bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous monitoring of SARS-CoV-2 RNA in urban wastewater from Porto, Portugal: sampling and analysis protocols
Authors: Tomasino Maria Paola , Semedo Miguel , Vieira Pedro , Ferraz Elza , Rocha Adelaide , Carvalho Maria F. , Magalhães Catarina , Mucha Ana P. 
Published: April 2021

AbstractResearch on the emerging COVID-19 pandemic is demonstrating that wastewater infrastructures can be used as public health observatories of virus circulation in human communities. Important efforts are being organized worldwide to implement sewage-based surveillance of SARS-CoV-2 that can be used for preventive or early warning purposes, informing preparedness and response measures. However, its successful implementation requires important and iterative methodological improvements, as well as the establishment of standardized methods. The aim of this study was to develop a continuous monitoring protocol for SARS-CoV-2 in wastewater, that could be used to model virus circulation within the communities, complementing the current clinical surveillance. Specific objectives included (1) optimization and validation of a sensitive method for virus quantification; (2) monitoring the time-evolution of SARS-CoV-2 in wastewater from two wastewater treatment plants (WWTPs) in the city of Porto, Portugal. Untreated wastewater samples were collected weekly from the two WWTPs between May 2020 and March 2021, encompassing two COVID-19 incidence peaks in the region (mid-November 2020 and mid-January 2021). In the first stage of this study, we compared, optimized and selected a sampling and analysis protocol that included RNA virus concentration through centrifugation, RNA extraction from both liquid and solid fractions and quantification by reverse transcription quantitative PCR (RT-qPCR). In the second stage, we used the selected methodology to track SARS-CoV-2 in the collected wastewater over time. SARS-CoV-2 RNA was detected in 39 and 37 out of 48 liquid and solid fraction samples of untreated wastewater, respectively. The copy numbers varied throughout the study between 0 and 0.15 copies/ng RNA and a good fit was observed between the SARS-CoV-2 RNA concentration in the untreated wastewater and the COVID-19 temporal trends in the study region. In agreement with the recent literature, the results from this study support the use of wastewater-based surveillance to complement clinical testing and evaluate temporal and spatial trends of the current pandemic.
Correcting Covid-19 PCR Prevalence for False Positives in the Presence of Vaccination Immunity
Authors: Halem Michael 
Published: April 2021

AbstractSince the first analysis was published on 7 April 2021 the PCR test positivity rate has dropped significantly below the then estimated false positive rate (FPR) of 1.16% using the exponential decay to FPR model. Therefore, the estimate has been rejected and a new model was developed.Using the ONS infection survey’s assumption (PCR FPR rate below 0.1%) the new model splits the test time series data into two periods based on a change in transmissibility that coincides with the reopening of England schools on 8 March. The new model provides for two base levels of exponential decay (for each period’s transmissibility) combined with a single decay rate increase dependent on vaccination.Because the FPR is relatively insignificant compared to current PCR test positives, it cannot be statistically separated using currently available England epidemic time series data by the non-linear least squares estimation technique. Therefore, the FPR factor is temporarily dropped in the least squares regression.The new model is stable in that it reasonably predicts through the most current available data (25 April) the future test prevalence using parameters estimated with 29 March data. Thus far, the estimate parameters remain within their original confidence intervals as successive days are added to the time series. Of potential usefulness is the current estimate for change in decay rate per mean vaccination rate, currently estimated at approximately 10.7% (CI: 8.8% - 12.6%). The estimate should be used with caution as other unforeseen factors could cause the model to misestimate.
Millennial-scale change on a Caribbean reef system that experiences hypoxia
Authors: Figuerola Blanca , Grossman Ethan L. , Lucey Noelle , Leonard Nicole D. , O’Dea Aaron 
Published: April 2021

AbstractCoastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi-enclosed system that experiences hypoxia in deeper waters which occasionally expand into shallow coral reefs, suffocating most aerobic benthic life. To explore the long-term history of reefs in the bay we extracted reef matrix cores from two reefs that today experience contrasting patterns of oxygenation. We constructed a 1800-year-long record of gastropod assemblages and isotope compositions from six U-Th chronologically-constrained reef matrix cores. We extracted two cores from each reef at 3 m water depth and two additional cores from a deeper part (4.8 m) of the hypoxia-exposed reef. Results show that the deeper part of the hypoxic reef slowed in growth and stopped accreting approximately 1500 years BP while the shallow part of the reef continued to accrete to the present day, in agreement with a model of expanding hypoxia at this time. Our proxy-based approach suggests that differences among these palaeoindicators in the two reefs may have been driven by an increase in hypoxia via eutrophication caused by either natural changes or human impacts. Similar patterns of increasing herbivores and decreasing carbon isotope values occurred in the shallow part of the hypoxic reef during the last few decades. This suggests that hypoxia may be expanding to depths as shallow as 3 m and that shallow reefs are experiencing greater risk due to increased human activity.
Sex and Gender Considerations in Reporting Guidelines of Health Research: A Systematic Review
Authors: Gogovor Amédé , Zomahoun Hervé Tchala Vignon , Ekanmian Giraud , Adisso Évèhouénou Lionel , Tardif Alèxe Deom , Khadhraoui Lobna , Rheault Nathalie , Moher David , Légaré France 
Published: April 2021

AbstractBackgroundDespite growing recognition of the importance of sex and gender considerations in health research, they are rarely integrated into research design and reporting. We sought to assess the integration of sex, as a biological attribute and gender as a socially constructed identity in published reporting guidelines.Methods and FindingsWe conducted a systematic review of published reporting guidelines listed on the EQUATOR website (www.equator-nework.org) from inception until December 2018. We selected all reporting guidelines (original and extensions) listed on the EQUATOR library. We used EndNote Citation Software to build a database of the statement of each guideline identified as ‘full bibliographic reference’ and retrieved the full texts. Reviewers independently extracted the data from the checklist/abstract/main text of guidelines. Data were analyzed using descriptive statistics and narrative synthesis. A total of 407 reporting guidelines were included; they were published between 1995 and 2018. Of the 407 guidelines, 159 (39%) mentioned “sex” and/or “gender” in the checklist/abstract/main text. Of these, 90 (22.1%) mentioned only “sex”, and 91 (22.4%) mentioned only “gender”. In the checklist of the reporting guidelines (n = 363), “sex” and “gender” were mentioned in 50 (13.8%) and 39 (10.7%), respectively. Only one reporting guideline met the three criteria of correct use of sex and gender concepts. Trends in the use of sex and gender in the checklists showed that the use of “sex” only started in 2003, while “gender” has been used since 1996.ConclusionsWe assessed the integration of sex and gender considerations in reporting guidelines based on the use of sex- and gender-related words. Our findings showed a low use and integration of sex and gender concepts in reporting guidelines. Authors of reporting guidelines should reduce this gap for a better use of research knowledge.Registration:PROSPERO no. CRD42019136491.
A fully adapted headstage for electrophysiological experiments with custom and scalable electrode arrays to record widely distributed brain regions
Authors: Mourão Flávio Afonso Gonçalves , de Oliveira Guarnieri Leonardo , Júnior Paulo Aparecido Amaral , Carvalho Vinícius Rezende , Mendes Eduardo Mazoni Andrade Marçal , Moraes Márcio Flávio Dutra 
Published: April 2021

ABSTRACTElectrophysiological recordings lead amongst the techniques that aim to investigate the dynamics of neural activity sampled from large neural ensembles. However, the financial costs associated with the state-of-the-art technology used to manufacture probes and multi-channel recording systems make these experiments virtually inaccessible to small laboratories, especially if located in developing countries. Here, we describe a new method for implanting several tungsten electrode arrays, widely distributed over the brain. Moreover, we designed a headstage system, using the Intan®RHD2000 chipset, associated with a connector (replacing the expensive commercial Omnetics connector), that allows the usage of disposable and cheap cranial implants. Our results showed high-quality multichannel recording in freely moving animals (detecting local field, evoked responses and unit activities) and robust mechanical connections ensuring long-term continuous recordings. Our project represents an open source and inexpensive alternative to develop customized extracellular records from multiple brain regions.
Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins
Authors: Sharma Stuti , Zhou Ruoyu , Wan Li , Song KangKang , Xu Chen , Li Yanyan , Liao Maofu 
Published: April 2021

AbstractPresent in all bacteria, lipoproteins are central in bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of cytoplasmic membrane. In Gram-negative bacteria, many lipoproteins are transported to the outer membrane (OM), a process dependent on the ATP-binding cassette (ABC) transporter LolCDE which extracts the OM-targeted lipoproteins from the cytoplasmic membrane for subsequent trafficking across the periplasm. Lipid-anchored proteins pose a unique challenge for transport machinery as they have both hydrophobic lipid moieties and soluble protein component, and the underlying mechanism is poorly understood. Here we determined the cryo-EM structures of nanodisc-embedded LolCDE in the nucleotide-free and nucleotide-bound states at 3.8-Å and 3.5-Å resolution, respectively. The structural analyses, together with biochemical and mutagenesis studies, uncover how LolCDE specifically recognizes its substrate by establishing multiple interactions with the lipid and N-terminal peptide moieties of the lipoprotein, and identify the amide-linked acyl chain as the key element for LolCDE interaction. Upon nucleotide binding, the transmembrane helices and the periplasmic domains of LolCDE undergo large-scale, asymmetric movements, resulting in extrusion of the captured lipoprotein. Comparison of LolCDE and MacB reveals the conserved mechanism of type VII ABC transporters and emphasizes the unique properties of LolCDE as a molecule extruder of triacylated lipoproteins.
A CRISPRi screen of essential genes reveals that proteasome regulation dictates acetic acid tolerance inSaccharomyces cerevisiae
Authors: Mukherjee Vaskar , Lind Ulrika , St. Onge Robert P. , Blomberg Anders , Nygård Yvonne 
Published: April 2021

ABSTRACTCRISPR interference (CRISPRi) is a powerful tool to study cellular physiology under different growth conditions and this technology provides a means for screening changed expression of essential genes. In this study, aSaccharomyces cerevisiaeCRISPRi library was screened for growth in medium supplemented with acetic acid. Acetic acid is a growth inhibitor challenging the use of yeast for industrial conversion of lignocellulosic biomasses. Tolerance towards acetic acid that is released during biomass hydrolysis is crucial for cell factories to be used in biorefineries.The CRISPRi library screened consists of >9,000 strains, where >98% of all essential and respiratory growth-essential genes were targeted with multiple gRNAs. The screen was performed using the high-throughput, high-resolution Scan-o-matic platform, where each strain is analyzed separately. Our study identified that CRISPRi targeting of genes involved in vesicle formation or organelle transport processes led to severe growth inhibition during acetic acid stress, emphasizing the importance of these intracellular membrane structures in maintaining cell vitality. In contrast, strains in which genes encoding subunits of the 19S regulatory particle of the 26S proteasome were downregulated had increased tolerance to acetic acid, which we hypothesize is due to ATP-salvage through an increased abundance of the 20S core particle that performs ATP-independent protein degradation. This is the first study where a high-resolution CRISPRi library screening paves the way to understand and bioengineer the robustness of yeast against acetic acid stress.IMPORTANCEAcetic acid is inhibitory to the growth of the yeastSaccharomyces cerevisiae, causing ATP starvation and oxidative stress, which leads to sub-optimal production of fuels and chemicals from lignocellulosic biomass. In this study, where each strain of a CRISPRi library was characterized individually, many essential and respiratory growth essential genes that regulate tolerance to acetic acid were identified, providing new understanding on the stress response of yeast and new targets for the bioengineering of industrial yeast. Our findings on the fine-tuning of the expression of proteasomal genes leading to increased tolerance to acetic acid suggests that this could be a novel strategy for increasing stress tolerance, leading to improved strains for production of biobased chemicals.
Prevalence of SARS-CoV-2 antibodies in Denmark 2020: results from nationwide, population-based sero-epidemiological surveys
Authors: Espenhain Laura , Tribler Siri , Jørgensen Charlotte Sværke , Holm Hansen Christian , Wolff Sönksen Ute , Ethelberg Steen 
Published: April 2021

BackgroundSeroprevalence studies have proven an important tool to monitor the progression of the coronavirus disease 2019 (COVID-19) epidemic. We present results of consecutive population-based seroprevalence surveys performed in Denmark in 2020.MethodsInvitation letters including a questionnaire covering symptoms were sent to representatively drawn samples of the population in spring, late summer and autumn/winter of 2020. Blood samples from participants taken at public test-centers were analyzed for total Ig and seroprevalence estimates per population segment calculated and compared to other surveillance parameters.ResultsFrom 34,081 participating individuals (response rate 33%), we obtained seroprevalence estimates increasing from 1.1% (95%CI: 0.7%–1.7) in May to 4.0 % (95%CI: 3.4%–4.7%) in December 2020. By December 2020, 1.5% of the population 12 years and older had tested positive by PCR. Seroprevalence estimates were roughly 3 times higher in those aged 12-29 compared to 65+ and higher in metropolitan municipalities. Among seropositives, loss of taste/smell were the more specific symptoms, 32%-56% did not report any symptoms. In half of seroconverted families, we did not see evidence of transmission between generations. Infected individuals in older age groups were hospitalized several fold more often than in younger.ConclusionsSeroprevalence increased during 2020; younger age groups were primarily infected in the autumn/winter surge. Approximately half were asymptomatically infected. Denmark has a high per capita test rate; roughly two undiagnosed infections of COVID-19 were estimated to occur for each diagnosed case. The epidemic appears to have progressed relatively modestly during 2020 in Denmark.summaryWe describe population-based COVID-19 seroprevalence surveys performed in Denmark in 2020. The seroprevalence increased during the year, particularly in adolescents and young adults, but was overall low. Roughly two undiagnosed cases per PCR-confirmed case were detected by December 2020.
PepVAE3: variational autoencoder framework for antimicrobial peptide generation and activity prediction
Authors: Dean Scott N. , Alvarez Jerome Anthony E. , Zabetakis Dan , Walper Scott A. , Malanoski Anthony P. 
Published: April 2021

AbstractNew methods for antimicrobial design are critical for combating pathogenic bacteria in the post-antibiotic era. Fortunately, competition within complex communities has led to the natural evolution of antimicrobial peptide (AMP) sequences that have promising bactericidal properties. Unfortunately, the identification, characterization, and production of AMPs can prove complex and time consuming. Here we report a peptide generation framework, PepVAE3, based around variational autoencoder (VAE) and antimicrobial activity prediction models for designing novel AMPs using only sequences and experimental minimum inhibitory concentration (MIC) data as input. Sampling from distinct regions of the learned latent space allows for controllable generation of new AMP sequences with minimal input parameters. Extensive analysis of the PepVAE3-generated sequences paired with antimicrobial activity prediction models supports this modular design framework as a promising system for development of novel AMPs, demonstrating controlled production of AMPs with experimental validation of predicted antimicrobial activity.
Keratin dynamics govern the establishment of the maternal-fetal interface
Authors: Nahaboo Wallis , Eski Sema Elif , Vermeersch Marjorie , Saykali Bechara , Monteyne Daniel , Magin Thomas M. , Schwarz Nicole , Zwijsen An , Perez-Morga David , Pal Singh Sumeet , Migeotte Isabelle 
Published: April 2021

SUMMARYAfter implantation, the mouse embryo undergoes gastrulation and forms mesoderm and endoderm. Mesoderm participates in embryonic and extra-embryonic tissues including the amnion, yolk sac, chorion and allantois, the umbilical cord precursor.Extra-embryonic mesoderm is rich in intermediate filaments. Two-photon live imaging of keratin 8-eYFP knock-in embryos allowed recording nucleation and elongation of keratin filaments, which formed apical cables coordinated across multiple cells in amnion, allantois, and blood islands. Embryos lacking all keratins displayed a deflated exocoelomic cavity, a narrow thick amnion, and a short allantois, indicating a hitherto unknown role for keratin filaments in post-implantation extra-embryonic membranes morphogenesis.Single-cell RNA sequencing of mesoderm cells, microdissected amnion, chorion, and allantois provided an interactive atlas of transcriptomes with germ layer and regional information. Keratin 8highmesenchymal cells in contact with the exocoelom shared a cytoskeleton and adhesion expression profile that might explain the adaptation of extra-embryonic structures to the increasing mechanical pressure.GRAPHICAL ABSTRACT
Maternal age affects equine Day 8 embryo gene expression both in trophoblast and inner cell mass
Authors: Derisoud E. , Jouneau L. , Dubois C. , Archilla C. , Jaszczyszyn Y. , Legendre R. , Daniel N. , Peynot N. , Dahirel M. , Auclair-Ronzaud J. , Wimel L. , Duranthon V. , Chavatte-Palmer P. 
Published: April 2021

AbstractBackgroundBreeding a mare until she is not fertile or even until her death is common in equine industry but the fertility decreases as the mare age increases. Embryo loss due to reduced embryo quality is partly accountable for this observation. Here, the effect of mare’s age on blastocysts’ gene expression was explored. Day 8 post-ovulation embryos were collected from multiparous young (YM, 6-year-old, N = 5) and older (OM, > 10-year-old, N = 6) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure or inner cell mass (ICM) enriched trophoblast, obtained by embryo bisection, were RNA sequenced. Deconvolution algorithm was used to discriminate gene expression in the ICM from that in the trophoblast. Differential expression was analyzed with embryo sex and diameter as cofactors. Functional annotation and classification of differentially expressed genes and gene set enrichment analysis were also performed.ResultsMaternal aging did not affect embryo recovery rate, embryo diameter nor total RNA quantity. In both compartments, the expression of genes involved in mitochondria and protein metabolism were disturbed by maternal age, although more genes were affected in the ICM. Mitosis, signaling and adhesion pathways and embryo development were decreased in the ICM of embryos from old mares. In trophoblast, ion movement pathways were affected.ConclusionsThis is the first study showing that maternal age affects gene expression in the equine blastocyst, demonstrating significant effects as early as 10 years of age. These perturbations may affect further embryo development and contribute to decreased fertility due to aging.
The quantitative genetics of the prevalence of infectious diseases: hidden genetic variation due to Indirect Genetic Effects dominates heritable variation and response to selection
Authors: Bijma Piter , Hulst Andries D. , de Jong Mart C. M. 
Published: April 2021

AbstractInfectious diseases have profound effects on life, both in nature and agriculture. Despite the availability of well-established epidemiological theory, however, a quantitative genetic theory of the host population for the endemic prevalence of infectious diseases is almost entirely lacking. While several studies have demonstrated the relevance of the transmission dynamics of infectious diseases for heritable variation and response to selection of the host population, our current theoretical framework of quantitative genetics excludes these dynamics. As a consequence, we do not know which genetic effects of the host population determine the prevalence of an infection, and have no concepts of breeding value and heritable variation for endemic prevalence.Here we integrate quantitative genetics and epidemiology, and propose a quantitative genetic theory forR0and for the endemic prevalence of an infectious disease. We first identify the genetic factors that determine the prevalence of an infection, using an approach founded in epidemiological theory. Subsequently we investigate the population level consequences of individual genetic variation, both forR0and for the endemic prevalence. Next, we present expressions for the breeding value and heritable variation, for both prevalence and individual binary disease status, and show that these parameters depend strongly on the level of the prevalence. Results show that heritable variation for endemic prevalence is substantially greater than currently believed, and increases when prevalence approaches zero, while heritability of individual disease status goes to zero. As a consequence, response of prevalence to selection accelerates considerably when prevalence goes down, in contrast to predictions from classical theory. Finally, we show that most of the heritable variation for the endemic prevalence of an infection is hidden due to indirect genetic effects, suggesting a key role for kin-group selection both in the evolutionary history of current populations and for genetic improvement strategies in animals and plants.