Miracle-dz/UniFAR-FTUs huggingface dataset:
Frequentist and Bayesian Regression Approaches for Determining Risk Factors of Child Mortality in Ghana

Background Child mortality is a global health problem. The United Nations' 2018 report on levels and trends on child mortality indicated that under-five mortality is one of the major public health problems in Ghana with a rate of 60 deaths per 1000 live births. To further mitigate this problem, it is important to identify the drivers of under-five mortality in order to achieve the United Nations SDG Goal 3 target 2. Methods In this study, we investigated the effects of some selected risk factors on child mortality using data from the 2014 Ghana Demographic Health Survey. We modelled the relationship between child mortality and the risk factors using a logistic regression model under the frequentist and Bayesian frameworks. We used the Metropolis-Hastings Algorithm to simulate parameter estimates from the posterior distributions, and statistical analyses were carried out using STATA version 14.1. Results Results from the frequentist framework are in line with those from the Bayesian framework. The results showed an increased risk of death among children who were delivered through caesarean and reduced relative odds of death among children whose sizes are average or large at birth and whose mothers have formal education. Conclusions There is a need for improved health facilities for better health-care for mothers and children. Education should, among other things, emphasise on the need for mothers to go for regular check-ups during antinatal and postnatal periods for improved mother and child health.
Coexistence of Axial Spondyloarthritis and Idiopathic Inflammatory Myopathy

Both axial spondyloarthritis (axSpA) and idiopathic inflammatory myopathy (IIM) are infrequent, and their coexistence is even rarer; there are a few reported cases in the literature. The aim of this study was to assess their association and clinical and laboratory features in our patients. The clinical data of patients with axSpA and IIM diagnosed in China-Japan Friendship Hospital from July 2015 to February 2019 were retrospectively analyzed. This study included 7 patients with axSpA who met the IIM criteria, including 3 males and 4 females. The age of onset was 16 to 39 years. Four patients were HLA-B27 positive, and three were negative. All patients were first diagnosed as axSpA, and then IIM was detected after 0.5–20 years (mean ± SD, 9.9 ± 5.0 years). After being diagnosed to have axSpA and IIM, those patients were given prednisone and immunosuppressant drugs, and their symptoms gradually improved. Our study provides further evidence of the coexistence of IIM with axSpA. In patients with axSpA who have skin rash, interstitial lung disease (ILD), myalgia, or muscle weakness, we should suspect that they may have IIM.
Heisenberg-limited Bayesian multiphase estimation algorithm

Quantum phase estimation (QPE) is ubiquitous in quantum technologies. It is the key subroutine of several quantum computing algorithms as well as a central ingredient in quantum computational chemistry and quantum simulation. While QPE strategies have focused on the estimation of a single phase, one can envisage applications where the simultaneous estimation of multiple phases may bring substantial advantages, for instance in presence of spatial or temporal constraints. In this work, we study a Bayesian QPE algorithm for the parallel (simultaneous) estimation of multiple arbitrary phases. The algorithm allows the estimation of each phase, as well as any arbitrary linear combination, with Heisenberg-limited sensitivity with respect to the total number of quantum resources. The parallel estimation protocol gives access to correlations in the Bayesian multiphase distribution that allow to surpass the sensitivity of sequential single phase estimation strategies for optimal combinations of phases. Furthermore, the algorithm proves a certain noise resilience, and can be implemented using single photons and standard optical elements in currently accessible experiments.
Anemia and Kidney Function Decline among the Middle-Aged and Elderly in China: A Population-Based National Longitudinal Study

Chronic kidney disease (CKD) is a public health burden, and anemia is common among patients with CKD. However, less is known regarding the longitudinal association between anemia and deterioration of kidney function among the general population. The China Health and Retirement Longitudinal Study is a nationally representative survey for households with members aged ≥ 45 years. Participants without creatinine and demographic data in 2011 and 2015 were excluded. Anemia was defined according to definitions of the World Health Organization. Rapid decline in kidney function was defined as a ≥16.9% (quartile 3) decline in estimated glomerular filtration rate (eGFR), calculated using the CKD-EPI equation during 2011-2015. Multivariate logistic regression and restricted cubic splines were used to explore their relationship. Altogether, 7210 eligible participants were included in the analysis, with a mean age of 58.6 ± 8.8 years. Rapid decline in kidney function occurred among 1802 (25.0%) participants. Those with kidney function decline were more likely to be older, male, and have anemia, lower eGFRs, hypertension, and cardiovascular disease (P < 0.05). Anemia, or hemoglobin, was independently associated with rapid decline in kidney function after adjusting for potential confounding factors (OR = 1.64, 95% CI, 1.32-2.04; OR = 0.90, 95% CI, 0.87-0.94, respectively). Restricted cubic splines showed a nonlinear relationship between hemoglobin and rapid decline in kidney function, especially for men with anemia (P < 0.05). In conclusion, anemia is an independent risk factor for progression of kidney function among the middle-aged and elderly population. Attentive management and intervention strategies targeting anemia could be effective to reduce the risk of kidney failure and improve the prognosis of the general population.
POPULATION STRUCTURE OF PORBEAGLE (LAMNA NASUS) IN THE ATLANTIC OCEAN AS INFERRED FROM MITOCHONDRIAL DNA CONTROL REGION SEQUENCES

SUMMARY Genetic population structure of porbeagle, Lamna nasus, in the Atlantic Ocean was investigated using nucleotide sequence of the mitochondrial DNA. We analyzed sequence variation of 293bp of the D-Loop region of 53 sharks from the North (4) and South (49) Atlantic Ocean. Neighbor-joining and UPGMA trees revealed that North and South Atlantic populations are genetically subdivided. Porbeagles prefer cold water, lower than 15℃, and they do not occur in equatorial seas. This biological information indicates restriction of gene flow between the North and South Atlantic populations. Concordance between genetic and biological suggestion is taken as robust evidence of population structure and is considered that two populations should be managed independently. In this study, the UGPMA tree suggested that there are two sub-populations in the South Atlantic while the neighbor-joining tree unidentified sub-population structure. At this moment, we cannot make it clear whether or not two sub-populations exist. Further analyses of population using genetic, biological and tagging techniques may provide additional information on the population structure and management units of porbeagle. RESUME
Herbivore community determines the magnitude and mechanism of nutrient effects on subtropical and tropical seagrasses

Numerous studies have examined the combined effects of nutrients (bottom‐up control) and consumers (top‐down control) on ecosystem structure and functioning. While it is recognized that both can have important effects, there remains a limited understanding of how their relative importance shifts across large spatial scales where consumer functional types can vary. Using seagrasses as a model ecosystem, we explore the effects of ambient variation in herbivore functional composition on the relative importance of bottom‐up and top‐down forcings. Distributed experiments were conducted across four Western Atlantic sites that encompassed a gradient in consumer composition. Herbivores at two subtropical sites were predominantly comprised of small crustacean invertebrates (mesograzers that consume epiphytic algae), while herbivores at two tropical sites were dominated by large macrograzers (sea urchins and herbivorous fishes that directly consume seagrass biomass). To test the relative importance of bottom‐up and top‐down factors at each site, we manipulated nutrient supply, mesograzer abundance, and the presence of macrograzers (mainly herbivorous fishes) in a fully factorial design over a 14‐week growing season. Seagrass above‐ground biomass, shoot density, canopy cover, leaf productivity and epiphyte mass were measured as indicators of habitat structure and productivity. Overall, nutrient addition elicited a strong response across sites, causing widespread loss of seagrass biomass and shoot density. However, the mechanisms driving these declines strongly varied as a function of resident herbivore identity. Seagrass loss at tropical sites was attributable to macrograzers, which increased their direct consumption of fertilized, nutrient‐rich seagrass. Conversely, at the subtropical sites, nutrient loading caused seagrass declines associated with the proliferation of epiphytic algae, but only in locations where mesograzer abundance was low. Synthesis. Our results confirm that nutrient enrichment generally has negative effects on seagrasses, but that the underlying mechanisms vary and may depend upon herbivore presence and functional identity. Along a subtropical to tropical gradient, the adverse effects of nutrient loading may switch from competitive algal overgrowth to a stimulation of seagrass consumption. Thus, in the tropics, top‐down and bottom‐up factors can act in combination, and in the same direction, to contribute to habitat loss.
Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports

Background Many scholarly journals have established their own data-related policies, which specify their enforcement of data sharing, the types of data to be submitted, and their procedures for making data available. However, except for the journal impact factor and the subject area, the factors associated with the overall strength of the data sharing policies of scholarly journals remain unknown. This study examines how factors, including impact factor, subject area, type of journal publisher, and geographical location of the publisher are related to the strength of the data sharing policy. Methods From each of the 178 categories of the Web of Science’s 2017 edition of Journal Citation Reports, the top journals in each quartile (Q1, Q2, Q3, and Q4) were selected in December 2018. Of the resulting 709 journals (5%), 700 in the fields of life, health, and physical sciences were selected for analysis. Four of the authors independently reviewed the results of the journal website searches, categorized the journals’ data sharing policies, and extracted the characteristics of individual journals. Univariable multinomial logistic regression analyses were initially conducted to determine whether there was a relationship between each factor and the strength of the data sharing policy. Based on the univariable analyses, a multivariable model was performed to further investigate the factors related to the presence and/or strength of the policy. Results Of the 700 journals, 308 (44.0%) had no data sharing policy, 125 (17.9%) had a weak policy, and 267 (38.1%) had a strong policy (expecting or mandating data sharing). The impact factor quartile was positively associated with the strength of the data sharing policies. Physical science journals were less likely to have a strong policy relative to a weak policy than Life science journals (relative risk ratio [RRR], 0.36; 95% CI [0.17–0.78]). Life science journals had a greater probability of having a weak policy relative to no policy than health science journals (RRR, 2.73; 95% CI [1.05–7.14]). Commercial publishers were more likely to have a weak policy relative to no policy than non-commercial publishers (RRR, 7.87; 95% CI, [3.98–15.57]). Journals by publishers in Europe, including the majority of those located in the United Kingdom and the Netherlands, were more likely to have a strong data sharing policy than a weak policy (RRR, 2.99; 95% CI [1.85–4.81]). Conclusions These findings may account for the increase in commercial publishers’ engagement in data sharing and indicate that European national initiatives that encourage and mandate data sharing may influence the presence of a strong policy in the associated journals. Future research needs to explore the factors associated with varied degrees in the strength of a data sharing policy as well as more diverse characteristics of journals related to the policy strength.
Genetic diversity and breed proportions of Indian stud cattle

India is the world’s leading milk producer, however, average milk yield per animal is low. Most of India’s cattle milk is produced by indigenous breeds, followed by crossbred cows. Crossbreeding intensified in the 1960s and 70s with a large influx of Holstein Friesian and Jersey bulls, and an increased use of artificial insemination. Based on genotypes generated from the 50K v2 BovineHD BeadChip assay, we analysed the genetic diversity and breed composition of 242 breeding cattle sampled from the BAIF breed herds, including indigenous, exotic dairy, and crossbred animals. We compared these animals to indigenous and animals used in smallholder systems in East Africa. Key findings were: confirmation that Indian Zebu breeds are pure Bos indicus in contrast to African Zebu and Sanga breeds, which are admixtures of Bos indicus and African Bos taurus; as found elsewhere, many apparently pure animals contain some admixture from imported breeds; crossbred animals exhibit a wider range of breed composition than intended, reflecting the lack of pedigree when sampling bull mothers from smallholder farms; breed composition of purebred and crossbred animals can in future be tested using SNP data, and only those meeting the desired composition retained for breeding.
Evaluation of cropping method for perennial ratoon rice: Adaptation of SALIBU to triple-cropping in Vietnam

Background: Generally, the yield of ratoon rice is at most 50% of the main crop. However, a cropping method “SALIBU” achieved more yield than the main crop and enables the perennial cropping. Although the SALIBU method is implementing 10 additional management practices to conventional method in Indonesia, the effect of each management practice is unclear. Methodology: We evaluated the effect size using an L 16 orthogonal array design pot experiment in triple-cropping rice in Vietnam. The robustness was checked by duplicating the experiment under standard and poor conditions. Results and Discussion: Positive large effects were shown in the poor conditions only. Cutting twice most affected the number of ratoon tillers. Importantly, the effect was positive under poor conditions but negative under standard conditions. Late irrigation had a robust negative effect. No treatment is effective in the triple-cropping of standard conditions. The SALIBU includes practices with unstable, negative, or minimal effects. The unstable effects show the interaction with the condition. The practices that have negative effects should exclude. Using practice on small effect size should depend on a cost-benefit analysis. Conclusions: No additional practice is effective for changing the triple-cropping to perennial ratoon cropping except harvesting near the ground. However, further work will be conducted to clarify the interaction between cutting twice and the cultivation condition.
Repellency of the essential oil extracted from the leaves of a local variety of Artimisia scoparia Waldst. & Kit. against Aedes aegypti L. using modified Y-tube olfactometer

Essential oil from Artemisia scoparia leaves was assayed for repellency against adult female Aedes aegypti L. using a modified Y-tube olfactometer. Three concentrations consisting of 10, 20, and 30 μl of the essential oil placed in 1x1 cm filter paper were separately assayed in the olfactometer against female A. aegypti adult mosquitoes. Results showed that 10 and 20 μl A. scoparia essential oil were effective repellent against Aedes aegypti as compared to control in one-way ANOVA (Fcal 13.57>Fcrit 4.96, P, 0.004, P= 0.004219) (Fcal, 69.39>Fcrit,4.96, P= 8.25x10) at 0.05% confidence level. Comparison of 30 μl A. scoparia essential oil repellency with a DEET-based commercial mosquito repellent showed comparable performance (fcalc 0.019<fcrit 4.30, P=0.89). On the basis of these results, it is concluded that A. scoparia essential oil is a potent repellent against Aedes aegypti and has comparable efficacy to the current DEET-based commercial mosquito repellent.
Effect of LPS remodeling and LPS-binding proteins on outer membrane vesicle production and composition

Effect of LPS Remodeling and LPS-binding Proteins on Outer Membrane Vesicle Production and Composition by Katherine Elizabeth Bonnington Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Meta J. Kuehn, Supervisor ___________________________ Michael Boyce ___________________________ Richard G. Brennan ___________________________ Kenneth Kreuzer ___________________________ Thomas McIntosh An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry in the Graduate School of Duke University 2017 Copyright by Katherine Elizabeth Bonnington 2017
Chlamydia trachomatis Infection, when Treated during Pregnancy, Is Not Associated with Preterm Birth in an Urban Safety-Net Hospital

Preterm birth is a major public health problem, occurring in more than half a million births per year in the United States. A number of maternal conditions have been recognized as risk factors for preterm birth, but for the majority of cases, the etiology is not completely understood. Chlamydia trachomatis is one of the most prevalent sexually transmitted infections in the world. However, its role in adverse pregnancy outcome in women is still debated. In order to determine if genitourinary tract infection with C. trachomatis during pregnancy was associated with preterm birth, we conducted a case-control study on women who delivered at Boston Medical Center, an urban “safety-net” hospital that serves a socioeconomically disadvantaged and racially diverse population. Women with known risk factors for preterm birth or immune suppression were excluded. Variables collected on enrolled subjects included demographics; diagnosis of C. trachomatis during or prior to pregnancy; tobacco, alcohol, and illicit substance use; gestational age; and birthweight and gender of the newborn. We also collected urine for chlamydia testing at the time of delivery and placental biopsies for nucleic acid amplification and histological studies. A total of 305 subjects were enrolled: 100 who delivered preterm and 205 who delivered full term. Among those subjects, we identified 19 cases of pregnancy-associated C. trachomatis infection: 6/100 preterm and 13/205 full term, a difference which was not statistically significant. Only two cases of untreated chlamydia infection were identified postpartum, and both occurred in women who delivered at term. We conclude that genitourinary tract infection with C. trachomatis during pregnancy, when appropriately treated, is not associated with preterm birth.
Review of Clinically Relevant Drug Interactions with Next Generation Hepatitis C Direct-acting Antiviral Agents

Abstract In this review, we examine the pharmacokinetics and clinically relevant drug interactions of the newer generation direct-acting antivirals (DAAs) for the treatment of chronic hepatitis C, specifically sofosbuvir/velpatasvir (Epclusa®), sofosbuvir/velpatasvir/voxilaprevir (Vosevi®), glecaprevir/pibrentasvir (Maviret®), and elbasvir/grazoprevir (Zepatier®). We searched MEDLINE (1948-January 2020), Embase (1964-January 2020), Google, and GoogleScholar using the terms pharmacokinetics, drug interaction, drug metabolism, sofosbuvir, velpatasvir, Epclusa, voxilaprevir, Vosevi, glecaprevir, pibrentasvir, Maviret, elbasvir, grazoprevir, and Zepatier, from inception to January 13, 2020. The search was limited to randomized controlled trials, in vitro studies, prospective and retrospective human studies, drug monographs, abstracts, and conference proceedings. All relevant published literature on pharmacokinetic and pharmacodynamic interactions involving DAAs were reviewed and the data extracted. Numerous clinically relevant drug-drug interactions (DDIs) were identified with the newer generation DAAs and commonly prescribed drugs. NS3/4A protease inhibitors are more likely to be involved in DDIs, followed by NS5A inhibitors and NS5B polymerase inhibitor. The majority of clinically relevant DDIs are predictable, according to known pharmacokinetic, pharmacodynamics, and physicochemical properties of DAAs; however, in select cases, unpredictable DDIs do occur. As expected, many drug interactions exist between newer generation DAAs and commonly prescribed medications. While the majority of clinically relevant interactions are predictable, many require therapeutic dose adjustment or careful selection of non-interacting drugs. In select cases, severe and unpredictable drug interactions can occur. Clinicians should consult hepatitis C virus pharmacotherapy experts and tertiary drug interaction resources when initiating DAA therapy in patients taking other medications.
NKAINs: A Novel Family of Membrane Proteins that Interact with the Na, K-ATPase and Affect Membrane Excitability

A novel family of Na,K-ATPase interacting (NKAIN) proteins was cloned and characterized. These proteins are highly conserved across species and do not resemble any known proteins in the genome. Aside from the conserved transmembrane domains, NKAINs contain no known functional domains. Striking amino acid conservation in the first two transmembrane domains suggests that the function of these proteins is concentrated in the membrane bilayer. NKAINl, 2, 3 and a splice form of NKAIN4 are brain and testis specific; another splice form of NKAIN4 is expressed ubiquitously. In the central nervous system, NKAINs localize to neurons. The C-terminal tail of NKAIN proteins interacts with the p subunit of the Na,K-ATPase. The Na,K-ATPase pi subunit, NKAINl and another p subunit interacting protein MONaKA form a complex in transfected cells. Since MONaKA shares sequence similarity with the C-terminal part of the Drosophila NKAIN homolog (dNKAIN), it is proposed that dNKAIN function is carried out by two mammalian proteins NKAIN and MONaKA. Flies with decreased dNKAIN expression show temperature-sensitive seizures, motor deficit and paralysis a phenotype of neuronal hyperexcitability. In contrast, dNKAIN overexpression leads to a phenotype identical to the phenotype of flies with inhibited cellular excitability. Thus, dNKAIN function is likely to decrease membrane excitability, possibly by affecting the Na,K-ATPase function. Neuronal expression of NKAIN proteins and a possible role in membrane excitability strongly suggest that this novel protein family could be critical for