bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term sonographic evaluation of the peritoneum in peritoneal dialysis patients: A retrospective cohort study
Authors: Taguchi Shinya , Ohtake Takayasu , Mochida Yasuhiro , Ishioka Kunihiro , Moriya Hidekazu , Hidaka Sumi , Kobayashi Shuzo 
Published: April 2020

Abstract

Background

Long-term peritoneal dialysis (PD) causes morphological changes to the peritoneum. However, the sequential morphological changes of the peritoneum remain unclear due to the invasiveness and ethical dilemmas surrounding peritoneal biopsies. We aimed to evaluate these long-term morphological peritoneal changes using sonography, which was recently reported to be useful for morphological peritoneal evaluation.
Methods

We retrospectively identified 115 PD patients who underwent sonographic peritoneal membrane thickness (PMT) measurement. Univariate and multivariate linear regression analyses identified factors related to PMT at baseline (bPMT), at last measurement (lPMT), and the PMT change rate. Of the 115 patients, 42 patients had at least two PMT measurements, including a bPMT measurement. We evaluated the PMT change between bPMT and lPMT. We also evaluated the annual PMT change for 3 years before PD withdrawal in patients who discontinued PD due to peritoneal dysfunction. Clinical characteristics and parameters were analyzed according to PMT change rates (≤ 0 [n = 28] or > 0 [n = 20]).
Results

The mean age at PD introduction and mean PD duration were 63.7 ± 12.7 years and 40.5 ± 30.1 months, respectively. There was a significant positive correlation between the dialysate to plasma ratio of creatinine (D/P Cr) and lPMT (r = 0.386, p = 0.004), but not bPMT (r=-0.114, p = 0.326). In the multivariate analyses, D/P Cr remained an independent predictor of lPMT (r = 0.478, p = 0.001) after adjusting for age, sex, body mass index, PD duration, diabetes, and peritonitis rate. The mean bPMT and lPMT were 0.67 ± 0.15 mm and 0.69 ± 0.10 mm, respectively, without statistical difference (p = 0.49). Annual PMTs for 3 years before PD withdrawal were 0.67 ± 0.13 mm, 0.66 ± 0.11 mm, and 0.67 ± 0.08 mm, respectively, with no significant differences among measurements (p = 0.967). There were no differences in PD duration, the use of a dialysate containing over 2.5% glucose or icodextrin, and the peritonitis rate between groups divided by the PMT change rate.
Conclusions

PMT, measured by sonography, was positively correlated with peritoneal permeability. Repeated evaluation of the peritoneum by sonography will enable the recognition of transition in peritoneal function in real time and allow for more appropriate PD management. Furthermore, the peritoneum was not necessarily thickened regardless of PD duration or cause of withdrawal.
Effect of Chemical-Hydrothermal Pretreatments on Compositional and Morphological Changes of Spruce Wood Exploited in Biogas Systems
Authors: Rahimi-Ajdadi Fatemeh , Esmaili Masoomeh 
Published: April 2020

Abstract
Agricultural crops and forest residues are of valuable resources to produce biofuel due to anaerobic digestion. But, the recalcitrance nature of these lignocellulose residues limits its enzymatic degradation and decreases biogas production. Therefore, efficient pretreatments prior to anaerobic digestion are essential. In present study, hydrothermal-chemical pretreatments using Phenol (Ph), Sodium Hydroxide (SH) and Phosphoric Acid (PA), and combined pretreatments included Ph + SH and Ph + PA as chemical pretreatments were used for spruce wood. For hydrothermal pretreatments, the samples were put into the autoclave at 134 ºC for 20 min. Acid hydrolysis, FTIR and SEM analyses were carried out. The results indicated that all pretreatments were effective lignin removal having the highest value for Ph (42.362%). Adding Ph to PA, caused to increase lignin removal from 1.580–6.112%. Mixing Ph to SH represented the same trend in changing structure of spruce wood as compared to individually use of SH. All results proposed that when Ph contributed in binary pretreatment with SH and PA, it could be more effective on the morphological changes of spruce wood. In general, Ph was more effective on changing the crystalline structure of spruce wood than the others. After that, Ph + SH was more effective compared to Ph + PA on structural changes of spruce wood. In comparison between alkali and acidic pretreatments, SH represented more structural change in spruce wood than PA one. To have an intermediate state, it is recommended to use the combination of Ph with SH as infectious pretreatment instead of individually Ph. Because, this increases the biodegradation power of SH while the toxicity of Ph decreases. The obtained results are very important in biogas production systems.
Physiological and growth responses of two wheat (Triticum aestivum L.) varieties inoculated with a new strain of Bacillus siamensis under Cadmium (Cd) stress
Authors: Khan Imran , Linkai Huang , Awan Samrah Afzal , Rehman Abd ur , Raza Muhammad Ali , Rizwan Muhammad , Khan Aaqil , Tariq Rezwan , Akhtar Nosheen , Shah Ghulam Abbas , Ansar Muhammad , Sarwar Majid , Brestic Marian , Ilyas Nosheen 
Published: April 2020

Abstract
Bioavailability of cadmium (Cd) metal in the soils due to scarcity of good quality water and industrial waste could be the major limiting factors negatively influencing the growth and yield of crops needs prompt solution to fulfil the requirement of food for increasing world population. In the recent time, variable range of plant growth promoting rhizobacteria (PGPR) are being used on large scale in agriculture to reduce the risk of abiotic stresses on plants and increase crop productivity. Among them, the Bacillus siamensis has a huge potential to enhance the plant tolerance against abiotic stress but limited evidences are reported about the putative role of B.s in crop plants under heavy metal stress. The current study was aimed to investigate the potential of a new metal tolerant strain of B.s on two wheat (Triticum aestivum L.) varieties (NARC-2009 and NARC-2011) grown in Cd contaminated soil at different treatments i.e Cd (0, 20, 30 and 50 ppm) and Cd (0, 20, 30 and 50 ppm) + B.s. Our results depicted that Cd stress decreased the wheat growth related attributes, biomass, and photosynthetic parameters (Chlorophyll a, b and a + b) which increased in both wheat varieties upon inoculation with B.s. Moreover, Cd stress caused significant membrane damage and negatively affected the water content, water potential, and osmotic potential of leaf. However, PGPR considerably increased the soluble sugars to reduce the Cd toxicity. Overall, the plants inoculated with B.s enhanced their tolerance index of root and shoot and found better in NARC-2009 than NARC-2011. Therefore, microorganisms efficiently increase the plant growth by reducing the metal toxicity.
Whole exome sequencing reveals a combination of rare high and low penetrance variants that correlates with familial breast cancer relative risk
Authors: rekaya Mariem Ben , Hamdi Yosr , Labidi Soumaya , Mejri Nessrine , Jaidane Olfa , Ayari Jihene , Nasr Sonia Ben , Dallali Hamza , Messaoud Olfa , Meddeb Rym , Haddaoui Abderazek , Mrad Ridha , Boussen Hamouda , Abdelhak Sonia 
Published: April 2020

Abstract
Background: Genetic risk factors of breast cancer are very heterogeneous and complex. They vary according to the familial relative risk, the age of cancer diagnosis of the index case and the age of the affected relatives.Objectives: We aimed to investigate and identify simultaneously all rare pathogenic and common variants in unrelated BC cases with different relative risk ratios for breast cancer and evaluate the contribution of these variants in genetic susceptibility to breast cancer.Patients and Methods: All frequent mutations in BRCA genes previously identified in Tunisia have been excluded by Sanger sequencing in 42 women affected with high family risk having at least 3 cancer affected related individuals. Two unrelated cases having two different family histories (in terms of different numbers of affected first-degree relatives and young age onset) have been selected for whole exome sequencing. The first family is composed of three sisters F1.1, F1.2 and F1.3 affected at 46, 50, and 32 years old, respectively. The second has only two breast cancer cases, F2.2 and F2.4, affected at late age 61 and 70 years old, respectively, in addition to other 5 members affected by different kinds of cancer. Selected high risk variants were confirmed and segregation analysis was performed using Sanger sequencing. Results and discussion: For F1.1 case, we identified a pathogenic frame-shift loss of function variant in BRCA2 p.Val1283Lysfs. For F2.2 we identified a pathogenic rare variant in OGG1, p.Arg46Gln that co-segregates with a rare non sense variant in BRCA2 p.K3326X, only in the breast cancer affected cases. Moreover, F2.2 patient has 9 other common low penetrant variants in different loci known to represent independently minor, but cumulatively significant, increased risk for breast cancer.Conclusion: Family history and the young age at onset for patient F1.1 correlate with the presence of a rare high penetrant variant (p.Val1283Lysfs) in BRCA2 gene. However, the late age at onset and the less severe phenotype for patient F2.2 are probably the consequence of the presence of a pathogenic variant p.Arg46Gln in OGG1 gene that co-segregate with a low penetrant variant Lys3326X in BRCA2 only in breast cancer cases.
Comprehensive Characterization of RNA Editing in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis
Authors: Behroozi Javad , Shahbazi Shirin , Bakhtiarizadeh Mohammad Reza , Mahmoodzadeh Habibollah 
Published: April 2020

Abstract
RNA editing is a post-transcriptional nucleotide modification in humans. Of the various types of RNA editing, the adenosine to inosine substitution is the most widespread in higher eukaryotes, which is mediated by ADAR family enzyme. Inosine is recognized by the biological machineries as guanosine, therefore, editing can potentially rendering substantial functional effects throughout the genome, depending on where it located. RNA editing could contribute to cancer by either exclusive editing of tumor suppressor/promoting genes or by introducing transcriptomic diversity to promote cancer progression. Here, we provided a comprehensive overview of the RNA editing sites in gastric adenocarcinoma and highlighted some of their possible contributions to gastric cancer. RNA-seq data corresponding to 8 gastric adenocarcinoma and their paired non-tumor counterparts were retrieved from GEO database. After pre-possessing and variant calling steps, a stringent filtering pipeline was employed to distinguish potential RNA editing sites from SNPs. The identified potential editing sites were annotated and compared with those in DARNED database. Totally, 12362 high-confidence adenosine to inosine RNA editing sites were detected across all samples. Of these, 12105 and 257 were known and novel editing events, respectively. These editing sites were unevenly distributed across genomic regions, nearly half of them were located in 3´UTR. Indeed, 4868, 3985 and 3509 editing sites were found to be common in both tissue, normal specific and cancer specific, respectively. Further analysis revealed significant number of differentially edited events among these sites, which were located in protein coding genes and microRNAs. Given the distinct pattern of RNA editing in gastric adenocarcinoma and adjacent normal tissue, edited sites have the potential to serve as biomarkers and therapeutic targets in gastric cancer diagnose, management and treatment.
Network Pharmacology-Based Identification of Pharmacological Mechanisms of Inula japonica Thunb. on Non-small Cell Lung Cancer
Authors: Qian Huiqin , Wang Bai-Ling , Zhang Ling-Yun , Li Jia-Xiang , Huang Xiu-Xiu 
Published: April 2020

Abstract
Background

Inula japonica Thunb. (IJT) is an extensively applied herbal medicine for treating non-small cell lung cancer (NSCLC) due to its anti-asthma, antitussive, and expectorant properties. However, the mechanism of IJT against NSCLC remains to be elucidated.
Methods

Network pharmacology analysis was applied to determine the function mechanism of IJT against NSCLC. Databases were used to collect compounds and their related and known therapeutic targets. The compound–target (C–T) and target–target networks were then constructed to screen the kernel compounds and NSCLC-related targets of IJT. Moreover, the NSCLC-related targets of IJT were input in the DAVID Bioinformatics Resources (version 6.8) for Gene Ontology Biological Processes (GOBP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, the binding affinity of major compounds with the NSCLC-relevant targets of IJT was further verified by molecular docking.
Results

Two active compounds (quercetin and luteolin) and six putative targets (RAC-alpha serine/threonine-protein kinase, G1/S-specific cyclin-D1, cyclin-dependent kinase inhibitor 2A, epidermal growth factor receptor, receptor tyrosine-protein kinase erbB-2, and cellular tumor antigen p53) were screened as the effective compounds and NSCLC-related targets of IJT. GOBP and KEGG enrichment analysis indicated that NSCLC was the major pathway of IJT in the treatment of NSCLC and the mediation of apoptosis, cell cycle, tumor progression, and proliferation of biological processes, including the Ras, ERBB, MAPK, PI3K–Akt, calcium, and p53 signaling pathways. The results of molecular docking validated that 10 of the 12 pairs of compound-target had effective binding.
Conclusions

The mechanisms of IJT against NSCLC through multi-compounds, multi-targets, and multi-pathways were elucidated.
Short-term renoprotective effect of SGLT-2 inhibitor for renal function and albuminuria in type 2 diabetes
Authors: Kubota Mitsunobu , SHiroyama Eri , Tanaka Kanako , Yoshii Yoko 
Published: April 2020

Abstract
Background

Progression of diabetic nephropathy in type 2 diabetic patients is a factor that determines the prognosis of life. Empagliflozin and canagliflozin, two oral diabetic SGLT-2 inhibitors, have shown improved renal outcomes in type 2 diabetic patients with chronic kidney disease in a large clinical study. These results suggest that SGLT-2 inhibitors could be used not only for hypoglycemic effects, but also for renal protective effects in patients with type 2 diabetes. It is not fully understood in which contexts the use of SGLT-2 inhibitors is likely to exert its renal protective effects. The purpose of this study was to clarify the profiles of patients in whom SGLT-2 inhibitors are more likely to exert a renal protective effect in clinical practice. We examined renal function and urinary albumin changes in short-term use of SGLT-2 inhibitors by patient background.
Methods

We retrospectively analyzed the chart information of sixty-three type 2 diabetic patients (33 males, 30 females, average age 53.0 ± 13.0 years) who were given usual doses of a SGLT-2 inhibitor. We investigated changes in body weight, blood pressure, glucose metabolism index, lipid metabolism index, estimated glomerular filtration rate (eGFR) and albuminuria (urinary albumin-to-creatinine ratio, UACR) three months before and after administration of a SGLT-2 inhibitor.
Results

Three months after administration of an SGLT-2 inhibitor, there were improvements in glucose tolerance, weight loss, blood pressure, and lipid indices. In all cases, there was no significant change in eGFR, but UACR decreased significantly. UACR decreased regardless of Angiotensin II Receptor Blocker medication and significantly decreased in the nephropathy stage 2 and 3 groups. UACR decreased only in the group in which blood pressure, body weight, and HbA1c decreased before and after administration of the SGLT-2 inhibitor.
Conclusions

Our study shows that SGLT-2 inhibitors are independent of renin-angiotensin system (RAS) inhibitors, and in addition to direct renal protection, the comprehensive effects of SGLT-2 inhibitors, which lower body weight, blood pressure, and blood glucose, are also important for their renal protection effects.
Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains
Authors: Wu Ting-Ying , Müller Marlen , Gruissem Wilhelm , Bhullar Navreet K. 
Published: April 2020

Abstract
Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular in different contributions of grain tissues to these process, are not understood.Main text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development.Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.
Articular chondrocyte derived exosomes promote cartilage differentiation of human umbilical cord mesenchymal stem cells by activation of autophagy
Authors: Ma Ke , Zhu Bo , Wang Zetao , Cai Peian , He Mingwei , Ye Danyan , Yan Guohua , Zheng Li , Yang Lujun , Zhao Jinmin 
Published: April 2020

Abstract
Background
Umbilical cord mesenchymal stem cells (HUCMSCs)-based therapies were previously predicated in cartilage regeneration due to the chondrogenic potential of MSCs. However, chondrogenic differentiation of HUMSCs is limited by administration of growth factors like TGF-β that may cause cartilage hypertrophy. It has been reported the exosomes could modulate phenotypic expression of stem cells. However, the role of human chondrogenic derived exosomes (C-EXO) in chondrogenic differentiation of HUCMSCs has not been reported.
Results
In this study, we successfully isolated chondrocyte-derived exosomes (C-EXO) from human multi-finger cartilage and found that C-EXO efficiently promoted the proliferation and chondrogenic differentiation of HUCMSCs, evidenced by highly expressed aggrecan (ACAN), COL2A and SOX-9. Also, the expression of the fibrotic marker, COL1A and hypertrophic marker, COL10, was significantly lower than that induced by TGF-β. In vivo, stimulation of C-EXO accelerated HUCMSCs-mediated cartilage repair in rabbit models. Furthermore, C-EXO led to increasing autophagosomes during the process of chondrogenic differentiation, indicating that C-EXO promoted cartilage regeneration might be through the activation of autophagy.
Conclusions
This study suggests that C-EXO has an essential role in fostering chondrogenic differentiation and proliferation of HUCMSCs, which may be a stable supply for articular cartilage repair.
pH Sensitive Lipid-Polymer Hybrid Nanoparticles Mediated Delivery of Docetaxel: A Viable Approach for Breast Cancer Therapeutic Intervention Development
Authors: Yuan Ye , Song Jia-Xing , Zhang Mei-Na , Yuan Baoshan 
Published: April 2020

Abstract
Present study was planned for the development of pH sensitive lipid polymer hybrid nanoparticles (pHS-LPHNPs) loaded with docetaxel (DTX) for guided and target specific cytosolic-delivery delivery of docetaxel (DTX). pHS-LPHNPs were formulated to entrap DTX by self-assembled nano-precipitation technique and characterised with respect to zeta potential, particle-size, entrapment efficiency, PDI as well as invitro drug release. The cell viability, apoptosis, cellular-uptake, pharmacokinetics, bio-distribution in vital organs, % changes in tumour volume and survival of breast cancer bearing animals were used for the evaluation of efficacy of the formulation. In-vitro studies showed increased cytotoxicity at lower IC50 and better cellular-uptake of pHS-LPHNPs mediated drug by breast cancer cell lines. We saw the better rate of apoptosis of breast cancer cells via Annexin V/Propidium iodide staining. Moreover, in-vivo studies demonstrated improved pharmacokinetics and targetability with minimum drug circulation in deep-seated organs upon delivery of DTX via pHS-LPHNPs in comparison with LPHNPs-DTX and free DTX. We observed sizeable % reduction in tumour-burden with pHS-LPHNPs-DTXthan that withLPHNPs-DTX &free DTX. In brief, pHS-LPHNPs mediated delivery of DTX exhibited promising approach for developing therapeutic-interventions against breast-cancer.
PARPBP is a prognostic marker and confers chemotherapeutic resistance to breast cancer
Authors: Chen Bo , Lai Jianguo , Dai Danian , Chen Rong , Liao Ning , Tang Hailin 
Published: April 2020

Abstract
Background: PARPBP (PARP1 Binding Protein) is an important homologous recombination inhibitor of human cells during DNA repair. But the expression and function of PARPBP in breast cancer remain unclear.Methods: We evaluated the expression and prognostic value of PARPBP in breast cancer by immunohistochemical analysis in our patients (n=137) and public available datasets. Multiple in vitro and in vivo animal models characterized its functions.Results: In the present study, we demonstrated that PARPBP was significantly upregulated in breast cancer tissues compared with normal breast tissues. PARPBP high expression group had poor overall survival (OS) compared to the PARPBP low expression group. Similar results got in TCGA and KM Plotter overall survival analysis. Knockdown of PARPBP suppressed breast cancer cell growth proliferation and colony formation. Furthermore, we found that high expression of PARPBP related with chemotherapy resistance in breast cancer. Depletion of PARPBP increases breast cancer cell apoptosis and DNA damage caused by chemotherapy drugs. Transcription factor forkhead box M1(FOXM1) activated PARPBP expression by directly binding to the promoter of PARPBP. Moreover, tumor xenograft experiments further demonstrated that PARPBP was involved in breast cancer chemoresistance. Conclusions: Taken together, our results highlight PARPBP is a prognostic marker and confers chemotherapeutic resistance to breast cancer.