bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influential and Highest Cited Shoulder Instability Articles: A Bibliometric Analysis
Authors: Allahabadi Sachin , Eftekhari Ava , Feeley Sonali E. , Feeley Brian T. , Lansdown Drew A. 
Published: March 2021

Background: In orthopaedic surgery and other fields, the effect of influential journal articles has been evaluated by their citation counts and their correlation with methodological quality. Purpose: To identify and characterize the 50 most cited articles on shoulder instability, examine trends in publication characteristics, and evaluate the correlation of citations with quality of evidence. Study Design: Cross-sectional study. Methods: The Web of Science and Scopus online databases were searched to identify the top 50 most cited articles on shoulder instability, based on the average number of citations from each database. Article characteristics were recorded, and level of evidence and methodological quality were assessed using the modified Coleman Methodology Score (mCMS), Jadad scale, and Methodological Index for Non-Randomized Studies (MINORS). Spearman correlation was used to evaluate relationships between citations or citation density (citations/y) and level of evidence or methodological scoring. Top cited articles from recent years were also aggregated. Results: The top 50 most cited papers had a mean ± SD number of citations of 381.5 ± 166.7, with a mean of 15.0 ± 8.8 citations/y. Overall, 15 articles (30%) were biomechanical/cadaveric studies, and 15 (30%) were case series. Only 3 (6%) were considered to have level 1 evidence. The mean ± SD mCMS was 54.4 ± 12.7, mean ± SD Jadad score was 3.1 ± 1.4, and mean ± SD MINORS score was 10.5 ± 3.3. There were no significant correlations between citation rank or density and methodological assessments. There were weak correlations between citation rank and publication year ( rs = 0.32; P = .022) and between rank and level of evidence ( rs = –0.38; P = .047). The correlation between citation density and publication year was moderate ( rs = 0.70; P < .0001). There was no difference in citation density of the top 10 articles from 2010 to 2020 compared with the top 10 from the overall list (23.8 ± 5.3 vs 28.8 ± 9.5; P = .16). Conclusion: Influential articles in shoulder instability included a high proportion of biomechanical/cadaveric studies. The majority of top cited articles had lower evidence levels and poorer methodological quality without strong correlation with citations or citation density. There was a moderate correlation between citation density and year of publication.
SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints
Authors: Zhang Yiqun , Chen Fengju , Creighton Chad J. 
Published: March 2021

Abstract
Background
Combined whole-genome sequencing (WGS) and RNA sequencing of cancers offer the opportunity to identify genes with altered expression due to genomic rearrangements. Somatic structural variants (SVs), as identified by WGS, can involve altered gene cis-regulation, gene fusions, copy number alterations, or gene disruption. The absence of computational tools to streamline integrative analysis steps may represent a barrier in identifying genes recurrently altered by genomic rearrangement.

Results
Here, we introduce SVExpress, a set of tools for carrying out integrative analysis of SV and gene expression data. SVExpress enables systematic cataloging of genes that consistently show increased or decreased expression in conjunction with the presence of nearby SV breakpoints. SVExpress can evaluate breakpoints in proximity to genes for potential enhancer translocation events or disruption of topologically associated domains, two mechanisms by which SVs may deregulate genes. The output from any commonly used SV calling algorithm may be easily adapted for use with SVExpress. SVExpress can readily analyze genomic datasets involving hundreds of cancer sample profiles. Here, we used SVExpress to analyze SV and expression data across 327 cancer cell lines with combined SV and expression data in the Cancer Cell Line Encyclopedia (CCLE). In the CCLE dataset, hundreds of genes showed altered gene expression in relation to nearby SV breakpoints. Altered genes involved TAD disruption, enhancer hijacking, and gene fusions. When comparing the top set of SV-altered genes from cancer cell lines with the top SV-altered genes previously reported for human tumors from The Cancer Genome Atlas and the Pan-Cancer Analysis of Whole Genomes datasets, a significant number of genes overlapped in the same direction for both cell lines and tumors, while some genes were significant for cell lines but not for human tumors and vice versa.

Conclusion
Our SVExpress tools allow computational biologists with a working knowledge of R to integrate gene expression with SV breakpoint data to identify recurrently altered genes. SVExpress is freely available for academic or commercial use at https://github.com/chadcreighton/SVExpress. SVExpress is implemented as a set of Excel macros and R code. All source code (R and Visual Basic for Applications) is available.
Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
Authors: Zhong Yizhi , Zhao Wenbin , Tang Zhangsheng , Huang Liming , Zhu Xiangxing , Liang Xiang , Yan Aifen , Lu Zhifa , Yu Yanling , Tang Dongsheng , Wang Dapeng , Lu Zhuanling 
Published: March 2021

Abstract
Background
The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely unknown. In this study, we identified four stages of P. clarkii ovary development, the previtellogenic stage (stage I), early vitellogenic stage (stage II), middle vitellogenic stage (stage III), and mature stage (stage IV) and compared the transcriptomics among these four stages through next-generation sequencing (NGS).

Results
The total numbers of clean reads of the four stages ranged from 42,013,648 to 62,220,956. A total of 216,444 unigenes were obtained, and the GC content of most unigenes was slightly less than the AT content. Principal Component Analysis (PCA) and Anosim analysis demonstrated that the grouping of these four stages was feasible, and each stage could be distinguished from the others. In the expression pattern analysis, 2301 genes were continuously increase from stage I to stage IV, and 2660 genes were sharply decrease at stage IV compared to stages I-III. By comparing each of the stages at the same time, four clusters of differentially expressed genes (DEGs) were found to be uniquely highly expressed in stage I (136 genes), stage II (43 genes), stage III-IV (49 genes), and stage IV (22 genes), thus exhibiting developmental stage specificity. Moreover, in comparisons between adjacent stages, the number of DEGs between stage III and IV was the highest. GO enrichment analysis demonstrated that nutrient reservoir activity was highest at stage II and that this played a foreshadowing role in ovarian development, and the GO terms of cell, intracellular and organelle participated in the ovary maturation during later stages. In addition, KEGG pathway analysis revealed that the early development of the ovary was mainly associated with the PI3K-Akt signaling pathway and focal adhesion; the middle developmental period was related to apoptosis, lysine biosynthesis, and the NF-kappa B signaling pathway; the late developmental period was involved with the cell cycle and the p53 signaling pathway.

Conclusion
These transcriptomic data provide insights into the molecular mechanisms of ovarian development in P. clarkii. The results will be helpful for improving the reproduction and development of this aquatic species.
A putative exosporium lipoprotein GBAA0190 of Bacillus anthracis as a potential anthrax vaccine candidate
Authors: Jeon Jun Ho , Kim Yeon Hee , Kim Kyung Ae , Kim Yu-Ri , Woo Sun-Je , Choi Ye Jin , Rhie Gi-eun 
Published: March 2021

Abstract
Background
Bacillus ancthracis causes cutaneous, pulmonary, or gastrointestinal forms of anthrax. B. anthracis is a pathogenic bacterium that is potentially to be used in bioterrorism because it can be produced in the form of spores. Currently, protective antigen (PA)-based vaccines are being used for the prevention of anthrax, but it is necessary to develop more safe and effective vaccines due to their prolonged immunization schedules and adverse reactions.

Methods
We selected the lipoprotein GBAA0190, a potent inducer of host immune response, present in anthrax spores as a novel potential vaccine candidate. Then, we evaluated its immune-stimulating activity in the bone marrow-derived macrophages (BMDMs) using enzyme-linked immunosorbent assay (ELISA) and Western blot analysis. Protective efficacy of GBAA0190 was evaluated in the guinea pig (GP) model.

Results
The recombinant GBAA0190 (r0190) protein induced the expression of various inflammatory cytokines including tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), monocyte chemoattractant protein-1 (MCP-1), and macrophage inflammatory protein-1α (MIP-1α) in the BMDMs. These immune responses were mediated through toll-like receptor 1/2 via activation of mitogen-activated protein (MAP) kinase and Nuclear factor-κB (NF-κB) pathways. We demonstrated that not only immunization of r0190 alone, but also combined immunization with r0190 and recombinant PA showed significant protective efficacy against B. anthracis spore challenges in the GP model.

Conclusions
Our results suggest that r0190 may be a potential target for anthrax vaccine.
The role of mGlu4 receptors within the nucleus accumbens in acquisition and expression of morphine-induced conditioned place preference in male rats
Authors: Ebrahimi Zahra , Kahvandi Nazanin , Komaki Alireza , Karimi Seyed Asaad , Naderishahab Marzieh , Sarihi Abdolrahman 
Published: March 2021

Abstract
Background
Several studies have shown that glutamate neurotransmission in the nucleus accumbens (NAc) is required for the development of morphine-induced conditional place preference (CPP). In addition, metabotropic glutamate receptors (mGluRs) in NAc play important roles in the reward pathways. However, the precise role of mGluR4 in different steps of the morphine-induced CPP is less well known. In the present study the effect of bilateral intra-accumbal infusion of VU0155041, as a specific mGluR4 agonist on the acquisition and expression of morphine induced CPP in male Wistar rats was investigated. The animals were bilaterally implanted with guide cannulae above the NAc. In the first step of the study, the VU0155041 was administered at doses of 10, 30 and 50 μg/0.5 μL saline per side into the NAc during the 3 days of morphine (5 mg/kg) conditioning (acquisition) phase of morphine-induced CPP. In the second step of the study, the rats bilaterally received VU0155041 at the dose of 50 μg/0.5 μL, 5 min before the post-conditioning test in order to check the effect of VU0155041 on the expression of morphine-induced CPP.

Results
The results showed that the intra-accumbal injection of VU0155041 inhibits the acquisition of morphine-induced CPP in a dose dependent manner, but had no effect on expression.

Conclusions
The data indicated that intra-NAc administration of VU0155041 dose dependently blocks the establishment of morphine-induced CPP and reduces the rewarding properties of morphine. These effects may be related to changes in glutamate activity in the NAC and/or learning dependent mechanism of glutamate neurotransmission in reward pathway(s).
Genome-wide identification of BAM genes in grapevine (Vitis vinifera L.) and ectopic expression of VvBAM1 modulating soluble sugar levels to improve low-temperature tolerance in tomato
Authors: Liang Guoping , He Honghong , Nai Guojie , Feng Lidan , Li Yanmei , Zhou Qi , Ma Zonghuan , Yue Yuan , Chen Baihong , Mao Juan 
Published: March 2021

Abstract
Background
Low temperature (LT) is one of the main limiting factors that affect growth and development in grape. Increasing soluble sugar and scavenging reactive oxygen species (ROS) play critical roles in grapevine resistance to cold stress. However, the mechanism of β-amylase (BAM) involved in the regulation of sugar levels and antioxidant enzyme activities in response to cold stress is unclear.

Results
In this study, six BAM genes were identified and clustered into four groups. Multiple sequence alignment and gene structure analysis showed that VvBAM6 lacked the Glu380 residue and contained only an exon. The transcript abundance of VvBAM1 and VvBAM3 significantly increased as temperature decreased. After LT stress, VvBAM1 was highly expressed in the leaves, petioles, stems, and roots of overexpressing tomato lines. The total amylase and BAM activities increased by 6.5- and 6.01-fold in transgenic plants compared with those in wild-type tomato plants (WT) subjected to LT, respectively. The glucose and sucrose contents in transgenic plants were significantly higher than those in WT plants, whereas the starch contents in the former decreased by 1.5-fold compared with those in the latter under LT stress. The analysis of transcriptome sequencing data revealed that 541 genes were upregulated, and 663 genes were downregulated in transgenic plants. One sugar transporter protein gene (SlSTP10), two peroxidase (POD)-related genes (SlPER7 and SlPER5), and one catalase (CAT)-related gene (SlCAT1) were upregulated by 8.6-, 3.6-, 3.0-, and 2.3-fold in transgenic plants after LT stress, respectively.

Conclusions
Our results suggest that VvBAM1 overexpression promotes ROS scavenging and improves cold tolerance ability by modulating starch hydrolysis to affect soluble sugar levels in tomato plants.
Prenatal diagnosis of a rare variant of harlequin ichthyosis with literature review
Authors: Zhou Yi , Li Liang , Wang Ling , Zhang Chaoxue 
Published: March 2021

Abstract
Background
Harlequin ichthyosis (HI) is a rare and severe genetic skin disorder that occurs within the developing foetus. Due to the extremely poor prognosis, prenatal diagnosis becomes very important, especially for foetuses with no family history. There are few reports on prenatal diagnosis in PubMed.

Case presentation
We report two cases of HI with no family history who were diagnosed by prenatal ultrasound. We searched for reports on the prenatal ultrasonic diagnosis of HI over nearly two decades and summarized the sonographic features of HI, the reasons for missed diagnoses and matters needing attention. A total of 10 articles of congenital harlequin ichthyosis diagnosed by prenatal ultrasound in PubMed were retrieved. There have been even fewer reports of late-trimester disease with no family history. Combining the two cases we reported with the literature review, we summarize the ultrasonic image characteristics of HI.

Conclusion
HI can be easily detected by 2D ultrasound combined with 3D, but attention should be paid to a systematic examination in the third trimester of pregnancy according to the clinical characteristics of the disease.
Corneal endothelial cells changes in different stages of Keratoconus: a multi-Centre clinical study
Authors: Elmassry Ahmed , Osman Ahmed , Sabry Moataz , Elmassry Mohamed , Katkat Mai , Hatata Mohamed Yousry , El-Kateb Mohamed 
Published: March 2021

Abstract
Purpose
To assess the corneal endothelial cells morphology and count in keratoconus patients and their correlation with different stages of keratoconus.

Methods
Prospective non randomized multi-centric clinical study included 150 eyes of 150 keratoconus patients. Four centers in Egypt participated in this study included: Departments of Ophthalmology in Alexandria University, Tanta University and Port Said University and Alex I-Care hospital. Pentacam (Wavelight Oculyzer II) and specular microscopy (Tomey EM-3000) were done to all eyes. Keratoconic eyes were classified according to Amsler classification into stage 1, 2 and 3. Stage 1 included 99 eyes, stage 2 included 32 eyes & stage 3 included 19 eyes.

Results
The mean age of keratoconus patients was 24.07 ± 6.154 years. Forty five cases were males (30%) and 105 cases were females (70%). There was statistically significant difference in endothelial cell density (p < 0.001) and coefficient of variation (p = 0.012) between different stages of keratoconus eyes. Regarding cell surface area, there was statistically significant difference in cell surface area between different stages of keratoconus eyes (p < 0.001). In addition, for cell morphology, there was statistically significant difference between different stages of keratoconus eyes (p < 0.001).

Conclusions
Qualitative and quantitative structural changes were seen in endothelial cells of keratoconus eyes by using specular microscopy. For stages 1 and 2, keratoconus may not affect the corneal endothelim significantly. The endothelium in stage 3 shows significant changes regarding polymegathism and pleomorphism.
Parental bonding styles in schizophrenia, depressive and bipolar patients: a comparative study
Authors: Abbaspour Aidin , Bahreini Masoud , Akaberian Sherafat , Mirzaei Kamran 
Published: March 2021

Abstract
Background
Numerous bio-psychosocial factors play a role in the etiology of psychiatric disorders. In this regard, the relationship between parents and their children is significantly involved in developing the offspring mental health. However, there is no clear-cut answer as to which parental bonding style is more strongly associated with psychiatric diseases of patients. This study aimed to compare parental bonding styles in patients with schizophrenia, depression, and bipolar disorder in Bushehr province, Iran in 2018.

Methods
In this cross-sectional comparative study, 130 patients with schizophrenia, depression, and bipolar disorder who referred to four outpatients psychiatric centers in Bushehr were selected using quota sampling. The patients were assessed and compared in terms of parental bonding styles. Data were collected using a valid and reliable parental bonding instrument (PBI). Data were analyzed using SPSS software (ver. 22), Chi-square and Kruskal-Wallis tests at a significant level of 0.05.

Results
Results showed that the optimal parental bonding style (low control, high care) in bipolar disorder (43.05%), major depression (47.7%), and schizophrenia (38.5%) was the most prevalent style of parental bonding; however, 62.30% of the above patients suffered from inefficient paternal bonding styles and 51.53% from inefficient maternal bonding styles. Furthermore, the patients’ maternal bonding styles were significantly different (p = 0.007) while their paternal bonding styles did not show any significant differences (p = 0.848).

Conclusions
Most of the patients with psychiatric disorders were affected by ineffective parenting styles. The results also confirmed that despite the several bio-psycho-social factors involved in the development of psychiatric disorders, the crucial roles of parents, especially mothers, should not be ignored. It was further suggested that parents and parental bonding were important and fundamental factors for mental health promotion.
Take-home naloxone programs for suspected opioid overdose in community settings: a scoping umbrella review
Authors: Moustaqim-Barrette Amina , Dhillon Damon , Ng Justin , Sundvick Kristen , Ali Farihah , Elton-Marshall Tara , Leece Pamela , Rittenbach Katherine , Ferguson Max , Buxton Jane A. 
Published: March 2021

Abstract
Background
Opioid related overdoses and overdose deaths continue to constitute an urgent public health crisis. The implementation of naloxone programs, such as ‘take-home naloxone’ (THN), has emerged as a key intervention in reducing opioid overdose deaths. These programs aim to train individuals at risk of witnessing or experiencing an opioid overdose to recognize an opioid overdose and respond with naloxone. Naloxone effectively reverses opioid overdoses on a physiological level; however, there are outstanding questions on community THN program effectiveness (adverse events, dosing requirements, dose-response between routes of administration) and implementation (accessibility, availability, and affordability). The objective of this scoping review is to identify existing systematic reviews and best practice guidelines relevant to clinical and operational guidance on the distribution of THN.

Methods
Using the Arksey & O’Malley framework for scoping reviews, we searched both academic literature and grey literature databases using keywords (Naloxone) AND (Overdose) AND (Guideline OR Review OR Recommendation OR Toolkit). Only documents which had a structured review of evidence and/or provided summaries or recommendations based on evidence were included (systematic reviews, meta-analyses, scoping reviews, short-cut or rapid reviews, practice/clinical guidelines, and reports). Data were extracted from selected evidence in two key areas: (1) study identifiers; and (2) methodological characteristics.

Results
A total of 47 articles met inclusion criteria: 20 systematic reviews; 10 grey literature articles; 8 short-cut or rapid reviews; 4 scoping reviews; and 5 other review types (e.g. mapping review and comprehensive reviews). The most common subject themes were: naloxone effectiveness, safety, provision feasibility/acceptability of naloxone distribution, dosing and routes of administration, overdose response after naloxone administration, cost-effectiveness, naloxone training and education, and recommendations for policy, practice and gaps in knowledge.

Conclusions
Several recent systematic reviews address the effectiveness of take-home naloxone programs, naloxone dosing/route of administration, and naloxone provision models. Gaps remain in the evidence around evaluating cost-effectiveness, training parameters and strategies, and adverse events following naloxone administration. As THN programs continue to expand in response to opioid overdose deaths, this review will contribute to understanding the evidence base for policy and THN program development and expansion.