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opencc-by-4.0May 2023View details →

Analysis on CD8+/FOXP3+Ratio and Its Association with Primary Endocrine Therapy Resistance in Indonesian Luminal B Her-2 Negative BC Patients

Analysis on CD8+/FOXP3+Ratio and Its Association with Primary Endocrine Therapy Resistance in Indonesian Luminal B Her-2 Negative BC Patients

opencc-zeroJun 2023View details →

Scalable Bayesian divergence time estimation with ratio transformations

<div class="page"> <div class="layoutArea"> <div class="column"> Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian phylogenetic studies have analyzed hundreds to thousands of sequences. Such large-scale analyses challenge divergence time reconstruction by requiring inference on highly-correlated internal node heights that often become computationally infeasible. To overcome this limitation, we explore a ratio transformation that maps the original N - 1 internal node heights into a space of one height parameter and N - 2 ratio parameters. To make the analyses scalable, we develop a collection of linear-time algorithms to compute the gradient and Jacobian-associated terms of the log-likelihood with respect to these ratios. We then apply Hamiltonian Monte Carlo sampling with the ratio transform in a Bayesian framework to learn the divergence times in four pathogenic viruses (West Nile virus, rabies virus, Lassa virus and Ebola virus) and the coralline red algae. Our method both resolves a mixing issue in the West Nile virus example and improves inference efficiency by at least 5-fold for the Lassa and rabies virus examples as well as for the algae example. Our method now also makes it computationally feasible to incorporate mixed-effects molecular clock models for the Ebola virus example, confirms the findings from the original study and reveals clearer multimodal distributions of the divergence times of some clades of interest. </div> </div> </div>

opencc-zeroDec 2022View details →

Normalised absorbance ratios of IgG for myxoma and rabbit hemorrhagic disease viruses: Longitudinal dataset wild European rabbits

This study addresses the long-term dynamics of humoral immunity to two viral pathogens of the European rabbit, an endangered keystone species of major ecological relevance. Such studies are particularly challenging in free-ranging species, and a combination of longitudinal capture-mark-recapture and semi-quantitative serology was used to address this question. Over 600 normalised absorbance ratios of indirect ELISA, obtained from 505 individual rabbits in 7 populations over five years were analysed using linear mixed models. The results support a lifelong acquired humoral immunity to myxoma virus and rabbit hemorrhagic disease virus upon natural infection and suggest the presence of maternal immunity to the latter in wild juvenile rabbits. These results contribute to understanding the epidemiology of two viral diseases threatening this keystone species and assist in developing conservation programs.

opencc-zeroJun 2023View details →

Data for: Mechanisms that can cause population decline under heavily skewed male-biased adult sex ratios

<ol> <li>While adult sex ratio (ASR) is a crucial component for population management, there is still a limited understanding of how its fluctuation affects population dynamics. To demonstrate mechanisms that hinder population growth under a biased ASR, we examined changes in reproductive success with ASR using a decapod crustacean exposed to female-selective harvesting. </li> <li> We examined the effect of ASR on the spawning success of females. A laboratory experiment showed that the number of eggs carried by females decreased as the proportion of males in the mating groups increased. Although the same result was not observed in data collected over 25 years in the wild, the negative effect of ASR was suggested when success in carrying eggs was considered as a spawning success. These results indicate that a surplus of males results in females failing to carry eggs, probably due to sexual coercion, and the negative effect of ASR can be detected at the population level only when the bias increases because failure in spawning success occurs in part of population. </li> <li>We experimentally examined how male-biased sex ratios affected the maintenance of genetic diversity in a population. The diversity of paternity in a clutch increased with the number of candidate fathers. However, over 50% of a clutch was fertilised by a single male regardless of the sex ratio, and the degree of diversity was less than half of the highest diversity expected in each mating group. </li> <li>We also experimentally examined the mating ability of males during the breeding season. The experiment showed that multiple mating by males could not compensate for the risk that their genotypes would be lost when multiple males competed for one female. These results suggest that a male-biased ASR could trigger a decline of genetic diversity in a population.</li> <li>We show that ASR skewed by female-selective harvesting decreases reproductive success not only of males that have few mating opportunities but also of females. We discuss that we may still underestimate the significance of ASR on population persistence due to the difficulty of revealing the effect of ASR.</li> </ol>

opencc-zeroJul 2023View details →

Multiple paternity is related to adult sex ratio and sex determination system in reptiles

The adult sex ratio (ASR, the proportion of males in the adult population) is an emerging predictor of reproductive behaviour, and recent studies in birds and humans suggest it is a major driver of social mating systems and parental care. ASR may also influence genetic mating systems. For instance, male-skewed ASRs are expected to increase the frequency of multiple paternity (defined here as a clutch or litter sired by two or more males) due to higher rates of coercive copulations by males and/or due to females exploiting the opportunity of copulation with multiple males to increase genetic diversity of their offspring. Here we evaluate this hypothesis in reptiles that often exhibit high frequency of multiple paternity, although its ecological and life-history predictors have remained controversial. Using a comprehensive dataset of 81 species representing all four non-avian reptile orders, we show that increased frequency of multiple paternity is predicted by more male-skewed ASR, and this relationship is robust to simultaneous effects of several life-history predictors. Additionally, we show that the frequency of multiple paternity varies with the sex determination system: species with female heterogamety (ZZ/ZW sex chromosomes) exhibit higher levels of multiple paternity than species with male heterogamety (XY/XX) or temperature-dependent sex determination. Thus, our across-species comparative study provides the first evidence that genetic mating system depends on ASR in reptiles. We call for further investigations to uncover the complex evolutionary associations between mating systems, sex determination systems and ASR.

opencc-by-4.0Aug 2023View details →

Concentrations and isotope ratios of N2O and related substrates with hydrographical data obtained in the eastern Indian Ocean in November, 2018

A spreadsheet that includes data presented in the following publication. Sakae Toyoda, Kotaro Terajima, Naohiro Yoshida, Chisato Yoshikawa, Akiko Makabe, Fuminori Hashihama, and Hiroshi Ogawa,  Extensive Accumulation of Nitrous Oxide in the Oxygen Minimum Zone in the Bay of Bengal, Global Biogeochemical Cycles, accepted for publication on August 8, 2023.

opencc-by-4.0Jun 2023View details →

Fig. 8 in Sex-ratio and body size plasticity in two cold-adapted ground beetles co-occurring in a periglacial area of the European Alps (Coleoptera: Carabidae)

Fig. 8 – Linear regression graph between elytra width of Nebria castanea females and the soil pH.

opencc-by-4.0Jun 2023View details →

Fig. 1 in Sex-ratio and body size plasticity in two cold-adapted ground beetles co-occurring in a periglacial area of the European Alps (Coleoptera: Carabidae)

Fig. 1 – Sampling plan: distribution of pitfall traps at the Lazaunkar site.

opencc-by-4.0Sep 2023View details →

High CD8 + / FOXP3+ Ratio is Significantly Associated with Primary Endocrine Therapy Resistance Occurrence in Locally Advanced Luminal B Her-2 Negative Breast Cancer Patients

High CD8 + / FOXP3+ Ratio is Significantly Associated with Primary Endocrine Therapy Resistance Occurrence in Locally Advanced Luminal B Her-2 Negative Breast Cancer Patients

openother-openSep 2023View details →

Wildfire Information and Trace Gas Enhancement Ratios

Wildfire Information, FRP statistics, TROPOMI ∆NO2/∆CO, and TROPOMI ∆HCHO/∆CO from "Analyzing the Impact of Evolving Combustion Conditions on the Composition of Wildfire Emissions Using Satellite Data"

opencc-zeroSep 2023View details →

Association of fat-to-muscle ratio with non-alcoholic fatty liver disease: a single-centre retrospective study

Objectives: Sarcopenia is a known risk factor for non-alcoholic fatty liver disease (NAFLD). Studies evaluating the association between the fat-to-muscle ratio (FMR) and NAFLD are limited. Therefore, the aim of our study was to investigate the association between FMR and NAFLD. Design: A retrospective study was conducted on the individuals who underwent health examination in Wuhan Union Hospital between January 2020 and November 2021. Clinical data were collected from electronic medical records. Setting: Our study was conducted in a hospital in China. Participants: A total of 1,592 participants aged ≥40 years who underwent body composition analysis and liver ultrasonography were retrospectively reviewed. Primary outcome measures: Liver ultrasonography was used to assess liver steatosis, and the Fibrosis-4 Index (FIB-4) was used to calculate the risk scores for liver fibrosis. The 10-year atherosclerotic cardiovascular disease (ASCVD) risk prediction model was used to calculate ASCVD risk scores. Results: The FMR was significantly higher in individuals with NAFLD than in those without NAFLD (P<0.001). The prevalence of NAFLD gradually increased from FMR tertile 1 (reference) to tertile 2 (OR=1.49, 95% CI: 1.13–1.97) and tertile 3 (OR=2.85, 95% CI: 2.08–3.90). In addition, patients with NAFLD in FMR tertile 3 had a significantly higher risk of liver fibrosis (OR=4.48, 95% CI: 2.12–9.50) and ASCVD (OR=4.63, 95% CI: 2.62–8.19) than those in FMR tertile 1 after adjustment for multiple confounders. Conclusion: In this study, we found a significant association between FMR and NAFLD. A higher FMR indicates a higher risk of NAFLD in the study population and a higher risk of liver fibrosis and ASCVD in NAFLD patients.

opencc-zeroOct 2023View details →

Offspring sex ratio is affected by pre-breeding rainfall and hatching order in a cooperative breeding bird

Selection may favour sex ratio adjustment when the fitness benefits of producing male or female offspring vary. In birds, sex ratio bias at hatching has been particularly well-studied in cooperative breeding species, primarily in helper-at-the-nest systems wherein young remain with their parents and help raise subsequent broods. In these systems, breeding females are expected to skew offspring sex ratio in favour of the helping sex if sufficient resources exist. In communal laying systems multiple group members breed and raise the young and offspring dispersal varies, making it difficult to predict whether and how breeders should skew offspring sex ratio. We tested for sex ratio bias in smooth-billed anis (Crotophaga ani), a communal laying cuckoo with low within-group relatedness, high offspring dispersal, and high annual turnover in group membership. One male performs nocturnal incubation and sires more offspring, suggesting these males may have higher reproductive variance and thus that it may be beneficial for his mate to produce more male offspring. We hypothesized that pre-breeding rainfall influences food availability and thus offspring sex ratio, predicting that breeding females skew production towards the more beneficial sex (i.e., males) in high food years, consistent with the Trivers-Willard hypothesis. Females may also adjust sex ratio across the hatching order, so we predicted a male-bias in first hatched chicks in larger broods that should experience greater competition. Contrary to our first prediction, more male chicks hatched when pre-breeding rainfall was lower. In partial support of our second prediction, marginally more first hatched chicks were male in larger broods. Based on these results, we propose the nestling competition hypothesis and predict that when nestling competition is high (i.e., in poor years and in large joint broods), mothers should produce more of the more competitive sex.

opencc-by-4.0Oct 2023View details →

Supplementary data for paper "Extreme mass-ratio inspiral and waveforms for a spinning body into a Kerr black hole via osculating geodesics and near-identity transformations"

Radiation-reaction fluxes and NIT interpolant data for paper "Extreme mass-ratio inspiral and waveforms for a spinning body into a Kerr black hole via osculating geodesics and near-identity transformations"

opencc-zeroDec 2023View details →

How does the weekend catch-up sleep ratio affect the health and lifestyle of Korean adults? An age- and sex- matched study

The purpose of this study was to investigate the association between various levels of physical activity, self-perception, cardiometabolic risk factors, and weekend catch-up sleep ratio (CSR). Using raw data from the Korea National Health and Nutrition Examination Survey 2018 – 2021, all participants were divided into three groups (< 1.0, 1.0 ≤ CSR < 1.5, or ≥ 1.5) by CSR, which is the value calculated by dividing weekend sleep time by weekday sleep time. After matching age and sex, 2,484 Korean adults were selected as study participants. Descriptive statistics, chi-square test, ANOVA, and multinomial logistic regression analysis were performed to analyze the data. The results showed a significant association between weekend CSR and socioeconomic status, physical activity, self-perception levels, and cardiometabolic risk factors. Specifically, compared to the reference group (1 ≤ CSR < 1.5), those with a CSR < 1 were 2.42 times more likely to live in a single-family house (OR = 2.42, 95% CI = 1.77 – 3.32) and 1.71 times more likely to engage in vigorous physical activity meeting WHO guidelines (OR = 1.71, 95% CI = 1.20 – 2.46). They were also 1.33 times more likely to perceive themselves as 'obese' (OR = 1.33, 95% CI = 1.00 – 1.76). Conversely, those in the CSR ≥ 1.5 group were 3.93 times more likely to be 'pink-collar' workers (OR = 3.93, 95% CI = 2.70 – 5.71), 1.72 times more likely to perceive their stress levels as 'quite' (OR = 1.72, 95% CI = 1.20 – 2.47), and 1.87 times more likely to have diabetes (OR = 1.87, 95% CI = 0.97 – 3.60). Alterations in CSR could indicate changes in physical activity levels, sedentary behavior duration, and other health indicators, ultimately influencing overall well-being. Therefore, a comprehensive healthcare approach incorporating CSR considerations is increasingly essential.

Comparison of Bystander Fatigue and CPR Quality When Using Two Different CPR Ratios.

ClinicalTrials.gov study NCT00380757. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Is There Any Correlation Between Respiratory Variation Ratios of Internal Jugular Vein and Inferior Vena Cava?

ClinicalTrials.gov study NCT04173741. IPD Sharing: Not stated. Countries: 1. Publications: 4.

closedIPD-NOFeb 2026View details →

Neutrophil to Lymphocyte Ratio as a Predictor of Complicated Acute Diverticulitis

ClinicalTrials.gov study NCT04663490. IPD Sharing: NO. Countries: 1. Publications: 17.

controlledIPD-YESFeb 2026View details →

Efficacy and Safety of 8-weeks of Glecaprevir/Pibrentasvir in Treatment-Naïve Adults With HCV Genotype 1-6 and Aspartate Aminotransferase to Platelet Ratio Index (APRI) ≤1

ClinicalTrials.gov study NCT03212521. IPD Sharing: YES. Countries: 10. Publications: 1.

Anticoagulants Comparative Benefit-risk Ratio in Real Life

ClinicalTrials.gov study NCT02785354. IPD Sharing: Not stated. Countries: 1. Publications: 2.

SI + CC Versus 3:1 C:V Ratio During Neonatal CPR

ClinicalTrials.gov study NCT02858583. IPD Sharing: Not stated. Countries: 2. Publications: 31.