bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimum Dietary Diversity and Associated Factors among Lactating Mothers in Ataye District, North Shoa Zone, Central Ethiopia: A Community-based Cross-sectional Study
Authors: Getacher Lemma , Egata Gudina , Alemayehu Tadesse , Bante Agegnehu , Molla Abebaw 
Published: October 2020

AbstractBackgroundLow dietary diversity superimposed with poor quality monotonous diets is a major problem that often results in undernutrition, mainly micronutrient deficiencies. However, there is limited evidence on minimum dietary diversity and associated factors among lactating mothers in resource-poor settings, including the study area. Therefore, the objective of the study is to assess the prevalence of minimum dietary diversity and associated factors among lactating mothers in Ataye District, Ethiopia.MethodsA community-based cross-sectional study design was used among 652 lactating mothers aged 15-49 years from January 25 to April 30, 2018. Dietary diversity was measured by the minimum dietary diversity indicator for women (MDD-W) using the 24-hour dietary recall method. Data were entered into EpiData version 4.2.0.0 and exported to the statistical package for social science (SPSS) version 24 for analysis using the logistic regression model.ResultsThe prevalence of minimum dietary diversity among lactating mothers was 48.8%, (95% CI: (44.7%, 52.9%). Having formal education [(AOR=2.16, 95% CL: (1.14, 4.09)], a final say on household purchases [(AOR=5.39, 95% CI: (2.34, 12.42)], home gardening practices [(AOR=2.67, 95% CI: (1.49, 4.81)], a history of illness [(AOR=0.47, 95% CI: (0.26, 0.85), good knowledge of nutrition [(AOR=5.11, 95% CI: (2.68, 9.78)], being from food-secure households [(AOR=2.96, 95% CI: (1.45, 6.07)] and medium [(AOR=5.94, 95% CI: (2.82, 12.87)] and rich wealth indices [(AOR= 3.55, 95% CI: (1.76, 7.13)] were significantly associated with minimum dietary diversity.ConclusionThe prevalence of minimum dietary diversity among lactating mothers was low in the study area. It was significantly associated with mothers having a formal education, final say on the household purchase, home garden, good knowledge of nutrition, history of illness, food-secure households and belonging to medium and rich household wealth indices. Therefore, efforts should be made to improve the mothers decision-making autonomy, nutrition knowledge, household food security and wealth status.
Temporal course of SARS-CoV-2 antibody positivity in patients with COVID-19 following the first clinical presentation
Authors: Risch Martin , Weber Myriam , Thiel Sarah , Grossmann Kirsten , Wohlwend Nadia , Lung Thomas , Hillmann Dorothea , Ritzler Michael , Ferrara Francesca , Bigler Susanna , Egli Konrad , Bodmer Thomas , Imperiali Mauro , Salimi Yacir , Fleisch Felix , Cusini Alexia , Renz Harald , Kohler Philipp , Vernazza Pietro , Kahlert Christian , Paprotny Matthias , Risch Lorenz 
Published: October 2020

AbstractKnowledge of the sensitivities of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibody tests beyond 35 days after the clinical onset of COVID-19 is insufficient. We aimed to describe positivity rate of SARS-CoV-2 assays employing three different measurement principles over a prolonged period. Two hundred sixty-eight samples from 180 symptomatic patients with COVID-19 and a reverse transcription polymerase chain reaction (RT-PCR) test followed by serological investigation of SARS-CoV-2 antibodies were included.. We conducted three chemiluminescence (including electrochemiluminscence, ECLIA), four enzyme linked immunosorbent assay (ELISA), and one lateral flow immunoassay (LFIA) test formats. Positivity rates, as well as positive (PPV) and negative predictive values (NPV) were calculated for each week after the first clinical presentation for COVID-19. Furthermore, combinations of tests were assessed within an orthogonal testing approach employing two independent assays and predictive values were calculated. Heat maps were constructed to graphically illustrate operational test characteristics. During a follow-up period of more than 9 weeks, chemiluminescence assays and one ELISA IgG test showed stable positivity rates after the third week. With the exception of ECLIA, the PPVs of the other chemiluminescence assays were ≥95% for COVID-19 only after the second week. ELISA and LFIA had somewhat lower PPVs. IgM exhibited insufficient predictive characteristics. An orthogonal testing approach provided PPVs ≥95% for patients with a moderate pretest probability (e.g., symptomatic patients), even for tests with a low single test performance. After the second week, NPVs of all but IgM assays were ≥95% for patients with low to moderate pretest probability. The confirmation of negative results using an orthogonal algorithm with another assay provided lower NPVs than the single assays. When interpreting results from SARS-CoV-2 tests, the pretest probability, time of blood draw and assay characteristics must be carefully considered. An orthogonal testing approach increases the accuracy of positive, but not negative, predictions.
Spatial modelling of sand fly vector’s response to a synthetic sex-aggregation pheromone: impact on the incidence of visceral leishmaniasis in rural and urban settings
Authors: Retkute Renata , Dilger Erin , Hamilton James GC , Keeling Matt J , Courtenay Orin 
Published: October 2020

AbstractBackgroundVisceral leishmaniasis (VL) is a potentially fatal protozoan parasitic disease of humans and dogs. In the Americas, dogs are the reservoir and Lutzomyia longipalpis is the sand fly vector. A synthetic version of the vector’s sex-aggregation pheromone attracts conspecifics to co-located lethal insecticide, reducing reservoir infection and vector abundance. Mathematical models of spatially deployed interventions are lacking, thus best practise using this novel lure-and-kill vector control approach to reduce infection incidence has not been fully explored.MethodsWe developed a predictive mathematical model of vector host-seeking behaviour combined with spatially explicit transmission models to evaluate changes in human and canine spatial infection incidence under variable pheromone implementation scenarios and demographic conditions.ResultsThe risk of human infection increased exponentially with canine incidence, but at different rates between rural and urban settings with spatial clustering of high forces of human infection related to their proximity to canine infected households. A predicted 70% household coverage using a cost-effective amount (50mg) of pheromone, plus insecticide, reduced rural and urban setting infection incidence by approximately 44% and 50% in dogs, and by 64% and 68% in humans, within 1-2 years. Near or complete transmission elimination in dogs and humans was achieved after 10 years intervention using 50mg of pheromone under 70% household coverage in urban settings when newly acquired (immigrant) dogs had no pre-existing infections, but in rural settings required 90% coverage using 500mg. The willingness to pay (WTP) price per 10mg unit of pheromone is likely to be <$3 USD, making it a cost-beneficial intervention compared to current alternative strategies.ConclusionsIntegrated stochastic and spatial models capturing vector host-seeking behaviour, is a useful mathematical framework to evaluate spatially dependent intervention methods, fine-scale transmission dynamics, and to identify best practise.
Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of Covid-19 in England
Authors: Sherratt Katharine , Abbott Sam , Meakin Sophie R , Hellewell Joel , Munday James D , Bosse Nikos ,   CMMID Covid-19 working group, Jit Mark , Funk Sebastian 
Published: October 2020

AbstractThe time-varying reproduction number (Rt: the average number secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of Rt estimates to different data sources representing Covid-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups.We sourced public data on test-positive cases, hospital admissions, and deaths with confirmed Covid-19 in seven regions of England over March through August 2020. We estimated Rt using a model that mapped unobserved infections to each data source. We then compared differences in Rt with the demographic and social context of surveillance data over time.Our estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. Rt estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test-positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of disease.We highlight that policy makers could better target interventions by considering the source populations of Rt estimates. Further work should clarify the best way to combine and interpret Rt estimates from different data sources based on the desired use.
2008 financial crisis vs 2020 economic fallout: How COVID-19 might influence fertility treatment and live births
Authors: Gromski Piotr S. , Smith Andrew D.A.C , Lawlor Deborah A , Sharara Fady I. , Nelson Scott M 
Published: October 2020

AbstractBackgroundThe economic and reproductive medicine response to the COVID-19 pandemic in the United States has reduced the affordability and accessibility of fertility care. We sought to determine the impact of the 2008 financial recession and the COVID-19 recession on fertility treatments and cumulative live-births.MethodsWe examined annual US natality, CDC IVF cycle activity and live birth data from 1999 to 2018 encompassing 3,286,349 treatment cycles, to estimate the age-stratified reduction in IVF cycles undertaken after the 2008 financial recession, with forward quantitative modelling of IVF cycle activity and cumulative live-births for 2020 to 2023.ResultsThe financial recession of 2008 caused a four-year plateau in fertility treatments with a predicted 53,026 (95% CI 49,581 to 56,471) fewer IVF cycles and 16,872 (95% CI 16,713 to 17,031) fewer live births. A similar scale of economic recession would cause 67,386 (95% CI: 61,686 to 73,086) fewer IVF cycles between 2020 and 2023, with women younger than 35 years overall undertaking 22,504 (95% CI 14,320 to 30,690) fewer cycles, as compared to 4,445 (95% CI 3,144 to 5749) fewer cycles in women over the age of 40 years. This equates to overall 25,143 (95% CI: 22,408 to 27,877) fewer predicted live-births from IVF, of which only 490 (95% CI 381 to 601) are anticipated to occur in women over the age of 40 years.ConclusionsThe COVID-19 recession could have a profound impact on US IVF live-birth rates in young women, further aggravating pre-existing declines in total fertility rates.Trial registration numbernot applicable
Urine single cell RNA-sequencing in focal segmental glomerulosclerosis reveals inflammatory signatures in immune cells and podocytes
Authors: Latt Khun Zaw , Heymann Jurgen , Jessee Joseph H. , Rosenberg Avi Z. , Berthier Celine C. , Eddy Sean , Yoshida Teruhiko , Zhao Yongmei , Chen Vicky , Nelson George W. , Cam Margaret , Kumar Parimal , Mehta Monika , Kelly Michael C. , Kretzler Matthias ,   The Nephrotic Syndrome Study Network (NEPTUNE),   The Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) consortium, Cheryl, Winkler A. , Kopp Jeffrey B. 
Published: October 2020

AbstractThe diagnosis of focal segmental glomerulosclerosis (FSGS) requires a renal biopsy, which is invasive and can be problematic in children and in some adults. We used single cell RNA-sequencing to explore disease-related cellular signatures in 23 urine samples from 12 FSGS subjects. We identified immune cells, predominantly monocytes, and renal epithelial cells, including podocytes. Analysis revealed M1 and M2 monocyte subsets, and podocytes showing high expression of genes for epithelial-to-mesenchymal transition (EMT). We confirmed M1 and M2 gene signatures using published monocyte/macrophage data from lupus nephritis and cancer. Using renal transcriptomic data from the Nephrotic Syndrome Study Network (NEPTUNE), we found that urine cell immune and EMT signature genes showed higher expression in FSGS biopsies compared to minimal change disease biopsies. These results suggest that urine cell profiling may serve as a diagnostic and prognostic tool in nephrotic syndrome and aid in identifying novel biomarkers and developing personalized therapeutic strategies.
Alteration of coastal productivity and artisanal fisheries interact to affect a marine food-web
Authors: Ávila-Thieme M. Isidora , Corcoran Derek , Pérez-Matus Alejandro , Wieters Evie A. , Navarrete Sergio A. , Marquet Pablo A. , Valdovinos Fernanda S. 
Published: October 2020

ABSTRACTTop-down and bottom-up forces determine ecosystem function and dynamics. Fisheries as a top-down force can shorten and destabilize food-webs, while climate-change driven effects can alter the bottom-up forces of primary productivity. We assessed the response of a highly-resolved intertidal food-web to these two global-change drivers, using network analysis and bioenergetic modelling. We quantified the relative importance of artisanal fisheries as another predator species, and evaluated the independent and combined effects of fisheries and plankton-productivity changes on food-web dynamics. The food-web was robust to the loss of all harvested species but sensible to plankton-productivity decline. Interestingly, fisheries dampened the negative impacts of decreasing plankton productivity on non-harvested species, while plankton-productivity decline increased the sensitivity of harvested species to fishing. Our results show that strategies for new scenarios caused by climate change are needed to protect marine ecosystems and the wellbeing of local communities dependent on their resources.
An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
Authors: Chan Kui K. , Tan Timothy J.C. , Narayanan Krishna K. , Procko Erik 
Published: October 2020

ABSTRACTThe spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing
Authors: Savage Adam K. , Gutschow Miriam V. , Chiang Tony , Henderson Kathy , Green Richard , Chaudhari Monica , Swanson Elliott , Heubeck Alexander T. , Kondza Nina , Burley Kelli C. , Genge Palak C. , Lord Cara , Smith Tanja , Thomson Zachary , Beaubien Aldan , Johnson Ed , Goldy Jeff , Bolouri Hamid , Buckner Jane H. , Meijer Paul , Coffey Ernest M. , Skene Peter J. , Torgerson Troy R. , Li Xiao-jun , Bumol Thomas F. 
Published: October 2020

SummaryMulti-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMCs up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from nativein vivobiology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states.
Strain-level sample characterisation using long reads and MAPQ scores
Authors: Hall Grace A. , Speed Terence P. , Woodruff Christopher J. 
Published: October 2020

AbstractA simple but effective method for strain-level characterisation of microbial samples using long read data is presented. The method, which relies on having a non-redundant database of reference genomes, differentiates between strains within species and determines their relative abundance. It provides markedly better strain differentiation than that reported for the latest long read tools. Good estimates of relative abundances of highly similar strains present at less than 1% are achievable with as little as 1Gb of reads. Host contamination can be removed without great loss of sample characterisation performance. The method is simple and highly flexible, allowing it to be used for various different purposes, and as an extension of other characterisation tools. A code body implementing the underlying method is freely available.
Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules
Authors: Shams Arik , Higgins Sean A. , Fellmann Christof , Laughlin Thomas G. , Oakes Benjamin L. , Lew Rachel , Lukarska Maria , Arnold Madeline , Staahl Brett T. , Doudna Jennifer A. , Savage David F. 
Published: October 2020

AbstractProteins evolve through the modular rearrangement of elements known as domains. It is hypothesized that extant, multidomain proteins are the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for geneticminimization byiterativesize-exclusion andrecombination (MISER) that comprehensively assays all possible deletions of a protein. Using MISER, we generated a deletion landscape for the CRISPR protein Cas9. We found that Cas9 can tolerate large single deletions to the REC2, REC3, HNH, and RuvC domains, while still functioningin vitroandin vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
Tautomerization constrains the accuracy of codon-anticodon decoding
Authors: Kazantsev Andriy , Ignatova Zoya 
Published: October 2020

AbstractG○U(T) mismatch has the highest contribution to the error rate of base pair recognition in replication, as well as in codon-anticodon decoding in translation. Recently, this effect was unambiguously linked to keto-enol tautomerization, which enables the Watson-Crick (WC) geometry of the base pair. Structural studies of the ribosome revealing G○U in the WC geometry in the closed state of the A-site challenge the canonical induced-fit model of decoding and currently lack a physicochemical explanation.Using computational and theoretical methods, we address effects of the ribosomal A-site on the wobble↔WC tautomerization reaction in G○U (wb-WC reaction), and the consequent implications for the decoding mechanism in translation. The free energy change of the wb-WC reaction in the middle codon-anticodon position was calculated with quantum-mechanical/molecular-mechanical umbrella sampling simulations. The wb-WC reaction was endoergic in the open A-site, but exoergic in the closed state. This effect can be explained in part by the decreased polarity of the closed A-site.We developed a model of initial selection in translation that incorporates the wb-WC reaction parameters in the open and closed states of the A-site. In the new model, the exoergic wb-WC reaction is kinetically restricted by the decoding rates, which explains the observations of the WC geometry at equilibrium conditions. Moreover, the model reveals constraints imposed by the exoergic wb-WC reaction on the decoding accuracy: its equilibration counteracts the favorable contribution from equilibration of the open-closed transition. The similarity of the base-pair recognition mechanism in DNA polymerases allows extending this model to replication as well. Our model can be a step towards a general recognition model for flexible substrates.
Dysfunction of the histone demethylase IBM1 in Arabidopsis reshapes the root-associated bacteria community
Authors: Lv Suhui , Yang Yu , Peng Li , Tang Kai , Kaushal Richa , Zhang Huiming 
Published: October 2020

AbstractRoot-associated bacteria communities are influential to plant growth and stress tolerance. Epigenetic regulation plays important roles in many plant biological processes, but its potential impacts on the assembly of root microbiota remain unclear. Here we report that dysfunction of the histone demethylase IBM1 in Arabidopsis substantially alters root-associated soil bacteria community. We compared two alleles ofibm1mutant (ibm1-1andibm1-4) with wild type Arabidopsis regarding the root-associated bacteria community by 16S rRNA gene sequencing. The constrained principal coordinate analysis (PCoA) showed that theibm1mutants are both clearly separated from Col-0 along the major coordinates. Among the 29 families which have a relative abundance more than 0.5% in at least one sample, 10 and 11 families were commonly affected byibm1-1andibm1-4alleles in the rhizosphere and the endosphere compartment, respectively. Notably, the ACMs (Abundant Community members) belonging Pseudomonadaceae showed increased relative abundance in theibm1mutant alleles compared to Col-0 in both the rhizosphere and the endosphere compartments. The ACMs belonging to Oxalobacteraceae mostly showed decreased relative abundance inibm1mutants compared to Col-0 in endosphere compartment. These findings demonstrate an influential function of IBM1-mediated epigenetic regulation in shaping the root-associated microbiota.