bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research advances in the identification of regulatory mechanisms of surfactin production by Bacillus: a review
Authors: Qiao Junqing , Borriss Rainer , Sun Kai , Zhang Rongsheng , Chen Xijun , Liu Youzhou , Liu Yongfeng 
Published: April 2024

AbstractSurfactin is a cyclic hexalipopeptide compound, nonribosomal synthesized by representatives of the Bacillus subtilis species complex which includes B. subtilis group and its closely related species, such as B. subtilis subsp subtilis, B. subtilis subsp spizizenii, B. subtilis subsp inaquosorum, B. atrophaeus, B. amyloliquefaciens, B. velezensis (Steinke mSystems 6: e00057, 2021) It functions as a biosurfactant and signaling molecule and has antibacterial, antiviral, antitumor, and plant disease resistance properties. The Bacillus lipopeptides play an important role in agriculture, oil recovery, cosmetics, food processing and pharmaceuticals, but the natural yield of surfactin synthesized by Bacillus is low. This paper reviews the regulatory pathways and mechanisms that affect surfactin synthesis and release, highlighting the regulatory genes involved in the transcription of the srfAA-AD operon. The several ways to enhance surfactin production, such as governing expression of the genes involved in synthesis and regulation of surfactin synthesis and transport, removal of competitive pathways, optimization of media, and fermentation conditions were commented. This review will provide a theoretical platform for the systematic genetic modification of high-yielding strains of surfactin.
Graphical Abstract
Risk factors of 30-day and long-term mortality and outcomes in open repair of thoracoabdominal aortic aneurysm
Authors: Wang Sudena , Wang Chunrong , Gao Yuchen , Tian Yu , Liu Jia , Wang Yuefu 
Published: April 2024

Abstract
Background
Open repair of thoracoabdominal aortic aneurysm (TAAA) was characterized by significant risk of postoperative mortality and morbidity. The aim of this study was to determine the perioperative predictors of early and long-term mortality in patients undergoing open repair of TAAA. Besides, the postoperative outcomes in patients with open repair of TAAA were described.

Methods
This is a single-center retrospective study, and 146 patients with open repair of TAAA from January 4, 2011, to November 22, 2018 was involved. Categorical variables were analyzed by the Chi-square test or Fisher’s exact test, and continuous variables were analyzed by the independent sample t-test and the WilCoxon rank-sum test. Multivariate Logistic regression and Cox regression were applied to identify the predictors of 30-day and long-term mortality, respectively. The Kaplan Meier curves were used to illustrate survival with the Log-rank test.

Results
The 30-day mortality was 9.59% (n = 14). Older than 50 years, the intraoperative volume of red blood cell (RBC) and epinephrine use were independently associated with postoperative 30-day mortality in open repair of TAAA. Long-term mortality was 17.12% (n = 25) (median of 3.5 years (IQR = 2–5 years) of follow-up). Prior open thoracoabdominal aortic aneurysm (TAAA) repair, aortic cross-clamping (ACC) time, intraoperative volume of RBC and use of epinephrine were independently correlated with long-term mortality.

Conclusions
Identifying perioperative risk factors of early and long-term mortaliy is crucial for surgeons. Intraoperative volume of RBC and use of epinephrine were predictors of both early and long-term mortality. In addition, patients of advanced age, prior open repair of TAAA and prolonged ACC time should be paid more attention.
‘Nowhere and no one is safe’: spatial analysis of damage to critical civilian infrastructure in the Gaza Strip during the first phase of the Israeli military campaign, 7 October to 22 November 2023
Authors: Asi Yara , Mills David , Greenough P. Gregg , Kunichoff Dennis , Khan Saira , Hoek Jamon Van Den , Scher Corey , Halabi Saleem , Abdulrahim Sawsan , Bahour Nadine , Ahmed A. Kayum , Wispelwey Bram , Hammoudeh Weeam 
Published: April 2024

Abstract
Background
Since the Hamas attacks in Israel on 7 October 2023, the Israeli military has launched an assault in the Gaza Strip, which included over 12,000 targets struck and over 25,000 tons of incendiary munitions used by 2 November 2023. The objectives of this study include: (1) the descriptive and inferential spatial analysis of damage to critical civilian infrastructure (health, education, and water facilities) across the Gaza Strip during the first phase of the military campaign, defined as 7 October to 22 November 2023 and (2) the analysis of damage clustering around critical civilian infrastructure to explore broader questions about Israel’s adherence to International Humanitarian Law (IHL).

Methods
We applied multi-temporal coherent change detection on Copernicus Sentinel 1-A Synthetic Aperture Radar (SAR) imagery to detect signals indicative of damage to the built environment through 22 November 2023. Specific locations of health, education, and water facilities were delineated using open-source building footprint and cross-checked with geocoded data from OCHA, OpenStreetMap, and Humanitarian OpenStreetMap Team. We then assessed the retrieval of damage at and with close proximity to sites of health, education, and water infrastructure in addition to designated evacuation corridors and civilian protection zones. The Global Moran’s I autocorrelation inference statistic was used to determine whether health, education, and water facility infrastructure damage was spatially random or clustered.

Results
During the period under investigation, in the entire Gaza Strip, 60.8% (n = 59) of health, 68.2% (n = 324) of education, and 42.1% (n = 64) of water facilities sustained infrastructure damage. Furthermore, 35.1% (n = 34) of health, 40.2% (n = 191) of education, and 36.8% (n = 56) of water facilities were functionally destroyed. Applying the Global Moran’s I spatial inference statistic to facilities demonstrated a high degree of damage clustering for all three types of critical civilian infrastructure, with Z-scores indicating < 1% likelihood of cluster damage occurring by random chance.

Conclusion
Spatial statistical analysis suggests widespread damage to critical civilian infrastructure that should have been provided protection under IHL. These findings raise serious allegations about the violation of IHL, especially in light of Israeli officials’ statements explicitly inciting violence and displacement and multiple widely reported acts of collective punishment.
Potential mental health-related harms associated with the universal screening of anxiety and depressive symptoms in Australian secondary schools
Authors: Braund Taylor A. , Baker Simon T. E. , Subotic-Kerry Mirjana , Tillman Gabriel , Evans Nathan J. , Mackinnon Andrew , Christensen Helen , O’Dea Bridianne 
Published: April 2024

Abstract
Background
Anxiety and depressive disorders typically emerge in adolescence and can be chronic and disabling if not identified and treated early. School-based universal mental health screening may identify young people in need of mental health support and facilitate access to treatment. However, few studies have assessed the potential harms of this approach. This paper examines some of the potential mental health-related harms associated with the universal screening of anxiety and depression administered in Australian secondary schools.

Methods
A total of 1802 adolescent students from 22 secondary schools in New South Wales, Australia, were cluster randomised (at the school level) to receive either an intensive screening procedure (intervention) or a light touch screening procedure (control). Participants in the intensive screening condition received supervised self-report web-based screening questionnaires for anxiety, depression and suicidality with the follow-up care matched to their symptom severity. Participants in the light touch condition received unsupervised web-based screening for anxiety and depression only, followed by generalised advice on help-seeking. No other care was provided in this condition. Study outcomes included the increased risk of anxiety, depression, psychological distress, decreased risk of help-seeking, increased risk of mental health stigma, determined from measures assessed at baseline, 6 weeks post-baseline, and 12 weeks post-baseline. Differences between groups were analysed using mixed effect models.

Results
Participants in the intensive screening group were not adversely affected when compared to the light touch screening condition across a range of potential harms. Rather, participants in the intensive screening group were found to have a decreased risk of inhibited help-seeking behaviour compared to the light touch screening condition.

Conclusions
The intensive screening procedure did not appear to adversely impact adolescents’ mental health relative to the light touch procedure. Future studies should examine other school-based approaches that may be more effective and efficient than universal screening for reducing mental health burden among students.
Trial registration Australian and New Zealand Clinical Trials Registry (ACTRN12618001539224) https://anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375821.
Investigating the impact of regulatory B cells and regulatory B cell-related genes on bladder cancer progression and immunotherapeutic sensitivity
Authors: Zhou Jiawei , Zhou Ranran , Zhu Yuanchao , Deng Shikai , Muhuitijiang Bahaerguli , Li Chengyao , Shi Xiaojun , Zhang Ling , Tan Wanlong 
Published: April 2024

Abstract
Background
Regulatory B cells (Bregs), a specialized subset of B cells that modulate immune responses and maintain immune tolerance in malignant tumors, have not been extensively investigated in the context of bladder cancer (BLCA). This study aims to elucidate the roles of Bregs and Breg-related genes in BLCA.

Methods
We assessed Breg infiltration levels in 34 pairs of BLCA and corresponding paracancerous tissues using immunohistochemical staining. We conducted transwell and wound healing assays to evaluate the impact of Bregs on the malignant phenotype of SW780 and T24 cells. Breg-related genes were identified through gene sets and transcriptional analysis. The TCGA-BLCA cohort served as the training set, while the IMvigor210 and 5 GEO cohorts were used as external validation sets. We employed LASSO regression and random forest for feature selection and developed a risk signature using Cox regression. Primary validation of the risk signature was performed through immunohistochemical staining and RT-qPCR experiments using the 34 local BLCA samples. Additionally, we employed transfection assays and flow cytometry to investigate Breg expansion ability and immunosuppressive functions.

Results
Breg levels in BLCA tissues were significantly elevated compared to paracancerous tissues (P < 0.05) and positively correlated with tumor malignancy (P < 0.05). Co-incubation of SW780 and T24 cells with Bregs resulted in enhanced invasion and migration abilities (all P < 0.05). We identified 27 Breg-related genes, including CD96, OAS1, and CSH1, which were integrated into the risk signature. This signature demonstrated robust prognostic classification across the 6 cohorts (pooled HR = 2.25, 95% CI = 1.52–3.33). Moreover, the signature exhibited positive associations with advanced tumor stage (P < 0.001) and Breg infiltration ratios (P < 0.05) in the local samples. Furthermore, the signature successfully predicted immunotherapeutic sensitivity in three cohorts (all P < 0.05). Knockdown of CSH1 in B cells increased Breg phenotype and enhanced suppressive ability against CD8 + T cells (all P < 0.05).

Conclusions
Bregs play a pro-tumor role in the development of BLCA. The Breg-related gene signature established in this study holds great potential as a valuable tool for evaluating prognosis and predicting immunotherapeutic response in BLCA patients.
Stearoyl-CoA desaturase 1 inhibition induces ER stress-mediated apoptosis in ovarian cancer cells
Authors: Lee Juwon , Jang Suin , Im Jihye , Han Youngjin , Kim Soochi , Jo HyunA , Wang Wenyu , Cho Untack , Kim Se Ik , Seol Aeran , Kim Boyun , Song Yong Sang 
Published: April 2024

AbstractOvarian cancer is a leading cause of death among gynecologic tumors, often detected at advanced stages. Metabolic reprogramming and increased lipid biosynthesis are key factors driving cancer cell growth. Stearoyl-CoA desaturase 1 (SCD1) is a crucial enzyme involved in de novo lipid synthesis, producing mono-unsaturated fatty acids (MUFAs). Here, we aimed to investigate the expression and significance of SCD1 in epithelial ovarian cancer (EOC). Comparative analysis of normal ovarian surface epithelial (NOSE) tissues and cell lines revealed elevated SCD1 expression in EOC tissues and cells. Inhibition of SCD1 significantly reduced the proliferation of EOC cells and patient-derived organoids and induced apoptotic cell death. Interestingly, SCD1 inhibition did not affect the viability of non-cancer cells, indicating selective cytotoxicity against EOC cells. SCD1 inhibition on EOC cells induced endoplasmic reticulum (ER) stress by activating the unfolded protein response (UPR) sensors and resulted in apoptosis. The addition of exogenous oleic acid, a product of SCD1, rescued EOC cells from ER stress-mediated apoptosis induced by SCD1 inhibition, underscoring the importance of lipid desaturation for cancer cell survival. Taken together, our findings suggest that the inhibition of SCD1 is a promising biomarker as well as a novel therapeutic target for ovarian cancer by regulating ER stress and inducing cancer cell apoptosis.
Bento: a toolkit for subcellular analysis of spatial transcriptomics data
Authors: Mah Clarence K. , Ahmed Noorsher , Lopez Nicole A. , Lam Dylan C. , Pong Avery , Monell Alexander , Kern Colin , Han Yuanyuan , Prasad Gino , Cesnik Anthony J. , Lundberg Emma , Zhu Quan , Carter Hannah , Yeo Gene W. 
Published: April 2024

AbstractThe spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene–gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.
Species-aware DNA language models capture regulatory elements and their evolution
Authors: Karollus Alexander , Hingerl Johannes , Gankin Dennis , Grosshauser Martin , Klemon Kristian , Gagneur Julien 
Published: April 2024

Abstract
Background
The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution.

Results
Here, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA language models capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA language models reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery.

Conclusions
Collectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.
A key gene, violaxanthin de-epoxidase-like 1, enhances fucoxanthin accumulation in Phaeodactylum tricornutum
Authors: Li Chenjie , Pan Yufang , Yin Wenxiu , Liu Jin , Hu Hanhua 
Published: April 2024

Abstract
Background
Fucoxanthin has been widely investigated owing to its beneficial biological properties, and the model diatom Phaeodactylum tricornutum, possessing fucoxanthin (Fux) chlorophyll proteins as light-harvesting systems, is considered to have the potential to become a commercial cell factory for the pigment production.

Results
Here, we compared the pigment contents in 10 different P. tricornutum strains from the globe, and found that strain CCMP631 (Pt6) exhibited the highest Fux content but with a low biomass. Comparison of mRNA levels revealed that higher Fux content in Pt6 was related with the higher expression of gene violaxanthin de-epoxidase-like (VDL) protein 1 (VDL1), which encodes the enzyme catalyzing the tautomerization of violaxanthin to neoxanthin in Fux biosynthesis pathway. Single nucleotide variants of VDL1 gene and allele-specific expression in strains Pt1 (the whole genome sequenced strain CCMP632) and Pt6 were analyzed, and overexpressing of each of the 4 VDL1 alleles, two from Pt1 and two from Pt6, in strain Pt1 leads to an increase in downstream product diadinoxanthin and channels the pigments towards Fux biosynthesis. All the 8 VDL1 overexpression (OE) lines showed significant increases by 8.2 to 41.7% in Fux content without compromising growth, and VDL1 Allele 2 OE lines even exhibited the higher cell density on day 8, with an increase by 24.2–28.7% in two Pt1VDL1-allele 2 OE lines and 7.1–11.1% in two Pt6VDL1-allele 2 OE lines, respectively.

Conclusions
The results reveal VDL1, localized in the plastid stroma, plays a key role in Fux over-accumulation in P. tricornutum. Overexpressing VDL1, especially allele 2, improved both the Fux content and growth rate, which provides a new strategy for the manipulation of Fux production in the future.
Concordance between two monoclonal antibody-based antigen detection enzyme-linked immunosorbent assays for measuring cysticercal antigen levels in sera from pigs experimentally infected with Taenia solium and Taenia hydatigena
Authors: Arroyo Gianfranco , Toribio Luz , Garrido Sara , Chile Nancy , Lopez-Urbina Teresa , Gomez-Puerta Luis A. , Muro Miguel , Gilman Robert H. , Castillo Yesenia , Dorny Pierre , O’Neal Seth E. , Gonzalez Armando E. , Garcia Hector H. ,   for The Cysticercosis Working Group in Peru (CWGP)
Published: April 2024

Abstract
Background
Antigen detection in Taenia solium cysticercosis confirms viable infection in the intermediate host (either pig or human). The reference B158/B60 monoclonal antibody (mAb)-based Ag-enzyme-linked immunosorbent assay (ELISA) has acceptable levels of sensitivity and specificity in human neurocysticercosis with multiple brain cysts, although its sensitivity is lower in cases with single brain cysts, whereas in porcine cysticercosis the assay specificity is affected by its frequent cross-reaction with Taenia hydatigena, another common cestode found in pigs. Our group has produced 21 anti-T. solium mAbs reacting against antigens of the whole cyst, vesicular fluid, and secretory/excretory products, identifying TsW8/TsW5 as the most promising pair of mAbs for an Ag-ELISA.

Methods
We report the use of the TsW8/TsW5 Ag-ELISA to measure cysticercus antigen levels [expressed as optical density (OD) values] in two panels of sera collected from day 0 (baseline) to day 90 postinfection (PI) from pigs experimentally infected with T. solium (n = 26) and T. hydatigena (n = 12). At baseline and on days 28 and 90 PI, we used Bland–Altman (BA) analysis and Lin’s concordance correlation coefficients (CCC) to determine the concordance between the TsW8/TsW5 and the B158/B60 Ag-ELISA.

Results
The TsW8/TsW5 Ag-ELISA was able to efficiently measure circulating antigen levels in T. solium-infected pigs, similar to that obtained with the B158/B60 Ag-ELISA. Almost all paired log-OD differences between assays were within the limits of agreement (LoA) in the BA analysis at baseline and on days 28 and 90 PI (92.3%, 100%, and 100%, respectively), and a high concordance of log-ODs between assays was also found (Lin’s CCC: 0.69, 0.92, and 0.96, respectively, all P < 0.001). In pigs infected with T. hydatigena, almost all paired log-OD differences were within the LoA in the BA analysis, whereas the concordance of log-ODs between assays was low at baseline (Lin’s CCC: 0.24) but increased on days 28 and 90 PI (Lins’ CCC: 0.88 and 0.98, P < 0.001).

Conclusions/significance
The TsW8/TsW5 Ag-ELISA recognizes antigens in pigs with T. solium cysticercosis and is highly concordant with the B158/B60 Ag-ELISA. However, its diagnostic use is hampered by cross-reactions with T. hydatigena, as in other mAb-based Ag-ELISAs.

Graphical Abstract
Tick-borne bacterial agents in Hyalomma asiaticum ticks from Xinjiang Uygur Autonomous Region, Northwest China
Authors: Zhang Bing , Zhang Niuniu , Zheng Tao , Lu Miao , Baoli Bierk , Jie Runda , Wang Xiao , Li Kun 
Published: April 2024

Abstract
Background
Hyalomma ticks are widely distributed in semi-arid zones in Northwest China. They have been reported to harbor a large number of zoonotic pathogens.

Methods
In this study, a total of 334 Hyalomma asiaticum ticks infesting domestic animals were collected from four locations in Xinjiang, Northwest China, and the bacterial agents in them were investigated.

Results
A putative novel Borrelia species was identified in ticks from all four locations, with an overall positive rate of 6.59%. Rickettsia sibirica subsp. mongolitimonae, a human pathogen frequently reported in Europe, was detected for the second time in China. Two Ehrlichia species (Ehrlichia minasensis and Ehrlichia sp.) were identified. Furthermore, two Anaplasma species were characterized in this study: Candidatus Anaplasma camelii and Anaplasma sp. closely related to Candidatus Anaplasma boleense. It is the first report of Candidatus Anaplasma camelii in China.

Conclusions
Six bacterial agents were reported in this study, many of which are possible or validated pathogens for humans and animals. The presence of these bacterial agents may suggest a potential risk for One Health in this area.

Graphical Abstract