bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics analysis of paravertebral muscles atrophy in adult degenerative scoliosis
Authors: Rong Zhigang , Yang Zhong , Zhang Chengmin , Pu Rongxi , Chen Can , Xu Jianzhong , Luo Fei 
Published: January 2023

Abstract
Paravertebral muscles (PVM) act as one of the major dynamic factors to maintain human upright activities and play a remarkable role in maintaining the balance of the trunk. Adult degenerative scoliosis (ADS) has become one of the important causes of disability in the elderly population owing to the changes in spinal biomechanics, atrophy and degeneration of PVM, and imbalance of the spine. Previously, many studies focused on the physical evaluation of PVM degeneration. However, the molecular biological changes are still not completely known. In this study, we established a rat model of scoliosis and performed the proteomic analysis of the PVM of ADS. The results showed that the degree of atrophy, muscle fat deposition, and fibrosis of the PVM of rats positively correlated with the angle of scoliosis. The proteomic results showed that 177 differentially expressed proteins were present in the ADS group, which included 105 upregulated proteins and 72 downregulated proteins compared with the PVM in individuals without spinal deformities. Through the construction of a protein–protein interaction network, 18 core differentially expressed proteins were obtained, which included fibrinogen beta chain, apolipoprotein E, fibrinogen gamma chain, thrombospondin-1, integrin alpha-6, fibronectin-1, platelet factor 4, coagulation factor XIII A chain, ras-related protein Rap-1b, platelet endothelial cell adhesion molecule 1, complement C1q subcomponent subunit A, cathepsin G, myeloperoxidase, von Willebrand factor, integrin beta-1, integrin alpha-1, leukocyte surface antigen CD47, and complement C1q subcomponent subunit B. Further analysis of the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and immunofluorescence showed that the neutrophil extracellular traps (NETs) formation signaling pathway plays a major role in the pathogenesis of PVM degeneration in ADS. The results of the present study preliminarily laid the molecular biological foundation of PVM atrophy in ADS, which will provide a new therapeutic target for alleviating PVM atrophy and decreasing the occurrence of scoliosis.
WITHDRAWN: Histopathological effect of ranitidine (Zantac) on liver and kidneys in albino mice
Authors: Rashid Muna Salah 
Published: January 2023

Abstract
The purpose: This study was sought to determine the effect of ranitidine on the histological structure of liver and kidneys in the albino mice. The design: two groups of mice were administered Ranitidine 75mg/kg of and 150mg/kg respectively, we used (15) albino mice and administrated the doses orally for 10 consecutive 10 days.
Finding : The results showed some structural effects on tissues of liver and kidneys group two showed (75mg/kg of b. w.) desquamation of the wall of central vein of the liver, necrosis , accumulation of fibroblast, hemorrhage and aggregation of Kupffer cells .the kidneys exhibited necrosis in some regions, hemorrhage and existence of cast in the tubules and it seems that ranitidine has caused dilation between glomerulus and bowman corpuscles. Group three (150mg/kg of b. w.) revealed more damage in the wall of the central vein of the liver, infiltration of focal inflammatory in the area caused hemorrhage ,expansion in sinusoid , accumulation of fibroblast and necrosis in the liver tissue. Kidneys were severely affected in comparison to group one, and showed an extended hemorrhage and ruptures in glomerulus with dilatation, hyperplasia cells in tubules and cast, form this study we conclude that ranitidine with a dose of 75mg/kg has mild effect on the liver and kidneys and medium effect with a dose of with a dose of 150 mg/kg.
Originality/ value: the research is focus in histopathology effects of ranitidine on liver and kidneys
NEK2 could act as a circadian time-dependent tumor suppressor gene and biomarker in esophageal squamous cell carcinoma
Authors: Zeng Boning , Li Nan , Sun Chao , Xie Shouxia , Liu Xiaodi , Peng Yuying , Wang Shaoxiang , Wang Xiao 
Published: January 2023

Abstract
Background
As one of the most prevalent cancers worldwide, esophageal squamous cell carcinoma (ESCC) is characterized by rapid progression and poor prognosis, thus, it is essential to develop novel biomarkers to evaluate the diagnosis and prognosis of ESCC patients. NIMA-related kinase 2 (NEK2) is an oncogenic kinase that has been found to be upregulated in a variety of cancers, and is considered a potential therapeutic target. In addition, circadian rhythms have been shown to be closely related to the development of cancer. However, the relationship between NEK2, circadian rhythm and ESCC progression remain unknown.
Methods
The Cancer Genome Atlas (TCGA), and Gene Expression Omnibus (GEO) databases (GSE23400 and GSE53625) were employed to collected the gene expression in ESCC patients, gene expression data, and clinical information. Several bioinformatics methods, including the Gene Set Enrichment Analysis (GSEA) and survival analysis were utilized to explore the correlation between the expression patterns of NEK2 genes and the development of ESCC. RNA sequencing was performed to investigate the expression of circadian rhythm. The effects of INH6 on the growth and proliferation of ESCC cell lines were tested in vitro by the Cell Counting Kit 8 (CCK8), 5-ethynyl-2ʹ-deoxyuridine (EdU), and colony formation. Additionally, western blotting was used to examined the expression of NEK2, cell cycle and apoptosis related protein, such as P21and cleaved PARP. reverse transcription-quantitative PCR (RT-qPCR) was employed to confirm that core circadian gene Bmal1, and Rev-Erba expressed. The cell apoptosis was detected by flow cytometry.
Results
Here, we first found that NEK2 gene was identified as differentially expressed genes in both the three datasets. Additionally, NEK2 is overexpressed in ESCC tissues and inhibition of NEK2 impairs ESCC cell growth and proliferation. The analysis of the KEGG and GSEA pathways revealed that NEK2 is closely related to known and recognized pathways such as the cell cycle, but an interesting new pathway related to NEK2 was also identified: circadian rhythm. RNA sequencing identified that NEK2 exhibits circadian rhythmic expression, and further in vitro studies confirmed that NEK2 has circadian oscillation in synchronized ESCC cells. More importantly, we observed that INH6 efficacy correlated positively with NEK2 expression levels in ESCC, suggesting that it is well worthwhile to develop and optimize the in vivo efficacy evaluation of NEK2 inhibitors based on chronological administration.
Conclusions
According to this study, NEK2 is highly expressed in human EC, and NEK2 has circadian oscillation in synchronized ESCC cells, which could be used to increase INH6 response to esophageal cancer therapy. In a word, NEK2 acts as a time-dependent tumor suppressor gene and biomarker in ESCC.
Degradation potential, use and growth promotion and antioxidant properties of Haematococcus Pluvialis in algae cell culture system under the influence of phenol
Authors: Rezazadeh Hamzeh , Mansouri Hakimeh 
Published: January 2023

Abstract
In response to highly severe environmental conditions, the accumulation of vast levels of astaxanthin by Haematococcus Pluvialis is a recorded event. However, there is little investigation into the nature and possible interactions of the poisonous chemical factors on this pigment's synthesis. In this study, H. pluvialis was exposed to the environment phenol to determine cellular responses, synthesis of pigments, and astaxanthin. The phenol influences in different concentrations (0, 50, 100, and 150 mg l-1) were checked out by two ways; a treatment (14 days) and pre-treatment (7 days + 7 days) done on green and red stages of H. pluvialis. The amount of carotenoid, protein, and dry weight increased, but the amount of carbohydrates and chlorophyll reduced in treated green cells with a phenol. The pre-treatment increased the amount of chlorophyll a, carbohydrates, and carotenoids in green cells, but it did not significantly affect the dry weight, protein of green cells, and the amount of protein in red cells. The phenol treatment also enhanced the carotenoid, carbohydrate, dry weight, and protein of red cells. In general, the treatment and pre-treatment of phenol in the green phase and low concentrations significantly affected the alga. However, the pre-treatment had a more considerable effect on red cells in high concentrations. While the treatment in the high concentrations had notable effects on the xanthophylls, pre-treatment had the same effects on the xanthophylls at low concentrations. These results show that H. pluvialis can adapt to toxic environments due to the xanthophylls.
Construction of a prognostic model for advanced non-small cell lung cancer using combined analysis of public databases
Authors: Yin Fangtian , Wu Min , Lu Xin , Zhu Jun , Wang Jiale , Zhang Xuewen , Chen Jie , Zheng Kaiman , Jiang Jun 
Published: January 2023

Abstract
Non-small cell lung cancer (NSCLC) has become a global health problem owing to its high incidence and poor treatment efficacy. This study aimed to establish a prognostic model for advanced NSCLC using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to evaluate the prognosis. Based on TCGA database, we obtained a dataset of 191 advanced NSCLC and 108 normal tissue samples after screening. We screened the differential expression between advanced NSCLC and normal tissues using the "limma" software package in R and identified differential expression genes. Weighted gene co-expression network analysis of differential genes was performed and the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes were used for pathway enrichment analysis of the key genes in the core modules. Finally, univariate Cox regression analysis was used to determine genes associated with prognosis, and multivariate Cox regression analysis was used to construct a prognostic model. We used the receiver operating characteristic curve (ROC), Kaplan-Meier curve, and multivariate Cox regression analysis to test the prognostic value of the model. The GEO database (GSE68465) was used to screen a cohort of clinical and gene expression data from 69 patients to further validate the prognostic value of the model. We constructed a five-gene (CKS1B, SLC7A5, SPATS2, SPDL1, and CHEK2) prognostic model to predict overall survival in patients with advanced NSCLC. Kaplan-Meier analysis, area under the ROC curve (AUC), and C-index had good predictive power for gene signatures in TCGA dataset (P<0.0001; C-index 0.710; 95% confidence interval (0.681–0.738); AUC at 1 year, 2 years, and 3 years were 0.76, 0.75, and 0.73, respectively). The risk score was an independent risk factor for survival in patients with advanced NSCLC, after adjusting for other routine clinical parameters. Finally, we constructed a nomogram that integrated gene signatures and clinicopathological parameters. The risk score model constructed from the five survival-related genes can be used as prognostic biomarkers. The nomogram was closely related to the overall survival of the patients. This result may help future individualized treatment and clinical decision making.
Association of maternal plasma manganese with the risk of spontaneous preterm birth: A nested case-control study based on the Beijing Birth Cohort Study (BBCS) in China
Authors: Han Weiling , Zheng Wei , Wang Aili , Chen Junxi , Wang Jia , Huang Junhua , An Hang , Ma Yuru , Zhang Kexin , Yang Ruihua , Yan Lailai , Li Zhiwen , Li Guanghui 
Published: January 2023

Abstract
Background
As an essential trace nutrient, the effect of plasma manganese (Mn) level on the risk of spontaneous preterm birth (SPB) remains debated. This study aimed to clarify the dynamic changes in plasma Mn concentration during pregnancy and its association with SPB.
Methods
A nested case-control study was conducted based on the Beijing Birth Cohort Study (BBCS).This cohort recruited women with a singleton pregnancy, aged 18-44, and intended to receive regular prenatal health care in Beijing Obstetrics and Gynecology Hospital between 2018 and 2020. 244 SPB with maternal plasma samples in the first or third trimester was selected as cases. 244 controls were randomly selected from full term birth mothers with plasma samples in the first or third trimester. Maternal social demographic characteristics and gestational information were obtained from clinical electrical records. Plasma samples were collected in the first and third trimesters for dynamic monitoring. Inductively coupled plasma mass spectrometry (ICP-MS) was used for laboratory analysis.Unconditional logistic regression was used to analyze the relationship between plasma Mn levels and SPB.
Results
A total of 488 pregnant women were included for final analysis (SPB N=244; term group N=244). Maternal plasma Mn con centrations increased with gestational age during pregnancy (median, 0.81 ng/ml in the first trimester vs. 1.23 ng/ml in the third trimester). After adjustment for confounders, the highest Mn level (3rdtertile) in the third trimester increased the SPB risk to 1.647(95%CI: 1.035-2.621).The association became much more significant when the population was stratified to normal weight women(OR: 2.066, 95%CI: 1.182-3.611) or non-premature rupture of membranes（PROM）women (OR: 3.929, 95% CI: 1.995-7.738).Moreover, a dose-dependent relationship exists between the SPB risk and plasma Mn concentration in non-PROMwomen (P trend＜0.001). After excluding women with vaginal group B streptococcus(GBS) infection, the risk association was still significant.
Conclusion
High plasma Mn level in the third trimester may be a risk factor for SPB, especially in women with normal weight and non-PROM. It would be helpful for SPB prevention to monitor Mn levels during pregnancy.
Trial registration
Beijing Birth Cohort Study (BBCS) was retrospectively registered (ChiCTR2200058395, 2022-04-08).
Outcomes Up to Age 36 Months after Congenital Zika Virus Infection – U.S. States
Authors: Neelam Varsha , Woodworth Kate R. , Chang Daniel J. , Roth Nicole M. , Reynolds Megan R. , Akosa Amanda , Carr Christopher P. , Anderson Kayla N. , Mulkey Sarah B. , DeBiasi Roberta L. , Biddle Cara , Lee Ellen H. , Elmore Amanda L. , Scotland Sarah J. , Sowunmi Similoluwa , Longcore Nicole D. , Ahmed Muhammad , Langlois Peter H. , Khuwaja Salma , Browne Shea Elizabeth , Lind Leah , Shim Kyoo , Gosciminski Michael , Blumenfeld Rachel , Khuntia Shreya , Halai Umme-Aiman , Locklear Autumn , Chan Mary , Willabus Teri' , Tonzel Julius , Marzec Natalie S. , Barreto Nianest Alers , Sanchez Connie , Fornoff Jane , Hale Shelby , Nance Amy , Adibhatla Sowmya N. , Potts Emily , Schiffman Elizabeth , Raman Devin , McDonald Morgan F. , Stricklin Brandi , Ludwig Elizabeth , Denson Lindsay , Contreras Dianna , Romitti Paul A. , Ferrell Emily , Marx Meghan , Signs Kimberly , Cook Amie , Beauregard Suzann , Orantes Lucia C. , Cronquist Laura , Roush Lesley , Godfred-Cato Shana , Gilboa Suzanne M. , Meaney-Delman Dana , Honein Margaret A. , Moore Cynthia A. , Tong Van T. 
Published: January 2023

Abstract
Background:
To characterize neurodevelopmental abnormalities in children up to 36 months of age with congenital Zika virus exposure.
Methods:
From the U.S. Zika Pregnancy and Infant Registry, a national surveillance system to monitor pregnancies with laboratory evidence of Zika virus infection, pregnancy outcomes and presence of Zika associated birth defects (ZBD) were reported among infants with available information. Neurologic sequelae and developmental delay were reported among children with ≥ 1 follow-up exam after 14 days of age or with ≥ 1 visit with development reported, respectively.
Results:
Among 2,248 infants, 9.9% were born preterm, and 10.0% were small-for-gestational age. Overall, 122 (5.4%) had any ZBD; 91.8% of infants had brain abnormalities or microcephaly, 23.0% had eye abnormalities, and 14.8% had both. Of 1,881 children ≥ 1 follow-up exam reported, neurologic sequelae were more common among children with ZBD (44.6%) vs. without ZBD (1.5%). Of children with ≥ 1 visit with development reported, 46.8% (51/109) of children with ZBD and 7.4% (129/1739) of children without ZBD had confirmed or possible developmental delay.
Conclusion:
Understanding the prevalence of developmental delays and healthcare needs these children with congenital Zika virus exposure can inform health systems and planning to ensure services are available for affected families.
User-centered design of a telehealth-enhanced hybrid cardiac rehabilitation program as hospital quality improvement
Authors: Duran Andrea T. , Keener-DeNoia Adrianna , Stavrolakes Kimberly , Fraser Adina , Blanco Luis V. , Fleisch Emily , Pieszchata Nicole , Cannone Diane , McKay Charles Keys , Whittman Emma , Edmondson Donald , Shelton Rachel C. , Moise Nathalie 
Published: January 2023

Abstract

Background Innovative program designs and strategies are needed to support the widespread uptake of cardiac rehabilitation (CR) programs in the post-COVID19 era. We combined user-centered design (UCD) and implementation science (ImS) principles to design a novel telehealth-enhanced hybrid (home and clinic-based) CR (THCR) program. Methods As part of a New York Presbyterian Hospital (NYPH) quality improvement initiative (March 2020-February 2022), we designed a THCR program using an iterative 3 step UCD process informed by the Theoretical Domains Framework and Consolidated Framework for Implementation Research to: 1) identify user and contextual barriers to CR uptake (stakeholder interviews), 2) design an intervention prototype (design workshops and journey mapping), and 3) refine the prototype (usability testing). The process was optimized for usability and implementation outcomes. Results Step 1: Semi-structured interviews with stakeholders (n = 9) at 3 geographically diverse academic medical centers revealed behavioral (e.g., self-efficacy, knowledge) and contextual (e.g., social distancing guidelines, physical space, staffing, reimbursement) barriers to uptake. Step 2: Design workshops (n = 20) and journey-mapping sessions (n = 3) with multi-disciplinary NYPH stakeholders (e.g., digital health team, CR clinicians, creative director) yielded a THCR prototype that leveraged NYPH’s investment in their remote patient monitoring (RPM) platform to optimize feasibility of home-based CR sessions. Step 3: Usability testing with CR clinicians (n = 2) administering and CR patients (n = 3) participating in home-based sessions revealed usability challenges (e.g., RPM devices/exercise equipment usability; Wi-Fi/Bluetooth connectivity/syncing; patient safety/knowledge and protocol flexibility). Design workshops (n = 24) and journey-mapping sessions (n = 3) yielded design solutions (e.g., onboarding sessions, safety surveys, fully supervised remote sessions) and a refined THCR prototype. Conclusion Combining UCD and ImS methods while engaging multi-disciplinary stakeholders in an iterative process yielded a theory-informed telehealth-enhanced hybrid CR program targeting user and contextual barriers to real-world CR implementation. We provide a detailed summary of the process, and guidance for incorporating UCD and ImS methods in early-stage intervention development. THCR may shrink the evidence-to-practice gap in CR implementation. A future hybrid type I effectiveness-implementation trial will determine its feasibility, acceptability, and effectiveness.
Distribution of number of genes in different bacteriophages
Authors: Ng Wenfa 
Published: January 2023

Abstract
Advent of low-cost, relatively fast DNA sequencing has opened up applications in genome sequencing. Besides benefiting sequencing of whole genomes of bacteria, archaea and fungi, it has also lend its weight to improve our understanding of bacteriophage genomes. Despite our vast amount of sequencing data, we still do not fully comprehend the generic principles that guide the evolution of genome architecture of the expansive number of bacteriophages in the microbial world. This work hopes to open a small glimpse into the mysteries surrounding the distribution of number of genes in the bacteriophage. Specifically, it attempts to construct a histogram distribution of number of genes in various bacteriophages in the hope of gleaning useful guiding principles that could help us better classify bacteriophages at the genome level. Using bacteriophage genome data obtained from GenBank, this work reveals that there is, in general, three main “size” classifications for bacteriophage genomes with genome size ranging from (43 to 143 genes), (143 to 243 genes) and (243 to 343 genes). Analysis in this study reveals that the smallest genome size is the most prevalent. Given the significant number of genes in the smallest bacteriophage genomes, there may be a need to rethink our understanding of bacteriophage, and whether they are the primitive microbial lifeforms that kickstarted the evolution of bacterial and, to a smaller extent, archaea life on Earth.
Enhancing the expression of a key mitochondrial enzyme at the inception of ischemia-reperfusion injury can boost recovery and halt the progression of acute kidney injury
Authors: Corridon Peter R. 
Published: January 2023

Abstract

Hydrodynamic fluid delivery has shown promise in influencing renal function in disease models. This technique provided pre-conditioned protection in acute injury models by upregulating the mitochondrial adaptation, while hydrodynamic injections of saline alone have improved microvascular perfusion. Accordingly, hydrodynamic mitochondrial gene delivery was applied to investigate the ability to halt progressive or persistent renal function impairment following episodes of ischemia-reperfusion injuries known to induce acute kidney injury (AKI). The rate of transgene expression was approximately 33% and 30% in rats with prerenal AKI that received treatments 1 (T1hr) and 24 (T24hr) hours after the injury was established, respectively. The resulting mitochondrial adaptation via exogenous IDH2 (isocitrate dehydrogenase 2 (NADP+) and mitochondrial) significantly blunted the effects of injury within 24 hours of administration: decreased serum creatinine (» 60%, p < 0.05 at T1hr; » 50%, p < 0.05 at T24hr) and blood urea nitrogen (»50%, p < 0.05 at T1hr; » 35%, p < 0.05 at T24hr) levels, and increased urine output (» 40%, p < 0.05 at T1hr; » 26%, p < 0.05 at T24hr) and mitochondrial membrane potential, Δψm, (» by a factor of 13, p < 0.001 at T1hr; » by a factor of 11, p < 0.001 at T24hr), despite elevated histology injury score (26%, p < 0.05 at T1hr; 47%, p < 0.05 at T24hr). Therefore, this study identifies an approach that can boost recovery and halt the progression of AKI at its inception.