bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Vaccine Hesitancy Among Patients with Inflammatory Bowel Disease on Biologic Therapies; A cross-sectional study
Authors: Shehab Mohammad , Zurba Yasmin , Abdulsalam Ali Al , Alfadhli Ahmad , Elouali Sara 
Published: December 2021

AbstractBackgroundCOVID-19 Vaccinations have been shown to be effective in reducing risk of severe infection, hospitalization, and death. They also have been shown to be safe and effective in patients with inflammatory bowel disease (IBD) on biologic therapies. In this study, we aimed to evaluate the prevalence of vaccination among patients with IBD on biologic therapies.MethodsA single-center prospective cross-sectional study conducted at a tertiary care inflammatory bowel disease center. Data from patients with inflammatory bowel disease (IBD) who attended the gastroenterology infusion clinic from June 1st, 2021 until October 31st, 2021 were retrieved. Patients received infliximab or vedolizumab at least 6 weeks before recruitment were included. The primary outcome was prevalence of COVID-19 vaccination. The secondary outcome was to assess whether prevalence of COVID-19 vaccination differed based sex, age, type of biologic therapy and citizenship status.ResultsThe total number of inflammatory bowel disease (IBD) patients enrolled in the study was 280 (56.0% male and 44.0% female). The median age was 33.2 years and BMI was 24.8 kg/m2. 112 patients with ulcerative colitis (40.0%) and 168 (60.0%) with Crohn’s disease. 117 (41.8%) were vaccinated with either BNT162b2 or ChAdOx1 nCoV-19 and 163 (58.2%) were not vaccinated. Female patients were more likely to receive the vaccine compared to male patients (83.0% vs. 63.8%, p < 0.001). In addition, older patients (above the age 50) were also more likely to receive the vaccine than younger patients, below the age of 50 (95.6% vs 31.2% p< 0.001). Expatriates were more likely to receive the vaccine than citizens (84.8% vs 25.0%, p < 0.001). There was no statistical difference between patients on Infliximab and vedolizumab in terms of prevalence of vaccination (40.0% vs 48.0%, p= 0.34).ConclusionThe overall prevalence of COVID-19 vaccination among patients with inflammatory bowel disease (IBD) on biologic therapies was lower than the general population and world health organization (WHO) recommendation. Female patients, patients above the age of 50, and expatriates were more likely to be vaccinated. On the other hand, male patients, patients below the age of 50, and citizens were less likely to be vaccinated.
Differential effects of soil conservation practices on arthropods and crop yields
Authors: Lichtenberg Elinor M. , Milosavljević Ivan , Campbell Alistair J. , Crowder David W. 
Published: December 2021

AbstractMany agricultural management tactics, such as reduced tillage, aim to promote biodiversity and ecosystem services. Responses to such tactics can be context dependent, however, and differentially impact (i) functional groups of service-providing organisms and (ii) crop yields. In canola (Brassica napusL.,B. rapaL.) crop fields we assessed how soil tillage and landscape context (amount of semi-natural habitat within 1 km of each field) affected arthropod biodiversity and crop yield. We assessed effects of full (multiple tillage passes that leave soil surface bare), intermediate (tilled once and some stubble remains), or no (seed planted directly into last year’s stubble) tillage on functional groups with unique diets and reproductive strategies: (i) herbivores, (ii) kleptoparasites, (iii) parasitoids, (iv) pollinators, and (v) predators. Effects of tillage and landscape context on arthropod abundance and diversity varied across functional groups. Pollinators responded strongest to tillage, benefitting from intermediate tillage. Predators and herbivores responded strongly to landscape context, as both were more abundant in landscapes with more semi-natural habitat. Our results suggest natural history differences among functional groups mediate effects of landscape context on biodiversity. However, variation in arthropod communities had little effect on canola crop yield. The effects of soil management practices on aboveground arthropods are complex, and practices thought to increase some aspects of agricultural sustainability may not be beneficial in other contexts. Identifying practices such as intermediate tillage that may increase soil quality and arthropod diversity is a key to designing agricultural ecosystems that will effectively benefit both biodiversity and human well-being.
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
Authors: Cao Yunlong , Wang Jing , Jian Fanchong , Xiao Tianhe , Song Weiliang , Yisimayi Ayijiang , Huang Weijin , Li Qianqian , Wang Peng , An Ran , Wang Jing , Wang Yao , Niu Xiao , Yang Sijie , Liang Hui , Sun Haiyan , Li Tao , Yu Yuanling , Cui Qianqian , Liu Shuo , Yang Xiaodong , Du Shuo , Zhang Zhiying , Hao Xiaohua , Shao Fei , Jin Ronghua , Wang Xiangxi , Xiao Junyu , Wang Youchun , Xie Xiaoliang Sunney 
Published: December 2021

AbstractThe SARS-CoV-2 B.1.1.529 variant (Omicron) contains 15 mutations on the receptor-binding domain (RBD). How Omicron would evade RBD neutralizing antibodies (NAbs) requires immediate investigation. Here, we used high-throughput yeast display screening1,2 to determine the RBD escaping mutation profiles for 247 human anti-RBD NAbs and showed that the NAbs could be unsupervised clustered into six epitope groups (A-F), which is highly concordant with knowledge-based structural classifications3-5. Strikingly, various single mutations of Omicron could impair NAbs of different epitope groups. Specifically, NAbs in Group A-D, whose epitope overlap with ACE2-binding motif, are largely escaped by K417N, G446S, E484A, and Q493R. Group E (S309 site)6 and F (CR3022 site)7 NAbs, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but still, a subset of NAbs are escaped by G339D, N440K, and S371L. Furthermore, Omicron pseudovirus neutralization showed that single mutation tolerating NAbs could also be escaped due to multiple synergetic mutations on their epitopes. In total, over 85% of the tested NAbs are escaped by Omicron. Regarding NAb drugs, the neutralization potency of LY-CoV016/LY-CoV555, REGN10933/REGN10987, AZD1061/AZD8895, and BRII-196 were greatly reduced by Omicron, while VIR-7831 and DXP-604 still function at reduced efficacy. Together, data suggest Omicron would cause significant humoral immune evasion, while NAbs targeting the sarbecovirus conserved region remain most effective. Our results offer instructions for developing NAb drugs and vaccines against Omicron and future variants.
Telomere length sensitive regulation of Interleukin Receptor 1 type 1 (IL1R1) by the shelterin protein TRF2 modulates immune signalling in the tumour microenvironment
Authors: Mukherjee Ananda Kishore , Dutta Subhajit , Singh Ankita , Sharma Shalu , Roy Shuvra Shekhar , Sengupta Antara , Chatterjee Megha , Vinayagamurthy Soujanya , Bagri Sulochana , Khanna Divya , Verma Meenakshi , Soni Dristhi , Budharaja Anshul , Bhisade Sagar Kailasrao , Vivekanand  , Perwez Ahmad , George Nija , Faruq Mohammed , Gupta Ishaan , Sabarinathan Radhakrishnan , Chowdhury Shantanu 
Published: December 2021

AbstractTelomeres are crucial for cancer progression. Immune signalling in the tumour microenvironment has been shown to be very important in cancer prognosis. However, the mechanisms by which telomeres might affect tumour immune response remain poorly understood. Here, we observed that interleukin-1 signalling is telomere-length dependent in cancer cells. Mechanistically, non-telomeric TRF2 (Telomeric Repeat binding Factor 2) binding at the IL-1-receptor type-1 (IL1R1) promoter was found to be affected by telomere length. Enhanced TRF2 binding at theIL1R1promoter in cells with short telomeres directly recruited the histone-acetyl-transferase (HAT) p300, and consequent H3K27 acetylation activated IL1R1. This altered NF-kappa B signalling and affected downstream cytokines likeIL6, IL8andTNF. Further,IL1R1expression was telomere-sensitive in triple-negative breast cancer (TNBC) clinical samples. Infiltration of tumour-associated macrophages (TAM) was also sensitive to the length of tumour cell telomeres and highly correlated withIL1R1expression. The use of both IL1 Receptor antagonist (IL1RA) andIL1R1targeting ligands could abrogate M2 macrophage infiltration in TNBC tumour organoids. In summary, using TNBC cancer tissue (>90 patients), tumour-derived organoids, cancer cells and xenograft tumours with either long or short telomeres, we uncovered a heretofore undeciphered function of telomeres in modulating IL1 signalling and tumour immunity.
AMAW: automated gene annotation for non-model eukaryotic genomes
Authors: Meunier Loïc , Baurain Denis , Cornet Luc 
Published: December 2021

AbstractSummaryTo support small and large-scale genome annotation projects, we present AMAW (Automated MAKER2 Annotation Wrapper), a program devised to annotate non-model unicellular eukaryotic genomes by automating the acquisition of evidence data (transcripts and proteins) and facilitating the use of MAKER2, a widely adopted software suite for the annotation of eukaryotic genomes. Moreover, AMAW exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2.AvailabilityAMAW is released both as a Singularity container recipe and a standalone Perl script (https://bitbucket.org/phylogeno/amaw/).Contactlmeunier@uliege.be or luc.cornet@sciensano.beSupplementary informationSupplementary data are available at Bioinformatics online.
In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing
Authors: Bourgonje Arno R. , Andreu-Sánchez Sergio , Vogl Thomas , Hu Shixian , Vila Arnau Vich , Gacesa Ranko , Leviatan Sigal , Kurilshikov Alexander , Klompus Shelley , Kalka Iris N. , van Dullemen Hendrik M. , Weinberger Adina , Visschedijk Marijn C. , Festen Eleonora A. M. , Faber Klaas Nico , Wijmenga Cisca , Dijkstra Gerard , Segal Eran , Fu Jingyuan , Zhernakova Alexandra , Weersma Rinse K. 
Published: December 2021

SummaryInflammatory bowel diseases (IBD), e.g. Crohn’s disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. We leveraged a high-throughput phage-displayed immunoprecipitation sequencing (PhIP-seq) workflow to identify antibodies against 344,000 antimicrobial, immune and food antigens in 497 IBD patients as compared to 1,326 controls. IBD was characterized by 373 differentially abundant antibodies (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD and 28% unique to UC. Antibodies against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (AUC=0.89), and similar discrimination was achieved when using only ten antibodies (AUC=0.87). IBD patients thus show a distinct antibody repertoire against selected peptides, allowing patient stratification and discovery of immunological targets.
LitRev: A data driven method for quick literature review from PubMed
Authors: Das Gourab 
Published: December 2021

ABSTRACTSummaryLitRev is a novel robust data driven approach, developed for quick literature review on a particular topic of interest. This method identifies common biological phrases that follow a power law distribution and important phrases which have the normalized point wise mutual information score greater than zero.Contactgourabdas0727@gmail.com
Stranded abroad during the COVID-19 pandemic: examining the psychological and financial impact of border restrictions
Authors: McDermid Pippa , Craig Adam , Sheel Meru , Blazek Katrina , Talty Siobhan , Seale Holly 
Published: December 2021

ABSTRACTObjectiveWith the easing of COVID-19-related international travel restrictions in late 2021 it is time to consider the direct and indirect social, emotional, and financial impacts that these border closures have had. The study aims to evaluate the psychological and financial distress reported by people stranded abroad due to international travel restrictions introduced in response to the COVID-19 pandemic.MethodsBetween July and September 2021, we implemented a cross-sectional online survey targeting individuals stranded abroad due to international travel restrictions. The survey collected data about COVID-19 travel restriction-related travel impacts; personal stress, anxiety, and depression (using the validated DASS-21tool); as well as impacts on housing and financial security; and demographic data.FindingsWe had 1054 participants complete the survey; most were trying to return to the Oceania region (75.4%), with 45% stranded in Europe. Overall, 64.2% reported financial distress while stranded abroad. 64.4% (x̄ =9.43, SD=5.81) reported either a moderate or severe (based on the DASS-21 classification) level of depression, 41.7% for anxiety (x̄ =5.46, SD=4.74), and 58.1% for stress (x̄ =10.64, SD=5.26). Statistically significant factors associated with moderate to extremely severe depression, anxiety, and stress were financial stress, an employment change, being <30yrs, having a high perceived risk of contracting COVID-19 abroad and being stranded for >2 months.ConclusionThe study is among the first to explore the psychological and financial distress-related impacts associated with being stranded abroad due to COVID-19 travel restrictions. It highlights a range of unintended consequences that arise from pandemic-related travel restriction, identifies the health and social needs for a particularly vulnerable population, and provides clues as to the types of support that may be adopted to best support them. This research will assist policymakers in identifying support packages for people stranded abroad due to global disaster.
Trust in the scientific research community predicts intent to comply with COVID-19 prevention measures: An analysis of a large-scale international survey dataset
Authors: Han Hyemin 
Published: December 2021

AbstractIn the present study, I explored the relationship between people’s trust in different agents related to prevention of spread of COVID-19 and their compliance with pharmaceutical and non-pharmaceutical preventive measures. The COVIDiSTRESSII Global Survey dataset, which was collected from international samples, was analysed to examine the aforementioned relationship across different countries. For data-driven exploration, network analysis and Bayesian generalized linear model (GLM) analysis were performed. The result from network analysis demonstrated that trust in the scientific research community was most central in the network of trust and compliance. In addition, the outcome from Bayesian GLM analysis indicated that the same factor, trust in the scientific research community, was most fundamental in predicting participants’ intent to comply with both pharmaceutical and non-pharmaceutical preventive measures. I briefly discussed the implications of the findings, the importance of trust in the scientific research community in explaining people’s compliance with measure to prevent spread of COVID-19.
Measurement of SARS-CoV-2 antigens in plasma of pediatric patients with acute COVID-19 or MIS-C using an ultrasensitive and quantitative immunoassay
Authors: Sigal George B. , Novak Tanya , Mathew Anu , Chou Janet , Zhang Yubo , Manjula Navaratnam , Bathala Predeepthi , Joe Jessica , Padmanabhan Nikhil , Romero Daniel , Allegri-Machado Gabriella , Joerger Jill , Loftis Laura L. , Schwartz Stephanie P. , Walker Tracie C. , Fitzgerald Julie C. , Tarquinio Keiko M. , Zinter Matt S. , Schuster Jennifer E. , Halasa Natasha B. , Cullimore Melissa L. , Maddux Aline B. , Staat Mary A. , Irby Katherine , Flori Heidi R. , Coates Bria M. , Crandall Hillary , Gertz Shira J. , Randolph Adrienne G. , Pollock Nira R. 
Published: December 2021

AbstractBackgroundDetection of SARS-CoV-2 antigens in blood has high sensitivity in adults with acute COVID-19, but sensitivity in pediatric patients is unclear. Recent data suggest that persistent SARS-CoV-2 spike antigenemia may contribute to multisystem inflammatory syndrome in children (MIS-C). We quantified SARS-CoV-2 nucleocapsid (N) and spike (S) antigens in blood of pediatric patients with either acute COVID-19 or MIS-C using ultrasensitive immunoassays (Meso Scale Discovery).MethodsPlasma was collected from inpatients (<21 years) enrolled across 15 hospitals in 15 US states. Acute COVID-19 patients (n=36) had a range of disease severity and positive nasopharyngeal SARS-CoV-2 RT-PCR within 24 hours of blood collection. Patients with MIS-C (n=53) met CDC criteria and tested positive for SARS-CoV-2 (RT-PCR or serology). Controls were patients pre-COVID-19 (n=67) or within 24h of negative RT-PCR (n=43).ResultsSpecificities of N and S assays were 95-97% and 100%, respectively. In acute COVID-19 patients, N/S plasma assays had 89%/64% sensitivity, respectively; sensitivity in patients with concurrent nasopharyngeal swab cycle threshold (Ct) ≤ 35 were 93%/63%. Antigen concentrations ranged from 1.28-3,844 pg/mL (N) and 1.65-1,071 pg/mL (S) and correlated with disease severity. In MIS-C, antigens were detected in 3/53 (5.7%) samples (3 N-positive: 1.7, 1.9, 121.1 pg/mL; 1 S-positive: 2.3 pg/mL); the patient with highest N had positive nasopharyngeal RT-PCR (Ct 22.3) concurrent with blood draw.ConclusionsUltrasensitive blood SARS-CoV-2 antigen measurement has high diagnostic yield in children with acute COVID-19. Antigens were undetectable in most MIS-C patients, suggesting that persistent antigenemia is not a common contributor to MIS-C pathogenesis.Key pointsIn a U.S. pediatric cohort tested with ultrasensitive immunoassays, SARS-CoV-2 nucleocapsid antigens were detectable in most patients with acute COVID-19, and spike antigens were commonly detectable. Both antigens were undetectable in almost all MIS-C patients.
Empowering Engineered Muscle Function by Extending Connexin 43 Duration with Reduced Graphene Oxides
Authors: Ko Eunkyung , Aydin Onur , Li Zhengwei , Gapinske Lauren , Huang Kai-Yu , Saif Taher , Bashir Rashid , Kong Hyunjoon 
Published: December 2021

ABSTRACTEngineered skeletal muscle act as therapeutics invaluable to treat injured or diseased muscle and a “living” material essential to assemble biological machinery. For normal development, skeletal myoblasts should express connexin 43, one of the gap junction proteins that promote myoblast fusion and myogenesis, during the early differentiation stage. However, myoblasts cultured in vitro often down-regulate connexin 43 before differentiation, limiting myogenesis and muscle contraction. This study demonstrates that tethering myoblasts with reduced graphene oxide (rGO) slows connexin 43 regression during early differentiation and increases myogenic mRNA synthesis. The whole RNA sequencing also confirms that the rGO on cells increases regulator genes for myogenesis, including troponin, while decreasing negative regulator genes. The resulting myotubes generated a three-fold larger contraction force than the rGO-free myotubes. Accordingly, a valveless biohybrid pump assembled with the rGO-tethered muscle increased the fluid velocity and flow rate considerably. The results of this study would provide an important foundation for developing physiologically relevant muscle and powering up biomachines that will be used for various bioscience studies and unexplored applications.
Early neural activity changes associated with visual conscious perception
Authors: Khalaf Aya , Kronemer Sharif I. , Christison-Lagay Kate , Kwon Hunki , Li Jiajia , Wu Kun , Blumenfeld Hal 
Published: December 2021

AbstractThe neural mechanisms of visual conscious perception have been investigated for decades. However, the spatiotemporal dynamics associated with the earliest neural responses following consciously perceived stimuli are still poorly understood. Using a dataset of intracranial EEG recordings, the current study aims to investigate the neural activity changes associated with the earliest stages of visual conscious perception. Subjects (N=10, 1,693 grey matter electrode contacts) completed a continuous performance task in which individual letters were presented in series and subjects were asked to press a button when they saw a target letter. Broadband gamma power (40-115Hz) dynamics were analyzed in comparison to baseline prior to stimulus and contrasted for target trials with button presses and non-target trials without button presses. Regardless of event type, we observed early gamma power changes within 30-150 ms from stimulus onset in a network including increases in bilateral occipital, fusiform, frontal (including frontal eye fields), and medial temporal cortex, increases in left lateral parietal-temporal cortex, and decreases in the right anterior medial occipital cortex. No significant differences were observed between target and non-target stimuli until >150 ms post-stimulus, when we saw greater gamma power increases in left motor and premotor areas, suggesting a possible role of these later signals in perceptual decision making and/or motor responses with the right hand. The early gamma power findings suggest a broadly distributed cortical visual detection network that is engaged at early times tens of milliseconds after signal transduction from the retina.