bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of chitosan on blood profile, inflammatory cytokines by activating TLR4/NF-κB signaling pathway in intestine of heat stressed mice
Authors: Mohyuddin Sahar Ghulam , Qamar Aftab , Hu Can-ying , Chen Sheng-Wei , Wen Jia-ying , Liu Xiao-xi , Ma Xing-bin , Yu Zhi-chao , Yong Yan-hong , Wu Lian-Yun , Bao Ming-Long , Ju Xiang Hong 
Published: October 2021

AbstractHeat stress can significantly affect the immune function of the animal body. Heat stress stimulates oxidative stress in intestinal tissue and suppresses the immune responses of mice. The protecting effects of chitosan on heat stress induced colitis have not been reported. Therefore, the aim of this study was to investigate the protective effects of chitosan on immune function in heat stressed mice. Mice were exposed to heat stress (40 °C per day for 4 h) for 14 consecutive days. The mice (C57BL/6J), were randomly divided into three groups including: control group, heat stress, Chitosan group (LD: group 300 mg/kg/day, MD: 600 mg/kg/day, HD: 1000 mg/kg/day). The results showed that tissue histology was improved in chitosan groups than heat stress group. The current study showed that the mice with oral administration of chitosan groups had improved body performance as compared with the heat stress group. The results also showed that in chitosan treated groups the production of HSP70, TLR4, p65, TNF-α, and IL-10 was suppressed on day 1, 7, and 14 as compared to the heat stress group. In addition Claudin-2, and Occludin mRNA levels were upregulated in mice receiving chitosan on day 1, 7, and 14 of heat stress. Furthermore, the IL-6, IL-10, and TNF-α plasma levels were down-regulated on day 1, 7, and 14 of heat stress in mice receiving the oral administration of chitosan. In conclusion, the results showed that chitosan has an anti-inflammatory ability to tolerate hot environmental conditions.
Integrative transcriptomic and gene co-expression network analysis of host responses upon Verticillium dahliae infection in Gossypium hirsutum
Authors: Zhang Guoli , Zhao Zengqiang , Ma Panpan , Qu Yanying , Sun Guoqing , Chen Quanjia 
Published: October 2021

AbstractWorldwide, Verticillium wilt is among the major harmful diseases in cotton production, causing substantial reduction in yields. While this disease has been extensively researched at the molecular level of the pathogen, the molecular basis ofV. dahliaehost response association is yet to be thoroughly investigated. In this study, RNA-seq analysis was carried out onV. dahliaeinfected twoGossypium hirsutumL. cultivars, Xinluzao-36 (susceptible) and Zhongzhimian-2 (disease resistant) for 0 h, 24 h, 72 h and 120 h time intervals. Statistical analysis revealed thatV. dahliaeinfection elicited differentially expressed gene responses in the two cotton varieties, but more intensely in the susceptible cultivar than in the resistant cultivars. Data analysis revealed 4241 differentially expressed genes (DEGs) in the LT variety across the three treatment timepoints whereas 7657 in differentially expressed genes (DEGs) in the Vd592 variety across the three treatment timepoints. Six genes were randomly selected for qPCR validation of the RNA-Seq data. Numerous genes encompassed in disease resistance and defense mechanisms were identified. Further, RNA-Seq dataset was utilized in construction of the weighted gene co-expression network and 11 hub genes were identified, that encode for different proteins associated with lignin and immune response, Auxin response factor, cell wall and vascular development, microtubule, Ascorbate transporter, Serine/threonine kinase and Immunity and drought were identified. This significant research will aid in advancing crucial knowledge on virus-host interactions and identify key genes intricate inG. hirsutumL. resistance toV. dahliaeinfection.
Brain age estimation at tract group level and its association with daily life measures, cardiac risk factors and genetic variants
Authors: Salih Ahmed , Boscolo Galazzo Ilaria , Raisi-Estabragh Zahra , Rauseo Elisa , Gkontra Polyxeni , Petersen Steffen E. , Lekadir Karim , Altmann André , Radeva Petia , Menegaz Gloria 
Published: October 2021

AbstractBrain age can be estimated using different Magnetic Resonance Imaging (MRI) modalities including diffusion MRI. Recent studies demonstrated that white matter (WM) tracts that share the same function might experience similar alterations. Therefore, in this work, we sought to investigate such issue focusing on five WM bundles holding that feature that is Association, Brainstem, Commissural, Limbic and Projection fibers, respectively. For each tract group, we estimated brain age for 15,335 healthy participants from United Kingdom Biobank relying on diffusion MRI data derived endophenotypes, Bayesian ridge regression modeling and 10 fold-cross validation. Furthermore, we estimated brain age for an Ensemble model that gathers all the considered WM bundles. Association analysis was subsequently performed between the estimated brain age delta as resulting from the six models, that is for each tract group as well as for the Ensemble model, and 38 daily life style measures, 14 cardiac risk factors and cardiovascular magnetic resonance imaging features and genetic variants. The Ensemble model that used all tracts from all fiber groups (FG) performed better than other models to estimate brain age. Limbic tracts based model reached the highest accuracy with a Mean Absolute Error (MAE) of 5.08, followed by the Commissural ($$\hbox {MAE}=5.23$$

MAE
=
5.23

), Association ($$\hbox {MAE}=5.24$$

MAE
=
5.24

), and Projection ($$\hbox {MAE}=5.28$$

MAE
=
5.28

) ones. The Brainstem tracts based model was the less accurate achieving a MAE of 5.86. Accordingly, our study suggests that the Limbic tracts experience less brain aging or allows for more accurate estimates compared to other tract groups. Moreover, the results suggest that Limbic tract leads to the largest number of significant associations with daily lifestyle factors than the other tract groups. Lastly, two SNPs were significantly (p value $$< 5\hbox {E}{-}8$$

<
5
E
-
8

) associated with brain age delta in the Projection fibers. Those SNPs are mapped to HIST1H1A and SLC17A3 genes.
Rosmarinic acid inhibits DNA glycation and modulates the expression of Akt1 and Akt3 partially in the hippocampus of diabetic rats
Authors: Alrubaye Ameer , Motovali-Bashi Majid , Miroliaei Mehran 
Published: October 2021

AbstractNon-enzymatic glycation of DNA and the associated effects are among pathogenic factors in diabetes mellitus. Natural polyphenols have anti-diabetic activity. Herein, the protective role of one of the phytochemicals, rosmarinic acid (RA), was evaluated in glycation (with fructose) of human DNA and expression of Akt genes in the hippocampus of diabetic rats. In-vitro studies using fluorescence, agarose gel electrophoresis, fluorescence microscopy, and thermal denaturation analyses revealed that glycation causes DNA damage and that RA inhibits it. In-vivo studies were performed by induction of diabetes in rats using streptozotocin. The diabetic rats were given RA daily through gavage feeding. The expression of Akt genes (inhibitors of apoptosis) in the hippocampus was evaluated using RT-qPCR. In diabetic rats, Akt1 and Akt3 were significantly down-regulated compared to the control group. Treating the diabetic rats with RA returned the expression of Akt1 and Akt3 relatively to the normal condition. Past studies have shown that diabetes induces apoptosis in the hippocampal neurons. Given that glycation changes the genes expression and causes cell death, apoptosis of the hippocampal neurons can be due to the glycation of DNA. The results also suggest that RA has reliable potency against the gross modification of DNA under hyperglycemic conditions.
A histidine kinase and a response regulator provide phage resistance to Marinomonas mediterranea via CRISPR-Cas regulation
Authors: Lucas-Elío Patricia , Molina-Quintero Luisa Raquel , Xu Hengyi , Sánchez-Amat Antonio 
Published: October 2021

AbstractCRISPR-Cas systems are used by many prokaryotes to defend against invading genetic elements. In many cases, more than one CRISPR-Cas system co-exist in the same cell. Marinomonas mediterranea MMB-1 possesses two CRISPR-Cas systems, of type I–F and III-B respectively, which collaborate in phage resistance raising questions on how their expression is regulated. This study shows that the expression of both systems is controlled by the histidine kinase PpoS and a response regulator, PpoR, identified and cloned in this study. These proteins show similarity to the global regulators BarA/UvrY. In addition, homologues to the sRNAs CsrB and CsrC and the gene coding for the post-transcriptional repressor CsrA have been also identified indicating the conservation of the elements of the BarA/UvrY regulatory cascade in M. mediterranea. RNA-Seq analyses have revealed that all these genetics elements are regulated by PpoS/R supporting their participation in the regulatory cascade. The regulation by PpoS and PpoR of the CRISPR-Cas systems plays a role in phage defense since mutants in these proteins show an increase in phage sensitivity.
Negative enrichment of circulating tumor cells from unmanipulated whole blood with a 3D printed device
Authors: Chu Chia-Heng , Liu Ruxiu , Ozkaya-Ahmadov Tevhide , Swain Brandi E. , Boya Mert , El-Rayes Bassel , Akce Mehmet , Bilen Mehmet Asim , Kucuk Omer , Sarioglu A. Fatih 
Published: October 2021

AbstractReliable and routine isolation of circulating tumor cells (CTCs) from peripheral blood would allow effective monitoring of the disease and guide the development of personalized treatments. Negative enrichment of CTCs by depleting normal blood cells ensures against a biased selection of a subpopulation and allows the assay to be applied on different tumor types. Here, we report an additively manufactured microfluidic device that can negatively enrich viable CTCs from clinically-relevant volumes of unmanipulated whole blood samples. Our device depletes nucleated blood cells based on their surface antigens and the smaller anucleated cells based on their size. Enriched CTCs are made available off the device in suspension making our technique compatible with standard immunocytochemical, molecular and functional assays. Our device could achieve a ~ 2.34-log depletion by capturing > 99.5% of white blood cells from 10 mL of whole blood while recovering > 90% of spiked tumor cells. Furthermore, we demonstrated the capability of the device to isolate CTCs from blood samples collected from patients (n = 15) with prostate and pancreatic cancers in a pilot study. A universal CTC assay that can differentiate tumor cells from normal blood cells with the specificity of clinically established membrane antigens yet require no label has the potential to enable routine blood-based tumor biopsies at the point-of-care.
Photoluminescence enhancement by deterministically site-controlled, vertically stacked SiGe quantum dots
Authors: Schuster Jeffrey , Aberl Johannes , Vukušić Lada , Spindlberger Lukas , Groiss Heiko , Fromherz Thomas , Brehm Moritz , Schäffler Friedrich 
Published: October 2021

AbstractThe Si/SiGe heterosystem would be ideally suited for the realization of complementary metal-oxide-semiconductor (CMOS)-compatible integrated light sources, but the indirect band gap, exacerbated by a type-II band offset, makes it challenging to achieve efficient light emission. We address this problem by strain engineering in ordered arrays of vertically close-stacked SiGe quantum dot (QD) pairs. The strain induced by the respective lower QD creates a preferential nucleation site for the upper one and strains the upper QD as well as the Si cap above it. Electrons are confined in the strain pockets in the Si cap, which leads to an enhanced wave function overlap with the heavy holes near the upper QD’s apex. With a thickness of the Si spacer between the stacked QDs below 5 nm, we separated the functions of the two QDs: The role of the lower one is that of a pure stressor, whereas only the upper QD facilitates radiative recombination of QD-bound excitons. We report on the design and strain engineering of the QD pairs via strain-dependent Schrödinger-Poisson simulations, their implementation by molecular beam epitaxy, and a comprehensive study of their structural and optical properties in comparison with those of single-layer SiGe QD arrays. We find that the double QD arrangement shifts the thermal quenching of the photoluminescence signal at higher temperatures. Moreover, detrimental light emission from the QD-related wetting layers is suppressed in the double-QD configuration.
A systematic review of smartphone-based human activity recognition methods for health research
Authors: Straczkiewicz Marcin , James Peter , Onnela Jukka-Pekka 
Published: October 2021

AbstractSmartphones are now nearly ubiquitous; their numerous built-in sensors enable continuous measurement of activities of daily living, making them especially well-suited for health research. Researchers have proposed various human activity recognition (HAR) systems aimed at translating measurements from smartphones into various types of physical activity. In this review, we summarized the existing approaches to smartphone-based HAR. For this purpose, we systematically searched Scopus, PubMed, and Web of Science for peer-reviewed articles published up to December 2020 on the use of smartphones for HAR. We extracted information on smartphone body location, sensors, and physical activity types studied and the data transformation techniques and classification schemes used for activity recognition. Consequently, we identified 108 articles and described the various approaches used for data acquisition, data preprocessing, feature extraction, and activity classification, identifying the most common practices, and their alternatives. We conclude that smartphones are well-suited for HAR research in the health sciences. For population-level impact, future studies should focus on improving the quality of collected data, address missing data, incorporate more diverse participants and activities, relax requirements about phone placement, provide more complete documentation on study participants, and share the source code of the implemented methods and algorithms.
Connecting MHC-I-binding motifs with HLA alleles via deep learning
Authors: Lee Ko-Han , Chang Yu-Chuan , Chen Ting-Fu , Juan Hsueh-Fen , Tsai Huai-Kuang , Chen Chien-Yu 
Published: October 2021

AbstractThe selection of peptides presented by MHC molecules is crucial for antigen discovery. Previously, several predictors have shown impressive performance on binding affinity. However, the decisive MHC residues and their relation to the selection of binding peptides are still unrevealed. Here, we connected HLA alleles with binding motifs via our deep learning-based framework, MHCfovea. MHCfovea expanded the knowledge of MHC-I-binding motifs from 150 to 13,008 alleles. After clustering N-terminal and C-terminal sub-motifs on both observed and unobserved alleles, MHCfovea calculated the hyper-motifs and the corresponding allele signatures on the important positions to disclose the relation between binding motifs and MHC-I sequences. MHCfovea delivered 32 pairs of hyper-motifs and allele signatures (HLA-A: 13, HLA-B: 12, and HLA-C: 7). The paired hyper-motifs and allele signatures disclosed the critical polymorphic residues that determine the binding preference, which are believed to be valuable for antigen discovery and vaccine design when allele specificity is concerned.
Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota
Authors: Ma Chenchen , Zhang Chengcheng , Chen Denghui , Jiang Shuaiming , Shen Siyuan , Huo Dongxue , Huang Shi , Zhai Qixiao , Zhang Jiachao 
Published: October 2021

AbstractThe adaptive evolution in indigenous intestinal microbes derived from probiotics is critical to safety and efficacy evaluation of probiotics, yet it is still largely underexplored. Here, through 11 publicly accessible datasets, we demonstrated that probiotic consumption can lead to widespread single-nucleotide variants (SNVs) in the native microbiota. Interestingly, the same probiotic strains introduced far more SNVs in mouse gut than humans. Furthermore, the pattern of probiotics-induced SNVs was highly probiotic-strain specific, and 17 common SNVs in Faecalibacterium prausnitzii genome were identified cross studies, which might lead to changes in bacterial protein structure. Further, nearly 50% of F. prausnitzii SNVs can be inherited for six months in an independent human cohort, whereas the other half only transiently occurred. Collectively, our study substantially extended our understanding of co-evolution of the probiotics and the indigenous gut microbiota, highlighting the importance of assessment of probiotics efficacy and safety in an integrated manner.
Sensitizing phosphorescent and radical emitters via triplet energy translation from CsPbBr3 nanocrystals
Authors: Chen Zongwei , Liang Guijie , Wu Kaifeng 
Published: October 2021

Colloidal CsPbBr3 nanocrystals effectively sensitize surface-attached molecular triplets which can further translate their energy to non-conventional light-emitting materials such as phosphorescent and radical molecules.
Computational and in vitro experimental analyses of the anti-COVID-19 potential of Mortaparib and MortaparibPlus
Authors: Kumar Vipul , Sari Anissa Nofita , Meidinna Hazna Noor , Dhanjal Jaspreet Kaur , Subramani Chandru , Basu Brohmomoy , Kaul Sunil C. , Vrati Sudhanshu , Sundar Durai , Wadhwa Renu 
Published: October 2021

Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has become a global health emergency. Although new vaccines have been generated and being implicated, discovery and application of novel preventive and control measures are warranted. We aimed to identify compounds that may possess the potential to either block the entry of virus to host cells or attenuate its replication upon infection. Using host cell surface receptor expression (angiotensin-converting enzyme 2 (ACE2) and Transmembrane protease serine 2 (TMPRSS2)) analysis as an assay, we earlier screened several synthetic and natural compounds and identified candidates that showed ability to down-regulate their expression. Here, we report experimental and computational analyses of two small molecules, Mortaparib and MortaparibPlus that were initially identified as dual novel inhibitors of mortalin and PARP-1, for their activity against SARS-CoV-2. In silico analyses showed that MortaparibPlus, but not Mortaparib, stably binds into the catalytic pocket of TMPRSS2. In vitro analysis of control and treated cells revealed that MortaparibPlus caused down-regulation of ACE2 and TMPRSS2; Mortaparib did not show any effect. Furthermore, computational analysis on SARS-CoV-2 main protease (Mpro) that also predicted the inhibitory activity of MortaparibPlus. However, cell-based antiviral drug screening assay showed 30–60% viral inhibition in cells treated with non-toxic doses of either MortaparibPlus or Mortaparib. The data suggest that these two closely related compounds possess multimodal anti-COVID-19 activities. Whereas MortaparibPlus works through direct interactions/effects on the host cell surface receptors (ACE2 and TMPRSS2) and the virus protein (Mpro), Mortaparib involves independent mechanisms, elucidation of which warrants further studies.
Epigenetic processes during preeclampsia and effects on fetal development and chronic health
Authors: Ashraf Usman M. , Hall Dalton L. , Rawls Adam Z. , Alexander Barbara T. 
Published: October 2021

Abstract
Preeclampsia (PE), the leading cause of maternal and fetal morbidity and mortality, is associated with poor fetal growth, intrauterine growth restriction (IUGR) and low birth weight (LBW). Offspring of women who had PE are at increased risk for cardiovascular (CV) disease later in life. However, the exact etiology of PE is unknown. Moreover, there are no effective interventions to treat PE or alleviate IUGR and the developmental origins of chronic disease in the offspring. The placenta is critical to fetal growth and development. Epigenetic regulatory processes such as histone modifications, microRNAs and DNA methylation play an important role in placental development including contributions to the regulation of trophoblast invasion and remodeling of the spiral arteries. Epigenetic processes that lead to changes in placental gene expression in PE mediate downstream effects that contribute to the development of placenta dysfunction, a critical mediator in the onset of PE, impaired fetal growth and IUGR. Therefore, this review will focus on epigenetic processes that contribute to the pathogenesis of PE and IUGR. Understanding the epigenetic mechanisms that contribute to normal placental development and the initiating events in PE may lead to novel therapeutic targets in PE that improve fetal growth and mitigate increased CV risk in the offspring.
A novel method for transformer fault diagnosis based on refined deep residual shrinkage network
Authors: Hu Hao , Ma Xin , Shang Yizi 
Published: October 2021

AbstractThis study proposes a novel method to improve the fault identification performance of transformers. First, to couple multiple factors, a high‐dimensional feature map composed of the feature gas concentrations and some associated variables is constructed. Second, the deep residual shrinkage network is revised using the updated alternating direction multiplier, and the newly constructed variable soft thresholding is proposed to eliminate constant deviations. In addition, the fast iterative shrinkage‐thresholding algorithm is adopted, as it can speed up the determination of the threshold. For the output end, the uniform manifold approximation and projection algorithm are adopted to ensure the integrity of the local optimal solution and the global solution. Compared with traditional dissolved gas analysis methods, the novel refined deep residual shrinkage network exhibits superior precision, which is justified through experiments. The results show that the recognition accuracy of the new model is more than 1.3% higher than that of the existing methods. The new method has good scalability in power applications and fault prevention.