bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel exosome biomarker candidates for Alzheimer´s disease unraveled through Mass Spectrometry analysis
Authors: Martins Tânia Soares , Marçalo Rui , Silva Cristóvão B. da Cruz e , Trindade Dário , Catita José , Amado Francisco , Melo Tânia , Rosa Ilka Martins , Vogelgsang Jonathan , Wiltfang Jens , Silva Odete A. B. da Cruz e , Henriques Ana Gabriela 
Published: October 2021

Abstract
Exosomes are small extracellular vesicles (EVs) present in human biofluids that can transport specific disease-associated molecules. Consequently blood-derived exosomes have emerged as important peripheral biomarker sources for a wide range of diseases, among them Alzheimer’s disease (AD). Although there is no effective cure for AD, an accurate diagnosis, relying on easily accessible peripheral biofluids, is still necessary to discriminate this disease from other dementias, test potential therapies and even monitor rate of disease progression. The ultimate goal is to produce a cost-effective and widely available alternative, which can also be employed as a first clinical screen. In this study, EVs with exosome-like characteristics were isolated from serum of Controls and AD cases through precipitation- and column-based methods, followed by mass spectrometry analysis. The resulting proteomes were characterized by Gene Ontology (GO) functional enrichment and multivariate analyses. Although GO terms were similar for exosomes proteomes of Controls and ADs, using both methodologies, a clear segregation of disease cases was obtained when using the precipitation-based method. Nine significantly different abundant proteins were identified between Controls and AD cases, representing putative biomarker candidate targets. Among them AACT and C4BPα, two Aβ-binding proteins, whose exosome levels were further validated in individuals from independent cohorts using antibody-based approaches. The findings discussed represent an important contribution to the identification of novel exosomal biomarker candidates useful as potential blood-based tools for AD diagnosis.
Air Quality of Work, Residential, and Traffic Areas During the COVID-19 Lockdown with Insights to Improve Air Quality
Authors: Alharbi Badr H , Alhazmi Hatem A , Aldhafeeri Zaid 
Published: October 2021

Abstract
This study investigated the concentrations of air pollutants (NO, NO2, NOx, SO2, CO, O3, PM10, and PM2.5) at three sites with different traffic loads (work, residential, and traffic sites) before, during, and after the COVID-19 lockdown. The main objective of this study was to evaluate the effects and associated potential pollution control implications of the lockdown on the quality of ambient air at three selected sites in the urban area of Riyadh City. The average concentrations of NO, NO2, NOx, and CO decreased during the lockdown period by 73%, 44%, 53%, and 32% at the work site, 222%, 85%, 100%, and 60% at the residential site, and 133%, 60%, 101%, and 103% at the traffic site relative to the pre-lockdown period, respectively. The average concentration of O3 increased by 6% at the work site, whereas the concentration of SO2 increased by 27% at the residential site and decreased by 6.5% at the work site. The changes in PM10 and PM2.5 varied and did not exhibit a clear pattern. The air quality index (AQI) results indicated that the contribution to “undesired” air quality by O3 was 35.29% of the lockdown period at the work site while contributions to undesired air quality by PM10 and PM2.5 were 75.6% and 100% at the work site, 94.5% and 100% at the residential site, and 96.7% and 100% at the traffic site, respectively. The findings of this study are useful for devising effective urban pollution abatement policies. Applying control measures comparable to the lockdown measures over one week will result in a decrease of approximately 19% and 15% in CO mean concentration and 25% and 18% in NO2 mean concentration at residential and traffic sites, respectively. Significant mitigation of urban air pollution could be accomplished through intermittent implementations of strict pollution control measures.
Multiple Roles of Bamboo As A Regulator of Cyanobacterial Bloom In Aquatic Systems
Authors: Hao Aimin , Su Mengyao , Kobayashi Sohei , Zhao Min , Iseri Yasushi 
Published: October 2021

Abstract
To understand the potential roles of terrestrial bamboo on controlling cyanobacterial blooms in aquatic systems, growth rates of the cyanobacterium Microcystis aeruginosa and its competitor algae were examined under different concentrations of bamboo extract. In mono-species cultures with unicellular algal strains, 5.0 g L−1 extract treatment suppressed M. aeruginosa growth, while it had little effect on the growth of green alga Scenedesmus obliquus or promoted the growth of diatom Nitzschia palea. In co-species cultures, the extract treatment increased the effect of S. obliquus and N. palea on the growth of M. aeruginosa. Under the extract treatment with a field-collected M. aeruginosa population, its cell density declined and its colony was etiolated and sank, while co-cultured N. palea increased explosively by invading the colony. These results suggest that bamboo forest stands along banks and artificially installed bamboo poles can affect the aquatic environment for phytoplankton community. Enhancing the growth of competitors, especially diatoms that can invade cyanobacterial colonies, by using extracts or by providing substrates for growth, was suggested to be the major way of the bloom control by bamboo.
Disseminated Strongyloides Stercoralis Hyperinfection in An Immunocompetent Patient First Diagnosed by Metagenomic Next-Generation Sequencing in Cerebrospinal Fluid: A Case Report
Authors: Qu Junyan , Zong Zhiyong 
Published: October 2021

Abstract
Background

Disseminated Strongyloides stercoralis hyperinfection is rarely described in immunocompetent individuals and can lead to fatal outcomes if not recognized and diagnosed early. Non-specific clinical manifestations, such as pneumonia and gastroenteritis, pose a diagnostic dilemma.
Case presentation:

We report a case of a 67-year-old Chinese male who presented with two months of abdominal pain, fever, headache, vomiting, constipation, and slight cough with sputum. He had been in good health and had no history of glucocorticoid use. He was diagnosed with enterococcal meningitis and intestinal obstruction at a local hospital and improved after treatment with vancomycin, but symptoms of headache and abdominal pain soon recurred. The metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid using Illumina X10 sequencer revealed 7 sequence reads matching Strongyloides stercoralis. Disseminated strongyloidiasis was suspected. Next, microscopic examination of gastric fluid revealed Larvae of S. stercoralis. DNA extracted of larvae, the presence of both S. stercoralis ribosomal DNA gene and mitochondrial cytochrome c oxidase subunit 1 gene was identified. Disseminated strongyloidiasis was diagnosed. Albendazole (400 mg, twice daily) was used and the patient recovered gradually.
Conclusions

S. stercoralis hyperinfection can occur in immunocompetent individuals, imposing challenges for diagnosis. mNGS may be a useful tool for detecting rare infectious disease. The case would help clinicians to raise awareness of strongyloidiasis in non-endemic areas and reduce fatality.
Expression of Early Growth Responsive Gene-1 in The Visual Cortex of Monocular Form Deprivation Amblyopic Kittens
Authors: Fan Haobo , Wang Ying , Tang Xiuping , Yang Liyuan , Song Weiqi , Zou Yunchun 
Published: October 2021

Abstract
Purpose
The present study compared the expression of early growth responsive gene-1 (Egr-1) in visual cortex between amblyopia kittens and normal kittens, and to explore the role of Egr-1 in the pathogenesis of amblyopia.
Methods
A total of 20 healthy kittens were randomly divided into deprivation group and control group with 10 kittens in each group. Raised in natural light, and cover the right eye of the deprived kittens with a black opaque covering cloth. Pattern visual evoked potentials (PVEP) were measured before and at the 1st, 3rd and 5th week after covering in all kittens. After the last PVEP test, all kittens were killed. The expression of Egr-1 in the visual cortex of the two groups was compared by immunohistochemistry and in situ hybridization.
Results
PVEP detection showed that at age of 6 and 8 weeks, the P100 wave latency in the right eye of deprivation group was higher than that in the left eye of deprivation group (P < 0.05) and the right eye of control group (P < 0.05), while the amplitude decreased (P < 0.05). The number of positive cells (P < 0.05) and mean optical density (P < 0.05) of Egr-1 protein expression in visual cortex of 8-week-old deprivation group were lower than those of normal group, as well as the number (P < 0.05) and mean optical density of Egr-1 mRNA-positive cells (P < 0.05).
Conclusions
Monocular form deprivation amblyopia can lead to the decrease of Egr-1 protein and mRNA expression in visual cortex, and then promote the occurrence and development of amblyopia.
YOD1 Serves as a Potential Prognostic Biomarker For Pancreatic Cancer
Authors: Zhang Zhishuo , Zhao Wenxia , Li Yiming , Li Yang , Liu Yang , Liu Hao , Shao Rongguang 
Published: October 2021

Abstract
Background Ubiquitination is a basic post-translational modification of intracellular proteins and can be reversed enzymatically by DUBs (deubiquitinating enzymes). More than 90 DUBs have been identified. Among them, the deubiquitinating enzyme YOD1, a member of the ovarian tumor domain protease (OTUs) subfamily, is involved in the regulation of endoplasmic reticulum (ER)-related degradation pathways. In fact, it is reported that YOD1 is an important proliferation and metastasis-inducing gene, which can stimulate the characteristics of cancer stem cells and maintain circulating tumor cells (CTC). However, the expression level, prognostic effect, biological function and mechanism of YOD1 in pancreatic cancer are still unclear. ResultsIn the GEO and TCGA databases, YOD1 mRNA expression is significantly up-regulated in a variety of human pancreatic cancer tissues. Survival analysis showed that the up-regulation of YOD1 can predict poor prognosis of pancreatic cancer. Cox analysis showed that high YOD1 expression is an independent prognostic factor of pancreatic cancer. ROC analysis shows that YOD1 has significant diagnostic value. The immunohistochemistry (IHC) results showed that the protein expression level of YOD1 in pancreatic cancer tissue was higher than that in neighboring non-pancreatic cancer tissues (P<0.001). In addition, we found that YOD1 expression is negatively correlated with the infiltration level of CD8+ T cells, macrophages, neutrophils and dendritic cells (DC) in pancreatic cancer. The expression of YOD1 has a strong correlation with the different immune marker sets in PAAD. Co-expression network and functional enrichment analysis indicate that YOD1 may participate in the development of pancreatic cancer through cell adhesion molecules, p53, Hippo, TGF-β and other pathways. The experimental results of EDU, Transwell and Western blot indicate that YOD1 is highly expressed in pancreatic cancer cells and pancreatic cancer tissues, and its overexpression can promote the proliferation and metastasis of pancreatic cancer cells.Conclusion Our results indicate that YOD1 may be a useful biomarker for the prognosis of human pancreatic cancer, and it may also be a potential molecular target for the diagnosis and treatment of pancreatic cancer.
Hi-C-LSTM: Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of 3D genome conformation
Authors: Dsouza Kevin , Maslova Alexandra , Al-Jibury Ediem , Merkenschlager Matthias , Bhargava Vijay , Libbrecht Maxwell 
Published: October 2021

Abstract
Despite the availability of chromatin conformation capture experiments, discerning the relationship between the 1D genome and 3D conformation remains a challenge, which limits our understanding of their affect on gene expression and disease. We propose Hi-C-LSTM, a method that produces low-dimensional latent representations that summarize intra-chromosomal Hi-C contacts via a recurrent long short-term memory (LSTM) neural network model. We find that these representations contain all the information needed to recreate the original Hi-C matrix with high accuracy, outperforming existing methods. These representations enable the identification of a variety of conformation-defining genomic elements, including nuclear compartments and conformation-related transcription factors. They furthermore enable in-silico perturbation experiments that measure the influence of cis-regulatory elements on conformation.
Validation of Responsiveness of Physicians Scale (ROP-Scale) for Hospitalized COVID-19 Patients in Bangladesh
Authors: Joarder Taufique , Islam Mohammad Aminul , Islam Md Shariful , Mostari Shabnam , Hasan Md. Tanvir 
Published: October 2021

Abstract
BackgroundResponsiveness of Physicians (ROP) is defined as the social actions by physicians aimed at meeting the legitimate expectations of healthcare users. Even though patients’ expectations regarding ROP have increased during the COVID-19 pandemic, the psychometrically-validated ROP-Scale is difficult to apply in hospital settings. The goal of this study is to validate the existing ROP-Scale to measure the responsiveness of hospital physicians during the ongoing COVID-19 pandemic in Bangladesh.MethodsWe conducted a cross-sectional phone survey involving 213 COVID-19 hospital patients, randomly selected from the government database. We applied the Delphi method for content validity, exploratory factor analysis for construct validity, Cronbach's alpha and corrected item-total correlation for internal consistency reliability, and Pearson's correlation between the scale and overall patient satisfaction for concurrent validity.ResultsAfter removing survey items based on data sufficiency, collinearity, factor loading, and internal consistency, the final version of the COVID-19 ROP-Scale consisted of 12 items, grouped under Courteousness, Informativeness, Financial Sensitivity, and Treatment Provision Sensitivity domains. The scale was internally consistent, with a Cronbach's alpha coefficient of 0.83. The corrected item-total correlation ranged between 0.37 and 0.72. Concurrent validity was ascertained by the high correlation (0.78) between patient satisfaction and the COVID-19 ROP-Scale. Based on the median domain score, the highest- and the lowest-scoring responsiveness domain was 'Courteousness' (7.45) and 'Financial sensitivity' (1.85), respectively, whereas the highest- and the lowest-scoring item was 'Respect during the consultation' (8.16), and 'Providing treatment cost estimate before starting treatment' (1.78).ConclusionsThe 12-item COVID-19 ROP-Scale was demonstrated to be feasible, valid, and internally consistent. Therefore, at a time when many countries, including Bangladesh, have started experiencing new pandemic waves, its application can help amend past mistakes in health service provision and improve care for the hospitalised COVID-19 patients or other patients suffering from similar conditions. This study can contribute to the national decision-making regarding hospital care, open up further avenues in the health policy and system research, and eventually improve the quality of care provided to Bangladeshi patients seeking hospital services. Moreover, findings yielded by this study can be incorporated into doctors' medical education and in-service training.
Immune Features of COVID-19 Convalescent Individuals Revealed by a Single-cell RNA Sequencing
Authors: Zhao Pingsen , Zou Jiahua , Zhou Fan , Zhu Yanyan , Song Qibin , Yu Dongdong , Li Xiangpan 
Published: October 2021

Abstract
Background: The immune response to SARS-CoV-2 is critical in both controlling primary infection and preventing re-infection. However, it remains unclear whether immune responses following natural infection can be sustained or potentially prove critical for long-term immune protection against SARS-CoV-2 reinfection. Here, we systematically mapped the phenotypic landscape of SARS-CoV-2-specific immune responses in peripheral blood samples of 4 healthy donors and 13 convalescent patients with COVID-19, including moderate and severe cases, by single-cell RNA sequencing. Results: The relative percentage of the CD8+ effector memory subset was increased in both convalescent moderate and severe cases, but NKT-CD160 and maginal zone B clusters were decreased. Innate immune responses were attenuated reflected by decreased expression of genes involved in interferon-gamma, leukocyte migration and neutrophil mediated immune response in convalescent COVID-19 patients. Functions of T cell were strengthened in convalescent COVID-19 patients by clear endorsement of increased expression of genes involved in biological processes of regulation of T cell activation, differentiation and cell-cell adhesion. In addition, T cell mediated immune responses were enhanced with remarkable clonal expansions of TCR and increased transition of CD4+ effector memory and CD8+ effector-GNLY in severe subjects. B cell immune responses displayed sophisticated and dual functions during convalescence of COVID-19, providing a novel mechanism that B cell activation was observed especially in moderate while humoral immune response was weakened. Interestingly, HLA class I genes displayed downregulation while HLA class II genes upregulation in both T and B cell subsets in convalescent individuals. Notably, some unique IGV genes in severe patients may facilitate the design of vaccines. Conclusions: Our collective dataset showed that innate immunity was declined but SARS-CoV-2-specific T cell responses were retained even strengthened whereas sophisticated and dual functions of B cells, including declined humoral immunity were presented at several months following infections, which provided insights into evaluation of possibility of reinfection of exposed individuals with COVID-19 and facilitation to design of effective therapeutics and vaccines.
Nintedanib reduces corticosteroid resistance pulmonary fibrosis induced by bleomycin in mice by increasing the expression of β3 &amp; β6 integrins
Authors: alghamdi doha omar , Kawy Hala S Abdel , Damanhouri zuhair A 
Published: October 2021

Abstract
Background: Corticosteroid resistance pulmonary fibrosis is a major health problem. This study aimed to determine the effectiveness of nintedanib on corticosteroid resistance pulmonary fibrosis induced by bleomycin in mice. Methods: The mice were divided into five groups 12 mice each. control group, BLM group received single dose of bleomycin (BLM), BLM+MP group received BLM and methylprednisolone (MP), BLM+NIN group received BLM and nintedanib(NIN) and BLM + NIN + MP group. The lung tissues were obtained for biochemical analysis, gene expression and histopathological examination on day 7 and day 28. Results: after 7 days, both NIN groups showed a significant decrease in the levels of interleukin-2, interleukin-4, interferon-gamma, lung tumor necrosis factor-alpha, Malondialdehyde and lung water content with a significant increase in the Glutathione level in lung tissues compared to MP group. After 28 days, both NIN groups showed a significant reduction in hydroxyproline, and Trans-forming Growth Factor beta lung tissues contents compared to MP group, and they showed a positive effect on the expression of β 3 &β6 integrins compared to the negative effect of MP group. Histopathologically, both NIN groups showed significant improvement compared to MP group by H&E and Masson’s trichrome stains. Immunohistochemical staining revealed negative BCL-2 expression in the cytoplasm of bronchiolar epithelium in both NIN groups after 7 and 28 days of treatment. Lung tissue morphometric studies showed significant improvement of pathological changes induced by BLM in both NIN groups. Conclusions: Altogether, our data indicates that nintedanib overcame corticosteroid resistance pulmonary fibrosis induced by bleomycin.
DE-T1 On The Blastocyst Obtained Rate and Live Births Rates in Women Receiving IVF-ET Treatment
Authors: SHAO Hui , YAMAGUCHI Yoji , NOZAKI Toshiaki , BAI Li , DONG Xi , YANG Dongzi , JIAO Shuang , OTSUKI Junko , KOKEGUCHI Shoji , SHIOTANI Masahide 
Published: October 2021

Abstract
Background
Our objective was to retrospectively analyze the influence of DE-T1, a type of amino-polysaccharide extracted from dandelions, on the rates of blastocysts obtained and live births in women undergoing IVF-ET treatment.
Methods
This was a retrospective cohort study, conducting a total of 1014 patients over the age of 30, who received IVF treatment at Hanabusa Women’s clinic from Aug. 1, 2012 to Feb. 29, 2020. The patients were divided into two groups, based on their own choice regarding DE-T1 supplementation, which is available as over the counter medicine at the Clinic. The two groups’ overall rates of blastocysts obtained were compared and the rates of blastocysts obtained in patients with different ages and Anti-Mullerian hormone (AMH) levels were also compared using an Intention-to-treat (ITT) analysis. Among the patients who completed embryo transfers (ET), the live birth rate was compared between the supplementation group and the non-supplementation group using a Chi-squared test.
Results
The blastocyst obtained rate in the supplementation group was 75.98%, which was significantly higher than that of 57.28% in the non-supplementation group (P=2.4×109). The blastocyst obtained rate across the range of ages in the supplementation group were significantly higher than those of the non-supplementation group (≥30 and <35 years of age: 90.97% vs 74.32%, P=0.001;≥35 and <40 years of age: 82.40% vs 69.79%, P= 0.010; ≥40 and <43 years of age: 72.90% vs 52.11%, P=0.002; ≥43 years of age: 53.29% vs 22.95%, P= 5.7×105). The blastocyst obtained rate for both AMH levels in the supplementation group were significantly higher than those of the non-supplementation group (AMH≤1.1: 56.47% vs 40.44%, P=0.002; AMH> 1.1: 88.48% vs 71.08%, P=2.52×107). The live birth rate of the supplementation group was significantly higher than that of the non-supplementation group (57.53% vs. 40.0%, P=0.045).
Conclusion
DE-T1 supplementation might be an influence on improving the blastocyst obtained rate and live birth rates in women receiving IVF-ET treatment. DE-T1 supplementation might be of benefit to women of different ages and AMH levels.
Productivity Spillovers From Foreign Direct Investment To Ethiopian Manufacturing Sector
Authors: Wajebo Temesgen Woldamanuel 
Published: October 2021

Abstract
The study attempted to investigate productivity spillover from FDI to domestic firms in Ethiopian manufacturing industries. The analysis was conducted using panel data for the years 2011 up to 2016 on 260 large and medium scale-manufacturing firms deployed under 24 industries. The System Generalized Method of Moments (SYS-GMM) estimator was employed to conduct the analysis. Accordingly, the study found that a coexistence of both negative and positive effects from FDI through productivity spillover to domestically owned firms using absorptive capacity as determining factor of spillover occurrence in moderate level. Specifically, foreign presence in industry contributed a positive and significant horizontal and backward productivity spillover effect to domestic firms within the industry in average level. The horizontal productivity spillover transmitted to local firms through demonstration and competition effects in moderate level. Likewise, vertical productivity spillover occurred through the channel of sales of intermediate goods and services to foreign firms. Finally, we can conclude that technology gap is critical factor among those factors that determines the productivity spillover occurrence.