bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weighted Gene Co-Expression Network Analysis Revealed The Cellular Senescence Signaling Pathway Associated With Non-Obstructive Azoospermia
Authors: Wang Ye Copper , Xia Leilei , Yi Xingpeng , Lu Jianping , Shen Dan 
Published: December 2020

Abstract
BackgroundNon-obstructive azoospermia (NOA) in males is a disease commonly associated with infertility, and is characterized by a disorder in spermogenesis, which may be caused by chromosomal abnormalities, orchitis, or chemical therapy. Spermogenesis is a process tightly regulated by precise gene expression patterns. However, the key genes and signaling pathways contributing to NOA remain unclear.MethodsIn this study, weighted gene co-expression network analysis was performed to identify NOA-associated gene clusters, and combined with the KEGG pathway assay and biological research.ResultsOur results revealed that the cellular senescence signaling pathway may play important roles in NOA. Indeed, cellular senescence is a complex biological process, often associated with disorder in cellular function. Using different expression genes (DEGs), the core, NOA-associated gene set in the cellular senescence pathway was identified; it contained SMAD2, which was upregulated, and HIPK4, which was downregulated. Consequently, the database was divided based on the expression levels of SMAD2 and HIPK4, and the GSEA (Gene Set Enrichment Analysis) assay, as well as the GO and KEGG assays of genes co-expressing with SMAD2 and HIPK4, showed that these two genes may take part in the regulation of cellular senescence, sperm differentiation and development, and energy metabolism.ConclusionsThe two genes, SMAD2 and HIPK4, took part in the regulation of senescence, and indicated that the cellular senescence of sertoli cells may play important roles in the NOA. This research can help us understand the mechanisms underlying NOA, and suggest anti-senescence therapeutic approaches that target these associated genes, especially SMAD2 and HIPK4.
Strategy for Mass Production of Lytic Staphylococcus Aureus Bacteriophage pSa-3: Contribution of Multiplicity of Infection
Authors: Kim Sang Guen , Kwon Jun , Giri Sib Sankar , Yun Saekil , Kim Hyoun Joong , Kim Sang Wha , Kang Jung Woo , Lee Sung Bin , Jung Won Joon , Park Se Chang 
Published: December 2020

Abstract
BackgroundAntibiotic-resistant bacteria have emerged as a serious problem; bacteriophages have, therefore, been proposed as a therapeutic alternative to antibiotics. Several authorities, such as pharmacopeia, FDA, have confirmed their safety, and some bacteriophages are commercially available worldwide. The demand for bacteriophages is expected to increase exponentially in the future; hence, there is an urgent need to mass-produce bacteriophages economically. Unlike the replication of non-lytic bacteriophages, lytic bacteriophages are replicated by lysing host bacteria, which leads to the termination of phage production; hence, strategies that can prolong the lysis of host bacteria in bacteria-bacteriophage co-cultures are required.ResultsIn the current study, we manipulated the inoculum concentrations of Staphylococcus aureus and phage pSa-3 (multiplicity of infection, MOI), and their energy sources to delay the bactericidal effect while optimizing phage production. We examined an increasing range of bacterial inoculum concentration (2 × 108 to 2 × 109 CFU/mL) to decrease the lag phase, in combination with a decreasing range of phage inoculum (from MOI 0.01 to 0.00000001) to delay the lysis of the host. Bacterial concentration of 2 × 108 CFU/mL and phage MOI of 0.0001 showed the maximum final phage production rate (1.68 × 1010 plaque forming unit (PFU)/mL). With this combination of phage-bacteria inoculum, we selected glycerol, glycine, and calcium as carbon, nitrogen, and divalent ion sources, respectively, for phage production. After optimization using response surface methodology, the final concentration of lytic Staphylococcus phage was 8.63 × 1010 ± 9.71 × 109 PFU/mL (5.13 fold increase).ConclusionsTherefore, Staphylococcus phage pSa-3 production can be maximized by increasing the bacterial inoculum and reducing the seeding phage MOI, which this combinatorial strategy could decrease phage production time. Further, we suggest that response surface methodology has the potential for optimizing mass production of lytic bacteriophages.
The Dynamic Landscape of Parasitaemia Dependent Intestinal Microbiota Shifting at Species Level and the Correlated Gut Transcriptome During Plasmodium Yoelii Infection
Authors: Zong Yawen , Cheng Lei , Cheng Xiangyun , Liao Binyou , Ye Xingchen , Liu Taiping , Li Jiyao , Zhou Xuedong , Xu Wenyue , Ren Biao 
Published: December 2020

Abstract
BackgroundMalaria, caused by Plasmodium infection, is a global life-threatening infection disease especially during the COVID-19 pandemic. However, it is still unclear about the dynamic change and the interactions of the intestinal microbiota and immunity during the whole parasite infection. Here, we investigated the change of intestinal microbiome and transcriptome during the whole Plasmodium infection process in mice to analyze the dynamic landscape of parasitaemia dependent intestinal microbiota shifting and related to host immunity.ResultsThere were significant parasitaemia dependent changes of intestinal microbiota and transcriptome, and the microbiota was significantly correlated to the intestinal immunity. We found that (i) the diversity and composition of the intestinal microbiota represented a significant correlation along with the Plasmodium infection in family, genus and species level; (ii) particularly, Erysipelotrichaceae bacterium canine oral taxon 255, Sutterella*, Ruminococcus 1* and Eubacterium plexicaudatum ASF492 were specific during the parasitaemia rising state, while Eubacterium nodatum group* was specific in the recovering phase at species level; (iii) the up-regulated genes from the intestinal transcriptome were mainly enriched in immune cell differentiation pathways along with the malaria development, particularly, naive CD4+ T cells differentiated into Th1, Th2 and Tfh cells in the early immune response and into Th17 cells in the later response, while B cells were activated during the whole Plasmodium infection process; (iv) the abundance of the parasitaemia phase-specific microbiota represented a high correlation with the phase-specific immune cells development, particularly, Th1 cell with family Bacteroidales BS11 gut group, genera Prevotella 9, Ruminococcaceae UCG 008, Moryella and specie Sutterella* , Th2 cell with specie Sutterella*, Th17 cell with family Peptococcaceae , genus Lachnospiraceae FCS020 group and spices Ruminococcus 1*, Ruminococcus UGG 014* and Eubacterium plexicaudatum ASF492, Tfh and B cell with genera Moryella and species Erysipelotrichaceae bacterium canine oral taxon 255.Conclusion﻿There were a remarkable dynamic landscape of the parasitaemia dependent shifting of intestinal microbiota and immunity, and a notable correlation between the abundance of intestinal microbiota, especially at species level, and immune cells.
Data Quality Assessment and Subsampling Strategies to Correct Distributional Bias in Prevalence Studies.
Authors: D'Ambrosio Angelo , Garlasco Jacopo , Quattrocolo Francesca , Vicentini Costanza , Zotti Carla Maria 
Published: December 2020

Abstract
BackgroundHealthcare-associated infections (HAIs) represent a major Public Health issue. Hospital-based prevalence studies are a common tool of HAI surveillance, but data quality problems and non-representativeness can undermine their reliability.MethodsThis study proposes three algorithms that, given a convenience sample and variables relevant for the outcome of the study, select a subsample with specific distributional characteristics, boosting either representativeness (Probability and Distance procedures) or risk factors' balance (Uniformity procedure). A "Quality Score" (QS) was also developed to grade sampled units according to data completeness and reliability. The methodologies were evaluated through bootstrapping on a convenience sample of 135 hospitals collected during the 2016 Italian Point Prevalence Survey (PPS) on HAIs.ResultsThe QS highlighted wide variations in data quality among hospitals (median QS 52.9 points, range 7.98-628, lower meaning better quality), with most problems ascribable to ward and hospital-related data reporting. Both Distance and Probability procedures produced subsamples with lower distributional bias (Log-likelihood score increased from 7.3 to 29 points). The Uniformity procedure increased the homogeneity of the sample characteristics (e.g., -58.4% in geographical variability). The procedures selected hospitals with higher data quality, especially the Probability procedure (lower QS in 100% of bootstrap simulations). The Distance procedure produced lower HAI prevalence estimates (6.98% compared to 7.44% in the convenience sample), more in line with the European median.ConclusionsThe QS and the subsampling procedures proposed in this study could represent effective tools to improve the quality of prevalence studies, decreasing the biases that can arise due to non-probabilistic sample collection.
A Novel Graphical Evaluation of Agreement
Authors: Kim Jongphil , Lee Ji-Hyun 
Published: December 2020

Abstract
Background: The Bland-Altman plot with limit of agreement has been widely used as a visual tool for assessing test-retest reliability or reproducibility between two measurements. We have observed, however, that in certain circumstances the limit of agreement approach may mislead practitioners. Particularly, if the acceptable difference is not available and two readers are highly concordant but the common variance of the data is large, the broad width of the limit of agreement plot may incorrectly indicate a lack of agreement. Methods: This paper proposes a novel, scaled index-based guidance for graphical evaluation of reproducibility or reliability. We create a reference band from two measurements, which is based on the concordance correlation coefficient.Results: Simulation studies have been carried out to demonstrate the benefits of our method over the limit of agreement. We also consider the application to the real examples, including the peak expiratory flow rate data in Bland and Altman's paper and the test-retest reproducibility data of Radiomics study.Conclusions: In absence of acceptable difference, we found that the limit of agreement seems to derive subjective inference and may not be consistent with concordance correlation coefficient. Our simulation study results and real data application show that the proposed method can provide practitioners with a novel graphical evaluation method which is consistent with results from concordance correlation coefficient approach than the limit of agreement approach.
The Feasibility of Selective High-Risk Area Irradiation for Supraglottic Laryngeal Carcinoma With Positive Lymph Nodes Only in Areas II and IIIThe&nbsp;Feasibility of Selective High-Risk Area Irradiation for Supraglottic Laryngeal Carcinoma With Positive Lymph Nodes Only in Areas II and III
Authors: zhou jianfeng , Wang hongyong , Bian li , Wang tiejun 
Published: December 2020

Abstract
ObjectiveTo study the prognosis of patients with positive lymph nodes in area II and III after supraglottic laryngocarcinoma surgery and to evaluate the feasibility of selective irradiation of a high-risk area. MethodsFrom February 2010 to March 2015, the complete clinical data for 181 patients treated for supraglottic laryngeal cancer at the Radiotherapy Department of the Second Hospital of Jilin University were analysed retrospectively. Among them, 100 patients were treated with whole neck prophylactic irradiation and 81 patients were treated with selective high-risk irradiation; i.e., lymph drainage of areas II and III. ResultsThe median follow-up time was 38.5 months; the 5-year OS, PFS, and NFS were 67.9%,58.1%,64.6% respectively. Among them, there were 6 cases of lymph node recurrence, 4 cases of local recurrence, 8 cases of distant metastasis and 58 deaths. However, there was no significant difference in recurrence between the selective high-risk radiation group and the total neck prophylactic radiation group. The OS, PFS and NFS of the two groups were 67.9% vs. 68%, 58.02% and 58%, and 62.9% and 66%, respectively, and the P values were 0.9161, 0.8916 and 0.7333,respectively. For late toxicity resulting from radiotherapy, the incidence of cervical fibrosis (2.47% vs. 10%, P = 0.043) and the incidence of throat mucosa injury (6.17% vs. 24%, P = 0.001) in patients in the selective high-risk area irradiation group were reduced. ConclusionThe preliminary data show that selective high-risk area irradiation is safe and feasible for patients with supraglottic laryngeal cancer accompanied by positive lymph nodes only in areas II and III, and the treatment can reduce the long-term adverse reactions and improve the quality of life. However, more evidence is needed.
Effect of Prenatal Phthalate Exposure on Childhood Atopic Dermatitis: a Systematic Review and a Meta-analysis of Birth Cohort Studies
Authors: Jung Minyoung , Kim Min-ji , Kim Seonwoo , Kyung Yechan , Kim Minji , Lee Ji Young , Jeong Hye-In , Lee Bo Ra , Kim Jihyun , Ahn Kangmo , Park Yong Mean 
Published: December 2020

Abstract
Background: The association between prenatal exposure to phthalate and childhood atopic dermatitis (AD) has been previously investigated; however, the results are inconsistent. We aimed to perform a systematic review and meta-analysis of birth cohort studies to investigate whether prenatal exposure to phthalate increases the risk of developing AD in children.Methods: We performed an electronic search of the MEDLINE, Embase, and Cochrane library databases. Studies were critically appraised, and meta-analyses were performed.Results: Among 129 articles identified, 11 studies met the eligibility criteria. Included studies originated from Europe (n = 5), USA (n = 4), and Asia (n = 2). The study sample size ranged from 147 to 1024 mother-child pairs. Quality assessment using the Newcastle–Ottawa scale of all studies had scores of six or greater. A meta-analysis of data from eight selected studies suggested that monobenzyl phthalate (MBzP) exposure was significantly associated with the risk of AD development (odds ratio 1.16, 95% confidence interval 1.04-1.31, I2 = 17.36%). However, AD development was not associated with other phthalate metabolites such as mono-(2-ethylhexyl) phthalate, monoethyl phthalate, mono-isobutyl phthalate, mono-n-butyl phthalate, and the sum of di-[2-ethylhexyl] phthalate on the development of AD (all P-values > 0.05).Conclusions: Our study suggests a positive association between prenatal exposure to MBzP and the development of childhood AD.
The Effect of Adenomyosis on the Outcome of Fresh Embryo Transfer in ICSI Cycles: a Retrospective Case-control Study
Authors: Nagireddy Siddhartha , Reddy Nellepalli Sanjeeva , Pandurangi Monna , Vembu Radha , Muthusamy Tamizharasi , Kasinathan Kanomozhi 
Published: December 2020

Abstract
Background: Adenomyosis is known to cause reduced clinical pregnancies and increased miscarriage rates in ART (Assisted Reproductive Technology) cycles. The detrimental effect was found to be enhanced if these women would undergo fresh embryo transfer without optimal suppression by GnRH agonist treatment. Several mechanisms were proposed as causative factors such as increased myometrial contractions, decreased implantation and altered endometrial receptivity. But the conclusions from previous studies were mutually conflicting. To ensure adequate regression of the disease prior to embryo transfer, these women would commonly undergo freeze-all and subsequent frozen embryo transfer. On contrary to this, fresh embryo transfer may be necessary in certain justifiable clinical situations. The present study was designed as a retrospective case-control study to compare the ICSI-fresh embryo transfer outcomes of women with adenomyosis to those with tubal factor infertility. This study is aimed to find the extent to which adenomyosis compromises the outcomes of fresh embryo transfer in ICSI cycles. Methods: The data of the eligible patients as per the study criteria, was obtained from the hospital medical records of a tertiary care University teaching hospital, in Chennai, South India. The study groups (Group A: women with adenomyosis, GroupB; women with tubal factor infertility) were compared for the fresh embryo transfer outcomes such as pregnancy rate, clinical pregnancy rate, miscarriage and live birth rates. SPSS version 17 software was used and and P<0.05 was considered statistically significant.Results: The data of 89 women included in the study (Group A: 47, and Group B: 42) were analysed. The data analysis showed significantly reduced pregnancy, clinical pregnancy, implantation and live birth rates in Group A compared to Group B (25.7 vs. 52.4%; 23.4 vs. 52.4%; 7.6% vs. 26.2%; 17.0 vs. 47.6%, respectively).Conclusions: We found that adenomyosis is associated with a less favourable outcome in ICSI -fresh embryo transfer. Though these results are justifiable if performed with appropriate indications, the cost-effectiveness and indications of such an approach needs to be evaluated on a larger prospective data.
Successful Birth After Preimplantation Genetic Testing for a Couple With Two Different Reciprocal Translocations and Review of the Literature
Authors: Liu Dun , Chen Chuangqi , Zhang Xiqian , Dong Mei , He Tianwen , Dong Yunqiao , Lu Jian , Yu Lihua , Yang Chuanchun , Liu Fenghua 
Published: December 2020

Abstract
Background: Preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) is widely applied in couples with single reciprocal translocation to increase the chance for a healthy live birth. However, limited knowledge is known on the data of PGT-SR when both parents have a reciprocal translocation. Here, we for the first time present a rare instance of PGT-SR for a non-consanguineous couple in which both parents carried an independent balanced reciprocal translocation and show how relevant genetic counseling data can be generated.Methods: The precise translocation breakpoints were identified by whole genome low-coverage sequencing (WGLCS) and Sanger sequencing. Next-generation sequencing (NGS) combining with breakpoint-specific polymerase chain reaction (PCR) was used to define 24-chromosome and the carrier status of the euploid embryos.Results: Surprisingly, 66.7% day-5 blastocysts were found to be balanced for maternal reciprocal translocation while being normal for paternal translocation and thus transferable. The transferable embryo rate was significantly higher than that which would be expected theoretically. Transfer of one balanced embryo resulted in the birth of a healthy boy. Conclusion(s): Our data of PGT-SR together with a systematic review of the literature should help in providing couples carrying two different reciprocal translocations undergoing PGT-SR with more appropriate genetic counseling.
Knowledge, Attitudes, and Practices of Patients with type 2 Diabetes Mellitus with Regard to their Disease: A Cross-Sectional Study Among Palestinians of the West Bank
Authors: Shawahna Ramzi , Samaro Saed , Ahmad Zaid 
Published: December 2020

Abstract
Background: In Palestine, type 2 diabetes mellitus (T2DM) is a rapidly growing health concern. This study was conducted to evaluate current knowledge, attitudes, and practices among Palestinian patients with T2DM in the West Bank and to assess association between knowledge, attitudes, and practices with sociodemographic and clinical characteristics of the patients. Methods: This cross-sectional observational study was conducted in primary healthcare facilities frequently visited by patients with T2DM across the West Bank of Palestine. A pre-validated interviewer administered questionnaire was used to determine knowledge, attitudes and practices of patients with T2DM with regard to their disease.Results: Data were collected from 220 patients with T2DM. Patients who were younger than 55 years old (p-value = 0.002), male (p-value = 0.038), never married (p-value = 0.001), employed (p-value = 0.003), had university degree (p-value <0.001), had higher income (p-value <0.001), diagnosed less than 7 years ago (p-value = 0.009), and had usual fasting plasma glucose of less than 140 mg/dL (p-value = 0.027) tended to score more than 50% in the knowledge items. Patients who had higher income tended to have higher positive attitudes (p-value = 0.041) toward their disease. Patients who were younger than 55 years old (p-value = 0.002), employed (p-value = 0.003), had university degree (p-value <0.001), diagnosed less than 7 years ago (p-value = 0.009), had usual fasting plasma glucose of less than 140 mg/dL (p-value = 0.027), had usual postprandial plasma glucose of less than 200 mg/dL (p-value = 0.027), had usual HbA1c of less than 7% (p-value = 0.027) tended to score more than 80% in the practice items.Conclusions: The study established correlation between knowledge, attitude, and practice scores with sociodemographic and clinical characteristics of patients with T2DM in Palestine. Findings of this study highlighted the need for appropriately designed interventions to increase knowledge of T2DM and its complications, address the negative attitudes toward the disease, and promote healthy practices with regard to the disease. Future studies are still needed to assess if such interventions could be effective in improve health outcomes and quality of life of patients with T2DM in Palestine.
Cardiorespiratory Fitness is Associated with Multiple other Physical Fitness Components in 7-14-year-olds: A Cross-Sectional Study
Authors: Kasović Mario , Štefan Lovro , Petrić Vilko , Štemberger Vesna , Blažević Iva 
Published: December 2020

Abstract
BackgroundAlthough evidence suggests that cardiorespiratory fitness is the most important component associated with future health, little is known of how it is associated with multiple other physical fitness components. Since various physical fitness aspects do not change the same as cardiorespiratory fitness during childhood, it is necessary to establish possible associations between cardiorespiratory fitness and other physical fitness components in children. Therefore, the main purpose of the study was to test the associations between cardiorespiratory fitness with motor performance and body size in 7-14-year-old children.MethodsIn this cross-sectional study, we recruited 1612 children (52.5% girls). Health-related physical fitness components included: 1) body-mass index (kg/m2) calculated from height and weight (measure of body size), 2) sit-and-reach test (measure of flexibility), 3) standing long jump (measure of explosive strength), 4) sit-ups in 30 sec (measure of repetitive strength), 5) 10x5 shuttle run test (measure of agility) and 6) 20-m shuttle run test (measure of aerobic capacity). The associations were performed using generalized estimating equations with β coefficients.ResultsAfter adjusting for age, cardiorespiratory fitness was associated with sit-and-reach test (β=0.13, p<0.001), standing long jump (β=0.59, p<0.001), sit-ups in 30 sec (β=0.53, p<0.001) and 10x5 shuttle run test (β=-0.56, p<0.001) in boys. In girls, cardiorespiratory fitness was associated with body-mass index (β=-0.12, p<0.001), sit-and-reach test (β=0.21, p<0.001), standing long jump (β=0.25, p<0.001), sit-ups in 30 sec (β=0.36, p<0.001) and 10x5 shuttle run test (β=-0.40, p<0.001). No significant associations between cardiorespiratory fitness and body-mass index in boys were observed.ConclusionsAlthough significant, cardiorespiratory fitness is weakly to moderately associated with other physical fitness components, pointing out that such measure should be tested separately from other aspects of physical fitness in school-aged children.