bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining manipulation of integration loci and secretory pathway on expression of an Aspergillus niger glucose oxidase gene in Trichoderma reesei
Authors: Ji Wangli , Wang Xiaolu , Liu Xiaoqing , Wang Yuan , Liu Fangui , Xu Bo , Luo Huiying , Tu Tao , Zhang Wei , Xu Xinxin , Su Xiaoyun 
Published: February 2023

AbstractTrichoderma reesei (T. reesei) is well-known for its excellent ability to secret a large quantity of cellulase. However, unlike the endogenous proteins, little is known about the molecular mechanisms governing heterologous protein production. Herein, we focused on the integration loci and the secretory pathway, and investigated their combinatorial effects on heterologous gene expression in T. reesei using a glucose oxidase from Aspergillus niger as a model protein. Integration in the cel3c locus was more efficient than the cbh1 locus in expressing the AnGOx by increasing the transcription of AnGOx in the early stage. In addition, we discovered that interruption of the cel3c locus has an additional effect by increasing the expression of the secretory pathway component genes. Accordingly, overexpressing three secretory pathway component genes, that were snc1, sso2, and rho3, increased AnGOx expression in the cbh1 transformant but not in the cel3c transformant.
Chorioallantoic membrane assay revealed the role of TIPARP (2,3,7,8-tetrachlorodibenzo-p-dioxin-inducible poly (ADP-ribose) polymerase) in lung adenocarcinoma-induced angiogenesis
Authors: Miura Kenji , Koyanagi-Aoi Michiyo , Maniwa Yoshimasa , Aoi Takashi 
Published: February 2023

Abstract
Background
The chorioallantoic membrane (CAM) assay is a well-established technique to evaluate tumor invasion and angiogenesis and may overcome the shortcoming of the patient-derived xenograft (PDX) mouse model. Currently, few reports have described lung cancer invasion and angiogenesis in the CAM assay. We therefore used the CAM assay in the evaluation of lung cancer.

Method
Lung cancer cell line-derived organoids or lung cancer cell lines were transplanted into the CAM on embryonic development day (EDD) 10, and an analysis was performed on EDD 15. Microscopic and macroscopic images and movies of the grafts on the CAM were captured and analyzed. The relationships between the graft and chick vessels were evaluated using immunohistochemistry.

Results
We transplanted lung cancer cell lines and cell line-derived organoid into a CAM to investigate angiogenesis and invasion. They engrafted on the CAM at a rate of 50–83%. A549-OKS cells showed enhanced cell invasion and angiogenesis on the CAM in comparison to A549-GFP cells as was reported in vitro. Next, we found that A549-TIPARP cells promoted angiogenesis on the CAM. RNA-seq identified 203 genes that were upregulated more than twofold in comparison to A549-GFP cells. A pathway analysis revealed many upregulated pathways related to degradation and synthesis of the extracellular matrix in A549-TIPARP cells.

Conclusions
The CAM assay can be used to evaluate and research invasion and angiogenesis in lung cancer. The elevated expression of TIPARP in lung cancer may induce angiogenesis by remodeling the extracellular matrix.
Adherence to severe malaria treatment guidelines in children at a Ugandan regional hospital: a baseline assessment for a malaria treatment quality improvement project
Authors: Moffitt Cynthia A. , Olupot-Olupot Peter , Onen Joan Wamulugwa , O’Brien Nicole 
Published: February 2023

Abstract
Background
Malaria is one of the most common causes of hospital admission and death in children under the age of five. The World Health Organization (WHO) has issued guidelines for the identification and treatment of severe malaria. Evidence has shown that adherence to standardized malaria treatment protocols improves outcomes. As a baseline assessment in preparation for a malaria treatment quality improvement project, this study aimed to determine adherence to the WHO severe malaria treatment guidelines in children at a Ugandan Regional Referral Hospital.

Methods
A retrospective review was performed on a convenience sample of children discharged between June 2021 and March 2022 from the Mbale Regional Referral Hospital Paediatrics Ward with a diagnosis of severe malaria. Data were collected using a standardized case report form. Demographics, presenting symptoms, laboratory results, treatments, length of stay, and mortality were extracted. Comparison of treatments received to items recommended in the WHO guidelines was undertaken to determine adherence.

Results
147 patients were included. The median age was 5 years (IQR 2–7 years), and 55% were male. The most common features of severe malaria were haemoglobinuria (49%), haemoglobin < 5 mg/dL (34%), and altered mentation (24%). Median hospital length of stay was 3 days (IQR 2–4 days), and the mortality rate was 27% (n = 40). Overall adherence to all aspects of the WHO severe malaria guidelines was achieved in 3% (n = 4) of patients. The most common areas of deficiency were not testing to confirm malaria diagnosis (34%) and inadequate administration of artesunate (82%). Fewer than the three recommended doses of artesunate occurred in 22% of patients. Additionally, a delay in the administration of the second dose occurred in 67% (n = 78) and in the third dose in 77% (n = 71) of patients. While the recommended time between doses is 12 h, the median interval between dose one and dose two was 15 h (12–20) and the median interval from dose two to dose three was 17 h (14–25).

Conclusions
Current adherence to severe malaria treatment guidelines in children at this Ugandan regional referral hospital is poor, but this study has identified target areas for improvement.
Racial/ethnic disparities in opioid overdose prevention: comparison of the naloxone care cascade in White, Latinx, and Black people who use opioids in New York City
Authors: Khan Maria R. , Hoff Lee , Elliott Luther , Scheidell Joy D. , Pamplin John R. , Townsend Tarlise N. , Irvine Natalia M. , Bennett Alex S. 
Published: February 2023

Abstract
Background
Drug overdose mortality is rising precipitously among Black people who use drugs. In NYC, the overdose mortality rate is now highest in Black (38.2 per 100,000) followed by the Latinx (33.6 per 100,000) and white (32.7 per 100,000) residents. Improved understanding of access to harm reduction including naloxone across racial/ethnic groups is warranted.

Methods
Using data from an ongoing study of people who use illicit opioids in NYC (N = 575), we quantified racial/ethnic differences in the naloxone care cascade.

Results
We observed gaps across the cascade overall in the cohort, including in naloxone training (66%), current possession (53%) daily access during using and non-using days (21%), 100% access during opioid use (20%), and complete protection (having naloxone and someone who could administer it present during 100% of opioid use events; 12%). Naloxone coverage was greater in white (training: 79%, possession: 62%, daily access: 33%, access during use: 27%, and complete protection: 13%, respectively) and Latinx (training: 67%, possession: 54%, daily access: 22%, access during use: 24%, and complete protection: 16%, respectively) versus Black (training: 59%, possession: 48%, daily access:13%, access during use: 12%, and complete protection: 8%, respectively) participants. Black participants, versus white participants, had disproportionately low odds of naloxone training (OR 0.40, 95% CI 0.22–0.72). Among participants aged 51 years or older, Black race (versus white, the referent) was strongly associated with lower levels of being trained in naloxone use (OR 0.20, 95% CI 0.07–0.63) and having 100% naloxone access during use (OR 0.34, 95% CI 0.13–0.91). Compared to white women, Black women had 0.27 times the odds of being trained in naloxone use (95% CI 0.10–0.72).

Conclusions
There is insufficient protection by naloxone during opioid use, with disproportionately low access among Black people who use drugs, and a heightened disparity among older Black people and Black women.
Low expression of ZSCAN4 predicts unfavorable outcome in urothelial carcinoma of upper urinary tract and urinary bladder
Authors: He Hong-Lin , Lai Hong-Yue , Chan Ti-Chun , Hsing Chung-Hsi , Huang Steven K. , Hsieh Kun-Lin , Chen Tzu-Ju , Li Wan-Shan , Kuo Yu-Hsuan , Shiue Yow-Ling , Li Chien-Feng 
Published: February 2023

Abstract
Background
With the advance in genome-wide analyses, genetic alternations have been found to play an important role in carcinogenesis and aggressiveness of UC. Through bioinformatic analysis of gene expression profiles of urinary bladder urothelial carcinoma (UBUC) from publicly available GEO dataset (GSE31684), Zinc finger and SCAN domain containing 4 (ZSCAN4) was identified as a significant downregulated gene in muscle-invasive bladder cancer when compared with non-muscle-invasive bladder cancer.

Methods
The expression of ZSCAN4 was evaluated by immunohistochemistry in 340 upper urinary tract urothelial carcinomas (UTUCs) and 295 UBUCs. The expression profiles of ZSCAN4 and potential signaling pathways were analyzed bioinformatically.

Results
In UTUC, low expression of ZSCAN4 was significantly associated with advanced primary pT stage (P = 0.011), increased nodal metastasis (P = 0.002) and increased vascular invasion (P = 0.019). In UBUC, low expression of ZSCAN4 was significantly correlated with advanced primary pT stage (P < 0.001), increased nodal metastasis (P = 0.001), high histological grade (P = 0.003) and increased vascular invasion (P = 0.003). In survival analysis, low expression of ZSCAN4 acted as an independent negative prognostic factor for disease-specific survival and metastasis-free survival both in UTUC and UBUC. Gene ontology analysis showed that ZSCAN4 mRNA and its co-downregulated genes are associated with the mitotic cell cycle.

Conclusions
Low expression of ZSCAN4 predicted worse outcome in urothelial carcinoma and might have potential regulatory role in cell mitosis.
Global landscape of SARS-CoV-2 mutations and conserved regions
Authors: Abbasian Mohammad Hadi , Mahmanzar Mohammadamin , Rahimian Karim , Mahdavi Bahar , Tokhanbigli Samaneh , Moradi Bahman , Sisakht Mahsa Mollapour , Deng Youping 
Published: February 2023

Abstract
Background
At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management.

Methods
10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence.

Results
Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508–635(0.77%) and aa 381–508 (0.43%). The highest frequency of mutation was observed in aa 66–88 (2.19%), aa 7–14, and aa 164–246 (2.92%) in M, E, and N proteins, respectively.

Conclusion
Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS‐CoV‐2 diagnostic efficiency and design safe and effective vaccines against emerging variants.
Integrated multi-omics analyses and functional validation reveal TTK as a novel EMT activator for endometrial cancer
Authors: Miao Yu , Konno Yosuke , Wang Baojin , Zhu Lin , Zhai Tianyue , Ihira Kei , Kobayashi Noriko , Watari Hidemichi , Jin Xin , Yue Junming , Dong Peixin , Fang Mingyan 
Published: February 2023

Abstract
Background
Cancer-testis antigens (CTAs) are often expressed in tumor and testicular tissues but not in other normal tissues. To date, there has been no comprehensive study of the expression and clinical significance of CTA genes associated with endometrial cancer (EC) development. Additionally, the clinical relevance, biological role, and molecular mechanisms of the CTA gene TTK protein kinase (TTK) in EC are yet to be fully understood.

Methods
Using bioinformatics methods, we comprehensively investigated the genomic, transcriptomic, and epigenetic changes associated with aberrant TTK overexpression in EC samples from the TCGA database. We further investigated the mechanisms of the lower survival associated with TTK dysregulation using single-cell data of EC samples from the GEO database. Cell functional assays were used to confirm the biological roles of TTK in EC cells.

Results
We identified 80 CTA genes that were more abundant in EC than in normal tissues, and high expression of TTK was significantly linked with lower survival in EC patients. Furthermore, ROC analysis revealed that TTK could accurately distinguish stage I EC tissues from benign endometrial samples, suggesting that TTK has the potential to be a biomarker for early EC detection. We found TTK overexpression was more prevalent in EC patients with high-grade, advanced tumors, serous carcinoma, and TP53 alterations. Furthermore, in EC tissue, TTK expression showed a strong positive correlation with EMT-related genes. With single-cell transcriptome data, we identified a proliferative cell subpopulation with high expression of TTK and known epithelial–mesenchymal transition (EMT)-related genes and transcription factors. When proliferative cells were grouped according to TTK expression levels, the overexpressed genes in the TTKhigh group were shown to be functionally involved in the control of chemoresistance. Utilizing shRNA to repress TTK expression in EC cells resulted in substantial decreases in cell proliferation, invasion, EMT, and chemoresistance. Further research identified microRNA-21 (miR-21) as a key downstream regulator of TTK-induced EMT and chemoresistance. Finally, the TTK inhibitor AZ3146 was effective in reducing EC cell growth and invasion and enhancing the apoptosis of EC cells generated by paclitaxel.

Conclusion
Our findings establish the clinical significance of TTK as a new biomarker for EC and an as-yet-unknown carcinogenic function. This present study proposes that the therapeutic targeting of TTK might provide a viable approach for the treatment of EC.
Chronic kidney disease promotes cerebral microhemorrhage formation
Authors: Fang Chuo , Lau Wei Ling , Sun Jiahong , Chang Rudy , Vallejo Adrian , Lee Donghy , Liu Jihua , Liu Han , Hung Yu-Han , Zhao Yitong , Paganini-Hill Annlia , Sumbria Rachita K. , Cribbs David H. , Fisher Mark 
Published: February 2023

AbstractBackgroundChronic kidney disease (CKD) is increasingly recognized as a stroke risk factor, but its exact relationship with cerebrovascular disease is not well-understood. We investigated the development of cerebral small vessel disease using in vivo and in vitro models of CKD.MethodsCKD was produced in aged C57BL/6J mice using an adenine-induced tubulointerstitial nephritis model. We analyzed brain histology using Prussian blue staining to examine formation of cerebral microhemorrhage (CMH), the hemorrhagic component of small vessel disease and the neuropathological substrate of MRI-demonstrable cerebral microbleeds. In cell culture studies, we examined effects of serum from healthy or CKD patients and gut-derived uremic toxins on brain microvascular endothelial barrier.ResultsCKD was induced in aged C57BL/6J mice with significant increases in both serum creatinine and cystatin C levels (p < 0.0001) without elevation of systolic or diastolic blood pressure. CMH was significantly increased and positively correlated with serum creatinine level (Spearmanr = 0.37,p < 0.01). Moreover, CKD significantly increased Iba-1-positive immunoreactivity by 51% (p < 0.001), induced a phenotypic switch from resting to activated microglia, and enhanced fibrinogen extravasation across the blood–brain barrier (BBB) by 34% (p < 0.05). On analysis stratified by sex, the increase in CMH number was more pronounced in male mice and this correlated with greater creatinine elevation in male compared with female mice. Microglial depletion with PLX3397 diet significantly decreased CMH formation in CKD mice without affecting serum creatinine levels. Incubation of CKD serum significantly reduced transendothelial electrical resistance (TEER) (p < 0.01) and increased sodium fluorescein permeability (p < 0.05) across the endothelial monolayer. Uremic toxins (i.e., indoxyl sulfate, p-cresyl sulfate, and trimethylamine-N-oxide) in combination with urea and lipopolysaccharide induced a marked drop in TEER compared with the control group (p < 0.0001).ConclusionsCKD promotes the development of CMH in aged mice independent of blood pressure but directly proportional to the degree of renal impairment. These effects of CKD are likely mediated in part by microglia and are associated with BBB impairment. The latter is likely related to gut-derived bacteria-dependent toxins classically associated with CKD. Overall, these findings demonstrate an important role of CKD in the development of cerebral small vessel disease.
Bifocal versus trifocal bone transport for the management of tibial bone defects caused by fracture-related infection: a meta-analysis
Authors: Liu Kai , Zhang Hongyan , Maimaiti Xiayimaierdan , Yusufu Aihemaitijiang 
Published: February 2023

Abstract
Background
The purpose of this meta-analysis was to compare the efficacy and outcomes of bifocal bone transport (BFT) and trifocal bone transport (TFT) for the treatment of tibial bone defects caused by fracture-related infection (FRI).

Methods
The literature searches of Cochrane Library, Embase, Google Scholar databases, PubMed/Medline, and Web of Science for literature published up to September 20, 2022, were performed. The quality of the included studies was evaluated according to the MINORS scale. Patients were divided into the BFT group and the TFT group, depending on the site of the osteotomy. The demographic data, defect size (DS), external fixation time (EFT), external fixation index (EFI), bone and functional results, complications, and autologous bone grafting (ABG) were extracted and analyzed using the Review Manager software (version 5.3).

Results
Five studies included 484 patients with tibial bone defects treated by bone transport investigated in this meta-analysis, with a mean bone defect of 9.3 cm. There were statistical differences in DS (MD =  − 2.38, 95% CI − 3.45 to − 1.32, P < 0.0001), EFT (MD = 103.44, 95% CI 60.11 to 146.77, P < 0.00001), and EFI (MD = 26.02, 95% CI 14.38 to 37.65, P < 0.00001) between BFT group and TFT group. There was no statistical difference in bone results (RR = 0.98, 95% CI 0.91 to 1.06, P = 0.67), functional results (RR = 0.94, 95% CI 0.82 to 1.07, P = 0.37), complications (OR = 1.57, 95% CI 0.59 to 4.14, P = 0.36), and ABG (RR = 1.2, 95% CI 0.78 to 1.84, P = 0.42) between two groups.

Conclusions
TFT was a feasible and practical method in the treatment of massive tibial bone defects caused by FRI to receive shorter EFT and satisfactory bone and functional results.
Maternal separation and TNBS-induced gut inflammation synergistically alter the sexually differentiated stress response in rats
Authors: Hasegawa Ryoko , Saito-Nakaya Kumi , Gu Li , Kanazawa Motoyori , Fukudo Shin 
Published: February 2023

Abstract
Background
Neonatal maternal separation (MS) has been used to model long-lasting changes in behavior caused by neuroplastic changes associated with exposure to early-life stress. Earlier studies showed that transient gut inflammation can influence the development of irritable bowel syndrome (IBS). A prevailing paradigm of the etiology of IBS is that transient noxious events lead to long-lasting sensitization of the neural pain circuit, despite complete resolution of the initiating event. This study characterizes the changes in behaviors and neuroendocrine parameters after MS and early-phase trinitrobenzene sulfonic acid (TNBS)-induced colitis. We tested the hypothesis that MS and gut inflammation synergistically induce (1) hyperactivity in male rats and anxiety-like behaviors in female rats and (2) activation of the HPA axis in female rats and deactivation of the HPA axis in male rats after colorectal distention (CRD).

Methods
Male and female rat pups were separated from their dams for 180 min daily from postnatal day (PND) 2 to PND 14 (MS). Early-phase colitis was induced by colorectal administration with TNBS on PND 8. The elevated plus-maze test was performed at 7 weeks. Tonic CRD was performed at 60 mmHg for 15 min at 8 weeks. Plasma ACTH and serum corticosterone were measured at baseline or after the CRD. Analysis of variance was performed for comparison among controls, TNBS, MS, and MS + TNBS.

Results
In male rats, the time spent in open arms significantly differed among the groups (p < 0.005). The time spent in open arms in male MS + TNBS rats was significantly higher than that of controls (p < 0.009) or TNBS rats (p < 0.031, post hoc test). Female rats showed no difference in the time spent in open arms among the groups. MS and gut inflammation induced an increase in plasma ACTH in female rats but not in male rats at baseline.

Conclusions
These findings suggest that MS and gut inflammation synergistically induce hyperactive behavior or exaggerated hypothalamic–pituitary–adrenal axis function depending on sex.
Association between self-rated depressive symptoms and mucosal expression of NF-κ B in patients with upper gastrointestinal symptoms
Authors: Staab Julia , Vonhören Lara , Schwörer Harald , Meyer Thomas 
Published: February 2023

Abstract
Background
Previous clinical studies have reported elevated levels of depressive symptoms in selected samples of patients with gastritis. The objective of this study was to examine the associations of specific biomarkers of inflammation expressed in mucosal tissue from the stomach with mood and anxiety symptoms in adult patients with upper gastrointestinal symptoms.

Methods
In this monocentric, observational study, a total of 32 study participants were included who were referred for a routine diagnostic upper endoscopic assessment based on the suspected clinical diagnosis of gastritis. All participants completed the Hospital Anxiety and Depression Scale (HADS) before undergoing gastroscopy. Immunohistochemical stainings from biopsy sections were performed to evaluate the expression level of nuclear factor kappa B (NF-κ B), myeloperoxidase (MPO) and inducible nitric oxide synthase (iNOS).

Results
Our findings confirmed that nearly half of the study cohort (n = 13; 41%) displayed positive HADS depression scores above the clinically relevant cut-off level of ≥ 8. Regression models demonstrated that depressive symptoms were significantly and positively associated with the expression level of NF-κ B in biopsies from the upper gastrointestinal tract.

Conclusions
In summary, our study showed a significant association between NF-κ B expression and clinically relevant depressive symptoms in patients with gastritis, as assessed by a self-rated psychometric questionnaire. Further investigations are needed to confirm this relationship and to identify the pathophysiological mechanisms involved.