bluuebunny/crossref_metadata_2025_split huggingface dataset:
Categorization of differences of sex development among Egyptian children and the role of antimullerian hormone and inhibin B
Authors: Abdelghaffar Shereen , AbdelMoneam Engy Nasr , Hassanein Samah A. , Radwan Noha Abdelhalim , Mira Marwa Farouk 
Published: January 2023

BackgroundDifferences of sex development (DSD) are congenital conditions linked to atypical development of chromosomal, gonadal, or anatomical sex.ObjectiveThe aim of this study was to demonstrate our experiences at the Diabetes Endocrine and Metabolism Pediatric Unit (DEMPU), Faculty of Medicine, Cairo University in the field of DSD by focusing on the clinical presentation, laboratory profile, classification, and etiological diagnosis of these conditions. In addition, the present study intended to delineate the importance of serum anti-Müllerian hormone (AMH) and inhibin B in detecting the presence of functioning testicular tissue.MethodsThis cohort study included 451 infants and children with various clinical presentations of DSD. The study performed a retrospective analysis on medical records of established DSD cases to evaluate the clinical importance of AMH and inhibin B. In addition, newly diagnosed patients were prospectively analyzed.ResultsThree hundred thirty-six (74.5%) patients were 46,XY DSD, 98 (21.7%) were 46,XX DSD, 14 patients had other karyotypes and 3 had missing karyotypes. Among the 46XY DSD patients, the most common cause was partial androgen insensitivity. In contrast, congenital adrenal hyperplasia constituted the most common diagnosis in 46,XX DSD cases. The cut off value of serum AMH was 14.5 ng/ml with 100% sensitivity and 55.1% specificity.ConclusionPartial androgen insensitivity was the most important cause of 46,XY DSD in Egyptian children, and congenital adrenal hyperplasia was the most common cause of 46,XX DSD. AMH was valuable in detecting functioning testicular tissue.
Optimal operation of urban tidal drainage pumping station based on genetic algorithm coupled with head-water level successive approximation
Authors: Yi Gong , Wenhao Zou 
Published: January 2023

Aiming at the method of solving the optimization scheme for urban tidal drainage pumping stations during heavy rainfall below the urban drainage design standard, and the problems such as the mismatch between the head and water level of pumping stations at each divided time period during the solution process, a nonlinear mathematical model for optimal operation of urban tidal drainage pumping station was constructed which took the minimal operation cost of drainage pumping station during given operating period as the study target, and the blade angle of each pump unit in each divided time period as decision variables with the constraints of total water quantity of target drainage, matched motor power of each pump unit, water level of in the drainage area, number of switches and the shortest operation time of pump unit. For the problem of head-water level mismatch at each divided time period of pumping station, the genetic algorithm of coupled head-water level successive approximation is proposed, which can make the optimization scheme realize the matching of river network water level and pumping station operating head. Taking Guazhou Pumping Station in Yangzhou City of Jiangsu Province encountering 10% frequency designed rainfall as an example, optimization schemes under typical working conditions which included different starting drainage water levels and peak-valley electricity prices was obtained, as well as the influence of electricity price of divided time period, average head of each divided time period and inflow on the optimization scheme was carried out. The unit optimal operation drainage costs of Guazhou Pumping Station is 45.46 yuan/104 m3 and 51.32 yuan/104 m3 respectively when the starting drainage water level is set as 4.8 m and 4.6 m, which has the corresponding operation benefit of 15.34% and 4.40% less than that of conventional operation, and the water level variation of river network has dropped 6.61% and 7.85% than that of conventional operation. The constructed optimal operation model of urban tidal drainage pumping station and the proposed solution method can effectively improve the matching degree of pumping head and water level variation, and effectively make a compromise of economic operation of drainage pumping station and the safety requirements of water level control of river network in drainage area. The obtained optimization schemes can offer decision-making reference for relevant dispatching and management departments of drainage pumping stations.
Thermo-economic evaluation and optimization of solar-driven power-to-chemical systems with thermal, electricity, and chemical storage
Authors: Huang Shengwei , Zhang Yumeng , Guo Xinyu , Qian Meng , Zhao Yongming , Li Liang , Zhou Xing 
Published: January 2023

This paper evaluates the thermo-economics of power-to-chemicals using solar energy, with the chemicals being methane, methanol, and gasoline. In addition to the optimal technology sizing and heat cascade utilization, this paper also considers the optimal molten-salt solar power tower (MSPT) design, as the MSPT significantly affects the levelized product cost. A bi-level optimization is proposed, employing mixed-integer linear programming at the lower level with heat and mass integration for optimizing sizes and operating strategies of technologies, and with heat cascade utilization and a genetic algorithm at the upper level for optimizing the MSPT design. In the upper level, the full-load storage hours, design direct normal irradiance, solar multiple, and sizes of the MSPT are optimized. The electricity sources considered are the MSPT, photovoltaic (PV) with daily electricity storage, and the electrical grid as a complementary technology to satisfy the targeted daily product demand. Cost-competitiveness of solar-driven chemical synthesis is thoroughly assessed via considering sensitivity analysis on 1) regional solar resource endowments and actual local demands; 2) electricity sources, that is, PV vs. MSPT; and 3) the scale effect represented by different chemicals’ yield. The results show that the levelized methane cost ranges from 4.5 to 8.5 €/kg, depending on the location, plant size, and annual power contribution of concentrated solar power. Due to the larger mass production, the levelized cost of methanol and gasoline is lower: 1.5–2.2 €/kg for methanol and 4–6 €/kg for gasoline. The findings highlight the significance of location choice, that is, natural endowment of solar radiation and carbon sources. Using the syngas co-electrolysis pathway and direct solar radiation 100 kWh/m2 higher, the methane production cost is decreased by 2.4 €/kg. Sensitivity analysis performed on plant scale reveals that a compact, small-scale system is far too expensive. The levelized cost of methane could be decreased by 1.2 €/kg when the plant is scaled up from 4,000 to 20,000 kg/day H2. Due to its expensive electricity storage and limited working hours, PV is typically not chosen as a power source. Overall, solar fuels are unlikely to be cost-competitive in the near future when compared to market prices for all three compounds under consideration.
Differences in production decline characteristics of horizontal wells in tight gas sandstone reservoirs with different qualities: A case study of the Sulige gas field, Ordos Basin
Authors: Cheng Minhua , Wei Yunsheng , Ji Guang , Ning Bo , Zhao Meng 
Published: January 2023

Development of horizontal wells is one of the important means to improve the well production of the tight gas reservoir and realize the effective development of tight gas. Based on abundant static and dynamic data of a large number of horizontal wells that have been put into operation, structure characteristics of a tight reservoir carried out, detailed geologic analysis of the effective reservoir drilled by horizontal wells, and development dynamic analysis, three effective reservoir lateral distribution modes of the block concentrated development mode, medium layer, and thin layer superimposed mode and thin layer isolated model mode are proposed and their adaptability to the horizontal well deployment is evaluated. The drilled reservoir is divided into three types: high-quality reservoir, suboptimal reservoir, and poor reservoir, and the quantitative classification standard is established. On this basis, the decline rule and the difference of horizontal well drilling in different quality reservoirs are discussed, and the quantitative evaluation standard of the horizontal well development effect is established. The initial decline rates of the three types of horizontal wells are 32.9%, 35%, and 40%, and the estimate ultimate recoveries (EURs) of three types of horizontal wells are 89 million cm3, 68 million cm3, and 31 million cm3, respectively. The results of this study provide technical support for the optimal deployment of new horizontal wells in the Sulige gas field and a reference for the development of horizontal wells in the same types of gas reservoirs.
Positive regulation of innate immune response by miRNA-let-7a-5p
Authors: Ueta Mayumi , Nishigaki Hiromi , Komai Seitaro , Mizushima Katsura , Tamagawa-Mineoka Risa , Naito Yuji , Katoh Norito , Sotozono Chie , Kinoshita Shigeru 
Published: January 2023

Background: We have hypothesized that different factors are involved in the severity of ACD and AD because some but not all patients with atopic dermatitis (AD) present with allergic conjunctival disease (ACD) including severe types such as atopic keratoconjunctivitis (AKC) with/without giant papillae. We previously reported that plasma miR-628-3p was up-regulated in AD with severe ACD, but not in severe AD without severe ACD or in our healthy controls. In this study, to investigate the pathogenesis of AD with and without severe ACD, we performed comprehensive plasma miRNA analysis and studied the function of some miRNAs which were significantly up-regulated in ACD.Methods: Transcriptomics analysis of miRNA was performed using the microarray platform from the plasma of nine individuals (AD, severe ACD, controls: n = 3 each). To confirm up-regulation of the 12 miRNAs of the eight miRNA groups we focused on, we performed quantitative miRNA polymerase chain reaction (PCR) assays using 80 plasma samples (AD: 23, severe ACD: 17, controls: 40). To study the function of the eight miRNAs which were significantly up-regulated in ACD, we transfected their mimic to THP-1 cells, a monocyte cell line, and performed comprehensive gene expression analysis of them. The up-regulation of gene expression of interest in transfected THP-1 cells with the hsa-let-7a-5p miRNA mimic was confirmed by quantitative RT-qPCR assay.Results: Quantitative miRNA PCR assays showed that hsa-let-7a-5p, hsa-let-7days-3p, hsa-let-7e-5p, and hsa-miR-151a-5p were significantly up-regulated in both AD-ACD+ and AD-ACD- as were hsa-miR-130a-3p, hsa-miR-151a-3p, has-miR-27b-3p, and hsa-miR-146a-5p in AD-ACD+ but not in AD-ACD-. The functions of each miRNA were investigated by comprehensive gene expression analysis of THP-1 cells transfected with each miRNA mimic. Of the eight miRNAs, hsa-let-7a-5p, hsa-let-7e-5p, has-miR-27b-3p, and hsa-miR-146a-5p mimic-transfected THP-1 cells showed the up-regulation of CXCL10 (IP-10; interferon gamma-induced protein 10), which might be one of the innate immune-related genes. Quantitative RT-qPCR assays of transfected THP-1 cells with the hsa-let-7a-5p miRNA mimic showed that the 17 genes up-regulated more than 10-fold in the comprehensive gene expression analysis, and TLR3, RIG-I, and MDA5, important innate immune-related genes, were significantly up-regulated. TNFSF13B, AIM2, USP41, STAP1, GBP4, CCL8, and IFI27, reportedly down-regulated by the hsa-miR-628-3p mimic, were also significantly up-regulated in the transfected cells.Conclusion: Hsa-let-7a-5p, which was significantly up-regulated in AD-ACD+ and AD-ACD-, could positively regulate the important innate immune-related genes such as TLR3, RIG-I, and MDA5. It is possible that in an allergic disease such as atopic keratoconjunctivitis and/or dermatitis, innate immune responses might be positively regulated by hsa-let-7a-5p in the plasma.
Full-length transcriptome sequencing reveals the molecular mechanism of monoterpene and sesquiterpene biosynthesis in Cinnamomum burmannii
Authors: Hou Chen , Zhang Qian , Xie Peiwu , Lian Huiming , Wang Yingli , Liang Dongcheng , Cai Yanling , He Boxiang 
Published: January 2023

Essential oil of Cinnamomum burmannii is rich in monoterpenes and sesquiterpenes and is widely used in cosmetics and medicines. Knowledge about the enzymes that catalyze the formation of monoterpenes and sesquiterpenes in C. burmannii is insufficient. Therefore, anatomy observation of C. burmannii at the four developmental stages (7 days, CBS1; 14 days, CBS2; 21 days, CBS3, and 28 days, CBS4) were conducted to elucidate the origins of essential oil production. Twelve full-length transcriptomes of C. burmannii leaves at the four stages were generated using Oxford Nanopore Technologies. GC-MS analysis revealed 15 monoterpene and sesquiterpenes dramatically increased from CBS1 to CBS4. A weighted correlation network analysis (WGCNA) in association and differentially expressed genes across four developmental stages were performed. A total of 44 differentially expressed genes (DEGs) were involved in terpenoid syntheses during leaf development. Among them, the DEGs of the mevalonate acid (MVA) pathway were predominantly expressed at CBS1, while those of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway showed increased expression from CBS2 to CBS4. Besides, fourteen genes were associated with monoterpene synthesis and nine with sesquiterpene synthesis. Functions of these DEGs were further predicted with regard to gene expression profile and phylogenetic relationship with those characterized in previous studies. In addition, 922 long noncoding RNAs (lncRNAs) were detected, of which twelve were predicted to regulate monoterpene and sesquiterpene biosynthesis. The present study provided new insights the molecular mechanisms of monoterpenoid and sesquiterpenoid syntheses of C. burmannii.
Liquid biopsy in pediatric brain tumors
Authors: Tripathy Arushi , John Vishal , Wadden Jack , Kong Seongbae , Sharba Sana , Koschmann Carl 
Published: January 2023

Malignant primary brain tumors are the most common cancer in children aged 0–14 years, and are the most common cause of death among pediatric cancer patients. Compared to other cancers, pediatric brain tumors have been difficult to diagnose and study given the high risk of intracranial biopsy penetrating through vital midline structures, where the majority of pediatric brain tumors originate (Ostrom et al., 2015). Furthermore, the vast majority of these tumors recur. With limitations in the ability to monitor using clinical and radiographic methods alone, minimally invasive methods such as liquid biopsy will be crucial to our understanding and treatment. Liquid biopsy of blood, urine, and cerebrospinal fluid (CSF) can be used to sample cfDNA, ctDNA, RNA, extracellular vesicles, and tumor-associated proteins. In the past year, four seminal papers have made significant advances in the use of liquid biopsy in pediatric brain tumor patients (Liu et al., 2021; Cantor et al., 2022; Miller et al., 2022; Pagès et al., 2022). In this review, we integrate the results of these studies and others to discuss how the newest technologies in liquid biopsy are being developed for molecular diagnosis and treatment response in pediatric brain tumors.
Diagnostic application of exome sequencing in Chinese children with suspected inherited kidney diseases
Authors: Gao Min , Yu Fengling , Dong Rui , Zhang Kaihui , Lv Yuqiang , Ma Jian , Wang Dong , Zhang Hongxia , Gai Zhongtao , Liu Yi 
Published: January 2023

Background: Inherited kidney diseases (IKDs) are a group of kidney diseases characterized by abnormal kidney structure or function caused by genetic factors, but they are not easily diagnosed in childhood due to either nonspecific symptoms and signs or clinically silent symptoms in the early stages until the progressive stages, even end-stages. Early diagnosis of IKDs is very urgent for timely treatment and improving outcomes of patients. So far, the etiological diagnosis has been accelerated with the advance of clinical genetic technology, particularly the advent of next-generation sequencing (NGS) that is not only a powerful tool for prompt and accurate diagnosis of IKDs but also gives therapy guidance to decrease the risk of unnecessary and harmful interventions.Methods: The patients presenting with urinalysis abnormalities or structural abnormalities from 149 Chinese families were enrolled in this study. The clinical features of the patients were collected, and the potentially causative gene variants were detected using exome sequencing. The clinical diagnostic utility of the genetic testing was assessed after more detailed clinical data were analyzed.Result: In total, 55 patients identified having causative variants by exome sequencing were genetically diagnosed, encompassing 16 (29.1%) autosomal dominant IKDs, 16 (29.1%) autosomal recessive IKDs, and 23 (41.8%) X-linked IKDs, with 25 unreported and 45 reported variants. The diagnostic yield was 36.9%. The utility of the exome sequencing was accessed, 12 patients (21.8%) were confirmed to have suspected IKDs, 26 patients (47.3%) discerned the specific sub-types of clinical category, and 17 patients (30.9%) with unknown etiology or lack of typical manifestations were reclassified.Conclusion: Our study supported that genetic testing plays a crucial role in the early diagnosis for children with IKDs, which affected follow-up treatment and prognostic assessment in clinical practice. Moreover, the variant spectrum associated with IKDs was expanded.
Smoking, alcohol consumption, diabetes, body mass index, and peptic ulcer risk: A two-sample Mendelian randomization study
Authors: Liu Yi , Xiao Zhihan , Ye Kun , Xu Linlin , Zhang Yanping 
Published: January 2023

Background: Observational evidence has shown that smoking, alcohol consumption, type 2 diabetes, and body mass index (BMI) are risk factors for peptic ulcer disease (PUD), including gastric ulcer (GU) and duodenal ulcer (DU). However, the observed associations may be confounding factors. Herein, we use Mendelian randomization (MR) to examine causal associations such as smoking, alcohol, type 2 diabetes, BMI, and risks of PUD.Methods: We used 8,17,41,325,82, 231, and 616 identified genetic variants as proxies for age of smoking initiation (AgeSmk), smoking cessation (SmkCes, current/former), number of cigarettes smoked per day (CigDay), smoking status (SmkIni, ever/never), alcohol consumption, type 2 diabetes, and BMI to obtain unconfounded effect estimates on the GU and DU levels among 452,264 participants from the Gene ATLAS. The causal relationship was estimated by using inverse-variance weighted (IVW) as the main method. Sensitivity analysis includes Cochran’s Q test, the MR-Egger test, MR pleiotropy residual sum and outlier (MR-PRESSO), and MR-robust adjusted profile score (MR-RAPS). In addition, secondary MR analysis was conducted within summary data using genetic risk scores (GRSs) as instrumental variables (IVs).Results: In our two-sample MR analyses, genetic predisposition to smoking (SmkInit) and BMI were associated with an increased risk of GU. The beta values were 0.0035 (95% CI, 0.0021, 0.0049, p = 1.56E-06) for smoking (SmkInit) and 0.0021 (95% CI, 0.0009, 0.0033, p = 0.0008) for BMI. Genetic predisposition to smoking (SmkInit) and higher genetically predicted BMI were associated with an increased risk of DU. The beta values of DU were 0.0029 (95% CI, 0.0017, 0.0041, p = 2.43E-06) for smoking (SmkInit) and 0.0018 (95% CI, 0.0007, 0.0029, p = 0.001) for BMI. No other causal association between smoking (AgeSmk, CigDay, and SmkCes), alcohol consumption, type 2 diabetes, and GU or DU was observed. Consistent results were obtained in sensitivity analyses. Furthermore, the GRS approach showed similar results in the several MR methods.Conclusion: These findings do not support a causal role of AgeSmk, CigDay, SmkCes, alcohol consumption, and type 2 diabetes in the development of GU and DU. However, it is confirmed that SmkInit and BMI have a causal part in the development of GU and DU.
Clinical and immunological characteristics of TGM3 in pan-cancer: A potential prognostic biomarker
Authors: Zhang Wenqing , Wu Chenglong , Zhou Kaili , Cao Yu , Zhou Wange , Zhang Xue , Deng Dan 
Published: January 2023

Background: Recent studies have identified that transglutaminases (TGMs) are involved in a widespread epigenetic modification in tumorigenesis. However, it remains unclear how transglutaminase 3 (TGM3) affects in pan-cancer. The present study aimed to explore the clinical and prognostic function of TGM3 in pan-cancer as well as to explore the relationship of TGM3 expression with clinical stage, survival rate, prognosis condition, immune infiltration and mutation indicators.Methods: The relevant data of tumors were obtained from The Cancer Genome Atlas (TCGA), TARGET, Cancer Cell Line Encyclopedia (CCLE) and Genotype-Tissue Expression (GTEx) databases. According to the Human Protein Atlas (HPA) and TIMER databases, we evaluated the protein expression levels of TGM3 in different organs and tissues as well as their association with immune cell infiltration and immunotherapeutic response in pan-cancers. Expression differences between normal and tumor tissues as well as survival and prognosis situation, clinical data characteristics, tumor mutational burden (TMB), microsatellite instability (MSI), and RNA methylation were also assessed. Oncogenic analyses were also evaluated by GSEA.Results: Compared to normal tissues, some tumor tissues had a lower expression level of TGM3, while other tumor tissues had a high expression level of TGM3. Further studies showed that high TGM3 expression had a certain risk impact on pan-cancer as high TGM3 expression levels were detrimental to the survival of several cancers, except for pancreatic cancer (PAAD). High expression level of TGM3 was also related to higher clinical stages in most cancers. The expression level of TGM3 was significantly negatively correlated with the expression of immune infiltration-related cells, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages and dendritic cells (DCs). Furthermore, in most cancer types, TGM3 was inversely correlated with TMB, MSI, and methylation, suggesting that TGM3 expression can be used to assess potential therapeutic response, especially immune-related targeted therapy. GSEA analysis elucidated the biological and molecular function of TGM3 in various cancer types. Taken together, these bioinformatic analyses identified TGM3 as an important biomarker for clinical tumor prognosis and evaluation of treatment efficacy.Conclusion: We comprehensively analyzed the clinical characteristics, tumor stages, immune infiltration, methylation level, gene mutation, functional enrichment analysis and immunotherapeutic value of TGM3 in pan-cancer, providing implications for the function of TGM3 and its role in clinical treatment.