bluuebunny/crossref_metadata_2025_split huggingface dataset:
A RCT of a third dose CoronaVac or BNT162b2 vaccine in adults with two doses of CoronaVac
Authors: Pun Mok Chris Ka , Cheng Samuel M.S. , Chen Chunke , Yiu Karen , Chan Tat-On , Lai Kiu Cheung , Ling Kwun Cheung , Sun Yuanxin , Ho Lun Lai , Peiris Malik , Hui David S 
Published: November 2021

AbstractBackgroundPoor immunogenicity and antibody waning were found in vaccinees of CoronaVac. There is lack of randomized controlled trial (RCT) data to compare the immunogenicity and safety of schedules using homologous and heterologous vaccine as a booster dose.MethodsWe randomly assigned adults who had received 2 doses of CoronaVac with low antibody response to receive an additional booster dose of either BNT162b2 or CoronaVac. The local and systemic adverse reactions were recorded. Levels of SARS-CoV-2 neutralizing and spike binding antibody in plasma were measured.FindingsAt one month after the third dose of vaccine, BNT162b2 vaccines elicited significantly higher surrogate virus neutralizing test (sVNT), spike receptor binding, spike N terminal domain binding, spike S2 domain binding levels than CoronaVac. More participants from the BNT162b2 group reported injection site pain and swelling as well as fatigue and muscle pain than those who received CoronaVac as the third dose. The mean results of the sVNT against the wild type, beta, gamma and delta variants in the BNT162b2 boosted group was 96.83%, 92.29%, 92.51% and 95.33% respectively which were significantly higher than the CoronaVac boosted group (Wild type: 57.75%; Beta: 38.79 %; Gamma: 32.22%; Delta: 48.87%)ConclusionOur RCT study shows that BNT162b2 booster dose for those people who poorly responded to the previous vaccination of CoronaVac is significantly more immunogenic than a CoronaVac booster. BNT162b2 also elicits higher levels of SARS-CoV-2 specific neutralizing antibodies to different variants of concern. The adverse reactions were only mild and short-lived.At a Glance CommentaryScientific Knowledge on the SubjectPoor immunogenicity and antibody waning were found in vaccinees of CoronaVac. There is lack of randomized controlled trial (RCT) data to compare the immunogenicity and safety of schedules using homologous and heterologous vaccine as a booster dose.What This Study Adds to the FieldOur RCT study shows that BNT162b2 booster dose for those people who poorly responded to the previous vaccination of CoronaVac is significantly more immunogenic than a CoronaVac booster. The adverse reactions were only mild and short-lived.
Comprehensive RNA-Seq Reveals Molecular Changes in Kidney Malignancy Among People Living with HIV
Authors: Bao Juan , Ye Jianqing , Xu Jingjing , Liu Shanshan , Wang Lin , Li Zehuan , Li Qiuyue , Liu Feng , He Xiaomeng , Zou Heng , Feng Yanling , Corpe Christopher , Zhang Xiaoyan , Xu Jianqing , Zhu Tongyu , Wang Jin 
Published: November 2021

AbstractBackgroundMalignancy of the kidney is a rapidly progressive kidney disease and a major source of morbidity and mortality among people living with HIV (PLWH). Patients with HIV-associated kidey cancer experience higher cancer-specific mortality than the general population, and its mechanism remains poorly understood.MethodsTo heighten the awareness of kidney malignancy in patients with HIV infection to facilitate the early diagnosis of kidney cancer, we identified 2460 protein-coding transcripts in HIV-associated kidney cancer using comprehensive RNA sequencing (RNA-seq).ResultsKISS1R, CAIX, and NPTX2 mRNA expression levels were specifically increased in HIV-associated kidney cancer, and UMOD and TMEM213 mRNA were decreased in most cases based on real-time PCR analyses. These findings were similar to those noted for the general population with renal cell carcinoma. Immunohistochemical staining analysis also showed that a total of 16 of 18 kidney malignant cases among PLWH exhibited positive staining for KISS1R and CAIX.ConclusionPathway analysis of the differentially expressed mRNAs in HIV-associated kidney cancer revealed that several key pathways were involved, including voltage-gated chloride channel activity, distal tubule development, collecting duct development, fructose metabolic processes, and negative regulation of lipase activity. The identified molecular changes in kidney malignancy may offer a helpful explanation for cancer progression and open up new therapeutic avenues that may decrease mortality after a cancer diagnosis among PLWH.
Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas
Authors: Harpaz Nofar , Mittelman Tamir , Beresh Olga , Griess Ofir , Furth Noa , Salame Tomer-Meir , Oren Roni , Fellus-Alyagor Liat , Harmelin Alon , Alexandrescu Sanda , Marques Joana Graca , Filbin Mariella G. , Ron Guy , Shema Efrat 
Published: November 2021

SummaryCancer cells are highly heterogeneous at the transcriptional level and in their epigenetic state. Methods to study epigenetic heterogeneity are limited in throughput and information obtained per cell. Here, we adapted Cytometry by Time of Flight (CyTOF) to analyze a wide panel of histone modifications in primary tumor-derived lines of Diffused Intrinsic Pontine Glioma (DIPG). DIPG is a lethal glioma, driven by histone H3 lysine 27 mutation (H3-K27M). We identified two epigenetically distinct subpopulations in DIGP, reflecting inherent heterogeneity in expression of the mutant histone. These two subpopulations are robust across tumor lines derived from different patients and show differential proliferation capacity and expression of stem-cell and differentiation markers. Moreover, we demonstrate the use of this high-dimensional data to elucidate potential interactions between histone modifications and epigenetic alterations during the cell-cycle. Our work establishes new concepts for the analysis of epigenetic heterogeneity in cancer that could be applied to diverse biological systems.
Pseudomonas zeiradicisfrom corn andPseudomonas soyaefrom soybean, two newPseudomonasspecies and endophytes from agricultural crops
Authors: Lemaire Jacqueline , Seaton Sarah , Inderbitzin Patrik , Trujillo Martha E. 
Published: November 2021

ABSTRACTTwo novelPseudomonasspecies associated with healthy plants and other habitats are described from the United States. They arePseudomonas zeiradicisstrain PI116 from corn in Missouri, compost from Massachusetts, urban soil from Iowa and water of Lake Erie; andPseudomonas soyaestrain JL117 from soybean in Indiana and Wisconsin, and soil in Wyoming. No plant pathogenic strains are known for any of the novel species based on genome comparisons to assemblies in GenBank.
The role of the gut microbiota in the effects of early-life stress and dietary fatty acids on later-life central and metabolic outcomes in mice
Authors: Reemst Kitty , Tims Sebastian , Yam Kit-Yi , Mischke Mona , Knol Jan , Brul Stanley , Schipper Lidewij , Korosi Aniko 
Published: November 2021

AbstractEarly-life stress (ELS) leads to increased vulnerability for mental and metabolic disorders. We have previously shown that dietary low ω-6/ω-3 polyunsaturated fatty acid (PUFA) ratio is able to protect against ELS-induced cognitive impairments. Due to the importance of the gut microbiota as determinants of long-term health, we here study the impact of ELS and dietary PUFA’s on the gut microbiota, and how this relates to the previously described cognitive, metabolic and fatty acid profiles.Male mice were exposed to ELS via the limited bedding and nesting paradigm (postnatal day (P)2 – P9) and to an early diet (P2 – P42) with either high (15) or low (1) ω-6 linoleic acid to ω-3 alpha-linolenic acid ratio. 16S ribosomal RNA was sequenced and analyzed from fecal samples at P21, P42 and P180.ELS increased β-diversity at P42, which persisted into adulthood. The low ω-6/ω-3 diet prevented the ELS-induced increase in β-diversity, at P42. At the level of taxa abundance, for example, the abundance of the phyla Bacteroidetes increased while Actinobacteria and Verrucomicrobia decreased with age; ELS reduced the relative abundance of the genera RC9 gut group and Rikenella into adulthood and the low ω-6/ω-3 diet reduced the abundance of the Firmicutes Erysipelotrichia. At P42, species abundance correlated with body fat mass and circulating leptin (e.g. Bacteroidetes and Proteobacteria taxa) and fatty acid profiles (e.g. Firmicutes taxa).This study gives novel insights into the impact of age, ELS and dietary PUFAs on microbiota composition, providing potential targets for non-invasive (nutritional) modulation of the ELS-induced deficits.ImportanceEarly-life stress (ELS) leads to increased vulnerability to develop mental and metabolic disorders, however the biological mechanisms leading to such programming are not fully clear. Increased attention has been given to the importance of the gut microbiota as determinant of long term health and as potential target for non-invasive nutritional strategies to protect against the negative impact of ELS. Here we give novel insights in the complex interaction between ELS, early dietary ω-3 availability and the gut microbiota across ages and provides new potential targets for (nutritional) modulation of the long-term effects of the early-life environment via the microbiota.
Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction
Authors: Kimmel Gregory J. , Beck Richard J. , Yu Xiaoqing , Veith Thomas , Bakhoum Samuel , Altrock Philipp M. , Andor Noemi 
Published: November 2021

AbstractThe phenotypic efficacy of somatic copy number alterations (SCNAs) stems from their incidence per base pair of the genome, which is orders of magnitudes greater than that of point mutations. One mitotic event stands out in its potential to significantly change a cell’s SCNA burden–a chromosome missegregation. We present a general deterministic framework for modeling chromosome missegregations and use it to evaluate the possibility of missegregation-induced population extinction (MIE). The model predicts critical curves that separate viable from non-viable populations as a function of their turnover- and missegregation rates. Missegregation- and turnover rates estimated from a PAN-cancer scRNA-seq dataset of 15,464 cells are then compared to predictions. The majority of tumors across all cancer types had missegregation- and turnover rates that were within viable regions of the parameter space. When a dependency of missegregation rate on karyotype was introduced, karyotypes associated with low missegregation rates acted as a stabilizing refuge, rendering MIE impossible unless turnover rates are exceedingly high. Intra-tumor heterogeneity, including heterogeneity in missegregation rates, increases as tumors progress, rendering MIE unlikely.Author SummaryWhen a cell missegregates a chromosome while dividing, the chance is high that its two daughter cells will behave drastically different from each other and from their parental cell. Chromosome missegregations are therefore one of the most powerful forces of phenotypic diversity. We developed a mathematical model of chromosome missegregations that allows for this cell-to-cell diversity to be accounted for. The model serves to help understand how selection acts upon cells with versatile chromosome contents, as a tool for genotype-to-phenotype mapping in various microenvironments. As a first application example we used the model to address whether there exists an upper limit on missegregation rate, beyond which cancer populations collapse. Chromosome missegregations are common. They occur in 1.2-2.3% per mitosis in normal cells [1] and in cancer cells their rate is between one and two orders of magnitudes higher [2]. The model revealed that the upper limit of missegregation rate is a function of the tumor’s turnover rate (i.e. how fast the tumor renews itself). In heterogenous populations however, cells with low missegregation rates protect the population from collapse. Intra-tumor heterogeneity, including heterogeneity in missegregation rates, increases as tumors progress, rendering missegregation-induced extinction unlikely.
Synthesis and antimicrobial evaluation of new cephalosporin derivatives containing cyclic disulfide moieties
Authors: Shchelik Inga S. , Gademann Karl 
Published: November 2021

AbstractDue to a steady increase of microbial resistance, there is a need to increase the effectiveness of antibiotic performance by involving additional mechanisms of their penetration or retention for their better action. Cephalosporins are a successful group of antibiotics to combat pathogenic microorganisms, including drug-resistant strains. In this study, we investigated the effect of newly synthesized cephalosporin derivatives with cyclic disulfide modifications against several Gram-positive and Gram-negative strains as well as against biofilm formation. The incorporation of asparagusic acid was found to be effective in improving the activity of the drug against Gram-negative strains compared to the all carbon control compounds. Furthermore, we could demonstrate the successful reduction of biofilm formation forStaphylococcus aureusandPseudomonas aeruginosaat similar concentrations as obtained against planktonic cells. We propose that the incorporation of cyclic disulfides is one additional strategy to improve antibiotic activity and to combat bacterial infections.
QT-GILD: Quartet based gene tree imputation using deep learning improves phylogenomic analyses despite missing data
Authors: Mahbub Sazan , Sawmya Shashata , Saha Arpita , Reaz Rezwana , Rahman M. Sohel , Bayzid Md. Shamsuzzoha 
Published: November 2021

AbstractSpecies tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, for a combination of reasons (ranging from sampling biases to more biological causes, as in gene birth and loss), gene trees are often incomplete, meaning that not all species of interest have a common set of genes. Incomplete gene trees can potentially impact the accuracy of phylogenomic inference. We, for the first time, introduce the problem of imputing the quartet distribution induced by a set of incomplete gene trees, which involves adding the missing quartets back to the quartet distribution. We present QT-GILD, an automated and specially tailored unsupervised deep learning technique, accompanied by cues from natural language processing (NLP), which learns the quartet distribution in a given set of incomplete gene trees and generates a complete set of quartets accordingly. QT-GILD is a general-purpose technique needing no explicit modeling of the subject system or reasons for missing data or gene tree heterogeneity. Experimental studies on a collection of simulated and empirical data sets suggest that QT-GILD can effectively impute the quartet distribution, which results in a dramatic improvement in the species tree accuracy. Remarkably, QT-GILD not only imputes the missing quartets but it can also account for gene tree estimation error. Therefore, QT-GILD advances the state-of-the-art in species tree estimation from gene trees in the face of missing data. QT-GILD is freely available in open source form at https://github.com/pythonLoader/QT-GILD.
Sleep and Alcohol Use Patterns During Federal Holidays in the United States
Authors: Heacock Rachel M , Capodilupo Emily R , Czeisler Mark É , Weaver Matthew D , Czeisler Charles A , Howard Mark E , Rajaratnam Shantha MW 
Published: November 2021

AbstractWe conducted a retrospective observational study using remote wearable and mobile application data to identify US public holidays associated with significant changes in sleep behaviors, including sleep duration, bedtime and waketime, and the consistency of sleep timing, as well as changes in the point prevalence of alcohol use. These metrics were collected and analyzed from objective, high resolution sleep-wake data and survey responses of 24,250 US subscribers to the wrist-worn biometric device platform, WHOOP (Boston, Massachusetts, USA), who were active users during May 1, 2020 through May 1, 2021. Compared to baseline, statistically significant differences in sleep and alcohol measures were found on the US public holidays and their eves. For example, New Year’s Eve corresponded with a sleep consistency decrease of 13.8% (± 0.3), a sleep onset of 88.9 minutes (± 3.2) later, a sleep offset of 78.1 minutes (± 3.1), and more than twice as many participants reported alcohol consumption (138.0% ± 6.7) compared to baseline. The majority of US public holidays and holiday eves were associated with sample-level increases in sleep duration, decreases in sleep consistency, later sleep onset and offset, and increases in the prevalence of alcohol consumption.Significance StatementUS public holidays were associated with increased sleep duration, decreased sleep consistency, and later sleep timing among US adult users of an objective, validated commercial fitness tracker. Holidays were also associated with an increased prevalence of participants having reported alcohol use. Given the adverse health impacts of sleep timing variability on both weekends and during the transition to daylight savings time, and of increased alcohol use on weekends and public holidays, further investigation of the health impacts of these behavioral changes is warranted.
Prevalence of Antibodies to SARS-CoV-2 following natural infection and vaccination in Irish Hospital Healthcare Workers; changing epidemiology as the pandemic progresses
Authors: Allen Niamh , Brady Melissa , Riain Una Ni , Conlon Niall , Domegan Lisa , Carrion Martin Antonio Isidro , Walsh Cathal , Doherty Lorraine , Higgins Eibhlin , Kerr Colm ,   PRECISE Study Steering Group, Bergin Colm , Fleming Catherine 
Published: November 2021

AbstractBackgroundIn October 2020 SARS-CoV-2 seroprevalence among hospital healthcare workers (HCW) of two Irish hospitals was 15% and 4.1% respectively. We compare seroprevalence in the same HCW population six months later, assess changes in risk factors for seropositivity with progression of the pandemic and serological response to vaccination.MethodsAll staff of both hospitals (N=9038) were invited to participate in an online questionnaire and SARS-CoV-2 antibody testing in April 2021. We measured anti-nucleocapsid and anti-spike antibodies. Frequencies and percentages for positive SARS-CoV-2 antibodies were calculated and adjusted relative risks for participant characteristics were calculated using multivariable regression analysis.Results5085 HCW participated. Seroprevalence increased to 21% and 13% respectively; 26% of infections were previously undiagnosed. Black ethnicity (aRR 1.7, 95% CI 1.3-2.2, p<.001), lower level of education (aRR 1.4 for secondary level education, 95% CI 1.1-1.8, p=0.002), living with other HCW (aRR 1.2, 95% CI 1.0-1.4, p=0.007) were significantly associated with seropositivity. Having direct patient contact also carried a significant risk (being a healthcare assistant (aRR 1.8, 95% CI 1.3-2.3, p<.001), being a nurse (aRR 1.4, 95% CI 1.1-1.5, p=0.022), daily contact with COVID-19 patients (aRR 1.4, 95% CI 1.1-1.7, p=0.002), daily contact with patients without suspected or confirmed COVID-19 (aRR 1.3, 95% CI 1.1- 1.5, p=0.013) Breakthrough infection occurred in 23/4111(0.6%) of fully vaccinated participants; all had anti-S antibodies.ConclusionThe increase in seroprevalence reflects the magnitude of the third wave of the pandemic in Ireland. Genomic sequencing is needed to apportion risk to the workplace versus the household/community. Concerted efforts are needed to mitigate risk factors due to ethnicity and lower level of education, even at this stage of the pandemic. The undiagnosed and breakthrough infections call for ongoing infection prevention and control measures and testing of HCW in the setting of close contact. Vaccinated HCW with confirmed infection should be actively assessed, including SARS-CoV-2 whole genome sequencing (WGS), serology testing and assessment of host determinants, to advance understanding of the reasons for breakthrough infection.
Impaired ability in visual-spatial attention in Chinese children with developmental dyslexia
Authors: Tian Mengyu , Wang Runzhou , Bi Hong-Yan 
Published: November 2021

AbstractMany studies demonstrated that alphabetic language speaking children with developmental dyslexia had a deficit in visual-spatial attention, especially in rapid orienting of the attentional spotlight. Chinese, as a logographic language, is characterized as highly visual-spatial complexity. To date, few studies explored the visual-spatial attention of Chinese children with developmental dyslexia. The present study examined the visual-spatial attention of Chinese children with developmental dyslexia using the visual search task. The results showed that Chinese children with developmental dyslexia had poor performances in conjunction search, indicating that they had a deficit in the rapid orienting of visual-spatial attention. Meanwhile, only the conjunction search was a significant predictor of Chinese characters reading when other variables were controlled. These results indicated that Chinese dyslexic children had a deficit in visual-spatial attention, and visual-spatial attention played a special role in Chinese reading development.
Extracting multi-way chromatin contacts from Hi-C data
Authors: Liu Lei , Zhang Bokai , Hyeon Changbong 
Published: November 2021

AbstractThere is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions forn-body contact probabilities (n> 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.Author summaryThe importance of DNA looping is often mentioned as the initiation step of gene expression. However, there are growing evidences that ‘chromatin hubs’ comprised of multiple genes and enhancers play vital roles in gene expressions and regulations. Currently a number of experimental techniques to detect and identify multi-way chromosome interactions are available; yet detection of such multi-body interactions is statistically challenging. This study proposes a method to predict multi-way chromatin contacts from pair-wise contact frequencies available in Hi-C dataset. Since chromosomes are made of polymer chains, the pairwise contact probabilities are not entirely independent from each other, but certain types of correlations are present reflecting the underlying chromosome structure. We extract these correlations hidden in Hi-C dataset by leveraging theoretical argument based on polymer physics.