bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of STAT3 and phospho-STAT3 expression on the prognosis and clinicopathology of ovarian cancer: a systematic review and meta-analysis
Authors: Gao Shuo , Zhang Wenyuan , Yan Na , Li Min , Mu Xiaowei , Yin Huaxia , Wang Jinhua 
Published: November 2021

Abstract
Purpose
STAT3 and p-STAT3 are often overexpressed in various human tumours and participate in cancer development and progression. However, whether STAT3/p-STAT3 expression is associated with clinicopathologic characteristics and has prognostic significance for people suffering from ovarian cancer remains controversial. We conducted a systematic review and meta-analyses to clarify the associations between STAT3/p-STAT3 expression and clinicopathologic characteristics and prognostic factors of ovarian cancer.

Methods
A systematic electronic search in the PubMed, Embase, CNKI, and Wanfang databases was conducted to identify relevant articles published before 3 April 2021. All statistical analyses were performed using Stata 15.1.

Results
We included 16 eligible studies incorporating 1747 ovarian cancer patients. The expression of STAT3/p-STAT3 was upregulated in ovarian cancer samples versus normal ovarian tissue, benign tumours and borderline tumours (OR = 10.14, p < 0.00001; OR = 9.08, P < 0.00001; OR = 4.01, p < 0.00001, respectively). STAT3/p-STAT3 overexpression was significantly correlated with FIGO stage (I-II vs. III-IV) (OR = 0.36, p < 0.00001), tumour grade (G1 + G2 vs. G3) (OR = 0.55; p = 0.001) and lymph node metastasis (yes vs. no) (OR = 3.39; p < 0.00001). High STAT3/p-STAT3 expression was correlated with poorer prognosis of ovarian cancer patients for both overall survival (OS) (HR = 1.67, p < 0.00001) and progression-free survival (PFS) (HR = 1.40, p = 0.007).

Conclusion
The present meta-analysis indicated that high STAT3/p-STAT3 expression is likely predictive of an unfavourable prognosis in ovarian cancer patients. Nonetheless, prospective trials are required to confirm these associations.
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit
Authors: Wang Runze , Xue Yongsong , Fan Jing , Yao Jia-Long , Qin Mengfan , Lin Tao , Lian Qun , Zhang Mingyue , Li Xiaolong , Li Jiaming , Sun Manyi , Song Bobo , Zhang Jiaying , Zhao Kejiao , Chen Xu , Hu Hongju , Fei Zhangjun , Xue Cheng , Wu Jun 
Published: November 2021

AbstractBackgroundStone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.ResultsWe generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function ofPbrNSCin regulating lignocellulose formation using both pear fruit andArabidopsisplants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation.ConclusionsThis study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.
The effect of supplementation with vitamins A, B, C, D, and E on disease severity and inflammatory responses in patients with COVID-19: a randomized clinical trial
Authors: Beigmohammadi Mohammad Taghi , Bitarafan Sama , Hoseindokht Azin , Abdollahi Alireza , Amoozadeh Laya , Soltani Danesh 
Published: November 2021

Abstract
Background and objective
Because of the effect of vitamins on modulating the immune system function, we have evaluated the effect of supplementation with vitamins A, B, C, D, and E in ICU-admitted patients with COVID-19.

Methods
This study was a randomized and single-blinded clinical trial in which 60 subjects were randomly assigned to two groups. The intervention group (n=30) received vitamins, and the control group did not receive any vitamin or placebo. The intervention was included 25,000 IU daily of vitamins A, 600,000 IU once during the study of D, 300 IU twice daily of E, 500 mg four times daily of C, and one amp daily of B complex for 7 days. At baseline and after the 7-day intervention, the serum levels of inflammatory markers, vitamins, and the SOFA score were assessed. In addition, the mortality rate and duration of hospitalization were evaluated after the intervention (IRCT registration number: IRCT20200319046819N1/registration date: 2020-04-04, https://www.irct.ir/trial/46838).

Results
Significant changes were detected in serum levels of vitamins (p < 0.001 for all vitamins), ESR (p < 0.001), CRP (p = 0.001), IL6 (p = 0.003), TNF-a (p = 0.001), and SOFA score (p < 0.001) after intervention compared with the control group. The effect of vitamins on the mortality rate was not statistically significant (p=0.112). The prolonged hospitalization rate to more than 7 days was significantly lower in the intervention group than the control group (p=0.001). Regarding the effect size, there was a significant and inverse association between receiving the intervention and prolonged hospitalization (OR = 0.135, 95% CI 0.038–0.481; p=0.002); however, after adjusting for confounders, it was not significant (OR=0.402, 95% CI 0.086–1.883; p=0.247).

Conclusion
Supplementation with vitamins A, B, C, D, and E could improve the inflammatory response and decrease the severity of disease in ICU-admitted patients with COVID-19.
A comprehensive review on microbial production of 1,2-propanediol: micro-organisms, metabolic pathways, and metabolic engineering
Authors: Tao Yuan-ming , Bu Chong-yang , Zou Li-hua , Hu Yue-li , Zheng Zhao-Juan , Ouyang Jia 
Published: November 2021

Abstract1,2-Propanediol is an important building block as a component used in the manufacture of unsaturated polyester resin, antifreeze, biofuel, nonionic detergent, etc. Commercial production of 1,2-propanediol through microbial biosynthesis is limited by low efficiency, and chemical production of 1,2-propanediol requires petrochemically derived routes involving wasteful power consumption and high pollution emissions. With the development of various strategies based on metabolic engineering, a series of obstacles are expected to be overcome. This review provides an extensive overview of the progress in the microbial production of 1,2-propanediol, particularly the different micro-organisms used for 1,2-propanediol biosynthesis and microbial production pathways. In addition, outstanding challenges associated with microbial biosynthesis and feasible metabolic engineering strategies, as well as perspectives on the future microbial production of 1,2-propanediol, are discussed.
A geodatabase of blood pressure level and the associated factors including lifestyle, nutritional, air pollution, and urban greenspace
Authors: Mohammadi Alireza , Pishgar Elahe , Firouraghi Neda , Bagheri Nasser , Shamsoddini Ali , Abbas Jaffar , Kiani Behzad 
Published: November 2021

Abstract
Objectives
Hypertension is a prevalent chronic disease globally. A multifaceted combination of risk factors is associated with hypertension. Scientific literature has shown the association among individual and environmental factors with hypertension, however, a comprehensive database including demographic, environmental, individual attributes and nutritional status has been rarely studied. Moreover, an integrated spatial-epidemiological approach has been scarcely researched. Therefore, this study aims to provide and describe a geodatabase including individual-based and socio-environmental data related to people living in the city of Mashhad, Iran in 2018.

Data description
The database has been extracted from the PERSIAN Organizational Cohort study in Mashhad University of Medical Sciences. The data note includes three shapefiles and a help file. The shapefile format is a digital vector storage format for storing geometric location and associated attribute information. The first shapefile includes the data of population, air pollutants and amount of available green space for each census block of the city. The second shapefile consists of aggregated blood pressure data to the census blocks of the city. The third shapefile comprises the individual characteristics data (i.e., demographic, clinical, and lifestyle). Finally, the fourth file is a guide to the previous data files for users.
Investigation of bioluminescence-based assays for determination of kinetic parameters for the bifunctional Neisseria meningitidis serogroup W capsule polymerase
Authors: Sheikhi Moghaddam Laleh , Adegbite Ayobami , McCarthy Pumtiwitt C. 
Published: November 2021

Abstract
Objective
Neisseria meningitidis is a Gram-negative bacterium that causes meningitis. N. meningitidis serogroup W (NmW) capsule polymerase synthesizes capsular polysaccharide of this serogroup. This enzyme could be a tool for meningococcal glycoconjugate vaccine development. Our long-term goal is to control activity of the NmW capsule polymerase for production of defined carbohydrates for vaccines. The enzyme lacks a simple, high-throughput activity assay. Here, we describe the use of high-throughput bioluminescence assays (CMP-Glo and UDP-Glo by Promega) to investigate NmW capsule polymerase activity. These assays detect free nucleotides produced during transfer of sugar from UDP-Galactose and CMP-Sialic Acid to an acceptor. Kinetic studies using NmW hydrolyzed polysaccharide (PS) acceptor are described as well as preliminary work with a sialic acid trimer (DP3) acceptor.

Results
In CMP-Glo kinetic studies, with constant donor (80 µM) and varied NmW hydrolyzed polysaccharide (0–2000 µg/mL), a Km of 629.2 ± 101.4 µg/mL and a Vmax of 0.8965 ± 0.05823 µM/min was obtained. Using UDP-Glo, Km and Vmax values of 13.84 ± 9.675 µM and 0.6205 ± 0.1331 µM/min were obtained with varied CMP-NeuNAc (0–80 µM) and constant acceptor (400 µg/mL) and UDP-Gal (80 µM). This is the first report of using bioluminescence assays for NmW kinetics.
Immunomagnetic B cell isolation as a tool to study blood cell subsets and enrich B cell transcripts
Authors: Henning Amanda N. , Green Daniel , Baumann Ryan , Grandinetti Patrick , Highfill Steven L. , Zhou Huizhi , De Giorgi Valeria 
Published: November 2021

Abstract
Objective
Transcriptional profiling of immune cells is an indispensable tool in biomedical research; however, heterogenous sample types routinely used in transcriptomic studies may mask important cell type-specific transcriptional differences. Techniques to isolate desired cell types are used to overcome this limitation. We sought to evaluate the use of immunomagnetic B cell isolation on RNA quality and transcriptional output. Additionally, we aimed to develop a B cell gene signature representative of a freshly isolated B cell population to be used as a tool to verify isolation efficacy and to provide a transcriptional standard for evaluating maintenance or deviation from traditional B cell identity.

Results
We found RNA quality and RNA-sequencing output to be comparable between donor-matched PBMC, whole blood, and B cells following negative selection by immunomagnetic B cell isolation. Transcriptional analysis enabled the development of an 85 gene B cell signature. This signature effectively clustered isolated B cells from heterogeneous sample types in our study and naïve and memory B cells when applied to transcriptional data from a published source. Additionally, by identifying B cell signature genes whose functional role in B cells is currently unknown, our gene signature has uncovered areas for future investigation.
Pulmonary eosinophilia may indicate onset stage of allergic bronchopulmonary aspergillosis
Authors: Miki Mari , Ohara Yuko , Tsujino Kazuyuki , Kawasaki Takahiro , Kuge Tomoki , Yamamoto Yuji , Matsuki Takanori , Miki Keisuke , Kida Hiroshi 
Published: November 2021

Abstract
Background
Allergic bronchopulmonary aspergillosis (ABPA) and chronic eosinophilic pneumonia (CEP) both display peripheral eosinophilia as well as pulmonary infiltration, together described as pulmonary eosinophilia, and differentiation is sometimes problematic. This study therefore examined the distinctions between ABPA with and without CEP-like shadows.

Methods
This retrospective cohort study from a single center included 25 outpatients (median age, 65 years) with ABPA diagnosed between April 2015 and March 2019, using criteria proposed by the International Society of Human and Animal Mycology (ISHAM), which focuses on positive specific IgE for Aspergillus fumigatus. Patients were assigned to either the eosinophilic pneumonia (EP) group or Non-EP group, defined according to findings on high-resolution computed tomography (HRCT). The EP group included patients with HRCT findings compatible with CEP; i.e., the presence of peripheral consolidation (p-consolidation) or ground-glass opacities (GGO), with no evidence of high-attenuation mucus. The Non-EP group comprised the remaining patients, who showed classical findings of ABPA such as mucoid impaction. Differences between the groups were analyzed.

Results
Baseline characteristics, frequency of a history of CEP (EP, 50% vs. Non-EP, 26%) and tentative diagnosis of CEP before diagnosis of ABPA (67% vs. 16%) did not differ significantly between groups. Although elevated absolute eosinophil count and Aspergillus-specific immunoglobulin E titers did not differ significantly between groups, the Non-EP group showed a strong positive correlation between these values (R  = 0.7878, p  = 0.0003). The Non-EP group displayed significantly higher levels of the fungal marker beta-D glucan (median, 11.7 pg/ml; interquartile range, 6.7–18.4 pg/ml) than the EP group (median, 6.6 pg/ml; interquartile range, 5.2–9.3 pg/ml). Both groups exhibited frequent recurrence of shadows on X-rays but no cases in the EP group had progressed to the Non-EP group at the time of relapse.

Conclusions
The ABPA subgroup with imaging findings resembling CEP experienced frequent recurrences, as in typical ABPA. In pulmonary eosinophilia, even if there are no shadows indicating apparent mucous change, the Aspergillus-specific immunoglobulin E level is important in obtaining an accurate diagnosis and in the selection of appropriate therapies for this type of ABPA.
The role of the immune system in idiopathic nephrotic syndrome
Authors: Hackl Agnes , Zed Seif El Din Abo , Diefenhardt Paul , Binz-Lotter Julia , Ehren Rasmus , Weber Lutz Thorsten 
Published: November 2021

AbstractIdiopathic nephrotic syndrome (INS) in children is characterized by massive proteinuria and hypoalbuminemia and usually responds well to steroids. However, relapses are frequent, which can require multi-drug therapy with deleterious long-term side effects. In the last decades, different hypotheses on molecular mechanisms underlying INS have been proposed and several lines of evidences strongly indicate a crucial role of the immune system in the pathogenesis of non-genetic INS. INS is traditionally considered a T-cell-mediated disorder triggered by a circulating factor, which causes the impairment of the glomerular filtration barrier and subsequent proteinuria. Additionally, the imbalance between Th17/Tregs as well as Th2/Th1 has been implicated in the pathomechanism of INS. Interestingly, B-cells have gained attention, since rituximab, an anti-CD20 antibody demonstrated a good therapeutic response in the treatment of INS. Finally, recent findings indicate that even podocytes can act as antigen-presenting cells under inflammatory stimuli and play a direct role in activating cellular pathways that cause proteinuria. Even though our knowledge on the underlying mechanisms of INS is still incomplete, it became clear that instead of a traditionally implicated cell subset or one particular molecule as a causative factor for INS, a multi-step control system including soluble factors, immune cells, and podocytes is necessary to prevent the occurrence of INS. This present review aims to provide an overview of the current knowledge on this topic, since advances in our understanding of the immunopathogenesis of INS may help drive new tailored therapeutic approaches forward.
Autumn migration routes and wintering areas of juvenile Chinese Egrets (Egretta eulophotes) revealed by GPS tracking
Authors: Huang Zhijun , Zhou Xiaoping , Fang Wenzhen , Zhang Hailong , Chen Xiaolin 
Published: November 2021

AbstractBackgroundThe vulnerable Chinese Egret (Egretta eulophotes) is a long-distance migratory waterbird whose migration and wintering information is poorly understood. This study aims to identify the autumn migration routes and wintering areas of juvenile Chinese Egrets and determine the migration movement traits of this species.MethodsThirty-nine juvenile Chinese Egrets from the Fantuozi Island, an uninhabited offshore island with a large breeding colony of Chinese Egrets in Dalian, China, were tracked using GPS/GSM transmitters. Some feathers from each tracked juvenile were collected for molecular identification of sex in the laboratory. The GPS locations, recorded at 2-h intervals from August 2018 to May 2020, were used for the analyses.ResultsOf the 39 tracked juveniles, 30 individuals began their migration between September and November, and 13 successfully completed their autumn migration between October and November. The juveniles migrated southward via three migration routes, coastal, oceanic and inland, mainly during the night. The migration duration, migration distance, flight speed, and stopover duration of the 13 juvenile egrets that completed migration averaged 5.08 ± 1.04 days, 3928.18 ± 414.27 km, 57.27 ± 5.73 km/h, and 23.08 ± 19.28 h, respectively. These juveniles wintered in the coastal wetlands of Southeast Asia including those in the Philippines, Vietnam, and Malaysia, and only one successfully began its spring migration in June 2020.ConclusionsThis study newly finds that the oceanic route taken by juvenile Chinese Egrets, suggesting that the juveniles are able to fly over the Pacific Ocean without a stopover. Moreover, our novel data indicate that coastal wetlands along the East Asian–Australasian Flyway are important areas for both autumn migration stopover and the wintering of these juveniles, suggesting that international cooperation is important to conserve the vulnerable Chinese Egret and the wetland habitats on which it depends.
Partitioning tree water usage into storage and transpiration in a mixed forest
Authors: Liu Ziqiang , Liu Qianqian , Wei Zijun , Yu Xinxiao , Jia Guodong , Jiang Jiang 
Published: November 2021

Abstract
Background
Water migration and use are important processes in trees. However, it is possible to overestimate transpiration by equating the water absorbed through the plant roots to that diffused back to the atmosphere through stomatal transpiration. Therefore, it is necessary to quantify the water transpired and stored in plants.

Method
The δ2H/δ18O technique and heat ratio method were used to explore the water usage of coniferous and broad-leaved tree species, including the proportions of water used for transpiration and water storage.

Results
Platycladus orientalis and Quercus variabilis had strong plasticity in their water usage from different sources. Platycladus orientalis primarily used groundwater (30.5%) and the 60–100-cm soil layer (21.6%) throughout the experimental period and was sensitive to precipitation, absorbing water from the 0–20-cm layer (26.6%) during the rainy season. Quercus variabilis absorbed water from all sources (15.7%–36.5%) except from the 40–60-cm soil layer during the dry season. In addition, it did not change its water source but increased its groundwater uptake during the rainy season. The annual mean water fluxes of P. orientalis and Q. variabilis were 374.69 and 469.50 mm·year− 1, with 93.49% and 93.91% of the water used for transpiration, respectively. However, nocturnal sap flow in P. orientalis and Q. variabilis was mainly used for water storage in the trunk rather than transpiration, which effectively alleviated drought stress and facilitated the transport of nutrients.

Conclusions
The water stored in both species comprised 6%–7% of the total water fluxes and, therefore, should be considered in water balance models.
Slope stability analysis of a landfill subjected to leachate recirculation and aeration considering bio-hydro coupled processes
Authors: Feng Shi-Jin , Wu Shao-Jie , Fu Wen-Ding , Zheng Qi-Teng , Zhang Xiao-Lei 
Published: November 2021

AbstractDuring the operation of landfills, leachate recirculation and aeration are widely applied to accelerate the waste stabilization process. However, these strategies may induce high pore pressures in waste, thereby affecting the stability of the landfill slope. Therefore, a three-dimensional numerical analysis for landfill slope stability during leachate recirculation and aeration is performed in this study using strength reduction method. The bio-hydro coupled processes of waste are simulated by a previously reported landfill coupled model programmed on the open-source platform OpenFOAM and then incorporated into the slope stability analysis. The results show that both increasing the injection pressure for leachate recirculation and maximum anaerobic biodegradation rate will reduce the factor of safety (FS) of the landfill slope maximally by 0.32 and 0.62, respectively, due to increased pore pressures. The ignorance of both waste biodegradation and gas flow will overestimate the slope stability of an anaerobic bioreactor landfill by about 20–50%, especially when the landfilled waste is easily degradable. TheFSvalue of an aerobic bioreactor landfill slope will show a significant reduction (maximally by 53% in this study) when the aeration pressure exceeds a critical value and this value is termed as the safe aeration pressure. This study then proposes a relationship between the safe aeration pressure and the location of the air injection screen (i.e., the horizontal distance between the top of the injection screen and the slope surface) to avoid landfill slope failure during aeration. The findings of this study can provide insights for engineers to have a better understanding of the slope stability of a bioreactor landfill and to design and control the leachate recirculation and aeration systems in landfills.