Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of hub genes associated with cognition in the hippocampus of Alzheimer’s Disease

ABSTRACT Alzheimer’s Disease (AD) is a neurodegenerative disease featured by cognitive impairment. This bioinformatic analysis was used to identify hub genes related to cognitive dysfunction in AD. The gene expression profile GSE48350 in the hippocampus of AD patients aged >70 years was obtained from the Gene Expression Omnibus (GEO) database. A total of 96 differentially expressed genes (DEGs) were identified, and subjected to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses; a protein–protein interaction (PPI) network was constructed. The DEGs were enriched in synapse-related changes. A protein cluster was teased out of PPI. Furthermore, the cognition ranked the first among all the terms of biological process (BP). Next, 4 of 10 hub genes enriched in cognition were identified. The function of these genes was validated using APP/PS1 mice. Cognitive performance was validated by Morris Water Maze (MWM), and gene expression by RT-qPCR, Cholecystokinin (CCK), Tachykinin precursor 1 (TAC1), Calbindin 1 (CALB1) were downregulated in the hippocampus. These genes can provide new directions in the research of the molecular mechanism of AD.
Reduced mortality during the COVID-19 outbreak in Japan, 2020: a two-stage interrupted time-series design

Abstract Background Coronavirus disease 2019 (COVID-19) continues to be a major global health burden. This study aims to estimate the all-cause excess mortality occurring in the COVID-19 outbreak in Japan, 2020, by sex and age group. Methods Daily time series of mortality for the period January 2015–December 2020 in all 47 prefectures of Japan were obtained from the Ministry of Health, Labour and Welfare, Japan. A two-stage interrupted time-series design was used to calculate excess mortality. In the first stage, we estimated excess mortality by prefecture using quasi-Poisson regression models in combination with distributed lag non-linear models, adjusting for seasonal and long-term variations, weather conditions and influenza activity. In the second stage, we used a random-effects multivariate meta-analysis to synthesize prefecture-specific estimates at the nationwide level. Results In 2020, we estimated an all-cause excess mortality of −20 982 deaths [95% empirical confidence intervals (eCI): −38 367 to −5472] in Japan, which corresponded to a percentage excess of −1.7% (95% eCI: −3.1 to −0.5) relative to the expected value. Reduced deaths were observed for both sexes and in all age groups except those aged <60 and 70–79 years. Conclusions All-cause mortality during the COVID-19 outbreak in Japan in 2020 was decreased compared with a historical baseline. Further evaluation of cause-specific excess mortality is warranted.
Prevalence of sensitization to specific allergens in allergic patients in Beijing, China: A 7-year retrospective study.

BACKGROUND Knowledge of the prevalence of common sensitizing allergens may aid in overall management of allergic disease in a specified area. OBJECTIVE The aim of this study was to identify and analyse the prevalence of common inhaled and food sensitizing allergens in Beijing. METHODS This was a retrospective study, analysing demographic data and serum sIgE antibody test results from 59057 outpatients who presented to Beijing TongRen Hospital, from January 2013 to December 2019. RESULTS 28879 patients (48.9%) showed positive sIgE test results; with significantly more males aged under 16 years sensitized to at least one allergen than females, and most patients (53.62%) were sensitized to multiple allergens. The first inhaled sensitizing allergens was Artemisia grass (11910 (41.24%)); and the first food allergens was crab (3547 (12.28%)). For Artemisia sensitized patients, sIgE levels were mostly at level 5. The number of patients with ragweed allergy is increasing year by year. The detection rates for sIgE to Artemisia, common ragweed, and Humulus grass allergens were significantly higher in August and September. R package ggplot2 analysis, demonstrated strong correlations between tree allergens and common ragweed and Humulus grass allergens (phi coefficients = 0.50 and 0.46, respectively; both P < 0.01). CONCLUSIONS The prevalence of sensitization to different allergens in Beijing showed Artemisia grass was the most commonly inhaled sensitizing allergen, and the number of patients with ragweed grass allergy was increasing by year.
COVID-19 and Outcomes in Patients With Inflammatory Bowel Disease: Systematic Review and Meta-Analysis

Abstract Background Our understanding of coronavirus disease 2019 (COVID-19) and its implications for patients with inflammatory bowel diseases (IBD) is rapidly evolving. We performed a systematic review and meta-analysis to investigate the epidemiology, clinical characteristics, and outcomes in IBD patients with COVID-19. Methods We searched PubMed, EMBASE, Cochrane Central, Clinicaltrials.gov, Web of Science, MedRxiv, and Google Scholar from inception through October 2020. We included studies with IBD patients and confirmed COVID-19. Data were collected on the prevalence, patient characteristics, pre-infection treatments for IBD, comorbidities, hospitalization, intensive care unit (ICU), admission, and death. Results Twenty-three studies with 51,643 IBD patients and 1449 with COVID-19 met our inclusion criteria. In 14 studies (n = 50,706) that included IBD patients with and without COVID-19, the prevalence of infection was 1.01% (95% confidence interval [CI], 0.92-1.10). Of IBD patients with COVID-19, 52.7% had Crohn’s disease, 42.2% had ulcerative colitis, and 5.1% had indeterminate colitis. Nine studies (n = 687) reported outcomes according to IBD therapy received. Compared with patients on corticosteroids, those on antitumor necrosis factor (anti-TNF) therapy had a lower risk of hospitalization (risk ratio [RR], 0.24; 95% CI, 0.16-0.35; P < .01; I2 = 0%) and ICU admission (RR, 0.10; 95% CI, 0.03-0.37; P < .01) but not death (RR, 0.16; 95% CI, 0.02-1.71; P = .13; I2 = 39%). Compared with patients on mesalamine, those on antitumor necrosis factor therapy had a lower risk of hospitalizations (RR, 0.37; 95% CI, 0.25-0.54), ICU admissions (RR, 0.20; 95% CI, 0.07-0.58), and death (0.21; 95% CI, 0.04-1.00). Comparing patients on immunomodulators vs mesalamine or anti-TNF therapy, there was no difference in these outcomes. Conclusions The prevalence of COVID-19 in IBD patients was low. Use of corticosteroids or mesalamine was significantly associated with worse outcomes, whereas use of anti-TNFs was associated with more favorable outcomes. Further investigation clarifying the mechanisms of these disparate observations could help identify risk and adverse outcome-mitigating strategies for patients with IBD.
Stimulation Pattern Efficiency in Percutaneous Auricular Vagus Nerve Stimulation: Experimental Versus Numerical Data

Objective: Percutaneous electrical stimulation of the auricular vagus nerve (pVNS) is an electroceutical technology. The selection of stimulation patterns is empirical, which may lead to under-stimulation or over-stimulation. The objective is to assess the efficiency of different stimulation patterns with respect to individual perception and to compare it with numerical data based on in-silico ear models. Methods: Monophasic (MS), biphasic (BS) and triphasic stimulation (TS) patterns were tested in volunteers. Different clinically-relevant perception levels were assessed. In-silico models of the human ear were created with embedded fibers and vessels to assess different excitation levels. Results: TS indicates experimental superiority over BS which is superior to MS while reaching different perception levels. TS requires about 57% and 35% of BS and MS magnitude, respectively, to reach the comfortable perception. Experimental thresholds decrease from non-bursted to bursted stimulation. Numerical results indicate a slight superiority of BS and TS over MS while reaching different excitation levels, whereas the burst length has no influence. TS yields the highest number of asynchronous action impulses per stimulation symbol for the used tripolar electrode set-up. Conclusion: The comparison of experimental and numerical data favors the novel TS pattern. The analysis separates excitatory pVNS effects in the auricular periphery, as accounted by in-silico data, from the combination of peripheral and central pVNS effects in the brain, as accounted by experimental data. Significance: The proposed approach moves from an empirical selection of stimulation patterns towards efficient and optimized pVNS settings.
Does Sleep Apnea Affect the Outcome of Stroke Patients?

BACKGROUND Sleep apnea is described as an isolated risk factor for stroke or recurrent stroke which could be cause of death. In our study, the aim was to determine whether sleep apnea affects the outcome of stroke patients. SUBJECTS AND METHODS This is a prospective study in which a group of 110 patients in the acute phase of a stroke was evaluated sleep apnea. Acute stroke has been diagnosed either by computed tomography and magnetic resonance imaging of the brain. There was no significant difference in patient's age with or without sleep apnea neither in men nor women. Neurological, neuropsychiatric, pulmonary test were performed in all patients at five different time periods. In these time periods, all patients were evaluated: Glasgow scale, The American National Institutes of Health Scale Assessment, Mini Mental Test, The Sleep and snoring Questionnaire Test, The Berlin Questionnaire Test, The Epworth Sleepiness Scale, The Stanford Sleepiness Scale and The general sleep questionnaire. RESULTS One year after the onset of stroke, 91 (82.7%) of 110 patients with apnea survived. The survival rate of patients with sleep apnea is significantly lower than without sleep apnea (p=0.01). In men with apnea, the survival rate was significantly lower in patients without apnea (p=0.004). The largest number of survivors of apnea had diabetes mellitus, followed by survival of patients with heart disease, body mass index >29 kg/m2 and hypertension, with hyperlipoproteinemia and smoking. The highest number of survivors without apnea was body mass index >29 kg/m2, followed by survival of patients with hyperlipoproteinemia, heart disease, hypertension, smoking, and diabetes mellitus. CONCLUSION Patients with sleep apnea have a significant correlation in survival rates compared with sexually and age-matched subjects, associated with concomitant risk factors such as hypertension, body mass index, and smoking.
A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19

Abstract Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, over 100 million people have been infected by COVID-19, millions of whom have died. In the latest year, a large number of omics data have sprung up and helped researchers broadly study the sequence, chemical structure and function of SARS-CoV-2, as well as molecular abnormal mechanisms of COVID-19 patients. Though some successes have been achieved in these areas, it is necessary to analyze and mine omics data for comprehensively understanding SARS-CoV-2 and COVID-19. Hence, we reviewed the current advantages and limitations of the integration of omics data herein. Firstly, we sorted out the sequence resources and database resources of SARS-CoV-2, including protein chemical structure, potential drug information and research literature resources. Next, we collected omics data of the COVID-19 hosts, including genomics, transcriptomics, microbiology and potential drug information data. And subsequently, based on the integration of omics data, we summarized the existing data analysis methods and the related research results of COVID-19 multi-omics data in recent years. Finally, we put forward SARS-CoV-2 (COVID-19) multi-omics data integration research direction and gave a case study to mine deeper for the disease mechanisms of COVID-19.
The effects of rumination on internalising symptoms in the context of the COVID-19 pandemic among mothers and their offspring: a brief report

ABSTRACT As a result of the novel coronavirus (COVID-19) pandemic, anxiety and depressive symptoms have risen among children and adults. However, it remains unclear why the effects of the pandemic are so salient for certain individuals. This study examined rumination, a well-established risk factor for internalising disorders, as a predictor of prospective increases in anxiety and depression symptoms in mothers and their offspring. Change in rumination during the pandemic was also examined as a predictor of symptom transmission at the dyadic level. Fifty-three biological mother–child dyads were recruited from two longitudinal studies that had completed their respective baselines prior to the COVID-19 pandemic. Mothers and youth (ages 9–15 years, 77.4% female) completed measures of depression and anxiety symptoms and rumination before and during the pandemic. Results revealed baseline rumination was positively associated with internalising symptom changes for mothers, but not youth. Moreover, pre-to-peri pandemic changes in rumination were associated with prospective increases in mother and youth internalising symptoms. Finally, results revealed a significant correlation for pre-to-peri pandemic depressive symptom change among mothers and youth; however, rumination did not mediate this association. Findings highlight changes in rumination as a potential mechanism for internalising symptom risk during the COVID-19 pandemic across development.
Chronic inflammatory demyelinating polyneuropathy in Spain: a retrospective analysis of hospital incidence and medical costs

ABSTRACT Background Chronic inflammatory demyelinating polyneuropathy (CIDP) is a rare disorder that usually involves long-term impairment. Despite the chronic health-care needs that are often associated, research evaluating the economic burden of this disorder is still scarce. This study aimed to assess the characteristics of patients admitted with CIDP in Spanish hospitals and to determine the associated medical costs. Methods A retrospective multicenter study was designed analyzing records of hospital and ambulatory visits of patients with CIDP in Spanish hospitals between 2004 and 2018. Medical costs registered in hospital facilities were evaluated. Results Admission files corresponding to 2805 patients diagnosed with CIDP were extracted from the database: 64.7% of patients were males, and median age was 60 years. Patients presented comorbidities that included essential hypertension, hypercholesterolemia, and diabetes mellitus. The raw number of admissions for CIDP increased significantly over the study period, similarly to mean admission costs for all age groups. Consequently, total hospital medical costs associated with CIDP increased over the study period. The mean medical cost per admission was €3953. Conclusions The increasing number of hospital cases of CIDP is associated with rising medical costs. Further research will be required to fully evaluate the medical and societal burdens of this disorder.
MVIP: multi-omics portal of viral infection

Abstract Virus infections are huge threats to living organisms and cause many diseases, such as COVID-19 caused by SARS-CoV-2, which has led to millions of deaths. To develop effective strategies to control viral infection, we need to understand its molecular events in host cells. Virus related functional genomic datasets are growing rapidly, however, an integrative platform for systematically investigating host responses to viruses is missing. Here, we developed a user-friendly multi-omics portal of viral infection named as MVIP (https://mvip.whu.edu.cn/). We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc. We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc. In addition, we integrated these genome-wide signals into customized genome browsers, and developed multiple dynamic charts to exhibit the information, such as time-course dynamic and differential gene expression profiles, alternative splicing changes and enriched GO/KEGG terms. Furthermore, we implemented several tools for efficiently mining the virus-host interactions by virus, host and genes. MVIP would help users to retrieve large-scale functional information and promote the understanding of virus-host interactions.
Use of Social Media as a Platform for Education and Support for People With Diabetes During a Global Pandemic

Background: Patient education is a fundamental aspect of self-management of diabetes. The aim of this study was to understand whether a social media platform is a viable method to deliver education to people with diabetes and understand if people would engage and interact with it. Methods: Education sessions were provided via 3 platforms in a variety of formats. “Tweetorials” and quizzes were delivered on the diabetes101 Twitter account, a virtual conference via Zoom and video presentations uploaded to YouTube. Audience engagement during and after the sessions were analyzed using social media metrics including impressions and engagement rate using Twitter analytics, Tweepsmap, and YouTube Studio. Results: A total of 22 “tweetorial” sessions and 5 quizzes with a total of 151 polls (both in tweetorial and quiz sessions) receiving a total of 21,269 votes took place. Overall, the 1-h tweetorial sessions gained 1,821,088 impressions with an engagement rate of 6.3%. The sessions received a total of 2,341 retweets, 2,467 replies and 10,060 likes. The quiz days included 113 polls receiving 16,069 votes. The conference covered 8 topics and was attended live by over 100 people on the day. The video presentations on YouTube have received a total of 2,916 views with a watch time of 281 h and 8,847 impressions. Conclusion: Despite the limitations of social media, it can be harnessed to provide relevant reliable information and education about diabetes allowing people the time and space to learn at their own pace.
Similarity-Based Analysis of Allele Frequency Distribution among Multiple Populations Identifies Adaptive Genomic Structural Variants

Abstract Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip

Abstract Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence–structure–stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.
Analysis of immune-related key genes in Alzheimer’s disease

ABSTRACT This research revealed that 15 modules were obtained through weighted gene co-expression network analysis, among which the magenta and blue modules were significantly associated with Alzheimer’s Disease (AD). There were 121 genes in the magenta module and 1022 genes in the blue module. Through differently expressed genes analysis, significant differences were shown in 134 genes (88 were up-regulated and 46 were down-regulated). 34 immune-key genes were obtained after three types of genes were crossed. Functional enrichment analysis showed that genes were mainly enriched in cytokine receptor activity and immune receptor activity. Through protein–protein interaction (PPI) network analysis, 10 hub genes were obtained: SERPINE1, ZBTB16, CD44, BCL6, HMOX1, SLC11A1, CEACAM8, ITGA5, SOCS3, and IL4R. Through immune-infiltration analysis, significant differences were demonstrated in four immune cells: CD8 + T cells, resting NK cells, M2 macrophages, and activated dendritic cells, and a significant positive correlation was shown between CD8 + T cells and macrophages M2, or between the other two cells. CEACAM8 was positively correlated with CD8 + T cells and macrophages M2, and negatively correlated with the other two cells while the remaining nine genes showed the opposite. Receiver operating characteristic (ROC) curve analysis demonstrated that both the differential immune cells and 10 hub genes had good diagnostic values. In GSE122063, the hub genes were verified and BCL6, CD44, HMOX1, IL4R, ITGA5, and SOCS3 were up-regulated. Meanwhile, hub genes was up-regulated in the brain tissues of AD rats. This study is of great significance for the diagnosis and therapy of AD.
Characterizing the cortical pathways underlying visual trigger induced urinary urgency incontinence by functional MRI

Visual triggers have long been recognized clinically to stimulate urgency urinary incontinence (UUI). Current pathophysiology recognizes the importance of cortical control over micturition but there is no standardized methodology for clinicians to study the impact of visual triggers. Our aim was to develop an imaging protocol able to characterize the brain's response to personalized visual triggers, providing a methodology for evaluation on connectivity within the brain in patients with visually triggered urinary urgency.