bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline
Authors: Pandey Ayush , Rodriguez Makena L. , Poole William , Murray Richard M. 
Published: October 2022

AbstractWe present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parameterizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in cell-free protein expression system. We build on existing Python tools — BioCRNpyler, AutoReduce, and Bioscrape — to create this pipeline. For enzyme-mediated DNA recombination in cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model, hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parameterization.
Importance of agriculture for Crop Wild Relatives conservation in Switzerland
Authors: Petitpierre Blaise , Boserup Julie , Möhl Adrian , Römetsch Sibyl , Aubry Sylvain 
Published: October 2022

AbstractCrop Wild Relatives are a subset of the global plant diversity that is often neglected, as not the primary focus for conservationists or plant breeders. However, a relatively large portion of the wild flora, up to 60% in Switzerland for example, do share genetic relationships with cultivated species and therefore can be considered as Crop Wild Relatives. Their conservation appears simultaneously a challenge to conservation programmes but also a considerable levy to mobilize other sectors, like agriculture, to contribute to the conservation of biodiversity at large. Here, we provide a comprehensive checklist of Swiss Crop Wild Relatives representing 2,226 taxa, of which 285 prioritised taxa, referred to as “Crop wild relatives Of Concern”, were designated. Following a taxa-specific ecogeographic analysis, we analysed the extent to which CWR of concern are already contained in existing protected areas as well as their distribution in the agricultural area. Prioritised Crop Wild Relatives species richness was compared to modelled species richness to identify potential conservation gaps. About a fifth of CWR of concern is not significantly better protected than a random species by existing protected areas. However, 28.8 % and 15.5 % of these taxa are more frequently distributed in agricultural and summer grazing areas respectively than random expectations. A clear deficit of species richness for these Crop Wild Relatives of concern was inferred on low lands, possibly related to a lower sampling effort. We further identified a network of 39 sites that contains all taxa of Swiss CWR of concern and that could be used as a primary conservation infrastructure. More generally, our results could be generalized to other countries and support better consideration of CWR in agriculture areas, an important “reservoir” for expanding specific measures of conservation that are crucial to meet the future global goals of diversity conservation frameworks.
Philosophy of Maternity Nursing: Women Centered Care
Authors: Nastiti Aria Aulia , Pandin Moses Glorino Rumambo , Nursalam  
Published: October 2022

AbstractIntroductionMaternity nursing is a discipline part of nursing that focuses on the degree of health of women in this stage of life as the main object. Various women’s health problems that occur at this time along with the rapid development of technology have become a challenge for maternity nursing as a comprehensive care service to continue to develop for the better and collaborate with other sciences. The purpose of this paper is to explain the current conditions in Indonesia and the world regarding maternity nursing that supports women’s health and quality of life.MethodThis article was compiled through a literature search for the authenticity of this study using articles in English, Sciencedirect, PubMed, Scopus, Research Gate, and Google Scholar from 2015 to 2022.ResultThe results of the literature search show that currently, maternity nursing continues to develop and is centered on women at every stage of life. Research is currently being carried out on women’s welfare, autonomy and women’s empowerment, such as the decision to use contraception and the best care during pregnancy and childbirth.
Adverse birth outcomes and associated factors among newborns delivered in a western African country: a case‒control study
Authors: Vasconcelos Alexandra , Sousa Swasilanne , Bandeira Nelson , Alves Marta , Papoila Ana Luísa , Pereira Filomena , Machado Maria Céu 
Published: October 2022

AbstractBackgroundNewborns with one or more adverse birth outcomes (ABOs) are at greater risk of mortality or long-term morbidity with health impacts into adulthood. Hence, identifying ABO-associated factors is crucial for devising comprehensive and relevant interventions. The aim of this study was to identify factors that are associated with the occurrence of ABO – prematurity (PTB), low birth weight (LBW), macrosomia, congenital anomalies, asphyxia, and sepsis - among babies delivered at the only hospital of Sao Tome & Principe (STP), a resource-constrained sub-Saharan Western African country.MethodsHospital-based unmatched case‒control study conducted in STP among newborns from randomly selected mothers from July 2016 to November 2018. Newborns with one or more ABO (gestational age <37 weeks, LBW < 2.5 kg, BW >4 kg, 5-minute Apgar score <7, major congenital anomalies, and probable sepsis based on clinical criteria) were the cases (ABO group), while healthy newborns without ABO were the controls (no-ABO group). Data were collected by a face-to-face interview and abstracted from antenatal pregnancy cards and medical records. Multivariable logistic regression analysis was performed to identify ABO risk factors considering a level of significance α=0.05.ResultsA total of 519 newborns (176 with ABO and 343 with no-ABO) were enrolled. The mean gestational age and birth weight of cases and controls were 36 (SD=3.7) weeks with 2659 (SD=881.44) g and 39.6 (SD=1.0) weeks with 3256 (SD=345.83) g, respectively. In a multivariable analysis, twin pregnancy [aOR 4.92, 95% CI 2.25–10.74], prolonged rupture of membranes [aOR 3.43, 95% CI 1.69–6.95], meconium-stained amniotic fluid [aOR 1.59, 95% CI 0.97-2.62], and fewer than eight antenatal care (ANC) visits [aOR 0.33, 95% CI 0.18–0.60] were significantly associated with adverse birth outcomes.ConclusionModifiable factors were associated with ABOs in this study and should be considered in cost-effectiveness interventions. The provision of high-quality ANC with eight or more visits should be a priority at ANC service delivery in STP. Twin pregnancies as well as intrapartum factors such as prolonged rupture of membranes and meconium-stained amniotic fluid are red flags for adverse birth outcomes that should receive prompt intervention and follow-up.
Barriers to accessing mother, new-born and child health services in urban Gambia during COVID-19: An interview-based qualitative study
Authors: Bah Abdourahman , Russo Giuliano 
Published: October 2022

AbstractIntroductionEvidence is being consolidated that shows that the utilisation of mother, newborn, and child health (MNCH) services has declined in low-income countries (LICs) during the COVID-19 pandemic. Very little is known about the effects of the pandemic on MNCH service utilisation in the Gambia. We set out to explore the COVID-19-related factors affecting the utilisation of antenatal and immunisation services in the Gambia.MethodsA qualitative methodology was used to explore patients’ and providers’ experiences of MNCH services during the pandemic in two Local Government Areas (LGAs) in the Gambia. Thirty-one study participants were recruited from four health facilities, applying a theory-driven sampling framework, including health workers as well as female patients. Qualitative evidence was collected through theory-driven semi-structured interviews, and was recorded, translated into English, transcribed, and analysed thematically, applying a social-ecological framework.ResultsIn our interviews, we identified five main themes, ranging from individual factors to interpersonal, community, institutional and policy factors. Individual factors revolved around patients’ fear of being infected in the facilities, and of being quarantined, and their anxiety about passing on infections to family members. Interpersonal factors involved the reluctance of partners and family members, as well as perceived negligence and disrespect by health workers. Community factors included misinformation within the community and mistrust of vaccines. Institutional factors included the shortage of health workers, closures of health facilities, and the lack of personal protective equipment (PPEs) and essential medicines. Finally, policy factors revolved around the consequences of COVID-19 prevention measures, particularly the shortage of transport options and mandatory wearing of face masks.ConclusionsOur findings suggest that patients’ fears of contagion, perceptions of poor treatment in the health system, and a general anxiety around the imposing of prevention measures, undermined the uptake of MNCH services. In future emergencies, the government in the Gambia, and governments in other LICs, will need to consider the unintended consequences of epidemic control measures on the uptake of MNCH services.
Systematic Review and Meta-Analysis of the Efficacy and Effectiveness of Pneumococcal Vaccines in Adults
Authors: Farrar Jennifer L , Childs Lana , Ouattara Mahamoudou , Akhter Fahmina , Britton Amadea , Pilishvili Tamara , Kobayashi Miwako 
Published: October 2022

AbstractThe 13-valent pneumococcal conjugate vaccine (PCV13) and 23-valent pneumococcal polysaccharide vaccine (PPSV23) were previously recommended for adults in the United States. To help inform discussions on recently licensed 15- and 20-valent pneumococcal vaccine use among adults, we conducted a systematic review of PCV13 and PPSV23 efficacy or effectiveness. We conducted a search on PCV13 and PPSV23 efficacy or effectiveness (VE) studies against vaccine type (VT) invasive pneumococcal disease (IPD) and VT-pneumococcal pneumonia in adults. Nineteen studies were included: 13 on VT-IPD (four on PCV13, nine on PPSV23) and eight on VT-pneumococcal pneumonia (three on PCV13, four on PPSV23, one on PCV13 and PPSV23). One randomized-controlled trial (RCT) evaluated PCV13 and observed an efficacy of 75% and 45% against VT-IPD and VT-pneumococcal pneumonia, respectively. No RCTs reported PPSV23 efficacy. PCV13 effectiveness estimates against VT-IPD ranged from 47% to 68%. Pooled PPSV23 effectiveness against VT-IPD was 45% (95% CI: 37%, 51%; I2=0%). PCV13 VE estimates against VT-pneumonia ranged from –2 to 46%. Pooled PPSV23 VE against VT-pneumococcal pneumonia was 18% (95% CI: -4%, 35%; I2=0%). Evidence suggests PCV13 and PPSV23 are effective against VT-IPD and VT-pneumococcal pneumonia in adults; this was used to inform PCV15 and PCV20 policy decisions.
Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil
Authors: Miranda Thamiris dos Santos , Schiffler Francine Bittencourt , D’arc Mirela , Moreira Filipe Romero Rebello , Cosentino Matheus Augusto Calvano , Coimbra Amanda , Mouta Ricardo , Medeiros Gabriel , Girardi Déa Luiza , Wanderkoke Victor , Soares Caique Ferreira Amaral , Francisco Talitha Mayumi , Henry Malinda Dawn , Afonso Bianca Cardozo , Soffiati Flávio Landim , Ferreira Suelen Sanches , Ruiz-Miranda Carlos Ramon , Soares Marcelo Alves , dos Santos André Felipe Andrade 
Published: October 2022

AbstractViral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those free-living introduced, knowledge about viral diversity remains poorly studied. Therefore, through the use of metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, named Tritonambidensovirus due to telomeric structures at the 3’ and 5’ ends of the genome. The novel species received the name Fecalis tritonambidensovirus 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species of Betabaculovirus, named Callithrix fecalis granulovirus. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets’ diet. This identification in hosts’ feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
Impacts of Biostimulation and Bioaugmentation on Woodchip Bioreactor Microbiomes
Authors: Wang Hao , Feyereisen Gary W. , Wang Ping , Rosen Carl , Sadowsky Michael J. , Ishii Satoshi 
Published: October 2022

ABSTRACTWoodchip bioreactors (WBRs) are used to remove nutrients, especially nitrate, from subsurface drainage. The nitrogen removal efficiency of WBRs, however, is limited by low temperature and availability of labile carbon. Bioaugmentation and biostimulation are potential approaches to enhance nitrate removal of WBRs under cold conditions, but their effectiveness is still unclear. Here, we clarified the effects of bioaugmentation and biostimulation on the microbiomes and nitrate removal rates of WBRs. As a bioaugmentation treatment, we inoculated WBR-borne cold-adapted denitrifying bacteria Cellulomonas cellasea strain WB94 and Microvirgula aerodenitrificans strain BE2.4 into the WBRs located at Willmar, MN, USA. As a biostimulation treatment, acetate was added to the WBRs to promote denitrification. Woodchip samples were collected from multiple locations in each WBR before and after the treatments and used for the microbiome analysis. The 16S rRNA gene amplicon sequencing showed that the microbiomes changed by the treatments and season. The high-throughput quantitative PCR for nitrogen cycle genes revealed a higher abundance of denitrification genes at locations closer to the WBR inlet, suggesting that denitrifiers are unevenly present in WBRs. In addition, a positive relationship was identified between the abundance of M. aerodenitrificans strain BE2.4 and those of norB and nosZ in the WBRs. Based on generalized linear modeling, the abundance of norB and nosZ was shown to be useful in predicting the nitrate removal rate of WBRs. Taken together, these results suggest that the bioaugmentation and biostimulation treatments can influence denitrifier populations, thereby influencing the nitrate removal of WBRs.IMPORTANCENitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor’s nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor’s performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution.
Epithelial Outgrowth Through Mesenchymal Rings Drives Alveologenesis
Authors: Negretti Nicholas M. , Son Yeongseo , Crooke Philip , Plosa Erin J. , Benjamin John T. , Jetter Christopher S. , Bunn Claire , Mignemi Nicholas , Marini John , Hackett Alice N. , Ransom Meaghan , Nichols David , Guttentag Susan H. , Pua Heather H. , Blackwell Timothy S. , Zacharias William , Frank David B. , Kozub John A. , Mahadevan-Jansen Anita , Kropski Jonathan A. , Wright Christopher V.E. , Millis Bryan , Sucre Jennifer M. S. 
Published: October 2022

AbstractDetermining how alveoli are formed and maintained is critical to understanding lung organogenesis and regeneration after injury. While technological barriers have heretofore limited real-time observation of alveologenesis, we have now used scanned oblique plane illumination microscopy of living lung slices to observe specific cellular behaviors at high resolution over several days. Contrary to the prevailing paradigm that alveoli form by airspace subdivision via ingrowing septa, we find that alveoli form by ballooning epithelial outgrowth supported by stable mesenchymal ring structures. Our systematic analysis allowed creation of a computational model of finely-timed cellular structural changes that drive alveologenesis under normal conditions or with perturbed intercellular Wnt signaling. This new paradigm and platform can be leveraged for mechanistic studies and screening for therapies to promote lung regeneration.One-Sentence SummaryLong-term live analysis of neonatal lungs supports a dynamic epithelial outgrowth model for alveologenesis.
Inhibition of the proton-activated chloride channel PAC by PIP2
Authors: Mihaljević Ljubica , Ruan Zheng , Osei-Owusu James , Lü Wei , Qiu Zhaozhu 
Published: October 2022

AbstractProton-Activated Chloride (PAC) channel is a ubiquitously expressed pH-sensing ion channel that regulates endosomal acidification and macropinosome shrinkage by releasing chloride from the organelle lumens. It is also found at the cell surface, where it is activated under pathological conditions related to acidosis and contributes to acid-induced cell death. However, the pharmacology of the PAC channel is poorly understood. Here, we report that phosphatidylinositol (4,5)-bisphosphate (PIP2) potently inhibits PAC channel activity. We solved the cryo-electron microscopy structure of PAC with PIP2 at pH 4.0 and identified its binding site, which, surprisingly, locates on the extracellular side of the transmembrane domain (TMD). While the overall conformation resembles the previously resolved PAC structure in the desensitized state, the TMD undergoes remodeling upon PIP2-binding. Structural and electrophysiological analyses suggest that PIP2 inhibits the PAC channel by stabilizing the channel in a desensitized-like conformation. To our knowledge, PAC is the first chloride channel reported to be inhibited by PIP2. Our findings identify PIP2 as a new pharmacological tool for the PAC channel and lay the foundation for future drug discovery targeting this channel.
Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects
Authors: Qi Guanghao , Strober Benjamin J. , Popp Joshua M. , Ji Hongkai , Battle Alexis 
Published: October 2022

AbstractAllele-specific expression, which measures the expression of two alleles of a gene in a diploid individual, is a powerful signal to study cis-regulatory effects. Comparing ASE across conditions, or differential ASE, can reveal context-specific gene regulation. Recently, single-cell RNA sequencing (scRNA-seq) has allowed the measurement of ASE at the resolution of individual cells, but there is a lack of statistical methods to analyze such data. We develop DAESC, a statistical method for differential ASE analysis across any condition of interest using scRNA-seq data from multiple individuals. DAESC includes a baseline model based on beta-binomial regression with random effects accounting for multiple cells from the same individual (DAESC-BB), and an extended mixture model that incorporates implicit haplotype phasing (DAESC-Mix). We demonstrate through simulations that DAESC accurately captures differential ASE effects in a wide range of scenarios. Application to scRNA-seq data from 105 induced pluripotent stem cell lines identifies 657 genes that are dynamically regulated during endoderm differentiation. A second application identifies several genes that are differentially regulated in pancreatic endocrine cells between type 2 diabetes patients and controls. In conclusion, DAESC is a powerful method for single-cell differential ASE analysis and can facilitate the discovery of context-specific regulatory effects.
Comparison of COVID-19 Antigen Rapid Test (Oral Fluid) and Real-Time RT-PCR in the laboratory diagnosis of SARS-CoV-2 infection
Authors: Mense Lotte M. , Ouburg Sander 
Published: October 2022

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first diagnosed in December 2019. Since then this virus has caused an ongoing wide pandemic. Accurate diagnostic tests for SARS-CoV-2 are used to prevent the virus from spreading. However, these tests could not keep up with the demand and were not available in all places. Self-testing devices are easy-to-use-tests and reduce the demand in the diagnostic laboratories. The Antigen Rapid Test evaluated in this study uses oral fluid which is a non-invasive technique compared to nasopharyngeal swabs.In this study the COVID-19 Antigen Rapid Test (Oral fluid) was evaluated with 150 SARS-CoV-2 positive saliva specimens and 350 SARS-CoV-2 negative saliva specimens. The Antigen Rapid Test was performed according to the instruction manual. SARS-CoV-2 Real-time RT-PCR was used as Golden Standard.Although the criteria of the WHO are specific to nasal / nasopharyngeal samples (and not saliva), the specificity of the Antigen Rapid Test meets the criteria of the World Health Organization (WHO; specificity ≥ 97%). The test meets the WHO sensitivity criteria in samples with higher viral loads (Ct<30), showing the better performance of the test in highly positive samples. For positive SARS-CoV-2 specimens with a Ct value lower than 30 a sensitivity of 83.8% (95% CI: 80.1%-86.8%) and an accuracy of 95.9% (95% CI: 93.7%-97.4%) was observed. This shows that this assay with saliva samples is able to meet the high standards set by the WHO. The performance of the test is comparable to other antigen rapid tests reported in meta-analyses. Furthermore, the test allows self-testing which is non-invasive, affordable and straightforward. This antigen rapid test may provide an affordable, quick, and easy to perform method to differentiate between individuals with high and low viral loads.