bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protective effect of peroxisome proliferator-activated receptor-α in regulating the early inflammation response to extended hepatectomy from a comparative transcriptomic analysis
Authors: Shi Cheng-Cheng , Bai Yang , Yan Xin , Cheng Nuo , Guo Wen-Zhi , Zhang Shui-Jun , Shi Ji-Hua 
Published: July 2022

Abstract
Background
The regulation mechanism of post-operative hepatic failure and small-for-size syndrome remains unclear. Thus, we aimed to analyze the molecular profiles following extended hepatectomy and identify the therapeutic target.
Methods
Major hepatectomy and extended hepatectomy were performed in the rat model, and the remnant livers were obtained dynamically for the high-throughput transcriptome analysis to identify the differentially expressed genes (DEGs). The general framework for weighted gene co-expression network analysis (WGCNA) was employed to explore the expression patterns of DEGs. The expression and function of the selected DEG from the WGCNA was further verified following hepatectomy in the human and rat.
Results
DEGs after major hepatectomy and extended hepatectomy were detected by transcriptomics. WGCNA identified 10 distinct gene co-expression modules according to the correlation between module eigengene and different postoperative time-points. The magenta module (gene count: 289) and the lightcyan module (gene count: 484) were found positively correlated with major hepatectomy instead of extended hepatectomy. In the lightcyan module, peroxisome proliferator-activated receptor-α (PPARα) was selected and found the down-regulation in the remnant liver following extended (marginal) hepatectomy in rats and humans. Besides, administration of PPARα agonist attenuated hepatic inflammation injury while PPARα antagonist increased liver inflammation injury after extended hepatectomy in rats, marked by the significantly changed aminotransferases, tumor necrosis factor-α and interleukin-6 levels in the plasm, and histological Suzuki criteria.
Conclusion
DEGs and their molecular profiles after extended hepatectomy were identified, and PPARα could be a potential therapy target for small-for-size syndrome.
Adeno-Associated Virus based Caveolin-1 Delivery via Different Routes for the Prevention of Cholesterol Gallstone Formation
Authors: Li Sha , Chen Hongtan , Jiang Xin , Hu Fengling , Li Yiqiao , Xu Guoqiang 
Published: July 2022

Abstract
Background
The hepatic caveolin1 (CAV1) was reduced in cholesterol gallstone disease (CGD). And mice with CAV1 deficiency were prone to develop CGD. However, it remains unknown whether the restored hepatic CAV1 expression would prevent the development of CGD.
Methods
C57BL/6 mice were injected with adeno-associated virus 2/8 (AAV2/8) vectors carrying CAV1 gene (AAV2/8CAV1) via intravenous (i.v.) or intraperitoneal (i.p.) route and then were subjected to a lithogenic diet (LD) for 8 weeks. Uninjected mice were used as control. The functional consequences of rescuing CAV1 expression by either i.v. or i.p. AAV2/8CAV1 treatment on CGD prevention and its subsequent molecular mechanisms were examined.
Results
The CAV1 expression was reduced in liver and gallbladder of LD-fed-induced CGD mice. We discovered that AAV2/8CAV1 i.p. delivery results in higher transduction efficiency in the gallbladder than tail vein administration. And although either i.v. or i.p. injection of AAV2/8CAV1 improved the liver lipid metabolic abnormalities in CGD mice, they did not affect LD feeding-induced bile cholesterol supersaturation. In comparison with i.v. administration route, i.p. administration of AAV2/8CAV1 obviously increased CAV1 protein levels in the gallbladder of LD-fed mice. And i.p. delivery of AAV2/8CAV1 would partially improve gallbladder cholecystokinin receptor (CCKAR) responsiveness and impede bile cholesterol nucleation, via the activation of adenosine monophosphate-activated protein kinase (AMPK) signaling induced a reduction of gallbladder mucin-1 (MUC1) and MUC5ac expression and gallbladder cholesterol accumulation.
Conclusions
CGD prevention by i.p. AAV2/8CAV1 injection in LD-fed mice was associated with the improvement of gallbladder stasis, which again supported the notion that supersaturated bile is required but not sufficient for the formation of cholesterol gallstones. Additionally, AAV treatment via local i.p. injection offers particular advantages over the systemic i.v. route for much more effective gallbladder gene delivery, which will be an excellent tool for conducting preclinical functional studies on the maintenance of normal gallbladder function to prevent CGD.
A 2-D numerical study of contact angle effect on transient falling-film flow over horizontal tubes
Authors: Kandukuri Prudviraj , Deshmukh Sandip , Katiresan Supradeepan 
Published: July 2022

Abstract
The coverage of the liquid film over the horizontal tubes, particularly the wetting ratio, is important for heat transfer mechanism of gravity-driven evaporators and absorbers. A 2D, two-phase CFD model was developed to examine the falling-film hydrodynamics and transient flow mechanism for Reynolds numbers ranging from 100-500, contact angles spanning from 0°/30°/60°/90°, and inter tube spacing of 10 mm. The VOF method is used in this article to capture the gas-liquid interface. The findings showed that the complete spreading of the liquid film is difficult at low Reynolds numbers and high contact angles. The formation of dry regions on the tube wall as a result of insufficient liquid supply, liquid film breakage, and liquid film shrinkage. Furthermore, as the Reynolds number increases and contact angle decrease, the wetting ratio over the tube surface increases. It was worth noting that each contact angle must have a minimum Reynolds number in order to keep the surface completely wet. The research also found that for higher Reynolds numbers, the influence of contact angle on wettability of tube wall can be ignored. The liquid propagation time required to wet the tube surface increases as the contact angle value increases for the same Reynolds number. Fouling over the tubes can be aided by the formation of air voids near the lower stagnation zone.
Targeted, actionable and fair: reviewer reports as feedback and its effect on ECR career choices
Authors: Derrick Gemma , Zimmermann Alessandra , Greaves Helen , Best Jonathan , Klavans Richard 
Published: July 2022

Abstract

Background: Previous studies of the use of peer review for the allocation of competitive funding agencies have concentrated on questions of efficiency and how to make the ‘best’ decision, by ensuring that successful applicants are also the more productive or visible in the long term. This paper examines the components of feedback received from an unsuccessful grant application, is associated with motivating applicants career decisions to persist (reapply for funding), or to switch (not to reapply, or else leave academia).Methods: This study combined data from a survey of all applicants to ECR funding calls of The Wellcome Trust 2009-2019; with interviews with unsuccessful applicants (n=19), and manual coding of reviewer comments received by applicants (n=81).Results: Survey results show a high proportion of resubmissions, with 50% of unsuccessful applicants at T0 reapplying at T1, and with 35% of these achieving success with this reapplication. Here, peer-review-comments-as-feedback sends signals to applicants to encourage them to persist (continue) or switch (not continue) even when the initial application has failed. Feedback associated by unsuccessful applicants as motivating their decision to resubmit had 3 characteristics: actionable; targeted; and fair.Conclusions: The results lead to identification of standards of feedback for funding agencies and peer-reviewers to promote when providing reviewer feedback to applicants as part of their peer review process. The provision of quality reviewer-reports-as-feedback to applicants, ensures that peer review acts as a participatory research governance tool focused on supporting the development of individuals and their future research plans.
Non metastasis protein 2 (NME2) is a potential target for leukemia-specific immunotherapy
Authors: Däbritz Tobias , TSCHIEDEL Sabine , CROSS Michael , NIEDERWIESER Dietger 
Published: July 2022

Abstract
Background: NME2 is an immunogenic overexpressed tumor-associated antigen in chronic myeloid leukemia (CML). We evaluated NME2’s antigenicity in common HLA-backgrounds as a potential target for CML-specific immunotherapy. Methods: NME2-specific cytotoxic T-lymphocytes (CTL) were generated by stimulating cultured PBMCs with artificial antigen presenting cells (aAPC) expressing NME2 and the appropriate HLA-A antigen. Cultured PBMCs were obtained from healthy donors or CML-patients and priming with aAPCs was repeated weekly. IFNγ production from CD8+CTLs was evaluated by ELISpot assays. Results: NME2-specific CTLs were successfully generated both from healthy donors and from CML patients after hematopoietic stem cell transplantation. NME2-specific recognition by CTLs was HLA class I restricted (HLA-A 02, 03, 24) with no significant differences between the HLA-A backgrounds tested. The T315I TKI resistance mutation BCR::ABL1 did not affect susceptibility to CTL-mediated killing.Conclusions: NME2-specific CTLs can eradicate CML progenitor cells remaining after TKI-therapy or HSCT. Immunotherapy targeting NME2 may complement existing therapies.
Effect of Atmospheric Pressure Cold Plasma Gliding Arc Discharge Remote Treatment on Microbiological and Physicochemical Properties of Black Peppercorns (Piper nigrum)
Authors: Silva A. B.G.C.J. , Weerasinghe W. A.B.S. , Weeratunge H. D. , Milani M.D.Y. , Amunugoda P. N.R.J. , Gunawardena S. H. P. , de Alwis A.A.P. 
Published: July 2022

Abstract
The authors have requested that this preprint be removed from Research Square.
Prenatal diagnosis and genetic counseling of an inherited unbalanced chromosome abnormalities in a Chinese family
Authors: Zhang Ying , Chen Juan , Feng Zonghui , Li Wencheng 
Published: July 2022

Abstract
Background: Unbalanced chromosome abnormalities (UBCA) are either gains or losses or large genomic regions, but the affected person is not or only minimally clinically affected. Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. CNVs and UBCA identified in prenatal cases need careful considerations and correct interpretation if those are harmless or harmful variants from the norm.Case presentation: A 25-year-old, gravida 1, para 0, woman underwent amniocentesis at 18 weeks of gestation because the noninvasive prenatal testing (NIPT) results revealed a 6.8 Mb duplication from 2q11.1 to 2q11.2. Chromosomal microarray analysis (CMA) was performed on uncultured amniocytes. GTG-banding karyotype analysis on cultured amniocytes was performed. Results: Chromosomal GTG-banding of the cultured amniocytes revealed a karyotype of 46,XX. CMA detected a 6.8-Mb chromosomal duplication in the region of 2q11.1q11.2 (arr[GRCh37] 2q11.1q11.2(95,327,873_102,088,148)x3).Conclusion: Chromosomal microdeletions and microduplications are difficult to detect by conventional cytogenetics, combination of prenatal ultrasound, karyotype analysis, NIPT, CMA and genetic counseling is helpful for the prenatal diagnosis of UBCA and chromosomal microdeletions/microduplications..
Storage-induced changes in plasticizer emigration and structural properties of soybean isolate protein-based composite films
Authors: Zhu Tingwei , Fan Peipei , Li Qianyu , Ma Luyan , Wei Qian , Guo Xingfeng , Chen Fusheng 
Published: July 2022

Abstract
Previous study found soybean isolate protein (SPI)-based composite films added by corn starch (CS) (SPI:CS (4:1) composite film, SPI:CS (1:1) composite film) exhibited good mechanical property and better stability during the short-term storage pre-experiment. These properties were related to internal structure changes. In order to accordingly understanding the causes driving stability changes in performance and then controlling long-term stability of the SPI-based composite films, plasticizer emigration and structural properties of SPI-based composite films stored at different temperatures (5 ℃, 20 ℃, 35 ℃) and 54% relative humidity were systematically investigated over a period of time. High storage temperature (＞ 20 ℃) accelerated plasticizer emigration which reflected in increased migration rate of glycerol molecules and decreased moisture content. During the storage of SPI-based composite films, the decreased free SH partly formed new disulfide bonds and non-covalent inter-molecular interactions like hydrogen bonds changes significantly weakened the protein structure, which influenced mechanical properties changes during storage. PAGE and FTIR results explained the protein aggregation was bond with disulfide bonds and the reorganization of protein structure with prevalence of extended β-sheet conformation.
Role of Nrf2/ARE Signalling in Cadmium induced Alterations inNMDA ReceptorMediatedPostsynaptic Signalling inRat Hippocampus: Attenuation by Quercetin
Authors: Srivast Anugya , Kumari Anima , Jagdale Pankaj , Ayanur Anjaneya , Pant Aditya Bhushan , Khanna Vinay Kumar 
Published: July 2022

Abstract
Exposure tocadmium, a heavy metal distributed in the environment is a cause of concerndue to associated health effects in population world over. Continuing with the leadsdemonstrating alterations in brain cholinergic signalling in cadmium induced cognitive deficits;the study is focussed to understand involvement of N-Methyl-D-aspartate receptor (NMDA-R) and its post-synaptic signalling and Nrf2-ARE pathway in hippocampus. Also, the protective potential of quercetin, a polyphenolicbioflavonoid, was assessed in cadmium induced alterations. Cadmium treatment (5 mg/kg, body weight, p.o., 28 days)decreased mRNA expression and protein levels of NMDA receptor subunits (NR1, NR2A) in rat hippocampus, compared to controls. These rats also exhibited decrease in levels of NMDA-Rassociated downstream signalling proteins (CaMKIIα, PSD-95, TrkB, BDNF, PI3K, AKT, Erk1/2, GSK3β, and CREB) and increase in levels of SynGap, a negative regulator of Ras-MAPK in hippocampus. Alterations in protein levels of selected targets associated with AREsignalling (Nrf2, HO-1 and Keap1) and degeneration of pyramidal neurons were also evident in hippocampus of cadmium treated rats.Simultaneous treatment with quercetin (25 mg/kg body weight p.o., 28 days) was found to attenuate cadmium induced changes in hippocampus. No significantchange in any targetwas observed in hippocampus of ratstreated with quercetin alone.The results suggest that impairment in ARE signalling on exposure to cadmium may disrupt NMDA-R and its post-synaptic signaling in hippocampus and contribute in cadmium induced cognitive deficits in rats. Further, quercetin has the potential to protect cadmium induced changes in hippocampus possibly by modulating ARE signalling.
Gene Coverage Count and Classification (GC3): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum
Authors: Stabler Thomas C. , Dwivedi Ankit , Shrestha Biraj , Joshi Sudhaunshu , Schindler Tobias , Ouattara Amed , García Guillermo A. , Daubenberger Claudia , Silva Joana C. 
Published: July 2022

Abstract
Background
The ability of malaria rapid diagnostic tests (RDTs) to effectively detect active infections is being compromised by the presence of malaria strains with genomic deletions at the hrp2 and hrp3 loci, encoding the antigens most commonly targeted in diagnostics for Plasmodium falciparum (Pf) detection. The frequency of such deletions can be determined in publically available Pf whole genome sequencing (WGS) datasets. A computational approach was developed and validated, termed Gene Coverage Count and Classification (GC3), to analyze genome-wide sequence coverage data and provide informative outputs to assess presence and coverage profile of a target locus in WGS data. GC3 was applied to detect deletions at hrp2 and hrp3 (hrp2/3) and flanking genes in different geographic regions and across time points.
Methods
GC3 uses Python and R scripts to extract locus read coverage metrics from mapped WGS data according to user-defined parameters and generates relevant tables and figures. GC3 was tested using WGS data for laboratory reference strains with known hrp2/3 genotype, and its results compared to those of a hrp2/3-specific qPCR assay. Samples with at least 25% of coding region positions with zero coverage were classified as having a deletion. Publicly available sequence data was analyzed and compared with published deletion frequency estimates.
Results
GC3 results matched the expected coverage of known laboratory reference strains. Agreement between GC3 and a hrp2/3-specific qPCR assay reported 19/19 (100%) hrp2 deletions and 18/19 (94.7%) hrp3 deletions. Among Cambodian (n = 127) and Brazilian (n = 20) WGS datasets, which had not been previously analyzed for hrp2/3 deletions, GC3 identified hrp2 deletions in three and four samples, and hrp3 deletions in 10 and 15 samples, respectively. Plots of hrp2/3 coding regions, grouped by year of sample collection, showed a decrease in median standardized coverage among Malawian samples (n = 150) suggesting an increase in frequency of deletions between 2007-08 and 2014-15. Among Malian (n = 90) samples, median standardized coverage was lower in 2002 than 2010, indicating widespread deletions present at the gene locus in 2002.
Conclusions
The GC3 tool accurately classifies hrp2/3 deletions and provided informative tables and figures to analyze targeted gene coverage. GC3 is an appropriate tool when performing preliminary and exploratory assessment of locus coverage data.
High and low inferior mesenteric artery ligation in laparoscopic low anterior rectal resections: A retrospective study
Authors: Yu Jun , Yan Qian , Li Tong , Chen Yi , Sheng Bo , Zhen Zhuo , Zhang Jianbo , Zhu Peng 
Published: July 2022

Abstract
Purpose
The high or low inferior mesenteric artery (IMA) ligation in rectal cancer remains a great debate. This study retrospectively discussed the outcomes of the perioperative period, defecation and urinary function and long-term prognosis in rectal cancer patients with high or low IMA ligation.
Methods
This study enrolled 220 consecutive rectal cancer cases, including 134 with high IMA ligation and 86 with low ligation. A comparison between the two groups was made for anastomotic leakage, low anterior resection syndrome (LARS), international Prostate Symptom Score (IPSS), 5-year disease-free survival (DFS) and 5-year overall survival (OS).
Results
Low-ligation group had a longer operative time, and larger intraoperative blood loss. No significant difference was noted in anastomotic leakage incidence. In multivariable analysis, the male gender and tumor located at the lower rectum were identified as risk factors for anastomotic leakage. No significant differences were observed between groups in their LARS and IPSS questionnaire responses. The high-ligation versus the low-ligation 5-year OS and DFS were 78.3% versus 82.4% and 72.4% versus 76.6%, respectively, which were not statistically different.
Conclusion
The ligation level of the IMA had no significant effect on the anastomotic leakage incidence, defecation, urinary function, and long-term prognosis.
Unravelling synergetic removal of airborne carbonyls and inhibition of CO2 off-gas over robust amine-functionalised MnO2
Authors: Li Haiwei , Ho Wingkei , Cui Long , Lu Yanfeng , Li Xinwei , Wang Zhenyu , Ge Xinlei , Chen Mindong , Cao Junji , Lee Shuncheng , Huang Yu 
Published: July 2022

Abstract
Since the first standard available 2,4-dinitrophenylhydrazine (DNPH)-coated solid sorbents in the determination of carbonyls in the 1990s, studies of the ultrafast chemoselective reactions that form stable Schiff bases (C = N) in catalytic processes that remove airborne carbonyls have been scarce. Here, amine-functionalised MnO2 is engineered with a method involving freezing–thawing cycles, and interfacial structure and configuration of amino groups at the metal oxide surfaces that usually decay in nature are mechanically enhanced. Through molecular level characterisation and measurements, we find strong hydrogen bonds between robust amino groups and metal oxide sites in the well-ordered H5O2+ overlayer and the amino groups are negatively charged under environmental acidity. Compared with a DNPH control, we improve biocompatible amine-functionalised MnO2 to achieve the complete removal of sub-ppm formaldehyde, acetaldehyde and acetone synergically. Carbonyls and intermediate deprotonated hydrazones (–N = C(NH2)) are persistently chemosorbed and decomposed into recyclable bicarbonated amides (NH3+HCO3−), which are reservoirs or sinks of secondary aldehydes and routine CO2 off-gas.
Efficacy and Failure Patterns of Early SBRT to the Primary Tumor in Advanced EGFR Mutation-Positive Lung Cancer with EFGR-TKI treatment: A Prospective, Single Arm, Phase II Study
Authors: Shi Yangyang , Xu Hailing , Raynor William Y. , Ding Jiapei , Lin Ling , Zhou Chao , Wang Wei , Meng Yinnan , Wu Xiaomai , Chen Xiaofeng , Lv Dongqing , Yang Haihua 
Published: July 2022

Abstract
Introduction:
Early stereotactic body radiation therapy (SBRT) to the primary tumor combined with EFGR-TKI treatment may increase progression-free survive (PFS) by delaying resistance in patients with advanced EGFR-mutant NSCLC.
Methods
In this prospective, single arm phase II study, patients with advanced NSCLC were treated with EGFR TKI (Icotinib125mg tid or gefitinib 250mg qd) for one month followed by SBRT (40-60Gy/5-8F/5-10d) to the primary tumor with concurrent EGFR TKI until disease progression. The primary endpoint was PFS and the patterns of failure. Overall survival (OS) and adverse effects (AEs) were second endpoints.
Results
Overall 41 advanced NSCLC patients with EGFR mutations received treatment with 24.42 months of median follow-up time. On average, SBRT was initiated 1.49 months after EGFR-TKI administration. Tumors were found to have an average shrinkage rate of 42.50%. Median PFS was 15.23 months (95% CI 13.10-17.36), while median OS was 27.57 months (95% CI 23.05–32.09). Thirty-three patients were found to have disease progression, of which new site failure (NF) (22 patients, 66.66%) was the most common pattern, followed by original site failure (OF) (7 patients, 21.21%) and Simultaneous OF/NF (ONF) (4 patients, 12.12%). There was no AEs equal to or greater than grade 3 with the most frequent AE being radiation pneumonitis.
Conclusions
Administering therapy targeted at the primary tumor using early SBRT after EGFR-TKI initiation is a new potential safe and effective approach to treat EGFR-mutant advanced NSCLC.