bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel activation model for myofibroblasts derived from hepatic stellate cells in fibrotic liver
Authors: Yan Mengchao , Xie Ye , Yao Jia , Li Xun 
Published: July 2023

Abstract
Myofibroblasts in liver fibrosis originate from the activation of hepatic stellate cells (HSCs). Traditional activation model contains high expression of α-SMA and COL1A1. Based on traditional model, collagen deposition in the fibrotic liver should constructed in the way of patchy distribution, which is not consistent with the objective situation. We analyzed the expression of α-SMA and COL1A1 in the cell subpopulation with myofibroblast characteristics based on the Single-cell sequencing database Omnibrowser, and the result showed that α-SMA and COL1A1 were negatively correlated. After inducing myofibroblast characteristics of HSCs using fibrotic serum, further intervention with TGF-β1 promotes the expression of α- SMA simultaneously inhibits COL1A1 expression. Multicolor fluorescence of rat fibrotic liver tissue showed a network-like distribution of TGF-β1, while COL1A1 showed a patchy distribution in the TGF-β1 loop. COL1A1 expression was lower near the TGF-β1 loop and higher in the distant region, presenting a centripetal pattern. The difference is that α-SMA expression was mostly concentrated next to the TGF-β1 loop. Therefore, we propose the dual mode transition model of myofibroblasts in fiber liver (DMTM model). In the DMTM model, myofibroblasts have dual modes. Myofibroblasts obtain enhanced migration ability, accompanied by inhibition of COL1A1 expression in the high-concentration region of TGF-β1. When migrating to the periphery of the TGF-positive region, myofibroblasts convert to a high collagen secretion phenotype. The combination of migration to the periphery and collagen secretion promotes the continuous spread of collagen bundles and ultimately forms the observed fiber distribution pattern in the fibrotic liver.
Genetic divergence studies among sand pear (Pyrus pyrifolia (Burm) Nakai.) genotypes for yield and yield contributing traits in North-Western Himalayas
Authors: chauhan akriti , Thakur Dinesh S , Dogra RK , Rana VS 
Published: July 2023

Abstract

Germplasm assets are critical for hereditary breeding, investigation of complex traits and are conducive to the investigation and creation of unused germplasm. In order to effectively measure genetic divergence and character association for sand pear genetic improvement, yield and yield contributing variables were assessed for 125 genotypes during 2018–2021 in three districts of Himachal Pradesh, India (N-W Himalayas). The results indicated that estimates for eye basin, depth stalk cavity depth, fruit stalk length, non reducing sugars and leaf area high had high PCV and GCV values. High heritability and genetic gain both suggests the existence of additive gene action. The fruit's weight, sugar-to-acid ratio, and titratable acidity were reported, these qualities can be enhanced via direct selection. Fruit weight, total sugars, trunk diameter, total soluble solids (TSS), fruit length, fruit breadth, petiole length, and leaf area all have a high direct effect on plant yield, according to studies of association. Therefore, the overall result suggests that there is substantial diversity in the assessed attributes for them to serve as selection indices for genetic improvement of sand pear.
Predictive role of circulating tumor DNA and blood-based tumor mutational burden in esophageal squamous cell carcinoma receiving definitive chemoradiotherapy combined with toripalimab: Exploratory analyses of a phase II study (EC-CRT-001)
Authors: Xi Mian , Chen BaoQing , Liu Shiliang , Zhu Yujia , Wang Ruixi , Cheng Xingyuan , Chen Biqi , Dragomir Mihnea , Zhang Yaru , Hu Yonghong , Liu Mengzhong , Li Qiaoqiao , Yang Hong 
Published: July 2023

Abstract
The combination of toripalimab (an anti-PD-1 antibody) with definitive chemoradiotherapy (CRT) demonstrated encouraging efficacy against locally advanced esophageal squamous cell carcinoma (ESCC) in the EC-CRT-001 phase II trial. This exploratory analysis evaluated the role of circulating tumor DNA (ctDNA) and blood-based tumor mutational burden (bTMB) in predicting the response and survival. We found that ctDNA-negative patients achieved a higher clinical complete response rate (cCR) compared to those with detectable ctDNA during CRT (83%, 19/23 vs. 39%, 7/18; p=0.008) or post-CRT (78%, 21/27 vs. 30%, 3/10; p=0.017). Patients with detectable ctDNA during CRT had shorter progression-free survival (PFS) (p=0.014). Similarly, patients with post-CRT detectable ctDNA had a significantly shorter PFS (p=0.012) and worse overall survival (OS) (p=0.004). Moreover, patients with high bTMB levels during CRT had prolonged OS (p=0.027). In conclusion, ctDNA and bTMB has the potential for predicting treatment efficacy and survival in ESCC treated with CRT and immunotherapy.
Contribution of mine-derived airborne particulate matter to Ca, Fe, Mn and S content and distribution in the lichen Punctelia hypoleucites transplanted to Bajo de la Alumbrera mine, Catamarca (Argentina)
Authors: Hernández Juan Martín , Cañas Martha Susana , Brizuela Luis German Rodríguez , Fournière Emmanuel Marie de la , Debray Mario Ernesto , Ramos Cinthia Paula , Plá Rita Rosa , Jasán Raquel Clara , Ivernizzi Rodrigo 
Published: July 2023

Abstract
The aim of this work is to relate the contribution of mine-derived airborne particulate matter to Ca, Fe, Mn and S content and distribution in Punctelia hypoleucites transplanted to Bajo de la Alumbrera, an important open-pit mine in Catamarca, Argentina. Lichen samples were transplanted to four monitoring sites: two sites inside the mine, and two sites outside the mine. After three months, elemental distribution in samples were analyzed by micro-Particle induced X-ray emission, and elemental concentration was determined by specific techniques: Ca and Fe by instrumental neutron activation analysis; Mn by inductively coupled plasma atomic emission spectrometry; S by a turbidimetric method. As a result, a differential distribution of S and Ca in thalli transplanted inside-mine sites was detected compared to that of samples transplanted outside-mine sites. An overlap of Fe and S in the upper cortex of the apothecium section was observed, leading to infer a mineral association of both elements. Similar association was observed for Ca and S. In addition to these results, the significantly higher concentration detected for S and Mn in inside-mine sites samples suggests a contribution of Fe, S, Ca and Mn of mining origin to the content and distribution of these elements in P. hypoleucites. Micro PIXE complemented with Mössbauer spectroscopy analysis determined the presence of pyrite particles together with other iron-bearing minerals with different degrees of oxidation were detected. These results point out to a mining origin of the airborne particulate matter trapped by the lichen thalli transplanted to Bajo de la Alumbrera.
Convergent evolution in Afrotheria and non-afrotherians demonstrates high evolvability of the mammalian inner ear
Authors: Grunstra Nicole , Hollinetz Fabian , Morante Guillermo Bravo , Zachos Frank , Pfaff Cathrin , Winkler Viola , Mitteröcker Philipp , Maitre Anne Le 
Published: July 2023

Abstract

Evolutionary convergence in distantly related species is among the most convincing evidence of adaptive evolution. The mammalian ear, responsible for balance and hearing, is not only characterised by its spectacular evolutionary incorporation of several bones of the jaw, it also varies considerably in shape across modern mammals. Using a new multivariate approach, we show that in Afrotheria, a monophyletic clade with morphologically and ecologically highly disparate species, inner ear shape evolved similar adaptations as in non-afrotherian mammals. We identified four trait combinations that underlie this convergence. The high evolvability of the mammalian ear is surprising: nowhere else in the skeleton are different functional units so close together; it includes the smallest bones of the skeleton, and is encapsulated within the densest bone. We suggest that this evolvability is a direct consequence of the increased genetic and developmental complexity of the mammalian ear compared to other vertebrates.
ReaxFF-nn: A Reactive Machine Learning Potential in GULP and the Applications in the Thermal Conductivity Calculation of Carbon Nanostructures
Authors: Guo Feng , Ye Zhong-Hao , Chai Chuan-Guo , Wen Yu-Shi 
Published: July 2023

Abstract
ReaxFF-nn stands for Reactive Force Field (ReaxFF) with neural networks and is currently added to the General Utility Lattice Program (GULP) by modern FORTRAN programming. With GULP and ReaxFF-nn with parameters that are trained by our I-ReaxFF package, the thermal properties, crystal properties, energy minimization, etc., can be done with precision at the quasi-density functional theory (DFT) level. Compared to other Machine Learning Potentials (MLPs), we do not construct a thoroughly new machine learning potential, but just simply used a small neural network for the bond order and bond energy calculations, and the uncorrected bond orders are chosen as the input atomic feature vector. The advantage of To validate the model which we have coded in the GULP, we compared the forces of a random structure between the auto-differentiate package and our FORTRAN code, and the difference between them is about 10-6. Furthermore, we provided a systematical study of the thermal conductivity (κ) of graphene and carbon nanotubes (CNTs) through the phonon Boltzmann transport equation. The value of κ thermal conductivity of graphene is very close to the DFT calculations. Therefore, we declare that the potential we have trained for sp2 carbon can reach the quasi-DFT level. In this work, we report the thermal conductivity of CNTs calculated by ReaxFF-nn at quasi-DFT level are range from 107.032 to 310.019 W.m-1.K-1.
Identification of PPAR β/δ agonists using a drug-repurposing approach by computational HTVS and molecular docking/ dynamics simulation
Authors: Mandal Sumit , Muzaffar-Ur-Rehman Mohammed , Puri Sonakshi , Kumar Banoth Karan , Sharma Pankaj Kumar , Sankaranarayanan Murugesan , Deepa P. R. 
Published: July 2023

Abstract
Peroxisome proliferator-activated receptors (PPARs) play a crucial role in regulating carbohydrate and lipid metabolism and are considered as significant targets for treating metabolic syndrome and cancers. There is a need to identify new bioactive ligands that can activate specific PPAR subtypes, particularly PPARβ/δ, which is less studied compared to other PPAR isoforms (α and γ). Here, the ZINC database of clinically approved drugs was screened to target PPARβ/δ receptor, through virtual screening followed by molecular docking and molecular dynamics (MD) simulation. Among the screened ligands, the top five ligands with strong binding affinity towards the PPARβ/δ were canagliflozin, empagliflozin, lumacaftor, eprosartan, dapagliflozin. The top-scoring ligands showed stable protein-ligand complexation (PLC)with PPARβ/δ, as revealed by RMSD / RMSF analysis. The in silico ADMET prediction analysis assessed the pharmacokinetic profiles of these top five ligands, wherein they showed favourable drug-likeness properties. These promising results indicate scope for developing and validating the top-scoring PPARβ/δ agonists in specific disease models.
RtD-Net: Low-light image enhancement network based on deep learning
Authors: Wang Manli , Zhang Hang , Zhang Changsen 
Published: July 2023

Abstract

Existing low-light image enhancement techniques are mostly not only difficult to deal with both visual quality and computational efficiency but also are prone to detail loss and low contrast. in unknown complex scenarios. To solve these problems, we proposed an efficient low-light enhancement network for Removing the Darkness (denoted as RtD-Net). The network decomposes the image into two parts, the illumination branch is used to deal with light regulation and the reflection branch is used to deal with degradation removal. In this paper, we introduce the structure of RtD-Net, loss function, and training method of the model. First, the residual layer module is added to the network structure to improve the feature learning performance and the detail processing ability of the network; then a composite function including image reconstitution loss function, SSIM (Structural Similarity) loss function and TV loss function is used to optimize the contrast, brightness, color and saturation of the low-light image; Finally, segmental training is used to further improve the quality of the generated enhanced images. In the experimental comparison, the model demonstrates more advanced performance in both qualitative and quantitative comparisons, and is in an advantageous position when comparing with other low-light image enhancement models for image quality metrics. It can be proved through experiments that the proposed method has reached the state-of-the art in terms of processing speed and effect.
Probiotics and Diet Modifications: A Holistic Approach to Tackling Helicobacter pylori with the Help of the Gut Microbiota
Authors: Addissouky Tamer A. , Wang Yuliang , Sayed Ibrahim El Tantawy El , Khalil Ahmed A. 
Published: July 2023

Abstract
Background
Helicobacter pylori is a common gastrointestinal bacterium that can cause a range of diseases, including gastritis, peptic ulcer disease, and gastric cancer. The gut microbiota plays an important role in H. pylori colonization and associated diseases.
Main body:
Lifestyle factors, such as diet, stress, smoking, and alcohol consumption, can impact the gut microbiota composition and function, and may influence the risk of H. pylori colonization and H. pylori-associated diseases. Strategies to promote gut health, such as a healthy diet, stress reduction, smoking cessation, alcohol moderation, regular exercise, adequate sleep, antibiotic stewardship, and probiotic supplementation, may help to reduce the risk of H. pylori colonization and enhance the effectiveness of H. pylori eradication therapy. Furthermore, the gut microbiota may also be a potential target for H. pylori eradication, and personalized treatment approaches based on individual patient characteristics may be necessary to optimize H. pylori eradication rates and reduce the risk of adverse effects.
Conclusion
Further research is needed to better understand the role of the gut microbiota in H. pylori eradication and to develop more effective treatment strategies. By promoting gut health and developing personalized treatment approaches, we may be able to reduce the burden of H. pylori-associated diseases and improve patient outcomes.
An open-label single-center investigator-initiated exploratory clinical study in patients with refractory or recurrent solid tumors: ‘R-ISV-FOLactis’ trial
Authors: Dai Juanjuan , Wang Xiaolu , Chen Xinjie , Zhu Junmeng , Zhou Yingling , Min Limei , Qi Haoyue , Liu Qin , Shen Jie , Tian Manman , Shao Jie , Liu Baorui , Li Rutian 
Published: July 2023

Abstract
Background: As a breakthrough tool for cancer immunotherapy, the therapeutic cancer vaccine, which includes personalized neoantigen vaccine and in situ vaccine, is in rapid development. In situ vaccination can be realized by radiotherapy and intratumoral immune injection. Additionally, immune checkpoint inhibitor is a common treatment modality for tumors. This study proposes to combine intratumoral injection, radiotherapy, and PD-1 inhibitors for patients with recurrent or metastatic solid tumors and subsequently evaluate the efficacyand safety.
Methods/design: This exploratory clinical study is designed as an open-label, single-center trial aimed at treating patients with advanced solid tumors who are unresponsive or intolerable to standard treatment. Patients will be treated with hypofractionated radiotherapy, intratumoral injection of FOLactis, and PD-1 blockades. Additionally, 300mg cyclophosphamide will be added during intravenous administration of PD-1 blockades to inhibit regulatory T cells. Immune maintenance therapy with PD-1 blockades will be administered every three weeks until disease progression or the emergence of intolerable toxicity. The primary endpoint of this study is to observe the objective efficacy and safety of the combined regimen, with the secondary endpoint to evaluate abscopal effects and the correlation between the immunological rationale and efficacy.
Discussion: Both radiotherapy and intratumoral immune injection are approaches to conducting in situ vaccination. Their combination can enhance anti-tumor immunity by targeting multiple links of the cancer-immunity cycle. PD-1 blockade, a kind of immune checkpoint inhibitor, has garnered significant attention in tumor immunotherapy research in recent years. In this study, a triple combination of radiotherapy, intratumoral immune injection, and intravenous PD-1 inhibitor will be utilized to treat patients with advanced solid tumors to trigger antitumor immunity. The combined treatment is expected to be feasible and effective and provide a novel option for the comprehensive treatment of cancer.
Trial registration: ChiCTR. gov.cn: ChiCTR2200060660.
Sequencing methods to study the microbiome with antibiotic resistance genes in patients with pulmonary infections
Authors: Dong Tingyan , Wang Yongsi , Qi Chunxia , Fan Wentao , Xie Junting , Chen Haitao , Zhou Hao , Han Xiaodong , Wang Michael Xia 
Published: July 2023

Abstract
Background
Various antibiotic resistant bacteria are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of the spectrum of bacteria with antibiotic resistance genes (ARGs) can improve the antibiotic treatment efficiency. In this study, we induced metagenomic next-generation sequencing (mNGS) alignment and assembly methods in the bioinformatics analysis pipeline to reveal the profile of bacteria with ARGs (ARB) in samples from patients with pulmonary infections.
Methods
A retrospective analysis of 151 clinical samples from 144 patients with pulmonary infections was undertaken by mNGS and conventional microbiological detection methods. Positive ARB were determined according to the analysis results detected both by the alignment and assembly methods. Co-occurrence analysis of ARG-ARB network was conducted to investigate the attributions between ARGs and microbial taxa. We also evaluated the potential application conditions to predict ARGs using those two approaches.
Results
Compared to that using conventional detection methods, the false-positive detection rate of ARB was significantly higher using mNGS alignment method. The assembly method could assist the determining of the detected pathogens by the alignment method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network revealed the main ARGs in predominant ARB. A total of 361 ARGs were detected, which mostly belonged to the multidrug class and β-lactam antibiotic classes. Specifically, 101 ARGs (existing in two approaches) and 34 ARGs (detected only by assembly method) achieved a clear ARG-bacteria attribution and potentially could optimize the reference antibiotic resistance database. The most prevalent ARB and its corresponding ARG and drug classes were as follows in this study: Acinetobacter baumannii (ADE, multidrug), Pseudomonas aeruginosa (MEX, multidrug), Klebsiella pneumoniae (MDT, aminocoumarin; EMR, fluoroquinolone), Stenotrophomonas maltophilia (SME, multidrug) and Corynebacterium striatum (carA, MLSB).
Conclusion
Collectively, our findings demonstrated the applicability of mNGS alignment and assembly as antibiotic resistant diagnostic methods and uncovered pulmonary infection-associated ARB and ARGs, potentially, as antibiotic treatment targets for the pulmonary infection.
Evaluation of Anogeissus Leiocarpus (African Brich) Leaves Extract and its Wood Ash for Dyeing and Mordanting of Cotton Fabric
Authors: Leulseged Sawiros , Worku Amare 
Published: July 2023

Abstract
Now a day the coloration of textile materials is done by using mainly synthetic dyes. This is because synthetic dyes have better quality than natural dyes. However, these dyes are not eco-friends, and nearly the modern world has returned to using natural dyes as eco-friend dyeing alternatives. Unfortunately, these natural dyes have some drawbacks that directly correlate with quality. This research aimed to bring a qualified eco friend alternative dyes and mordants from A.leiocarpus tree leaves and wood ash respectively for coloring the cotton fabric. To examine the quality of the natural mordant it’s necessary to compare with synthetics mordants which are accepted globally. Here in this study 5% of Al2SO4 and 1% of FeSO4 were used as controls for comparison and then dyeing with three different methods of mordanting, which are pre, simultaneous, and post, to obtain better results on the color fastness and color strength. The maximum K/S value, which is 4.389, and color fastness, except light fastness, was obtained from Al2SO4 pre-mordanting methods. The ash-mordanted one showed dull yellowish color with good uniformly dyeing with the 2.664 K/S maximum value at the time of pre-mordanting. The color fastness has given almost the same fastness value in both wash and rub but the ash-mordanted fabric shows better light fastness which is 6, in pre mordanting method.
Prenatal diagnosis and molecular cytogenetic analyses of a homozygous Robertsonian translocation family with novel mosaic Robertsonian fission karyotype
Authors: Wu Qian , Liu Ruixue , Yu Chunjiao , Wang Bo , Luo Lan 
Published: July 2023

Abstract
Background
Approximately one person in 1,000 is a Robertsonian translocation carrier. Errors in the formation of eggs (or more rarely of sperms) may be the cause of Robertsonian translocation. Most Robertsonian translocation carriers are healthy and have a normal lifespan, but do have an increased risk of offsprings with trisomies and pregnancy loss. The fitness of rob translocation carries is reduced, but rob translocation can provide material for evolution.
Methods
We have done prenatal diagnosis and molecular cytogenetic analyses on this homozygous Robertson translocation family. We report a homozygous Robertson translocation family with previously undescribed mosaic Robertsonian fission karyotype.
Results
We identified six Robertsonian translocation carriers in this family. Four were heterozygous translocation carriers of 45,XX or XY,der(14;15)(q10;q10), one was a homozygous translocation carrier of a 44,XY,der(14;15)(q10;q10),der(14;15)(q10;q10) and one was a previously undescribed Robertsonian fission carrier of 45,XN,der(14;15)(q10;q10)[42]/46,XN[58] with normal phenotype.
Conclusion
We reported a previously undescribed mosaic Robertsonian fission karyotype. The homozygosity of Robertsonian translocation for speciation may be a potential mechanism of speciation in Humans. In theory, the carriers of homologous Robertsonian translocation can't produce normal gametes, but Robertson fission made it possible for them to produce normal gametes.