and the clinical characteristics of ccRCC patients to predict prognosis. Conclusions Patient survival is poor and immune cell infiltration is abnormal when TYMP is highly expressed in ccRCC, suggesting that ccRCC patients could benefit from using TYMP as a molecular diagnostic and therapeutic target.
Survey of Guideline Compliance and Attitude Toward Symptom Management in Japanese Intensive Care Units
Authors: Yamada Shuhei , Sakuramoto Hideaki , Aikawa Gen , Naya Kazuaki 
Published: December 2023

Introduction The Clinical Practice Guideline for the Management of Pain, Agitation, and Delirium in Adult Patients in the Intensive Care Unit (ICU) was revised in 2018 to include sleep disruption and immobility. Inadequate management of these symptoms can lead to negative consequences. A 2019 survey in Japan found that the guideline was recognized but needed to be consistently implemented. Objective This study aimed to examine compliance with the guideline for symptom management of pain, agitation, delirium, and sleep in Japanese ICUs. Methods This study included all ICUs in Japan and asked one representative from each unit to respond to the web survey from January 2022 to February 2022. Results Of a potential 643 units, 125 respondents from the ICU were included in the analysis (19.4% response rate). Compared to the guideline's recommendations, (a) pain assessment was performed in 86.3% of patients who could self-report, and in 72.0% of those who could not self-report; (b) agitation and sedation assessment was performed in 99% of patients; (c) only 66.1% of nurses reported assessing sleep quality on the units, and 9.1% performed the subjective sleep quality assessment; (d) the use of the recommended risk factor of the delirium assessment tool was low (9.6%). Additionally, according to the survey respondents, contrary to the guideline, many units administered medications to prevent and treat delirium, and approximately 30% used multiple non-drug interventions. The data are expressed as numbers and percentages. Some datasets were incomplete due to missing values. Conclusion Most units used drugs for delirium prevention and treatment, and only a few used non-drug interventions. There is a need to popularize the assessment of sleep and delirium risk factors and use non-drug interventions to promote patient-centered care in the future.
Psychometric Properties of the Spanish Burnout Inventory in University Teachers in Hybrid Education
Authors: Deroncele-Acosta Angel , Gil-Monte Pedro R. , Norabuena-Figueroa Roger P. , Gil-LaOrden Pedro 
Published: December 2023

Introduction The scientific literature argues the urgent need for adequate tools to assess burnout in human service professionals, however, little progress has been made on this in university teachers in hybrid environments, even though after the pandemic, these work scenarios are predominant. Objective To determine the psychometric properties of invariance between male and female teachers of hybrid education in the Spanish Burnout Inventory (SBI). Method The anonymous, self-administered SBI was administered to 1060 university teachers in Lima, Peru, from online random sampling. Of the total number of participants, 626 were women (59.1%) and 434 were men (40.9%), with an age range of 22 to 76 years, with a mean of 46.97 and a standard deviation of 10.256. It should be noted that 74.5% of the teachers worked full time. The analysis used the statistical programs AMOS v24, SPSS v26 and R-Project v4.1.2. First, a descriptive analysis of the data was performed, as well as a multivariate normality test of the data. Secondly, confirmatory factor analysis was performed; finally, a factorial invariance test was performed. Results Cronbach's alpha of the SBI was 0.827, and for each subscale: Enthusiasm toward the job (0.742), Psychological exhaustion (0.889), Indolence (0.819), Guilt (0.816). According to the fit indicators, the confirmatory factor model is adequate. The results supported configural invariance, metric invariance, scalar invariance, and strict invariance in the male and female groups, although further investigation of some items specific to the indolence factor is needed. Conclusion The SBI is a valid instrument to assess burnout in university teachers in hybrid environments. Studies associated with the SBI focus on its psychometric properties, burnout prevalence, related variables, and literature reviews. The validation of the SBI in various countries and service areas is discussed, as well as future implications for intervention in burnout prevention and mastery.
CSF1R inhibition promotes neuroinflammation and behavioral deficits during graft-versus-host disease in mice
Authors: Adams Rachael C. , Carter-Cusack Dylan , Llanes Genesis T. , Hunter Christopher R. , Vinnakota Janaki Manoja , Ruitenberg Marc J. , Vukovic Jana , Bertolino Patrick , Chand Kirat K. , Wixey Julie A. , Nayler Samuel P. , Hill Geoffrey R. , Furlan Scott N. , Zeiser Robert , MacDonald Kelli P. A. 
Published: December 2023

Abstract
Chronic graft-versus-host disease (cGVHD) remains a significant complication of allogeneic hematopoietic stem cell transplantation. Central nervous system (CNS) involvement is becoming increasingly recognized, in which brain-infiltrating donor major histocompatibility complex (MHC) class II+ bone marrow–derived macrophages (BMDM) drive pathology. BMDM are also mediators of cutaneous and pulmonary cGVHD, and clinical trials assessing the efficacy of antibody blockade of colony-stimulating factor 1 receptor (CSF1R) to deplete macrophages are promising. We hypothesized that CSF1R antibody blockade may also be a useful strategy to prevent/treat CNS cGVHD. Increased blood-brain barrier permeability during acute GVHD (aGVHD) facilitated CNS antibody access and microglia depletion by anti-CSF1R treatment. However, CSF1R blockade early after transplant unexpectedly exacerbated aGVHD neuroinflammation. In established cGVHD, vascular changes and anti-CSF1R efficacy were more limited. Anti-CSF1R–treated mice retained donor BMDM, activated microglia, CD8+ and CD4+ T cells, and local cytokine expression in the brain. These findings were recapitulated in GVHD recipients, in which CSF1R was conditionally depleted in donor CX3CR1+ BMDM. Notably, inhibition of CSF1R signaling after transplant failed to reverse GVHD-induced behavioral changes. Moreover, we observed aberrant behavior in non-GVHD control recipients administered anti-CSF1R blocking antibody and naïve mice lacking CSF1R in CX3CR1+ cells, revealing a novel role for homeostatic microglia and indicating that ongoing clinical trials of CSF1R inhibition should assess neurological adverse events in patients. In contrast, transfer of Ifngr–/– grafts could reduce MHC class II+ BMDM infiltration, resulting in improved neurocognitive function. Our findings highlight unexpected neurological immune toxicity during CSF1R blockade and provide alternative targets for the treatment of cGVHD within the CNS.
Loss of CD20 expression as a mechanism of resistance to mosunetuzumab in relapsed/refractory B-cell lymphomas
Authors: Schuster Stephen J. , Huw Ling-Yuh , Bolen Christopher R. , Maximov Victor , Polson Andrew G. , Hatzi Katerina , Lasater Elisabeth A. , Assouline Sarit E. , Bartlett Nancy L. , Budde L. Elizabeth , Matasar Matthew J. , Koeppen Hartmut , Piccione Emily C. , Wilson Deanna , Wei Michael C. , Yin Shen , Penuel Elicia 
Published: December 2023

Abstract
CD20 is an established therapeutic target in B-cell malignancies. The CD20 × CD3 bispecific antibody mosunetuzumab has significant efficacy in B-cell non-Hodgkin lymphomas (NHLs). Because target antigen loss is a recognized mechanism of resistance, we evaluated CD20 expression relative to clinical response in patients with relapsed and/or refractory NHL in the phase 1/2 GO29781 trial investigating mosunetuzumab monotherapy. CD20 was studied using immunohistochemistry (IHC), RNA sequencing, and whole-exome sequencing performed centrally in biopsy specimens collected before treatment at predose, during treatment, or upon progression. Before treatment, most patients exhibited a high proportion of tumor cells expressing CD20; however, in 16 of 293 patients (5.5%) the proportion was &lt;10%. Analyses of paired biopsy specimens from patients on treatment revealed that CD20 levels were maintained in 29 of 30 patients (97%) vs at progression, where CD20 loss was observed in 11 of 32 patients (34%). Reduced transcription or acquisition of truncating mutations explained most but not all cases of CD20 loss. In vitro modeling confirmed the effects of CD20 variants identified in clinical samples on reduction of CD20 expression and missense mutations in the extracellular domain that could block mosunetuzumab binding. This study expands the knowledge about the occurrence of target antigen loss after anti-CD20 therapeutics to include CD20-targeting bispecific antibodies and elucidates mechanisms of reduced CD20 expression at disease progression that may be generalizable to other anti-CD20 targeting agents. These results also confirm the utility of readily available IHC staining for CD20 as a tool to inform clinical decisions. This trial was registered at www.ClinicalTrials.gov as #NCT02500407.
Ongoing production of tissue-resident macrophages from hematopoietic stem cells in healthy adult macaques
Authors: Rahmberg Andrew R. , Wu Chuanfeng , Shin Taehoon , Hong So Gun , Pei Luxin , Markowitz Tovah E. , Hickman Heather D. , Dunbar Cynthia E. , Brenchley Jason M. 
Published: December 2023

Abstract
Macrophages orchestrate tissue immunity from the initiation and resolution of antimicrobial immune responses to the repair of damaged tissue. Murine studies demonstrate that tissue-resident macrophages are a heterogenous mixture of yolk sac–derived cells that populate the tissue before birth, and bone marrow–derived replacements recruited in adult tissues at steady-state and in increased numbers in response to tissue damage or infection. How this translates to species that are constantly under immunologic challenge, such as humans, is unknown. To understand the ontogeny and longevity of tissue-resident macrophages in nonhuman primates (NHPs), we use a model of autologous hematopoietic stem progenitor cell (HSPC) transplantation with HSPCs genetically modified to be marked with clonal barcodes, allowing for subsequent analysis of clonal ontogeny. We study the contribution of HSPCs to tissue macrophages, their clonotypic profiles relative to leukocyte subsets in the peripheral blood, and their transcriptomic and epigenetic landscapes. We find that HSPCs contribute to tissue-resident macrophage populations in all anatomic sites studied. Macrophage clonotypic profiles are dynamic and overlap significantly with the clonal hierarchy of contemporaneous peripheral blood monocytes. Epigenetic and transcriptomic landscapes of HSPC-derived macrophages are similar to tissue macrophages isolated from NHPs that did not undergo transplantation. We also use in vivo bromodeoxyuridine infusions to monitor tissue macrophage turnover in NHPs that did not undergo transplantation and find evidence for macrophage turnover at steady state. These data demonstrate that the life span of most tissue-resident macrophages is limited and can be replenished continuously from HSPCs.
Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene
Authors: Bajaj Priyanka , Bhasin Munmun , Varadarajan Raghavan 
Published: December 2023

Abstract
Background
Single synonymous codon mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth of ~ 200 single synonymous codon mutations in an operonic context by mutating almost all positions of ccdB, the 101-residue long cytotoxin of the ccdAB Toxin-Antitoxin (TA) operon to most degenerate codons. Phenotypes were assayed by transforming the mutant library into CcdB sensitive and resistant E. coli strains, isolating plasmid pools, and subjecting them to deep sequencing. Since autoregulation is a hallmark of TA operons, phenotypes obtained for ccdB synonymous mutants after transformation in a RelE toxin reporter strain followed by deep sequencing provided information on the amount of CcdAB complex formed.

Results
Synonymous mutations in the N-terminal region involved in translation initiation showed the strongest non-neutral phenotypic effects. We observe an interplay of numerous factors, namely, location of the codon, codon usage, t-RNA abundance, formation of anti-Shine Dalgarno sequences, predicted transcript secondary structure, and evolutionary conservation in determining phenotypic effects of ccdB synonymous mutations. Incorporation of an N-terminal, hyperactive synonymous mutation, in the background of the single synonymous codon mutant library sufficiently increased translation initiation, such that mutational effects on either folding or termination of translation became more apparent. Introduction of putative pause sites not only affects the translational rate, but might also alter the folding kinetics of the protein in vivo.

Conclusion
In summary, the study provides novel insights into diverse mechanisms by which synonymous mutations modulate gene function. This information is useful in optimizing heterologous gene expression in E. coli and understanding the molecular bases for alteration in gene expression that arise due to synonymous mutations.
Genome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity
Authors: Tian Xuechen , Teo Wee Fei Aaron , Wee Wei Yee , Yang Yixin , Ahmed Halah , Jakubovics Nicholas S. , Choo Siew Woh , Tan Geok Yuan Annie 
Published: December 2023

Abstract
Background
Actinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and characterization of Actinomyces species is crucial for human health, as they play an important role in dental plaque formation and biofilm-related infections. Two Actinomyces strains ATCC 49340 T and ATCC 51655 T have been utilized in various studies, but their accurate species classification and description remain unresolved.

Results
To investigate the genomic properties and taxonomic status of these strains, we employed both 16S rRNA Sanger sequencing and whole-genome sequencing using the Illumina HiSeq X Ten platform with PE151 (paired-end) sequencing. Our analyses revealed that the draft genome of Actinomyces acetigenes ATCC 49340 T was 3.27 Mbp with a 68.0% GC content, and Actinomyces stomatis ATCC 51655 T has a genome size of 3.08 Mbp with a 68.1% GC content. Multi-locus (atpA, rpoB, pgi, metG, gltA, gyrA, and core genome SNPs) sequence analysis supported the phylogenetic placement of strains ATCC 51655 T and ATCC 49340 T as independent lineages. Digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) analyses indicated that both strains represented novel Actinomyces species, with values below the threshold for species demarcation (70% dDDH, 95% ANI and AAI). Pangenome analysis identified 5,731 gene clusters with strains ATCC 49340 T and ATCC 51655 T possessing 1,515 and 1,518 unique gene clusters, respectively. Additionally, genomic islands (GIs) prediction uncovered 24 putative GIs in strain ATCC 49340 T and 16 in strain ATCC 51655 T, contributing to their genetic diversity and potential adaptive capabilities. Pathogenicity analysis highlighted the potential human pathogenicity risk associated with both strains, with several virulence-associated factors identified. CRISPR-Cas analysis exposed the presence of CRISPR and Cas genes in both strains, indicating these strains might evolve a robust defense mechanism against them.

Conclusion
This study supports the classification of strains ATCC 49340 T and ATCC 51655 T as novel species within the Actinomyces, in which the name Actinomyces acetigenes sp. nov. (type strain ATCC 49340 T = VPI D163E-3 T = CCUG 34286 T = CCUG 35339 T) and Actinomyces stomatis sp. nov. (type strain ATCC 51655 T = PK606T = CCUG 33930 T) are proposed.
Genome-wide identification, structural homology analysis, and evolutionary diversification of the phospholipase D gene family in the venom gland of three scorpion species
Authors: Baradaran Masoumeh , Salabi Fatemeh 
Published: December 2023

Abstract
Background
Venom phospholipase D (PLDs), dermonecrotic toxins like, are the major molecules in the crude venom of scorpions, which are mainly responsible for lethality and dermonecrotic lesions during scorpion envenoming. The purpose of this study was fivefold: First, to identify transcripts coding for venom PLDs by transcriptomic analysis of the venom glands from Androctonus crassicauda, Hottentotta saulcyi, and Hemiscorpius lepturus; second, to classify them by sequence similarity to known PLDs and motif extraction method; third, to characterize scorpion PLDs; fourth to structural homology analysis with known dermonecrotic toxins; and fifth to investigate phylogenetic relationships of the PLD proteins.

Results
We found that the venom gland of scorpions encodes two PLD isoforms: PLD1 ScoTox-beta and PLD2 ScoTox-alpha I. Two highly conserved regions shared by all PLD1s beta are GAN and HPCDC (HX2PCDC), and the most important conserved regions shared by all PLD2s alpha are two copies of the HKDG (HxKx4Dx6G) motif. We found that PLD1 beta is a 31–43 kDa acidic protein containing signal sequences, and PLD2 alpha is a 128 kDa basic protein without known signal sequences. The gene structures of PLD1 beta and PLD2 alpha contain 6 and 21 exons, respectively. Significant structural homology and similarities were found between the modeled PLD1 ScoTox-beta and the crystal structure of dermonecrotic toxins from Loxosceles intermedia.

Conclusions
This is the first report on identifying PLDs from A. crassicauda and H. saulcyi venom glands. Our work provides valuable insights into the diversity of scorpion PLD genes and could be helpful in future studies on recombinant antivenoms production.
Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae
Authors: Li Qian , Feng Peng , Tang Hao , Lu Fujia , Mou Borui , Zhao Lan , Li Nan , Yang Yaojun , Fu Chun , Long Wencong , Xiao Ximeng , Li Chaohao , Wu Wei , Wang Gang , Liu Beidong , Tang Tianle , Ma Menggen , Wang Hanyu 
Published: December 2023

AbstractIn bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60 mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
Targeted elimination of Vancomycin resistance gene vanA by CRISPR-Cas9 system
Authors: Tao Shuan , Hu Chunwei , Fang Yewei , Zhang He , Xu Yao , Zheng Lin , Chen Luyan , Liang Wei 
Published: December 2023

Abstract
Objective
The purpose of this study is to reduce the spread of the vanA gene by curing the vanA-harboring plasmid of vancomycin-resistant using the CRISPR-Cas9 system.

Methods
Two specific spacer sequence (sgRNAs) specific was designed to target the vanA gene and cloned into plasmid CRISPR-Cas9. The role of the CRISPR-Cas system in the plasmid elimination of drug-resistance genes was verified by chemically transformation and conjugation delivery methods. Moreover, the elimination efficiency in strains was evaluated by plate counting, PCR, and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by Etest strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance.

Results
In the study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the vanA gene. PCR and qPCR results indicated that recombinant pCas9-sgRNA plasmid can efficiently clear vanA-harboring plasmids. There was no significant correlation between sgRNA lengths and curing efficiency. In addition, the drug susceptibility test results showed that the bacterial resistance to vancomycin was significantly reduced after the vanA-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system. The CRISPR-Cas9 system can block the horizontal transfer of the conjugated plasmid pUC19-vanA.

Conclusion
In conclusion, our study demonstrated that CRISPR-Cas9 achieved plasmid clearance and reduced antimicrobial resistance. The CRISPR-Cas9 system could block the horizontal transfer of plasmid carrying vanA. This strategy provided a great potential to counteract the ever-worsening spread of the vanA gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.