bluuebunny/crossref_metadata_2025_split huggingface dataset:
Women’s knowledge, attitudes and views of preconception health and intervention delivery methods: A cross-sectional survey
Authors: Daly Michael P , White James , Sanders Julia , Kipping Ruth R 
Published: May 2022

AbstractBackgroundSeveral preconception exposures have been associated with adverse pregnancy, birth and postpartum outcomes. However, few studies have investigated women’s knowledge of and attitudes towards preconception health, and the acceptability of potential intervention methods.MethodsSeven GP practices in the West of England posted questionnaires to 4,330 female patients aged 18 to 48 years. Without providing examples, we asked women to list maternal preconception exposures that might affect infant and maternal outcomes, and assessed their knowledge of nine literature-derived risk factors. Attitudes towards preconception health (interest, intentions, self-efficacy and perceived awareness and importance) and the acceptability of intervention delivery methods were also assessed. Multivariable multilevel regression examined participant characteristics associated with these outcomes.ResultsOf those who received questionnaires, 835 (19.3%) responded. Women were most aware of the preconception risk factors of diet (86.0%) and physical activity (79.2%). Few were aware of weight (40.1%), folic acid (32.9%), abuse (6.3%), advanced age (5.9%) and interpregnancy intervals (0.2%), and none mentioned interpregnancy weight change or excess iron intake. After adjusting for demographic and reproductive covariates, women aged 18-25-years (compared to 40-48-years) and nulligravid women were less aware of the benefit of preconception folic acid supplementation (adjusted odds ratios (aOR) for age: 4.30 [2.10-8.80], gravidity: aOR 2.48 [1.70-3.62]). Younger women were more interested in learning more about preconception health (aOR 0.37 [0.21-0.63]) but nulligravid women were less interested in this (aOR 1.79 [1.30-2.46]). Women with the lowest household incomes (versus the highest) were less aware of preconception weight as a risk factor (aOR: 3.11 [1.65-5.84]) and rated the importance of preconception health lower (aOR 3.38 [1.90-6.00]). The most acceptable information delivery channels were websites/apps (99.5%), printed healthcare materials (98.6%), family/partners (96.3%), schools (94.4%), television (91.9%), pregnancy tests (91.0%) and doctors, midwives and nurses (86.8-97.0%). Dentists (23.9%) and hairdressers/beauticians (18.1%) were the least acceptable.ConclusionsOur findings demonstrate a need to promote awareness of preconception risk factors and motivation for preconception health changes, particularly amongst younger and nulligravid women and women with lower incomes. Interventions to improve preconception health should focus on communication from healthcare professionals, schools, family members, and digital media.
pyTCR: a comprehensive and scalable platform for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research
Authors: Peng Kerui , Moore Jaden , Brito Jaqueline , Kao Guoyun , Burkhardt Amanda M. , Alachkar Houda , Mangul Serghei 
Published: May 2022

AbstractT cell receptor (TCR) studies have grown substantially with the advancement in the sequencing techniques of T cell receptor repertoire sequencing (TCR-Seq). The analysis of the TCR-Seq data requires computational skills to run the computational analysis of TCR repertoire tools. However biomedical researchers with limited computational backgrounds face numerous obstacles to properly and efficiently utilizing bioinformatics tools for analyzing TCR-Seq data. Here we report pyTCR, a computational notebook-based platform for comprehensive and scalable TCR-Seq data analysis. Computational notebooks, which combine code, calculations, and visualization, are able to provide users with a high level of flexibility and transparency for the analysis. Additionally, computational notebooks are demonstrated to be user-friendly and suitable for researchers with limited computational skills. Our platform has a rich set of functionalities including various TCR metrics, statistical analysis, and customizable visualizations. The application of pyTCR on large and diverse TCR-Seq datasets will enable the effective analysis of large-scale TCR-Seq data with flexibility, and eventually facilitate new discoveries.
Magneto-acoustic protein nanostructures for non-invasive imaging of tissue mechanics in vivo
Authors: Kim Whee-Soo , Min Sungjin , Kim Su Kyeom , Kang Sunghwi , Davis Hunter , Bar-Zion Avinoam , Malounda Dina , Kim Yu Heun , An Soohwan , Lee Jae-Hyun , Bae Soo Han , Lee Jin Gu , Kwak Minsuk , Cho Seung-Woo , Shapiro Mikhail G. , Cheon Jinwoo 
Published: May 2022

AbstractMeasuring cellular and tissue mechanics inside intact living organisms is essential for interrogating the roles of force in physiological and disease processes, and is a major goal in the field of mechanobiology. However, existing biosensors for 3D tissue mechanics, primarily based on fluorescent emissions and deformable materials, are limited for in vivo measurement due to the limited light penetration and poor material stability inside intact, living organisms. While magneto-motive ultrasound (MMUS), which uses superparamagnetic nanoparticles as imaging contrast agents, has emerged as a promising modality for real-time in vivo imaging of tissue mechanics, it has poor sensitivity and spatiotemporal resolution. To overcome these limitations, we introduce magneto-gas vesicles (MGVs), a unique class of protein nanostructures based on gas vesicles and magnetic nanoparticles that produces differential ultrasound signals in response to varying mechanical properties of surrounding tissues. These hybrid protein nanostructures significantly improve signal strength and detection sensitivity. Furthermore, MGVs enable non-invasive, long-term, and quantitative measurement of mechanical properties within 3D tissues and organs in vivo. We demonstrated the performance of MGV-based mechano-sensors in vitro, in fibrosis models of organoids, and in vivo in mouse liver fibrosis models.
The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS-CoV-2 coronavirus
Authors: Oliver José L. , Bernaola-Galván Pedro , Perfectti Francisco , Martín Cristina Gómez , Castiglione Silvia , Raia Pasquale , Verdú Miguel , Moya Andrés 
Published: May 2022

Disclaimer textThe author has withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2021/467547. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Low heritability of crossover rate in wild sticklebacks
Authors: Kivikoski Mikko , Fraimout Antoine , Rastas Pasi , Löytynoja Ari , Merilä Juha 
Published: May 2022

AbstractCrossover rate is mostly studied with domesticated or lab-reared populations and little is known about its genetic variation in the wild. We studied the variation and genetic underpinnings of crossover rate in outbred wild nine- (Pungitius pungitius) and three-spined (Gasterosteus aculeatus) sticklebacks. In both species, the crossover rate of females exceeded that of males as did also its repeatability (RFemales=0.21–0.33,RMales=0.026–0.11), implying individual differences of crossover rate in females, but no or less so in males. However, in both species and sexes additive genetic variance and heritability of crossover rate were effectively zero. A review of the previously reported repeatability and heritability estimates revealed that the repeatabilities in stickleback females were moderately high, whereas those in males were very low. Genome-wide association analyses recovered a few candidate regions possibly involved with control of crossover rate. The low additive genetic variance of crossover rate in wild sticklebacks suggest limited evolvability of crossover rate.
Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5
Authors: Kimura Izumi , Yamasoba Daichi , Tamura Tomokazu , Nao Naganori , Oda Yoshitaka , Mitoma Shuya , Ito Jumpei , Nasser Hesham , Zahradnik Jiri , Uriu Keiya , Fujita Shigeru , Kosugi Yusuke , Wang Lei , Tsuda Masumi , Kishimoto Mai , Ito Hayato , Suzuki Rigel , Shimizu Ryo , Begum MST Monira , Yoshimatsu Kumiko , Sasaki Jiei , Sasaki-Tabata Kaori , Yamamoto Yuki , Nagamoto Tetsuharu , Kanamune Jun , Kobiyama Kouji , Asakura Hiroyuki , Nagashima Mami , Sadamasu Kenji , Yoshimura Kazuhisa , Kuramochi Jin , Schreiber Gideon , Ishii Ken J , Hashiguchi Takao ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda Terumasa , Saito Akatsuki , Fukuhara Takasuke , Tanaka Shinya , Matsuno Keita , Sato Kei 
Published: May 2022

AbstractAfter the global spread of SARS-CoV-2 Omicron BA.2 lineage, some BA.2-related variants that acquire mutations in the L452 residue of spike protein, such as BA.2.9.1 and BA.2.13 (L452M), BA.2.12.1 (L452Q), and BA.2.11, BA.4 and BA.5 (L452R), emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these L452R/M/Q-bearing BA.2-related Omicron variants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1 and BA.2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. Furthermore, infection experiments using hamsters indicated that BA.4/5 is more pathogenic than BA.2. Altogether, our multiscale investigations suggest that the risk of L452R/M/Q-bearing BA.2-related Omicron variants, particularly BA.4 and BA.5, to global health is potentially greater than that of original BA.2.HighlightsSpike L452R/Q/M mutations increase the effective reproduction number of BA.2BA.4/5 is resistant to the immunity induced by BA.1 and BA.2 infectionsBA.2.12.1 and BA.4/5 more efficiently spread in human lung cells than BA.2BA.4/5 is more pathogenic than BA.2 in hamsters
O-GlcNAc transferase plays a non-catalytic role in C. elegans male fertility
Authors: Konzman Daniel , Fukushige Tetsunari , Dagnachew Mesgana , Krause Michael , Hanover John A. 
Published: May 2022

AbstractAnimal behavior is influenced by the competing drives to maintain energy and to reproduce. The balance between these evolutionary pressures and how nutrient signaling pathways intersect with mating drive remains unclear. The nutrient sensor O-GlcNAc transferase, which post-translationally modifies intracellular proteins with a single monosaccharide, is responsive to cellular nutrient status and regulates diverse biological processes. Though essential in most metazoans, O-GlcNAc transferase (ogt-1) is dispensable in Caenorhabditis elegans, allowing genetic analysis of its physiological roles. Compared to control, ogt-1 males have a four-fold reduction in mean offspring, with nearly two thirds producing zero progeny. Interestingly, we found that isolated ogt-1 males are less likely to engage in mate-searching, and they initiate mating less often when exposed to mates. In addition, ogt-1 males which do initiate mating are less likely to continue with subsequent steps in the mating process, resulting in fewer successful sperm transfers. Lowering barriers to mating such as immobilizing mates or allowing more mating time significantly improves ogt-1 male mating. Surprisingly, we found high fertility levels for ogt-1 mutant males with hypodermal expression of wild-type ogt-1 and by ogt-1 harboring mutations that prevent the transfer of O-GlcNAc by OGT-1. This suggests OGT-1 serves a non-catalytic function in the hypodermis impacting the male mating drive. This study builds upon research on the nutrient sensor O- GlcNAc transferase and demonstrates a role it plays in the interplay between the evolutionary drives for reproduction and survival.Author SummaryAnimals must make decisions on whether to engage in reproduction or conserve energy. These decisions must take into account the energy available to the animal, therefore making the nutrient sensing enzyme OGT of particular interest. In response to nutrient levels in the cell, OGT transfers the GlcNAc sugar onto proteins to regulate their function. OGT is implicated in a number of human diseases including diabetes, cancer, and X-linked intellectual disability. By deleting the gene encoding OGT in the nematode C. elegans, we show OGT is required for male fertility. We assessed the behavior of these mutant male worms and found they have a reduced mating drive. Surprisingly, restoring OGT specifically in the hypodermis was able to raise male fertility and mating drive back to normal levels. In addition, missense mutations in the OGT catalytic domain which prevent the enzyme from transferring GlcNAc do not negatively impact fertility, suggesting a different function of OGT is important in this process. Our study demonstrates that OGT is important in critical behavioral decisions and that further investigation in C. elegans may help reveal new functions of the enzyme.
The inner nuclear membrane protein NEMP1 is required for nuclear envelope openings and enucleation of erythroblasts during erythropoiesis
Authors: Hodzic Didier , Wu Jun , Krchma Karen , Jurisicova Andrea , Tsatskis Yonit , Liu Yijie , Ji Peng , Choi Kyunghee , McNeill Helen 
Published: May 2022

ABSTRACTNuclear Envelope Membrane Proteins (NEMP) are a conserved family of nuclear envelope proteins that reside within the inner nuclear membrane. Even though Nemp1 knockout (KO) mice are overtly normal, they display a pronounced splenomegaly. This phenotype and recent reports describing a requirement for nuclear envelope openings during erythroblasts terminal maturation led us to examine a potential role for Nemp1 in erythropoiesis. Here, we report that Nemp1 knockout (KO) mice show peripheral blood defects, anemia in neonates, ineffective erythropoiesis, splenomegaly and stress erythropoiesis. The erythroid lineage of Nemp1 KO mice is overrepresented until the pronounced apoptosis of polychromatophilic erythroblasts. We show that NEMP1 localizes to the nuclear envelope of erythroblasts and their progenitors. Mechanistically, we discovered that NEMP1 accumulates into aggregates that localize near or at the edge of nuclear envelope openings and Nemp1 deficiency leads to a marked decrease of both nuclear envelope openings and ensuing enucleation. Together, our results for the first time demonstrate that NEMP1 is essential for nuclear envelope openings and erythropoietic maturation in vivo and provide the first mouse model of defective erythropoiesis directly linked to the loss of an inner nuclear membrane protein.
Vertical and horizontal transmission of cell fusing agent virus in Aedes aegypti
Authors: Logan Rhiannon A. E. , Quek Shannon , Muthoni Joseph N. , von Eicken Anneliese , Brettell Laura E. , Anderson Enyia R. , Villena Marcus E.N. , Hegde Shivanand , Patterson Grace T. , Heinz Eva , Hughes Grant L. , Patterson Edward I. 
Published: May 2022

AbstractCell fusing agent virus (CFAV) is an insect specific flavivirus (ISF) found in field and laboratory populations of Aedes aegypti. ISFs have recently demonstrated the ability to block the transmission of arboviruses such as dengue, West Nile and Zika viruses. It is thought that vertical transmission is the main route for ISF infections. This has been observed with CFAV, but there is evidence of horizontal and venereal transmission in other ISFs. Understanding the route of transmission can inform strategies to spread ISFs to wild vector populations as a method of controlling pathogenic arboviruses. We crossed individually reared male and female mosquitoes from both a naturally occurring CFAV-positive Ae. aegypti colony and its negative counterpart to provide information on maternal, paternal, and horizontal transmission. RT-PCR was used to detect CFAV in individual female mosquito pupal exuviae and was 89% sensitive, but only 41% in male mosquito pupal exuviae. This is a possible way to screen individuals for infection without destroying the adults. Female-to-male horizontal transmission was not observed during this study, however there was a 31% transmission rate from mating pairs of CFAV-positive males to negative female mosquitoes. Maternal vertical transmission was observed with a filial infection rate of 93%. The rate of paternal transmission was 85% when the female remained negative, 61% when the female acquired CFAV horizontally, and 76% overall. Maternal and paternal transmission of CFAV could allow the introduction of this virus into wild Ae. aegypti populations through male or female mosquito releases, and thus provides a potential strategy for ISF-derived arbovirus control.
CMV seropositivity in older adults changes the T cell repertoire, but does not prevent antibody or cellular responses to SARS-CoV-2 vaccination
Authors: Breznik Jessica A. , Huynh Angela , Zhang Ali , Bilaver Lucas , Bhakta Hina , Stacey Hannah D. , Ang Jann C. , Bramson Jonathan L. , Nazy Ishac , Miller Matthew S. , Denburg Judah , Costa Andrew P. , Bowdish Dawn M. E. ,   other members of the COVID-in-LTC Investigator Group
Published: May 2022

AbstractChronic infection with human cytomegalovirus (CMV) may contribute to poor vaccine efficacy in older adults. We assessed effects of CMV serostatus on antibody quantity and quality, as well as cellular memory recall responses, after 2 and 3 SARS-CoV-2 mRNA vaccine doses, in older adults in assisted living facilities. CMV serostatus did not affect anti-Spike and anti-RBD IgG antibody levels, nor neutralization capacity against wildtype or beta variants of SARS-CoV-2 several months after vaccination. CMV seropositivity altered T cell expression of senescence-associated markers and increased TEMRA cell numbers, as has been previously reported; however, this did not impact Spike-specific CD4+ T cell memory recall responses. CMV seropositive individuals did not have a higher incidence of COVID-19, though prior infection influenced humoral immunity. Therefore, CMV seropositivity may alter T cell composition but does not impede the durability of humoral protection or cellular memory responses after SARS-CoV-2 mRNA vaccination in older adults.Key PointsCMV seropositive older adults have more EMRA and terminally differentiated T cells CMV seropositivity does not prevent antibody maintenance after SARS-CoV-2 vaccination CMV seropositivity does not impede SARS-CoV-2 vaccine T cell memory recall responses
How early can an upcoming critical transition be detected?
Authors: Southall Emma , Tildesley Michael J , Dyson Louise 
Published: May 2022

AbstractNumerous studies have suggested the use of early warning signals (EWSs) of critical transitions to overcome challenges of identifying tipping points in complex natural systems. However, the real-time application of EWSs has often been overlooked; many studies show the presence of EWSs but do not detect when the trend becomes significant. Knowing if the signal can be detected early enough is of critical importance for the applicability of EWSs. Detection methods which present this analysis are sparse and are often developed anew for each individual study. Here, we provide a summary and validation of a range of currently available detection methods developed from EWSs. We include an additional constraint, which requires multiple time-series points to satisfy the algorithms’ conditions before a detection of an approaching critical transition can be flagged. We apply this procedure to a simulated study of an infectious disease system undergoing disease elimination. For each detection algorithm we select the hyper-parameter which minimises classification errors using receiver operating characteristic (ROC) analysis. We consider the effect of time-series length on these results, finding that all algorithms become less accurate as the amount of data decreases. We compare EWS detection methods with alternate algorithms found from the change-point analysis literature and assess the suitability of using change-point analysis to detect abrupt changes in a system’s steady state.
Comparing the predictive power of machine learning and semi-mechanistic models of endemic measles dynamics
Authors: Lau Max SY , Becker Alex , Waller Lance , Metcalf Jessica , Grenfell Bryan 
Published: May 2022

AbstractMeasles is one the best-documented and most-mechanistically-studied non-linear infectious disease dynamical systems. However, systematic investigation into the comparative performance of traditional mechanistic models and machine learning approaches in forecasting the transmission dynamics of this pathogen are still rare. Here, we compare one of the most widely used semi-mechanistic models for measles (TSIR) with a commonly used machine learning approach (LASSO), comparing performance and limits in predicting short to long term outbreak trajectories and seasonality for both regular and less regular measles outbreaks in England and Wales (E&W) and the United States. First, our results indicate that the proposed LASSO model can efficiently use data from multiple major cities and achieve similar short-to-medium term forecasting performance to semi-mechanistic models for E&W epidemics. Second, interestingly, the LASSO model also captures annual to biennial bifurcation of measles epidemics in E&W caused by susceptible response to the late 1940s baby boom. LASSO may also outperform TSIR for predicting less-regular dynamics such as those observed in major cities in US between 1932-45. Although both approaches capture short-term forecasts, accuracy suffers for both methods as we attempt longer-term predictions in highly irregular, post-vaccination outbreaks in E&W. Finally, we illustrate that the LASSO model can both qualitatively and quantitatively reconstruct mechanistic assumptions, notably susceptible dynamics, in the TSIR model. Our results characterize the limits of predictability of infectious disease dynamics for strongly immunizing pathogens with both mechanistic and machine learning models, and identify connections between these two approaches.
Association of vasopressors with mortality in critically ill patients with COVID-19: A systematic review and meta-analysis
Authors: Mermiri Maria , Mavrovounis Georgios , Laou Eleni , Papagiannakis Nikolaos , Pantazopoulos Ioannis , Chalkias Athanasios 
Published: May 2022

ABSTRACTPurposeThe effect of vasopressors on mortality of critically ill patients with COVID-19 has not been studied extensively.Materials and MethodsA systematic search of PubMed, Scopus, and clinicaltrials.gov was conducted for relevant articles until January 2022. Eligibility criteria were randomized controlled and non-randomized trials. The primary outcome was mortality at latest follow-up. The quality of studies was assessed using the MINORS tool. Paired meta-analysis was used to estimate the pooled risk ratios along with their 95% Confidence Interval.ResultsAnalyses of 21 studies (n=7900) revealed that vasopressor use is associated with mortality in patients who receive vasopressors compared to those who do not receive vasopressor therapy [RR (95%CI): 4.26 (3.15, 5.76); p<0.001]. In-hospital and 30-day mortality are significantly higher in patients who receive vasopressors [RR (95%CI): 4.60 (2.47, 8.55); p<0.001 and RR (95%CI): 2.97 (1.72, 5.14); p<0.001, respectively]. The highest mortality rate was observed with vasopressin or epinephrine, while the lowest mortality rate was observed with angiotensin-II. Also, analyses of data from 10 studies (n=3519) revealed that vasopressor use is associated with acute kidney injury [RR (95%CI): 3.17 (2.21, 4.54); p<0.001].ConclusionVasopressor use was associated with an increase in in-hospital mortality, 30-day mortality, and acute kidney injury in critically ill patients with COVID-19.