bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of Drp1- Fis1 interaction alleviates aberrant mitochondrial fragmentation and acute kidney injury
Authors: Song Zhixia , Xia Yao , Shi Lang , Zha Hongchu , Huang Jing , Xiang Xiaohong , Li Huiming , Huang Hua , Yue Ruchi , Wang Hongtao , Zhu Jiefu 
Published: March 2024

Abstract
Background
Acute kidney injury (AKI) is a common clinical disorder with complex etiology and poor prognosis, and currently lacks specific and effective treatment options. Mitochondrial dynamics dysfunction is a prominent feature in AKI, and modulation of mitochondrial morphology may serve as a potential therapeutic approach for AKI.

Methods
We induced ischemia–reperfusion injury (IRI) in mice (bilateral) and Bama pigs (unilateral) by occluding the renal arteries. ATP depletion and recovery (ATP-DR) was performed on proximal renal tubular cells to simulate in vitro IRI. Renal function was evaluated using creatinine and urea nitrogen levels, while renal structural damage was assessed through histopathological staining. The role of Drp1 was investigated using immunoblotting, immunohistochemistry, immunofluorescence, and immunoprecipitation techniques. Mitochondrial morphology was evaluated using confocal microscopy.

Results
Renal IRI induced significant mitochondrial fragmentation, accompanied by Dynamin-related protein 1 (Drp1) translocation to the mitochondria and Drp1 phosphorylation at Ser616 in the early stages (30 min after reperfusion), when there was no apparent structural damage to the kidney. The use of the Drp1 inhibitor P110 significantly improved kidney function and structural damage. P110 reduced Drp1 mitochondrial translocation, disrupted the interaction between Drp1 and Fis1, without affecting the binding of Drp1 to other mitochondrial receptors such as MFF and Mid51. High-dose administration had no apparent toxic side effects. Furthermore, ATP-DR induced mitochondrial fission in renal tubular cells, accompanied by a decrease in mitochondrial membrane potential and an increase in the translocation of the pro-apoptotic protein Bax. This process facilitated the release of dsDNA, triggering the activation of the cGAS-STING pathway and promoting inflammation. P110 attenuated mitochondrial fission, suppressed Bax mitochondrial translocation, prevented dsDNA release, and reduced the activation of the cGAS-STING pathway. Furthermore, these protective effects of P110 were also observed renal IRI model in the Bama pig and folic acid-induced nephropathy in mice.

Conclusions
Dysfunction of mitochondrial dynamics mediated by Drp1 contributes to renal IRI. The specific inhibitor of Drp1, P110, demonstrated protective effects in both in vivo and in vitro models of AKI.
Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant
Authors: Wu Lin-Fang , Zhu Wei-Guang , Yu En-Ping , Cao Hong-Lin , Wang Zheng-Feng 
Published: March 2024

Abstract
Objectives
Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation.

Data description
Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839 bp in length, with 92 contigs and an N50 of 22,379,495 bp. The repetitive elements in the assembly were 555,442,205 bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.
De novo genome assembly of a high-protein soybean variety HJ117
Authors: Liu Zhi , Yang Qing , Liu Bingqiang , Li Chenhui , Shi Xiaolei , Wei Yu , Guan Yuefeng , Yang Chunyan , Zhang Mengchen , Yan Long 
Published: March 2024

Abstract
Objectives
Soybean is an important feed and oil crop in the world due to its high protein and oil content. China has a collection of more than 43,000 soybean germplasm resources, which provides a rich genetic diversity for soybean breeding. However, the rich genetic diversity poses great challenges to the genetic improvement of soybean. This study reports on the de novo genome assembly of HJ117, a soybean variety with high protein content of 52.99%. These data will prove to be valuable resources for further soybean quality improvement research, and will aid in the elucidation of regulatory mechanisms underlying soybean protein content.

Data description
We generated a contiguous reference genome of 1041.94 Mb for HJ117 using a combination of Illumina short reads (23.38 Gb) and PacBio long reads (25.58 Gb), with high-quality sequence coverage of approximately 22.44× and 24.55×, respectively. HJ117 was developed through backcross breeding, using Jidou 12 as the recurrent parent and Chamoshidou as the donor parent. The assembly was further assisted by 114.5 Gb Hi-C data (109.9×), resulting in a contig N50 of 19.32 Mb and scaffold N50 of 51.43 Mb. Notably, Core Eukaryotic Genes Mapping Approach (CEGMA) assessment and Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results indicated that most core eukaryotic genes (97.18%) and genes in the BUSCO dataset (99.4%) were identified, and 96.44% of the genomic sequences were anchored onto twenty pseudochromosomes.
Resistance training modifies of serum levels of matrix metalloproteinase 2 and tissue inhibitor of matrix metalloproteinases in multiple sclerosis women - a randomized controlled trail
Authors: Nezhad Nasrin Niazi , Parnow Abdolhossein , Khamoushian Kianoosh , Eslami Rasoul , Baker Julien S 
Published: March 2024

AbstractThe objectives of the present study was to investigate the effects of resistance training (RT) on serum levels of controlling blood-brain barrier (BBB) permeability indices and cognitive performance in MS women (MS-W). In this randomized control trail study (IRCT registration code: IRCT20120912010824N3, 07.09.2023), twenty-five MS-W were randomly divided into sedentary (MS) and resistance exercise (12 weeks/3 times per week/ 60–80% of 1RM) (MS + RT) groups. Fifteen healthy aged-matched women participated as a control group (HCON). The serum level of matrix metalloproteinase-2 (MMP-2), matrix metallopeptidase-9 (MMP-9), tissue metalloproteinase inhibitors-1 (TIMP-1), tissue metalloproteinase inhibitors-2 (TIMP-2), and S100 calcium-binding protein B (S100B) were assessed. In addition, cognitive performance was assessed pre- and post- intervention with the Brief International Cognitive Assessment for MS (BICAMS). A significant reduction in MMP-2, TIMP-2 serum levels, and MMP-2/TIMP-2 ratio were observed in post-test for MS + RT group (p < 0.01) in comparison to the HCON and MS groups; however, no changes were observed in MMP-9, TIMP-1, S100B and MMP-9/TIMP-1 ratio after RT (p > 0.05). The verbal learning was improved in post-test for MS + RT group (p < 0.01), although no change were observed for visuospatial memory and information processing speed (p > 0.05). These findings suggest that resistance training can modify some indices of BBB permeability and improve verbal learning in MS-W. The findings may also be beneficial as a non-pharmacological intervention to reduce inflammation.
Effectiveness of tranexamic acid in burn patients undergoing surgery – a systematic review and meta-analysis
Authors: Slob Joeri , Gigengack Rolf K. , van Baar Margriet E. , Loer Stephan A. , Koopman Seppe S. H. A. , van der Vlies Cornelis H. 
Published: March 2024

Summary
Background
Reducing blood loss during excisional surgery in burn patients remains a challenge. Tranexamic acid during surgery can potentially reduce blood loss. The use of tranexamic acid during excisional surgery in burn patients has recently been described in a review and meta-analysis. However, quality assessment on studies included was not performed and this review did not apply independent reviewers. Quality assessment of studies investigating the effectiveness of tranexamic acid in burn patients is crucial before concusions can be drawn. Therefore, we conducted a systematic review and meta-analysis of the literature investigating the effectiveness of tranexamic acid in burn patients undergoing surgery.

Methods
A systematic review and meta-analysis of the literature was conducted. The study was pre-registered in PROSPERO database (CRD42023396183).

Results
Five studies including two randomised controlled trials (RCTs) with a total of 303 patients were included. Risk of bias of the included studies was moderate to high. Individual results of the studies were heterogeneous. In three studies of moderate quality the administration of tranexamic acid resulted in a reduction of blood loss per unit excised area, accounting as moderate level of evidence. In two low-quality studies and one moderate quality study the administration of tranexamic acid resulted in a reduction of transfused packed Red Blood Cells (pRBC’s), accounting for moderate level of evidence. Postoperative haemoglobin levels were higher after tranexamic acid administration in one study, accounting for insufficient evidence. Meta-analysis pooling overall blood loss from two separate RCTs failed to detect a statistically significant reduction. Substantial heterogeneity was observed.

Conclusions
Moderate level of evidence indicates that tranexamic acid reduces blood loss per unit of excised area and transfusion of packed Red Blood Cells. Results indicate that tranexamic acid can be beneficial in burn patients undergoing surgery. More high-quality research is needed to confirm these results. Future studies should focus on the dosing of tranexamic acid, the administration approaches, and even consider combining these approaches.

Trial Registration
PROSPERO: CRD42023396183
Nuclear respiratory factor 1 regulates super enhancer-controlled SPIDR to protect hepatocellular carcinoma cells from oxidative stress
Authors: Liu Baowang , Dou Jian , Cao Jinglin 
Published: March 2024

Abstract
Background
Cellular response to oxidative stress plays significant roles in hepatocellular carcinoma (HCC) development, yet the exact mechanism by which HCC cells respond to oxidative stress remains poorly understood. This study aimed to investigate the role and mechanism of super enhancer (SE)-controlled genes in oxidative stress response of HCC cells.

Methods
The GSE112221 dataset was used to identify SEs by HOMER. Functional enrichment of SE-controlled genes was performed by Metascape. Transcription factors were predicted using HOMER. Prognosis analysis was conducted using the Kaplan-Meier Plotter website. Expression correlation analysis was performed using the Tumor Immune Estimation Resource web server. NRF1 and SPIDR expression in HCC and normal liver tissues was analyzed based on the TCGA-LIHC dataset. ChIP-qPCR was used to detect acetylation of lysine 27 on histone 3 (H3K27ac) levels of SE regions of genes, and the binding of NRF1 to the SE of SPIDR. To mimic oxidative stress, HepG2 and Hep3B cells were stimulated with H2O2. The effects of NRF1 and SPIDR on the oxidative stress response of HCC cells were determined by the functional assays.

Results
A total of 318 HCC-specific SE-controlled genes were identified. The functions of these genes was significant association with oxidative stress response. SPIDR and RHOB were enriched in the “response to oxidative stress” term and were chosen for validation. SE regions of SPIDR and RHOB exhibited strong H3K27ac modification, which was significantly inhibited by JQ1. JQ1 treatment suppressed the expression of SPIDR and RHOB, and increased reactive oxygen species (ROS) levels in HCC cells. TEAD2, TEAD3, NRF1, HINFP and TCFL5 were identified as potential transcription factors for HCC-specific SE-controlled genes related to oxidative stress response. The five transcription factors were positively correlated with SPIDR expression, with the highest correlation coefficient for NRF1. NRF1 and SPIDR expression was up-regulated in HCC tissues and cells. NRF1 activated SPIDR transcription by binding to its SE. Silencing SPIDR or NRF1 significantly promoted ROS accumulation in HCC cells. Under oxidative stress, silencing SPIDR or NRF1 increased ROS, malondialdehyde (MDA) and γH2AX levels, and decreased superoxide dismutase (SOD) levels and cell proliferation of HCC cells. Furthermore, overexpression of SPIDR partially offset the effects of NRF1 silencing on ROS, MDA, SOD, γH2AX levels and cell proliferation of HCC cells.

Conclusion
NRF1 driven SPIDR transcription by occupying its SE, protecting HCC cells from oxidative stress-induced damage. NRF1 and SPIDR are promising biomarkers for targeting oxidative stress in the treatment of HCC.
Antimicrobial resistance patterns, virulence genes, and biofilm formation in enterococci strains collected from different sources
Authors: Ghazvinian Maryam , Asgharzadeh Marghmalek Saba , Gholami Mehrdad , Amir Gholami Sanaz , Amiri Elham , Goli Hamid Reza 
Published: March 2024

Abstract
Background
Currently, antibiotic-resistant strains of Enterococcus are considered to be one of the critical health challenges globally. This study aimed to investigate the antibiotic susceptibility pattern, biofilm formation capacity, and virulence genes of enterococci isolated from different sources.

Methods
In this cross-sectional study, environmental and fecal samples were collected from the hospital environment, volunteers, and hospital staff from October 2018 to August 2019. The isolates were identified by morphological and biochemical tests (gram staining, catalase, bile resistance, esculin hydrolysis, carbohydrate fermentation, growth in 6.5% NaCl, Pyrrolidonyl arylamidase, arginine dehydrolase), and PCR for ddl gene. An antimicrobial susceptibility test was performed by the standard disk agar diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Quantitative microplate assays were used to assess biofilm production. The bacterial DNAs were extracted by alkaline lysis method and polymerase chain reaction technique was used detect the esp, ace, and efaA virulence genes.

Results
Out of 145 isolates, 84 (57.9%) were identified as E. faecalis and 61 (42.1%) as E. faecium. Resistance to kanamycin and quinupristin-dalfopristin was 82.1% (69/84) and 85.7% (72/84), respectively, in E. faecalis isolates. Out of 61 E. faecalis isolates, 38 (62.4%) were resistant to kanamycin. Among the E. faecalis isolates, esp was the most dominant virulence gene (73.80%), followed by efaA, and ace, which were detected in 60.71%, and 30.95% isolates, respectively. In total, 68.27% of the strains were biofilm producers. Further, esp and efaA genes were more frequently found among E. faecalis strains with moderate and strong biofilm biomass.

Conclusions
According to the findings of our study, enterococci strains isolated from different samples possess distinctive patterns of virulence genes. The esp, ace, and efaA genes were more prevalent among E. faecalis than E. faecium. Besides, the high level antibiotic resistance of normal flora and environmental enterococci strains is alarming the researchers.
Diagnosis of multiple tuberculous muscle abscesses in a patient with systemic lupus erythematosus by metagenomic next-generation sequencing- a case report and literature review
Authors: Wentao Liu , Shuxia Xie , Guoxing Zhu , Qiaoping Chen , Peiran Chen , Angela Wu , Meirong Li , Songchao Yin , Peiying Feng 
Published: March 2024

Abstract
Background
Early diagnosis of muscular tuberculosis (TB) without coexistent active skeletal involvement is often challenging because the disease is very rare and its clinical manifestation is nonspecific and misleading. To raise the awareness and emphasize early diagnosis of muscular TB, we present a case of multiple tuberculous muscle abscesses in a systemic lupus erythematosus (SLE) female, but without pulmonary tuberculosis (PTB), in order to increase awareness of and stress the need of early detection of muscular TB.

Case presentation
A 44-year-old woman with a 6-year history of SLE who had been treated with methylprednisolone for a long time complained of erythema on her trunk and extremities for five months, along with edema and myalgia for two months, and fever for one month. The patient was first misdiagnosed as SLE overlap dermatomyositis. However, an ultrasound-guided drainage of muscle abscesses revealed positive acid-fast staining combined with positive deoxyribonucleic acid fragment of Mycobacterium tuberculosis using metagenomic next-generation sequencing (mNGS). The patient was cured and released following standard anti-tuberculosis medication, local puncture drainage, and an intravitreal injection of streptomycin. Literature search found only 19 cases of tuberculous muscle abscesses occurring in the extremities reported from 1999 to 2023.

Conclusions
Extrapulmonary TB with predominantly muscle involvement is rare and with no specific clinical presentation. Muscular tuberculosis may be disdiagnosed for dermatomyositis due to the high muscle enzyme levels, delaying diagnosis and treatment. mNGS technology is helpful in the early and rapid diagnosis of muscular TB. On the basis of traditional anti-tuberculosis treatment, an ultrasound-guided percutaneous puncture drainage and intracavitary injection of streptomycin for the treatment of tuberculous muscle abscess is easy to operate, safe and effective, which is worthy of clinical popularization and application.
Expanded clinical phenotype and untargeted metabolomics analysis in RARS2-related mitochondrial disorder: a case report
Authors: Walimbe Ameya S. , Machol Keren , Kralik Stephen F. , Mizerik Elizabeth A. , Gofin Yoel , Bekheirnia Mir Reza , Gijavanekar Charul , Elsea Sarah H. , Emrick Lisa T. , Scaglia Fernando 
Published: March 2024

Abstract
Background
RARS2-related mitochondrial disorder is an autosomal recessive mitochondrial encephalopathy caused by biallelic pathogenic variants in the gene encoding the mitochondrial arginyl-transfer RNA synthetase 2 (RARS2, MIM *611524, NM_020320.5). RARS2 catalyzes the transfer of L-arginine to its cognate tRNA during the translation of mitochondrially-encoded proteins. The classical presentation of RARS2-related mitochondrial disorder includes pontocerebellar hypoplasia (PCH), progressive microcephaly, profound developmental delay, feeding difficulties, and hypotonia. Most patients also develop severe epilepsy by three months of age, which consists of focal or generalized seizures that frequently become pharmacoresistant and lead to developmental and epileptic encephalopathy (DEE).

Case presentation
Here, we describe a six-year-old boy with developmental delay, hypotonia, and failure to thrive who developed an early-onset DEE consistent with Lennox-Gastaut Syndrome (LGS), which has not previously been observed in this disorder. He had dysmorphic features including bilateral macrotia, overriding second toes, a depressed nasal bridge, retrognathia, and downslanting palpebral fissures, and he did not demonstrate progressive microcephaly. Whole genome sequencing identified two variants in RARS2, c.36 + 1G > T, a previously unpublished variant that is predicted to affect splicing and is, therefore, likely pathogenic and c.419 T > G (p.Phe140Cys), a known pathogenic variant. He exhibited significant, progressive generalized brain atrophy and ex vacuo dilation of the supratentorial ventricular system on brain MRI and did not demonstrate PCH. Treatment with a ketogenic diet (KD) reduced seizure frequency and enabled him to make developmental progress. Plasma untargeted metabolomics analysis showed increased levels of lysophospholipid and sphingomyelin-related metabolites.

Conclusions
Our work expands the clinical spectrum of RARS2-related mitochondrial disorder, demonstrating that patients can present with dysmorphic features and an absence of progressive microcephaly, which can help guide the diagnosis of this condition. Our case highlights the importance of appropriate seizure phenotyping in this condition and indicates that patients can develop LGS, for which a KD may be a viable therapeutic option. Our work further suggests that analytes of phospholipid metabolism may serve as biomarkers of mitochondrial dysfunction.
Characteristics of patients with recurrent retinoblastoma: a survival analysis
Authors: Li Nan , Wang Yi-Zhuo , Zhang Yi , Zhang Wei-Ling , Huang Dong-Sheng 
Published: March 2024

Abstract
Background
Management guidelines and corresponding survival data for patients with recurrent retinoblastoma (RB) are lacking. This study aimed to summarize the clinical characteristics of patients with recurrent RB and analyze their survival outcomes.

Methods
We retrospectively analyzed 68 patients with recurrent RB who underwent treatment in our institution from January 2016 to December 2020. Patients were grouped according to location of recurrence: intraocular, orbital, and distant metastasis.

Results
The male:female ratio was 1.3:1 and the median age at recurrence was 37.5 months (range, 30.3–62.8). The number of patients in the intraocular recurrence, orbital recurrence, and metastasis groups was 13 (19.1%), 23 (33.8%), and 32 (47.1%), respectively. Thirty patients died, 36 were alive at last follow-up, and two were lost to follow-up. Eye enucleation was performed in 94.1% of patients. Five-year overall survival in patients with intraocular recurrence, orbital recurrence, and metastasis was 84.6%, 69.6%, and 31.3%, respectively (P = 0.001). Most deaths occurred within 2 years of recurrence. Presence of high-risk pathological factors, central nervous system invasion, and absence of combination therapy were independent predictors of worse 5-year overall survival.

Conclusion
The rate of eye preservation in survivors of recurrent RB was very low. Although 5-year overall survival in patients who underwent treatment for intraocular and orbital recurrence was high, it was low in those with metastasis. RB patients may need lifelong follow-up for recurrence and secondary malignancy.
Epstein-Barr virus-positive iris diffuse large B-cell lymphoma detected by metagenomic next-generation sequencing
Authors: Wang Xiao-na , Hong Jing , Xu Yong-gen , Zhang Pei , Li Ying-yu , Dou Hong-liang , Li Hai-ping 
Published: March 2024

Abstract
Purpose
Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) is a relatively rare subtype of DLBCL. Herein, we report a case of a patient with EBV-positive iris DLBCL after undergoing penetrating keratoplasty and discuss its possible pathogenesis.

Methods
A 72-year-old male patient presented to our hospital with progressive blurring of vision in the left eye for the past 4 months. Small white nodular lesions were observed on the iris and retinal surface of the left eye, with a white cloud-like opacity in the vitreous cavity.

Results
The patient was eventually diagnosed with EBV-positive iris DLBCL after undergoing pathological and metagenomic tests. After injecting methotrexate in the left vitreous cavity and administering systemic and local antiviral treatments, the ocular lesions disappeared.

Conclusion
EBV infection, drug immunosuppression, and aging-related immune deterioration may play significant roles in the pathogenesis of EBV-positive iris DLBCL.

Synopsis
Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) is a new subtype of DLBCL, which rarely occurs. Herein, we report a case of a patient with EBV-positive iris DLBCL after undergoing penetrating keratoplasty and discuss its possible pathogenesis.