bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMEM16A activation for the fast block to polyspermy in the African clawed frog does not require conventional activation of egg PLCs
Authors: Komondor Kayla M. , Bainbridge Rachel E. , Sharp Katherine G. , Rosenbaum Joel C. , Carlson Anne E. 
Published: September 2022

AbstractFertilization of an egg by more than one sperm, a condition known as polyspermy, leads to gross chromosomal abnormalities and is embryonic lethal for most animals. Consequently, eggs have evolved multiple processes to stop supernumerary sperm from entering the nascent zygote. For external fertilizers, such as frogs and sea urchins, fertilization signals a depolarization of the egg membrane, which serves as the fast block to polyspermy. Sperm can bind to, but will not enter, depolarized eggs. In eggs from the African clawed frog, Xenopus laevis, the fast block depolarization is mediated by the Ca2+ activated Cl− channel TMEM16A. To do so, fertilization activates a phospholipase C, which generates IP3 to signal a Ca2+ release from the ER. Currently, the signaling pathway by which fertilization activates PLC remains unknown. Here, we sought to uncover this pathway by targeting the canonical activation of the PLC isoforms present in the X. laevis egg: PLCγ and PLCβ. We observed no changes to the fast block in X. laevis eggs inseminated in inhibitors of tyrosine phosphorylation, used to stop activation of PLCγ, or inhibitors of Gαq/11 pathways, used to stop activation of PLCβ. These data suggest that the PLC that signals the fast block depolarization in X. laevis is activated by a novel mechanism.
Multi-tissue landscape of somatic mtDNA mutations indicates tissue specific accumulation and removal in aging
Authors: Sanchez-Contreras Monica , Sweetwyne Mariya T. , Tsantilas Kristine A. , Whitson Jeremy A. , Campbell Matthew D. , Kohrn Brendan F. , Kim Hyeon Jeong , Hipp Micheal J. , Fredrickson Jeanne , Nguyen Megan M. , Hurley James B. , Marcinek David J. , Rabinovitch Peter S. , Kennedy Scott R. 
Published: September 2022

ABSTRACTAccumulation of somatic mutations in the mitochondrial genome (mtDNA) during aging has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue and mutation type dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with Elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age indicates a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.
New algorithms for accurate and efficient de-novo genome assembly from long DNA sequencing reads
Authors: Gonzalez-Garcia Laura , Guevara-Barrientos David , Lozano-Arce Daniela , Gil Juanita , Díaz-Riaño Jorge , Duarte Erick , Andrade Germán , Bojacá Juan Camilo , Hoyos Maria Camila , Chavarro Christian , Guayazan Natalia , Chica Luis Alberto , Buitrago Acosta Maria Camila , Bautista Edwin , Trujillo Miller , Duitama Jorge 
Published: September 2022

AbstractProducing de-novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. In this paper, we present new algorithms for assembling long-DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mers distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function that is calculated from the inferred distributions of features on a subset of safe edges. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. The phasing procedure is used to remove edges connecting reads assigned to different haplotypes and to obtain a phased assembly by running the layout algorithm on the filtered graph. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from bacteria, yeast, Drosophila, rice, maize, and human samples. Our algorithms showed competitive efficiency and contiguity of assemblies, as well as superior accuracy in some cases, as compared to other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.
In vitro selection of Engineered Transcriptional Repressors for targeted epigenetic silencing and initial evaluation of their specificity profile
Authors: Migliara Alessandro , Cappelluti Martino Alfredo , Valsoni Sara , Merelli Ivan , Cittaro Davide , Lombardo Angelo 
Published: September 2022

ABSTRACTGene inactivation is instrumental to study gene function and represents a promising strategy for the treatment of a broad range of diseases. Among traditional technologies, RNA interference suffers from partial target abrogation and requirement for life-long treatments. On the other hand, artificial nucleases can impose stable gene inactivation through induction of DNA Double Strand Breaks, but recent studies are questioning the safety of this approach. Targeted epigenetic editing via Engineered Transcriptional Repressors (ETRs) may represent a solution, as a single administration of specific ETRs combinations can lead to durable silencing without DNA breaks induction. ETRs are proteins containing a programmable DNA Binding Domain (DBD) and effectors from naturally occurring transcriptional repressors. Specifically, a combination of three ETRs equipped with the KRAB domain of human ZNF10, the catalytic domain of human DNMT3A and human DNMT3Lwas shown to induce heritable repressive epigenetic states on the ETR-target gene. The hit-and-run nature of this platform, the lack of impact on the DNA sequence of the target, and the possibility to revert on-demand the repressive state by DNA demethylation, make epigenetic silencing a game-changing tool. A critical step is the identification of the proper position on the target gene where to tether the ETRs in order to maximize on target and minimizing off-target silencing. Performing this step in the final ex vivo or in vivo preclinical setting can be cumbersome. Taking CRISPR-Cas9 system as a paradigmatic DBD for ETRs, here we describe a protocol consisting in the in vitro screen of gRNAs coupled to the triple ETRs combination for efficient on-target silencing, followed by evaluation of the genome-wide specificity profile of top hits. This allows to reduce the initial repertoire of candidate gRNAs to a short list of promising ones, whose complexity is suitable for their final evaluation in the therapeutically relevant setting of interest.
Travel distance to the general practitioner. Do patients move closer to the services when starting to use them?1
Authors: Johed Rosanna N. I. , Telle Kjetil 
Published: September 2022

ObjectivesThe main objectives were 1) to calculate and describe travel time by car from the home of Norwegian residents to the office of their named general practitioner (GP); 2) to estimate changes in travel time for residents who started to visit the GP and, if so, to 3) to explore if the residents changed GP or moved to reduce their travel time.MethodsWe used nation-wide individual-level annual registry data 2009-2017 on the exact location of the home of every resident and the GP-office to calculate travel time in minutes by car from home to their assigned GP. First, using data for 2017 only, we calculated travel time at the median and 90th percentile, and by sex, age, immigrant background, county of residence and use of GP in 2017. Second, with annual data 2009-2017, and restricting the sample to residents who had not used their GP over the last two years (t-2 and t-1), we used a difference-indifferences model to estimate changes in travel time in the next two years (t+1 and t+1) for patients with a visit in year t compared with those with no visit in t. Separate models were run for those who changed GP and those who moved from t-2 to t., and for the 20% who lived farthest away in t-1.ResultsWe could calculate the travel time for 3,976,910 residents in 2017, with a median travel time from home to the GP of 4.9 minutes and a travel time at the 90th percentile of 18.3 minutes. In the most sparsely populated northern county of Norway, travel time was about 5 minutes at the median and below 45 minutes at the 90th percentile. Elderly residents and residents who used their GP in 2017 had a somewhat shorter travel time than other groups of the population. Using annual data for 2009-2017 in the difference-in-differences analysis (16,388,151 resident-year observations), travel time dropped by 2.5 minutes (95% confidence interval 2.4 to 2.6) in t+1 and t+2 for patients with a visit in t compared with similar patients with no visit in t. The drop was similar for patients who did and did not change GP, but larger for patients who moved (10.0 minutes; 95%CI 9.7 to 10.4) compared with those who did not move (0.6 minutes; 95%CI 0.5 to 0.7), and particularly large for the 20% living farthest away in t-1 (24.2 minutes; 95%CI 23.3 to 25.2).ConclusionsTravel time from home to ones GP is short for the vast majority of the population in the sparsely populated country of Norway. However, residents move closer to the GP when they start using the services, especially patients who used to live far away. This relocation may reflect strong preferences for proximity to the services, and we conclude that more knowledge is needed to enable transparent balancing of costs and benefits of centralizing GP-services, at least in rural areas.JEL classificationI10, E32, J6
Impact of COVID-19 and Effects of Vaccination with BNT162b2 on Patient-Reported Health-Related Quality of Life, Symptoms, and Work Productivity Among US Adult Outpatients with SARS-CoV-2
Authors: Fusco Manuela Di , Sun Xiaowu , Moran Mary M. , Coetzer Henriette , Zamparo Joann M. , Puzniak Laura , Alvarez Mary B. , Tabak Ying P. , Cappelleri Joseph C. 
Published: September 2022

ABSTRACTBackgroundAlthough there is extensive literature on the clinical benefits of COVID-19 vaccination, data on humanistic effects are limited. This study evaluated the impact of SARS-CoV-2 infection on symptoms, Health Related Quality of Life (HRQoL) and Work Productivity and Impairment (WPAI) prior to and one month following infection, and compared results between individuals vaccinated with BNT162b2 and those unvaccinated.MethodsSubjects with ≥1 self-reported symptom and positive RT-PCR for SARS-CoV-2 at CVS Health US test sites were recruited between 01/31/2022-04/30/2022. Socio-demographics, clinical characteristics and vaccination status were evaluated. Self-reported symptoms, HRQoL, and WPAI outcomes were assessed using questionnaires and validated instruments (EQ-5D-5L, WPAI-GH) across acute COVID time points from pre-COVID to Week 4, and between vaccination groups. Mixed models for repeated measures were conducted for multivariable analyses, adjusting for several covariates. Effect size (ES) of Cohen’s d was calculated to quantify the magnitude of outcome changes within and between vaccination groups.ResultsThe study population included 430 subjects: 197 unvaccinated and 233 vaccinated with BNT162b2. Mean (SD) age was 42.4 years (14.3), 76.0% were female, 38.8% reported prior infection and 24.2% at least one comorbidity. Statistically significant differences in outcomes were observed compared with baseline and between groups. The EQ-Visual analogue scale scores and Utility Index dropped in both cohorts at Day 3 and increased by Week 4, but did not return to pre-COVID levels. The mean changes were statistically lower in the BNT162b2 cohort at Day 3 and Week 4. The BNT162b2 cohort reported lower prevalence and fewer symptoms at index date and Week 4. At Week 1, COVID-19 had a large impact on all WPAI-GH domains: the work productivity time loss among unvaccinated and vaccinated was 65.0% and 53.8%, and the mean activity impairment was 50.2% and 43.9%, respectively. With the exception of absenteeism at Week 4, the BNT162b2 cohort was associated with statistically significant less worsening in all WPAI-GH scores at both Week 1 and 4.ConclusionsCOVID-19 negatively impacted HRQoL and work productivity among mildly symptomatic outpatients. Compared with unvaccinated, those vaccinated with BNT162b2 were less impacted by COVID-19 infection and recovered faster.
The causal relationship between gastro-esophageal reflux disease and idiopathic pulmonary fibrosis: A bidirectional two-sample Mendelian randomization study
Authors: Reynolds Carl J , Del Greco M Fabiola , Allen Richard J , Flores Carlos , Jenkins R Gisli , Maher Toby M , Molyneaux Philip L , Noth Imre , Oldham Justin M , Wain Louise V , An Jiyuan , Ong Jue-Sheng , MacGregor Stuart , Yates Tom A. , Cullinan Paul , Minelli Cosetta 
Published: September 2022

AbstractBackgroundGastro-esophageal reflux disease (GERD) is associated with idiopathic pulmonary fibrosis (IPF) in observational studies. It is not known if this association arises because GERD causes IPF, or IPF causes GERD, or because of confounding by factors, such as smoking, associated with both GERD and IPF. We used bidirectional Mendelian randomisation (MR), where genetic variants are used as instrumental variables to address issues of confounding and reverse causation, to examine how, if at all, GERD and IPF are causally related.Methods and resultsA bidirectional two-sample MR was performed to estimate the causal effect of GERD on IPF risk, and of IPF on GERD risk, using genetic data from the largest GERD (78,707 cases and 288,734 controls) and IPF (4,125 cases and 20,464 controls) genome-wide association meta-analyses currently available. GERD increased the risk of IPF, with an odds ratio (OR) of 1.6 (95% Confidence Interval, CI: 1.04-2.49; p=0.032). There was no evidence of a causal effect of IPF on the risk of GERD, with an OR of 0.99 (95%CI: 0.97-1.02; p=0.615).ConclusionWe found that GERD increases the risk of IPF, but found no evidence that IPF increases the risk of GERD. GERD should be considered in future studies of IPF risk, and interest in it as a potential therapeutic target should be renewed. The mechanisms underlying the effect of GERD on IPF should also be investigated.
Low levels of monkeypox virus neutralizing antibodies after MVA-BN vaccination in healthy individuals
Authors: Zaeck Luca M. , Lamers Mart M. , Verstrepen Babs E. , Bestebroer Theo M. , van Royen Martin E. , Götz Hannelore , Shamier Marc C. , van Leeuwen Leanne P.M. , Schmitz Katharina S. , Alblas Kimberley , van Efferen Suzanne , Bogers Susanne , Scherbeijn Sandra , Rimmelzwaan Guus F. , van Gorp Eric C.M. , Koopmans Marion P.G. , Haagmans Bart L. , GeurtsvanKessel Corine H. , de Vries Rory D. 
Published: September 2022

AbstractIn July 2022, the ongoing monkeypox (MPX) outbreak was declared a public health emergency of international concern by the World Health Organization. Modified vaccinia virus Ankara (MVA-BN, also known as Imvamune, Jynneos, or Imvanex) is a 3rd generation smallpox vaccine that was generated by serial passaging of the more pathogenic parental vaccinia virus (VACV), and is authorized as a vaccine against MPX in humans in a two-shot regimen. Up to now, there is a lack of data that demonstrate MPX virus (MPXV)-neutralizing antibodies in vaccinated individuals and vaccine efficacy data against MPXV infection. Here, we measure MVA-, VACV-, and MPXV-reactive binding and neutralizing antibodies with validated in-house assays in cohorts of historically smallpox-vaccinated, MPXV PCR-positive, and recently MVA-BN-vaccinated individuals. We show that MPXV neutralizing antibodies were detected across all cohorts in individuals with MPXV exposure as well as those who received historic (VACV) vaccination. However, a primary MVA-BN immunization series in non-primed individuals yields relatively low levels of MPXV neutralizing antibodies. As the role of MPXV neutralizing antibodies for protection against disease and transmissibility is currently unclear and no correlate of protection against MPXV infection has been identified yet, this raises the question how well vaccinated individuals are protected. Dose-sparing leads to lower antibody levels, whereas a third MVA vaccination further boosts the antibody response. Cohort studies following vaccinated individuals are necessary to further assess vaccine efficacy in risk populations and determine correlates of protection for this emerging pathogen.
Atherosclerotic Cardiovascular Disease and Health-Related Quality of Life Among Adults in the United States: National Health Interview Survey 2013-2017
Authors: Hagan Kobina K. , Javed Zulqarnain , Acquah Isaac , Yahya Tamer , Valero-Elizondo Javier , Hyder Adnan A. , Mossiolas Elias , Lahan Shubham , Cainzos-Achirica Miguel , Nasir Khurram 
Published: September 2022

ABSTRACTBackgroundA brief health-related quality of life (HRQoL) tool with construct validity for atherosclerotic cardiovascular disease (ASCVD) may facilitate integration into healthcare delivery. We examined ASCVD-related changes in the Health and Activity Limitation Index (HALex), a generic HRQoL measure comprising perceived health and activity limitation.MethodsUsing data of 155,130 respondents of the National Health Interview Survey 2013-2017, we evaluated HALex scores by ASCVD (angina, heart attack, and stroke). Lower HALex scores reflected worse HRQoL and a 0.03 change was regarded as the threshold for clinical significance. Multivariable two-part models were used to assess HALex changes (β, 95%CI) associated with ASCVD overall and in sex, age, and race/ethnicity groups.ResultsOverall, participants with ASCVD – 6.8%, representing 15.7 million adults – had lower HALex scores (0.67) than those without ASCVD (0.87). Females, age ≥ 65 years, and non-Hispanic Blacks had the lowest HALex scores. Overall, ASCVD was associated with a substantial decrement in HALex (−0.10, [−0.10, −0.09]). Interactions between ASCVD and sex, and race/ethnicity were both significant (p < 0.001). ASCVD-associated decrement in HALex was clinically greater in: females (−0.11, [−0.12, −0.10]) than in males (−0.08, [−0.09, −0.07]); and non-Hispanic Black (−0.13, [−0.15, −0.1]) than in non-Hispanic White (−0.09, [−0.10, −0.08]). Though ASCVD impact on HALex was greater in age 18-64 years (−0.09, [−0.10, −0.08]), it was not statistically different from the elderly (−0.06, [−0.07, −0.06]).ConclusionsASCVD was consistently associated with lower HRQoL, as measured by HALex, across major demographics. HALex presents a feasible HRQoL tool to implement in healthcare.
Mapping the adaptor protein complex interaction network in Arabidopsis identifies P34 as a common stability regulator
Authors: Wang Peng , Siao Wei , Zhao Xiuyang , Arora Deepanksha , Wang Ren , Eeckhout Dominique , Leene Jelle Van , Kumar Rahul , Houbaert Anaxi , Winne Nancy De , Mylle Evelien , Vandorpe Michael , Korver Ruud A. , Testerink Christa , Gevaert Kris , Vanneste Steffen , Jaeger Geert De , Damme Daniël Van , Russinova Eugenia 
Published: September 2022

AbstractAdaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargos and coated vesicle accessory proteins. Since in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargos of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins, and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.
mTOR pathway inhibition stimulates pharmacologically induced nonsense suppression
Authors: Wittenstein Amnon , Caspi Michal , Rippin Ido , Elroy-Stein Orna , Eldar-Finkelmn Hagit , Thoms Sven , Rosin-Arbesfeld Rina 
Published: September 2022

ABSTRACTA large number of human genetic diseases result from premature termination codons (PTCs) caused by splicing defects, insertions, deletions or point mutations also termed nonsense mutations. Nonsense mutations are the source of various genetic diseases, ranging from rare neuro-metabolic disorders to relatively common inheritable cancer syndromes and muscular dystrophies. Over the years, a wide spectrum of studies has shown that certain antibiotics and other synthetic molecules can act as nonsense mutation suppressors, by inducing readthrough of the stop-codon leading to the expression of a full-length protein. Unfortunately, most readthrough-inducing agents have limited effects and are toxic. Thus, efforts are made to improve the clinical outcome of nonsense mutation suppressors.Here we show that the mTOR pathway is involved in antibiotic-mediated readthrough of nonsense mutations at the level of protein translation initiation. We demonstrate that inhibition of the mTOR translation-initiation-controlling eIF4E branch induces antibiotic-mediated nonsense mutation readthrough, paving the way to the development of a novel therapeutic strategy for enhancing the restoration of these disease-causing mutated transcripts.
Voltage clamp fluorometry analysis of the P2×7 receptor suggests a limited conformational interplay between extracellular ATP binding and the intracellular ballast domain
Authors: Durner Anna , Durner Ellis , Nicke Annette 
Published: September 2022

AbstractThe large intracellular C-terminus of the pro-inflammatory P2×7 ion channel receptor (P2×7R) is associated with diverse P2×7R-specific functions. Cryo-EM structures of the closed and ATP-bound open full-length P2×7R recently identified a membrane-associated anchoring domain, an open-state stabilizing “cap” domain, and a globular “ballast domain” containing GTP/GDP and dinuclear Zn2+-binding sites with unknown functions. To investigate protein dynamics during channel activation, we improved incorporation of the environment-sensitive fluorescent unnatural amino acid L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (ANAP) into Xenopus laevis oocyte-expressed P2×7Rs and performed voltage clamp fluorometry (VCF). While we confirmed predicted conformational changes within the extracellular and the transmembrane domains, only three out of 41 mutants containing ANAP in the C-terminal domain resulted in ATP-induced fluorescence changes. We conclude that the ballast domain functions rather independently from the extracellular ATP binding domain and might require activation by additional ligands and/or protein interactions. Novel tools to study these are presented.