bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crosstalk between chromatin state and ATM signalling in DNA damage-induced transcription stress.
Authors: Tresini Maria , Salas-Armenteros Irene , Klunder Maarten , Vermeulen Wim 
Published: February 2024

Abstract
The DNA Damage Response (DDR) is a highly regulated cellular process that safeguards genomic integrity against DNA lesions. Increasing evidence supports a reciprocal influence between architectural features of damaged chromatin and signalling pathways that co-ordinate the DDR. However, the mechanisms governing such a relationship in response to DNA helix-distorting lesions, remain largely unexplored. Here, we show that stalling of RNA polymerase II at such lesions, induces local chromatin acetylation mediated primarily by the histone acetyltransferases p300 and PCAF. The resulting open chromatin stimulates dissociation from nascent RNA of late-stage, co-transcriptional spliceosomes and subsequent formation of RNA: DNA hybrids, leading to activation of ATM signalling. In turn, activated ATM modulates chromatin conformation by phosphorylating Histone H2A.X and stimulating p38MAPK/MSK1-dependent Histone H3S10 phosphorylation. Our findings highlight the cross-regulation between chromatin state and ATM signalling as an integral part of the cellular response to transcription stress.
A scale-invariant large-area single-mode topological photonic cavity
Authors: Xie Biye , Li Zhongfu , Li Shiqi , Yan Bei , Chan Hsun-Chi , Li Jing , Guan Jun , Bi Wengang , Xiang Yuanjiang , Gao Zhen , Zhang Shuang , Zhan Peng , Wang Zhenlin 
Published: February 2024

Abstract

Emergent collective modes in lattices give birth to many intriguing physical phenomena in condensed matter physics. Among these collective modes, large area modes typically feature small level spacings, whilst a single mode tends to be spatially tightly confined. Here, we theoretically propose and experimentally demonstrate a unique scale-invariant, large-area, and single-mode topological cavity mode in a two-dimensional photonic crystal. This mode emerges from the hybridization of the large-area fundamental Dirac mode and in-gap topological corner modes. Remarkably, we find that the scale-invariant, large-area, and single-mode topological cavity mode possesses unique chiralities and with a tunable mode area under the change of the mass term of the inner topological nontrivial lattice. We experimentally observe such topological cavity modes in a 2D photonic system and demonstrate the robustness by introducing disorders in the cavity structure. Our findings have propelled the forefront of higher-order topology research, transitioning it from single-lattice systems to multi-lattice systems and may support promising potential applications, particularly in vertical-cavity surface-emitting lasers.
Mechanism of gastric cancer cell-derived exosomal circPDSS1 promoting ferroptosis of natural killer cells by regulating miR-1278/GOT1 molecular axis
Authors: Li Yuejin , Zhu Yu , Sheng Ping , Guo Xiaodong , Li Xing , Li Ruoxi , Zhao Zhiyuan , Li Linhai , Gong Kunmei 
Published: February 2024

Abstract
Background: Gastric cancer (GC) is one of the malignant tumors, with complex molecular mechanisms. Ferroptosis plays an important regulatory role in the development of GC. But no studies have investigated the specific mechanism of ferroptosis in natural killer (NK) cells in GC. This study aims to elucidate the molecular mechanism of GC cells regulating ferroptosis in NK cells.
Methods: qRT-qPCR was used to test the expression of circular RNA decaprenyl diphosphate synthase subunit 1 (circPDSS1) and microRNA-1278 (miR-1278). The protein expressions of glutathione peroxidase 4 (GPX4) and aspartate aminotransferase 1 (GOT1) were tested by Western blot, used fluorescence in situ hybridization to analyse location of circPDSS1 expressions, and the level of reactive oxygen species (ROS) was detected by immunofluorescence. Malondialdehyde (MDA) levels were detected by MDA kit, dual luciferase reporter gene to analyze targeting relationship, CCK-8 analyze the cell proliferation, transwell analyze the cell migration, and cell apoptosis was detected by flow cytometry.
Results: circPDSS1 expression is elevated in GC tissues and peripheral blood, and that GC cells secrete circPDSS1 by exosomes. Exosomes of knockdown circPDSS1 significantly reduced ROS and MDA levels and elevated GPX4 expression in NK cells. More importantly, circPDSS1 can act as a sponge for miR-1278 in NK cells, inhibiting its up-regulation and promoting the expression of GOT1, thereby impaired NK cell function and ultimately induced GC progression.
Conclusion: The GC cells-derived exosomal circPDSS1 promotes ferroptosis of NK cells by regulating the miR-1278/GOT1 molecular axis, thereby inducing GC progression.
Does Green Finance Reform and Innovation affect Corporate Financialization? Evidence from China
Authors: Qi Shaozhou , Zhou Jingjie , Li Xinqiang , Li Kai 
Published: February 2024

Abstract
In 2017, China introduced the Green Finance Reform and Innovation Pilot Zones (GFRI) policy, underscoring its commitment to fostering sustainable and low-carbon economic growth. This pilot policy exerts a significant influence on corporate business strategies. Meanwhile, the financialization (CF) may hinder the sustainable development of traditional firms. By using dataset of China’s listed companies from 2012 to 2021, this study implements the difference-in-differences (DID) method to investigate the impact of GFRI on CF and its underlying mechanism. The main findings are as follows. (1) The implementation of GFRI has significantly enhanced CF. (2) The positive impact is particularly pronounced in corporates of the eastern regions, non-state-owned entities, those with low ESG scores, and whose manager team lacks financial expertise. (3) GFRI’s promotion effect on CF is a short-term speculative behavior driven by "reservoir" and profit maximization motivations. Our study clearly identifies the causal relationship between GFRI and CF and reveals the driving force behind corporate’s business strategy. Policy implications are put forward accordingly.
Zi Chong granules improve hydroxyurea-induced decrease in ovarian reserve function
Authors: Dong Wenran , Guo Xinyu , Lu Hua , Liu Zhibin , Xie Lan , Liu Yi , Wan Qian , Chen Ren , Liu Sui 
Published: February 2024

Abstract

Hydroxyurea (HU) is an antitumor drug. However, HU exposure is associated with diminished ovarian reserve (DOR). Zi Chong granules, a Chinese Medicine, can protect against DOR, but little is known regarding its underlying mechanisms of DOR treatment, and thus the target of the present study. Female KM mice were randomly divided into three groups: the control group (Con), the hydroxyurea group (HU), and the Zi Chong group (ZC). The ovaries and uterus of mice were examined histologically by H&E. The levels of anti-Mullerian hormone (AMH), estradiol (E2), and progesterone (P) were quantified using ELISA kits. The number and quality of oocytes were assessed, and endometrial receptivity was evaluated by immunohistochemistry. 16S rDNA gene sequencing was used to analyze the composition and abundance of gut microbiome in feces, and non-targeted metabolomics was performed to detect serum metabolite profiles. Correlation analysis was performed to explore the relationships between different gut microbiota and differential metabolites. The results showed that ZC granules increased the number of primordial follicles in the ovaries, reduced excessive follicular atresia, restored low AMH, upregulated estrogen and progesterone secretion, and increased the number of mature oocytes after ovulation promotion. It also increased thickness of uterine endometrium and the number of glands, resulting in increased endometrial microvessel density (MVD), enhanced endometrial blood supply, reduced CD138 expression levels and endometrial inflammation. HU decreased the abundance of Lactobacillus spp. in mouse intestines and decreased arachidonic acid metabolism, tryptophan metabolism, spermidine and spermine biosynthesis, steroidogenesis and nicotinate and nicotinamide metabolism. Correlation analysis revealed that HU exerted its side effects by altering the gut microbiome and bacteria-derived metabolites, while ZC granules could reverse DOR partly depends on regulating gut microbiota and metabolites. Together, ZC granules may be a potential therapy for alleviating HU-induced DOR.
Bioethanol production from lignocellulosic waste without pre-treatment employing vermicompost and earthworm gut-isolated bacteria: Insights on waste to wealth conversion efficiency towards cleaner lifestyle
Authors: Chowdhury Ratan , Hussain Nazneen , Mukherjee Sandip , Barman Soma , Mandal Himadri , Raul Prasanta Kumar , Bhattacharya Satya Sundar 
Published: February 2024

Abstract
Lignocellulosic wastes (LCW) have enormous potential to be recycled for bioethanol production. Although yeasts (Saccharomyces sp.) are commonly used bio-agents for fermentation, their efficiency is inhibited in cellulosic feedstocks. This study isolated novel ethanologenic bacteria from vermicomposting systems for bioenergy generation from fruit waste without pre-treatment. Initially, six strains out of 22, showing remarkable ethanol production ability, were characterized via 16S rRNA sequencing. Specifically, two strains (Bacillus alcalophilus C5 and Rhizobium spp. S10) produced more ethanol (5.5 and 15.7 g L− 1) than the yeast (5 g L− 1) from banana epicarps. These strains' dramatically high sedimentation rate and ethanol tolerance strongly justified their industrial applicability. Significant upregulation of alcohol dehydrogenase and acetyl CoA synthase endowed greater ethanol-producing capacity in C5 and S10 than in S. cerevisiae. The flow cytometry and confocal microscopy evidenced that ethanologenic bacteria uniquely defend the reactor-induced sugar and ethanol stresses through reverse/delayed apoptosis and robust membrane integrity. The waste-to-wealth conversion efficiency and cost-benefit analyses estimated that bacteria-mediated LCW-to-bioethanol conversion was a more profitable venture than vermicomposting or composting. Overall, this research demonstrated that the C5 and S10 isolates were more effective than widely used commercial yeast strains for bioethanol generation from LCW.
SRD5A2 in the development of benign prostatic hyperplasia mechanism and immune infiltration analysis
Authors: Zhu Xiaoyan , Xu Qiming , Gong Rui , Fang Yuhao , Liu Zongshun , Hu Libing 
Published: February 2024

Abstract

This study aimed to elucidate the pathological mechanism of Steroid 5 Alpha-Reductase 2 (SRD5A2) in benign prostatic hyperplasia (BPH) using various methods. BPH datasets from the Gene Expression Omnibus (GEO) database were analyzed, and correlations between SRD5A2 and other genes were calculated. Gene Set Enrichment Analysis (GSEA) identified potential functions of SRD5A2, and key pathways were determined by intersecting the enrichment results of differentially expressed genes (DEGs) in BPH and control samples with SRD5A2 enrichment. Single sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network analysis (WGCNA) identified key pathways-related genes. Candidate genes were defined as overlapping genes among SRD5A2-related genes, key pathways-related genes, and DEGs. Functional similarity analysis identified genes significantly associated with SRD5A2. Support Vector Machine (SVM) analysis based on these genes revealed four key genes (SLIT3, TCF21, MATN2, and PSMG4) with good diagnostic efficacy. Quantitative real-time PCR (qRT-PCR) confirmed statistically significant differential expression of MATN2 and PSMG4. In conclusion, this study explored the potential biological functions of SRD5A2-related genes in BPH, providing insights into its treatment.
Analysis of Rare Events in Outcomes Research Using Department of Defense Data: Intravenous Immune Globulin Therapy for Bullous Pemphigoid
Authors: Baser Onur , Yuce Huseyin , Samayoa Gabriela 
Published: February 2024

Abstract
Introduction:
Rare events data have proven difficult to explain and predict. Standard statistical procedures can sharply underestimate the probability of rare events, such as intravenous immune globulin therapy (IVIg) for bullous pemphigoid.
Methods
This retrospective cross-sectional study used Department of Defense TRICARE data to determine factors associated with IVIg therapy among bullous pemphigoid patients. We used prior and weighted correction methods for logit regression to solve rare event bias.
Results
We identified 2,720 individuals diagnosed with bullous pemphigoid from 2019 to 2022, of which 14 were treated with IVIg. Patients who received IVIg therapy were younger (65.07 vs. 75.85, P = .0016) and more likely to be female (13 vs. 1, P = .0036). The underestimation with the standard regression model for event probabilities ranged from 11–102% using the prior correction method and from 15–107% using the weighted correction method.
Conclusion
Rare events are low-frequency, high-severity problems that can have significant consequences. Rare diseases and rare therapies are individually unique but collectively contribute to substantial health and social needs. Therefore, correct estimation of the events is the first step toward assessing the burden of rare diseases and the pricing of their therapies.
Loss of Dynein Axonemal Heavy Chain 5 Causes Cortical Development Disorders and CSF Flow Stagnation
Authors: Sakamoto Koichiro , Miyajima Masakazu , Nakajima Madoka , Ogino Ikuko , Horikoshi Kou , Miyahara Ryo , Kawamura Kaito , Karagiozov Kostadin , Kamohara Chihiro , Nakamura Eri , Tada Nobuhiro , Kondo Akihide 
Published: February 2024

Abstract
Background: Dynein axonemal heavy chain 5 (Dnah5) has been identified as a key gene associated with primary ciliary dyskinesia in humans. Studies have demonstrated that mice lacking Dnah5 (Dnah5-/-) develop acute hydrocephalus shortly after birth due to impaired ciliary motility, resulting in cerebrospinal fluid (CSF) stagnation and ultimately death within approximately a month. Notably, such hydrocephalus has not been reported in humansharboring this mutation. We aimed to elucidate the pathogenesis of hydrocephalus in Dnah5-deficient mice and by that improve our understanding of the role these pathogenetic mechanisms play in human hydrocephalus.
Methods: Using CRISPR/Cas9, we targeted exon 2 of the Dnah5 gene on chromosome 15, introducing a 4-base pair deletion to generate Dnah5-/- mice. We analyzed gene expression in the cerebral cortex using microarrays. Subsequently, we performed immunostaining of the cerebral cortex and ventricular wall using specific antibodies against dynein, n-cadherin, and nestin, and determined the gene expression levels and protein quantities through real-time Polymerase Chain Reaction and Western blot analysis.
Results: Hydrocephalus was observed in all Dnah5-/- mice. Electron microscopy images revealed an absence of the axonemal outer dynein arm of the peripheral doublet microtubules. Ventricular size of Dnah5-/- mice was enlarged immediately after birth and it progressed through life. The number of mature neurons in the cerebral motor cortex of Dnah5-/- mice was reduced by approximately 25% compared to wild-type mice. The level ofexpression of the Dynein Cytoplasmic 1 Heavy Chain 1 (Dync1h1) gene was decreased. Cytoplasmic dynein in the cerebral cortex of Dnah5-/- mice showed a 60% decrease compared to the wild-type mice. It was also observed a 32% reduction in nestin and 35% reduction in N-cadherin in the lateral ventricular wall of Dnah5-/- mice.
Conclusion: The reduction of cytoplasmic dynein resulted in the suppression of axonal growth and disrupted neurogenesis, and, consequently, a decrease in cell density in the ventricular wall layers. Hydrocephalus in the Dnah5-/- mouse model may arise from the stagnation of CSF due to impaired motile cilia function, and cortical malformations caused by cytoplasmic dynein deficiency.
Research of wet string grid dust removal vehicle and creation of dust control area on tunnel working face
Authors: Deng Huan , Chen Shiqiang , Huang Junxin , Wu Zhirong , Rao Ying , Qiu Xinyi , Cheng Jiujun 
Published: February 2024

Abstract
The spread of blast dust throughout the tunnel becomes a common problem in drill and blast tunneling,the key to breaking through the problem is the creation of a dust control area on the working face.In view of this key problem, a wet string grid dust removal crawler vehicle was developed, the power of the vehicle came from the diesel generator, and further, the air cooler of the diesel generator was used to generate air, and the suction process formed by the on-board axial flow fan was coupled to create a dust control area of the working face after blasting.The results show that when the frequency of the axial flow fan is adjusted to 30 Hz, the wind speed of the wet chord grid section reaches 3.34 m/s, and the dust removal efficiency is the highest, with a value of 94.3%.Compared with the non-use of the dust removal vehicle, when the air outlet of the air cooler is front, horizontal front, horizontal rear, the dust concentration is reduced by 74.37%, 92.39% and 50.53%.Finally, the optimized wet grid dust removal crawler was installed in the Dading tunnel, and the actual dust reduction efficiency was about 78.49%. The results obtained provide an important technical way to improve the working environment of the drilling and blasting construction tunnel.
Clinical characteristics and outcomes of acute liver failure in neonates: a retrospective cohort in China
Authors: Xu Suhua , Zhang Peng , Ge Mengmeng , Shan Yuanyuan , Cheng Guoqiang 
Published: February 2024

Abstract

Currently, no literature is available regarding neonatal acute liver failure (NALF), as a rare disease with high mortality, in China. We attempted to analyze a NALF cohort to improve the prognosis of this disease. We included all patients diagnosed with NALF at our institution between 2016 and 2021 and retrospectively reviewed their electronic records. NALF was defined as an INR ≥ 2.0 due to liver disease 28 days after birth. Comparisons were made according to etiology and outcome. The Kaplan-Meier method was used to estimate survival. Fifty-eight patients were included in this study. Etiologies included hypoxic/ischemic injury (29.3%), infection (27.6%), gestational alloimmune liver disease with neonatal hemochromatosis (GALD-NH) (10.3%), inherited metabolic diseases (5.2%), hemophagocytic lymphohistiocytosis (1.7%), other etiologies (12.1%), and unidentified causes (13.8%). Enteroviruses constituted 87.5% of the viral infections, whereas herpes simplex virus accounted for no infections. The median INR was significantly lower in the infection group than in the GALD-NH group (P < 0.05 for multiple comparisons). At the last follow-up, none of the patients had undergone liver transplantation, and the overall mortality rate was 50%. Liver function completely recovered in 31% of the patients, all of whom survived. The overall median survival time was 48 days; 26 days for hypoxic/ischemic injury and 43 days for GALD-NH. The incidence of cholestasis was significantly greater among surviving patients (P = 0.018).
Conclusions: Hypoxic/ischemic injury and infection are the predominant etiologies of NALF in China. The overall prognosis of NALF is poor, but its short-term prognosis is determined by the etiology.
Clinical features and effectiveness of SARS-CoV-2 vaccine in children with omicron infection in a tertiary hospital during the Omicron wave in China, December 2022–January 2023
Authors: Zheng Sujie , Guo Hao , Liu Ning , Jiang Tao , Guo Zhen , He Fang 
Published: February 2024

Abstract
There are limited data about Omicron infection in children in China. Here, we evaluated the infection fatality rates, clinical features and efficacy of SARS-CoV-2 vaccine in children with Omicron infection in a tertiary hospital during the first wave of SARS-CoV-2 caused by Omicron in China, December 2022-January 2023.We used the week as a statistical unit, and the positive rate of NAT was 0.03% from December 1 to December 7, the week before the Zero-COVID strategy was relaxed. Following the repeal of the Zero-COVID policy, the positive rate of NAT rose to 8.3% in the first week, peaked at 85.2% in the third week, and then steadily fell.The NAT positive rate in children peaked (90.4%) in the third week following the termination of the Zero-COVID policy.43.6% (232/532) of the 532 pediatric patients received vaccinations, with the majority (95.3%, 221/232) receiving two doses and the remainder receiving one.532 of the 641 pediatric patients who tested positive for NAT were seen in the pediatric outpatient clinic. Eventually, 51 pediatric patients were admitted to hospitals. Overall, the symptoms of infection were mild, and the rate of severe disease was low, whereas vaccination had a favorable effect on lowering the risk of severe illness in children.
Adoptive transfer of T lymphocytes retrovirally transduced to express personalized neoantigen reactive T cell receptors can mediate tumor regression in patients with metastatic colorectal cancer
Authors: Parkhurst Maria , Goff Stephanie , Lowery Frank , Beyer Rachel , Halas Hyunmi , Robbins Paul , Gartner Jared , Sindiri Sivasish , Krishna Sri , Zacharakis Nikolaos , Ngo Lien , Ray Satyajit , Bera Alakesh , Shepherd Ryan , Levin Noam , Kim Sanghyun , Copeland Amy , Nah Shirley , Levi Shoshana , Parikh Neilesh , Kwong Mei Li , Klemen Nicholas , Yang James , Rosenberg Steven 
Published: February 2024

Abstract

Adoptive cell transfer (ACT) using neoantigen reactive T lymphocytes can mediate cancer regression. Here, we developed methods to isolate unique, personalized, neoantigen reactive T cell receptors (TCRs) from tumor infiltrating lymphocytes (TIL) from patients with metastatic gastrointestinal cancers and incorporate the TCR α and β chains into gamma retroviral vectors. We transduced autologous peripheral blood lymphocytes (PBL) using γ-retroviruses and adoptively transferred those cells into patients after lymphodepleting chemotherapy. We treated 7 patients with metastatic, mismatch-repair proficient colorectal cancers who had progressive disease following multiple prior therapies, and three patients had objective clinical responses by RECIST criteria including regressions of metastases to the liver, lung, and lymph nodes. All patients received T cell populations containing ≥50% TCR transduced cells, and all T cell populations were polyfunctional in that they secreted IFNα, GM-CSF, IL-2, and Granzyme B specifically in response to mutant peptides compared to wild type counterparts. TCR transduced cells were detected in the peripheral blood of 5 patients, including the three responders, at levels ≥10% of CD3+ cells approximately one month post-ACT. In one patient with a partial response to therapy, ~20% of CD3+ PBL expressed transduced TCRs more than two years after treatment. These studies demonstrate that ACT with T cells genetically modified to express personalized neoantigen reactive TCRs is safe and can mediate tumor regression in patients with metastatic solid epithelial cancers.