bluuebunny/crossref_metadata_2025_split huggingface dataset:
ribosomal DNA instability as a potential cause of karyotype evolution
Authors: Li Duojia , Gandhi Dhyey , Kumon Tomohiro , Yamashita Yukiko M. 
Published: July 2022

AbstractKaryotype refers to the configuration of the genome into a set of chromosomes. The karyotype difference between species is expected to impede various biological processes, such as chromosome segregation or meiotic chromosome pairing, potentially contributing to incompatibility. Karyotypes can rapidly change between closely related species and even among populations of the same species. However, the forces driving karyotype evolution are poorly understood. Here we describe a unique karyotype of a D. melanogaster strain isolated from the Seychelles archipelago. This strain has lost the ribosomal DNA (rDNA) locus on the X chromosome. Because the Y chromosome is the only other rDNA-bearing chromosome, all females carry at least one Y chromosome as the source of rDNA. Interestingly, we found that the strain also carries a truncated Y chromosome (YS) that is stably maintained in the population despite its inability to support male fertility. Our modeling and cytological analysis suggest that the Y chromosome has a larger negative impact on female fitness than the YS chromosome. Moreover, we generated an independent strain that lacks X rDNA and has a karyotype of XXY females and XY males. This strain quickly evolved multiple karyotypes: two new truncated Y chromosomes (similar to YS), as well as two independent X chromosome fusions that contain the Y-derived rDNA fragment, eliminating females’ dependence on the Y chromosome. Considering that Robertsonian fusions frequently occur at rDNA loci in humans, we propose that rDNA loci instability is a driving force of karyotype evolution.
Age-stratified seroprevalence of antibodies against SARS-CoV-2 in the pre- and post-vaccination era, February 2020–March 2022, Japan
Authors: Yamayoshi Seiya , Iwatsuki-Horimoto Kiyoko , Okuda Moe , Ujie Michiko , Yasuhara Atsuhiro , Murakami Jurika , Duong Calvin , Hamabata Taiki , Ito Mutsumi , Chiba Shiho , Kobayashi Ryo , Takahashi Satoshi , Mitamura Keiko , Hagihara Masao , Shibata Akimichi , Uwamino Yoshifumi , Hasegawa Naoki , Ebina Toshiaki , Izumi Akihiko , Kato Hideaki , Nakajima Hideaki , Sugaya Norio , Seki Yuki , Iqbal Asef , Kamimaki Isamu , Yamazaki Masahiko , Kawaoka Yoshihiro , Furuse Yuki 
Published: July 2022

AbstractJapan has reported a small number of COVID-19 cases relative to other countries. Because not all infected people receive diagnostic tests for COVID-19, the reported number of COVID-19 cases must be lower than the actual number of infections. Assessments of the presence of antibodies against the spike protein of SARS-CoV-2 can retrospectively determine the history of natural infection and vaccination. In this study, we assessed SARS-CoV-2 seroprevalence by analyzing over 60,000 samples collected in Japan from February 2020 to March 2022. The results showed that about 5% of the Japanese population had been infected with the virus by January 2021. The seroprevalence increased with the administration of vaccinations to adults; however, among the elderly, it was not as high as the vaccination rate, probably due to poor immune responses to the vaccines and waning immunity. The infection was spread during the epidemic waves caused by the SARS-CoV-2 Delta and Omicron variants among children who were not eligible for vaccination. Nevertheless, their seroprevalence was as low as 10% as of March 2022. Our study underscores the low incidence of SARS-CoV-2 infection in Japan and the effects of vaccination on immunity at the population level.
Impact of non-pharmaceutical interventions on COVID-19 incidence and deaths: cross-national natural experiment in 32 European countries
Authors: Costa Diogo , Rohleder Sven , Bozorgmehr med Kayvan 
Published: July 2022

AbstractPurposeNon-pharmaceutical interventions (NPIs) have been the cornerstone of COVID-19 pandemic control, but evidence on their effectiveness varies according to the methods and approaches taken to empirical analysis.We analysed the impact of NPIs on incident SARS-CoV-2 across 32 European countries (March-December 2020) using two NPI trackers: the Corona Virus Pandemic Policy Monitor – COV-PPM, and the Oxford Covid-19 Government Response Tracker – OxCGRT.MethodsNPIs were summarized through principal component analysis into three sets, stratified by two waves (C1-C3, weeks 5-25, and C4-C6, weeks 35-52). Longitudinal, multi-level mixed-effects negative binomial regression models were fitted to estimate incidence rate ratios for cases and deaths considering different time-lags and reverse causation (i.e. changing incidence causing NPIs), stratified by waves and geographical regions (Western, Eastern, Northern, Southern, Others).ResultsDuring the first wave, restrictions on movement/mobility, public transport, public events, and public spaces (C1) and healthcare system improvements, border closures and restrictions to public institutions (C2) reduced SARS-CoV-2 incidence after 28 and 35-days. Mask policies (C3) reduced SARS-CoV-2 incidence (except after 35-days). During wave 1, C1 and C2 reduced deaths after 49-days and C3 after 21, 28 and 35-days. During wave 2, restrictions on movement/mobility, public transport and healthcare system improvements (C5) decreased SARS-CoV-2 cases and deaths across all countries.ConclusionIn the absence of pre-existing immunity, vaccines or treatment options, the impact of NPIs on SARS-CoV-2 incidence and deaths varied by regions and waves but was consistent across components of NPIs derived from two policy trackers (CoV-PPM and OxCGRT).
Health impact of routine measles vaccination and supplementary immunisation activities in 14 high burden countries: a DynaMICE modelling study
Authors: Auzenbergs Megan , Fu Han , Abbas Kaja , Procter Simon R , Cutts Felicity , Jit Mark 
Published: July 2022

AbstractBackgroundWHO recommends ≥95% population coverage with two doses of measles-containing vaccine (MCV). Most countries used routine services to offer MCV1 and later, MCV2. Many countries conducted supplementary immunisation activities (SIAs), offering vaccination to all persons in a given age range irrespective of prior vaccination history. We estimated the relative impact of each dose and delivery route in 14 high burden countries.MethodsWe used an age-structured dynamic model (DynaMICE), to estimate the health impact of different vaccination strategies on measles susceptibility and burden over 2000-2020. We estimated their incremental impact using averted cases and deaths and their efficiency using number needed to vaccinate (NNV) to avert an additional measles case.FindingsCompared to no vaccination, MCV1 implementation averted 823 million cases and 9.5 million deaths, with a median NNV of 1.41. Adding routine MCV2 to MCV1 further averted 108 million cases and 0.4 million deaths, while adding SIAs to MCV1 led to 249 million averted cases and 4 million deaths. Despite a larger incremental impact, adding SIAs to MCV1 showed reduced efficiency compared to adding routine MCV2, with median NNVs of 6.15 and 5.41, respectively.InterpretationVaccination strategies including non-selective SIAs reach a greater proportion of unvaccinated children and reduce burden more than MCV2 alone, but efficiency is somewhat lower because of the wide age groups included in SIAs. This analysis provides insight to improve health impact and efficiency of measles vaccination.FundingGavi, the Vaccine Alliance, and the Bill & Melinda Gates Foundation (OPP1157270)
Prevalence of anti-DENV IgG among routine Bangladeshi blood donors, and strategies for the future
Authors: Hoque Ashraful , Basak Sushanta Kumar , Al-Mamun A.B.M. , Rahman Marufur , Islam Kashfia 
Published: July 2022

AbstractBackgroundDengue is the most common arthropod-borne sickness worldwide, impacting at least 50 million people each year. The dengue virus has four primary serotypes. Infection with one serotype confers homotypic immunity but not heterologous immunity, and secondary infections may be more severe. Although blood transfusions and organ donations have also been observed, the Aedes aegypti mosquito is the primary vector for the transmission of dengue. Infection causes a continuum of clinical illness, from asymptomatic infection to dengue fever, DHF, and dengue shock syndrome (DSS).AimTo assess the presence of anti DENV IgG and anti DENV IgM antibodies specific to the four dengue serotypes in blood donor service donors and the importance of pre-donation screening in routine blood collection procedures.Method3 mL of peripheral venous blood from 507 blood donors was collected in tubes with BD vacutainer gel tube for serum separation after epidemiological records were reviewed. After that, serum was separated and tests were performed by SD Bioline Dengue Duo. Participants in the study completed a social and epidemiological questionnaire that contained information such as age, gender, and dengue diagnosis.ResultOut of the 507 blood samples that were taken, 473 (93.3%) came from male blood donors, while the remaining 34 (6.7%) belonged to female blood donors. The ratio of males to females is 13.91 to 1. The age range is 18–60 years, and the mean and standard deviation are both 27.7 and 6.5. 183 of the 507 samples produced anti DENV IgG positivity, while 324 did not. The ratio of positive to negative was 1.25:2.ConclusionAccording to the findings of this study, quantitative methods for determining the presence of anti-dengue antibodies or detecting the dengue virus in blood donors in endemic areas should be devised in order to ensure the quality of blood transfusions.
Multi-omics provide evidence for an anti-inflammatory immune signature and metabolic alterations in patients with Long COVID Syndrome – an exploratory study
Authors: Kovarik Johannes J. , Bileck Andrea , Hagn Gerhard , Meier-Menches Samuel M. , Frey Tobias , Kaempf Anna , Hollenstein Marlene , Shoumariyeh Tarik , Skos Lukas , Reiter Birgit , Gerner Marlene C. , Spannbauer Andreas , Hasimbegovic Ena , Schmidl Doreen , Garhöfer Gerhard , Gyöngyösi Mariann , Schmetterer Klaus G. , Gerner Christopher 
Published: July 2022

AbstractDespite the increasing prevalence of patients with Long Covid Syndrome (LCS), to date the pathophysiology of the disease is still unclear, and therefore diagnosis and therapy are a complex effort without any standardization. To address these issues, we performed a broad exploratory screening study applying state-of-the-art post-genomic profiling methods to blood plasma derived from three groups: 1) healthy individuals vaccinated against SARS-CoV-2 without exposure to the full virus, 2) asymptomatic fully recovered patients at least three months after SARS-CoV-2 infection, 3) symptomatic patients at least 3 months after a SARS-CoV-2 infection, here designated as Long Covid Syndrome (LCS) patients. Multiplex cytokine profiling indicated slightly elevated cytokine levels in recovered individuals in contrast to LCS patients, who displayed lowest levels of cytokines. Label-free proteome profiling corroborated an anti-inflammatory status in LCS characterized by low acute phase protein levels and a uniform down-regulation of macrophage-derived secreted proteins, a pattern also characteristic for chronic fatigue syndrome (CFS). Along those lines, eicosanoid and docosanoid analysis revealed high levels of omega-3 fatty acids and a prevalence of anti-inflammatory oxylipins in LCS patients compared to the other study groups. Targeted metabolic profiling indicated low amino acid and triglyceride levels and deregulated acylcarnithines, characteristic for CFS and indicating mitochondrial stress in LCS patients. The anti-inflammatory osmolytes taurine and hypaphorine were significantly up-regulated in LCS patients. In summary, here we present evidence for a specific anti-inflammatory and highly characteristic metabolic signature in LCS which could serve for future diagnostic purposes and help to establish rational therapeutic interventions in these patients.One sentence SummaryMulti-omics plasma analyses demonstrate anti-inflammatory and hypo-metabolic signatures in patients with Long COVID Syndrome.
Validating the Breathing Vigilance Questionnaire for use in Dysfunctional Breathing
Authors: Steinmann Jennifer , Lewis Adam , Ellmers Toby , Jones Mandy , MacBean Vicky , Kal Elmar 
Published: July 2022

AbstractDysfunctional breathing (DB) is common among people with and without primary respiratory pathology. While anxiety contributes to DB, the underpinning mechanism is unclear. One explanation is that anxiety induces excessive conscious monitoring of breathing, disrupting ‘automatic’ breathing mechanics. We validated a new tool that quantifies such breathing-related ‘hypervigilance’: the Breathing Vigilance Questionnaire (Breathe-VQ).Three-hundred-and-forty healthy adults (Mage=27.3 years, range: 18-71; 161 men) were recruited online. We developed an initial Breathe-VQ (11 items, 1-5 Likert scale) based on the Pain Vigilance and Awareness Scale, using feedback from the target population and clinicians. At baseline, participants completed the Breathe-VQ, Nijmegen Questionnaire (NQ), State-Trait Anxiety Inventory (form 2), and Movement-Specific Reinvestment Scale (assessing general conscious processing). Eighty-three people repeated the Breathe-VQ two weeks later.We removed five items based on item-level analysis. The resulting six-item Breathe-VQ questionnaire (score range: 6-30) has excellent internal (alpha=.892) and test-retest reliability (ICC=.810), a minimal detectable change of 6.5, and no floor/ceiling effects. Concurrent validity was evidenced by significant positive correlations with trait anxiety and conscious processing scores (r’s=.35-.46). Participants at high-risk of having DB (NQ>23; N=76) had significantly higher Breathe-VQ score (M=19.1±5.0) than low-risk peers (N=225; M=13.8±5.4;p<.001). In this ‘high-risk’ group, Breathe-VQ and NQ-scores were significantly associated (p=.005), even when controlling for risk factors (e.g., trait anxiety).The Breathe-VQ is a valid and reliable tool to measure breathing vigilance. Breathing vigilance may contribute to DB, and could represent a therapeutic target. Further research is warranted to further test the Breathe-VQ’s prognostic value, and assess intervention effects.Key Findings– Dysfunctional breathing (DB) is highly prevalent in the general population as well as in people with respiratory conditions.– Anxiety is identified as a key factor contributing to DB, potentially because it induces conscious, anxious monitoring of breathing.– We developed a short self-reported outcome measure of such breathing-specific vigilance, the Breathe-VQ.– The Breathe-VQ was found to be a valid and reliable tool for use in the general population.– Breathe-VQ scores were positively associated with self-reported breathing problems, after correcting for known risk factors such as trait-anxiety.
Multi-site disease analytics with applications to estimating COVID-19 undetected cases in Canada
Authors: Parker Matthew R. P. , Cao Jiguo , Cowen Laura L. E. , Elliott Lloyd T. , Ma Junling 
Published: July 2022

AbstractEven with daily case counts, the true scope of the COVID-19 pandemic in Canada is unknown due to undetected cases. We estimate the pandemic scope through a new multi-site model using publicly available disease count data including detected cases, recoveries among detected cases, and total deaths. These counts are used to estimate the case detection probability, the infection fatality rate through time, as well as the probability of recovery, and several important population parameters including the rate of spread, and importation of external cases. We also estimate the total number of active COVID-19 cases per region of Canada for each reporting interval. We applied this multi-site model Canada-wide to all provinces and territories, providing an estimate of the total COVID-19 burden for the 90 weeks from 23 Apr 2020 to 6 Jan 2022. We also applied this model to the five Health Authority regions of British Columbia, Canada, describing the pandemic in B.C. over the 31 weeks from 2 Apr 2020 to 30 Oct 2020.
Changes in General Practice use and costs with COVID-19 and telehealth initiatives
Authors: Butler Danielle C , Joshy Grace , Douglas Kirsty A , Bin-Sayeed Muhammad-Shahdaat , Welsh Jennifer , Douglas Angus , Korda Rosemary J. ,   the ANU Telehealth in Primary Care study group
Published: July 2022

AbstractBackgroundIn response to the COVID-19 pandemic, general practice (GP) in Australia underwent a rapid transition, including the rollout of population-wide telehealth, with uncertain impacts on GP use and costs.ObjectiveTo describe how use and costs of GP services in Australia changed in 2020—following the pandemic and introduction of telehealth—compared to 2019, and how this varied across population subgroups.MethodData for ∼19M individuals from Census 2016 were linked to Medicare data for 2019-2020 through the Multi-Agency Data Integration Project. We used regression models to compare age-sex-adjusted GP use and out-of-pocket cost (OPC) over time, overall and by sociodemographic characteristics.ResultsThe number of people who visited a GP in Q2-Q4 of 2020 decreased by 4% compared to Q2-Q4 of 2019. The mean number of face-to-face GP services per quarter declined, while telehealth services increased, with overall use of GP services in Q4 2020 similar to or higher than Q4 2019. The proportion of total GP services by telehealth stabilised at ∼25% in Q4 2020. However, individuals aged 3-14 or ≥70 years and those with limited English proficiency used fewer GP services in 2020 compared to 2019, with a lower proportion by telehealth. Mean OPC-per-service was lower across all subgroups in 2020 compared to 2019.DiscussionIntroduction of widespread telehealth largely maintained use of GP services during the pandemic and minimised OPCs, but not for all population subgroups. This may indicate technological, social or other barriers in these populations, as well as pandemic-related changes in healthcare use.HOW THIS FITS INIn response to the COVID-19 pandemic, major telehealth initiatives were implemented to ensure access to primary healthcare while minimising disease transmission. Using routinely collected, whole-of-population data from Australia, we show that the introduction of telehealth during the pandemic largely maintained use of GP services while minimising costs. However, compared to pre-pandemic levels, GP use was lower among individuals aged 3-14 or ≥70 years and those not proficient in English, although these groups also saw the greatest reduction in out-of-pocket cost per service. As telehealth initiatives are integrated into standard GP care, it is vital to ensure telehealth is designed and funded to support these groups and the ongoing financial viability of practices.
Efficient generation of mNeonGreenPlasmodium falciparumreporter lines enables quantitative fitness analysis
Authors: Hoshizaki Johanna , Jagoe Hannah , Lee Marcus 
Published: July 2022

1AbstractCRISPR editing has enabled the rapid creation of fluorescentPlasmodiumtransgenic lines, facilitating a deeper understanding of parasite biology. The impact of genetic perturbations such as gene disruption or the introduction of drug resistance alleles on parasite fitness is typically quantified in competitive growth assays between the query line and a wild type reference. Although fluorescent reporter lines offer a facile and frequently used method to measure relative growth, this approach is limited by the strain background of the existing reporter, which may not match the growth characteristics of the query strains, particularly if these are slower-growing field isolates. Here, we demonstrate an efficient CRISPR-based approach to generate fluorescently labelled parasite lines using mNeonGreen derived from the LanYFP protein inBranchiostoma lanceolatum, which is one of the brightest monomeric green fluorescent proteins identified. Using a positive-selection approach by insertion of an in-frame blasticidin S deaminase marker, we generated a Dd2 reporter line expressing mNeonGreen under the control of thepfpare(P. falciparumProdrug Activation and Resistance Esterase) locus. We selected thepfparelocus as an integration site because it is highly conserved acrossP. falciparumstrains, expressed throughout the intraerythrocytic cycle, not essential, and offers the potential for negative selection to further enrich for integrants. The mNeonGreen@pareline demonstrates strong fluorescence with a negligible fitness defect. In addition, the construct developed can serve as a tool to fluorescently tag otherP. falciparumstrains forin vitroexperimentation.
Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil
Authors: Caro Tristan A. , McFarlin Jamie , Jech Sierra , Fierer Noah , Kopf Sebastian 
Published: July 2022

AbstractThe rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen stable isotope probing of lipids with2H-enriched water. This technique provides a taxa-agnostic quantification ofin situmicrobial growth from the degree of2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that average apparent generation times in soil are quite slow (20 to 64 days) but also highly variable at the compound-specific level (6 to 1137 days), suggesting differential growth rates between community subsets. We observe that low-biomass communities can exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.SignificanceGeneration times, how quickly organisms grow and reproduce, are a key feature of biology. However, there are few measurements of microbial generation times in soil, despite the crucial importance of soil microbes to terrestrial ecosystems. By measuring the rate at which isotopically labeled water is incorporated into microbial membranes, we find that the generation times of soil microorganisms are far longer than those typically observed in culture. Surprisingly, we observe that lower-biomass soils exhibited faster growth rates than high-biomass soils. More abundant microorganisms are not necessarily the fastest growing and most soil microorganisms are slow growers. Our results underscore the importance of considering slow and variable growth rates when studying microbial communities and their contributions to ecosystem processes.