Although the transvaginal route is the preferred method for the oocyte retrieval procedure, the transabdominal (TA) route may be preferred in certain conditions. In this opinion we presented our experience with TA oocyte pick-up in 101 patients across several different indications and assessed the safety of the procedure.
Predator-prey models in theoretical ecology have a long and complex history, spanning decades of research. Most of the models rely upon simple reproduction and mortality rates associated with different types of functional responses. A key development in this field occurred with the introduction of a density dependent reproduction rate, originally introduced by Allee. In this manuscript, a new function representing the Allee effect is introduced and justified from the ecological point of view. This paper aims to analyze predator-prey models incorporating Holling type-I and II functional responses, influenced by this new Allee function. A rich dynamics shows up in the presence of the said function, including the emergence of the limit cycles through the Hopf bifurcation for a particular parameter domain.
Sean T. Bresnahan, Shaun Mahony, Kate Anton
et al.
Abstract Background Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproductive queens or short-lived, facultatively sterile workers. Beyond environmental factors, intragenomic conflict between genes inherited from the mother (matrigenes) versus the father (patrigenes) is hypothesized to influence the underlying traits. In honey bees, the Kinship Theory of Intragenomic Conflict predicts selection on patrigenes to favor traits enhancing individual fitness, such as accelerated growth or increased body size—traits more active in queen-destined larvae. Although parent-of-origin effects have been reported in honey bees, the associated gene regulatory mechanisms remain unknown. While DNA methylation underlies parent-biased transcription in eutherians, angiosperms, and some insects, it is not operating in honey bees or other social insects. Results Allele-specific transcriptome analyses on queen- and worker-destined larvae at 192 h post-fertilization (hpf) reveal hundreds of genes with parent-of-origin effects, with queen-destined larvae showing overrepresentation of patrigene-biased transcription relative to worker-destined larvae. Genes with parent-biased transcription resemble imprinted genes in other taxa regarding genomic clustering, recombination rate, intron length, and CpG density, with a subset showing parent-biased transcription in 24 hpf eggs. Allele-specific ChIP-seq analyses demonstrate that parent-of-origin effects on caste-specific profiles of H3K27me3, H3K4me3, and H3K27ac are associated with parent-of-origin transcription. Conclusions These findings suggest that parent-of-origin intragenomic conflict may influence phenotypic plasticity and may be associated with histone post-translational modifications, suggesting a “noncanonical” genomic imprinting-like system in social insects.
Background Excess epicardial adipose tissue (EAT) has been associated with cardiovascular diseases such as atrial fibrillation, coronary artery disease, and heart failure. The metabolomic signature of EAT is not well studied. Methods Untargeted 1H nuclear magnetic resonance metabolomics profiling of serum was performed (1‐dimensional nuclear magnetic resonance, Carr–Purcell–Meiboom–Gill Echo Train Acquisition, lipidomics) and EAT was measured with computed tomography in MESA (Multi‐Ethnic Study of Atherosclerosis; N=3936) and the Rotterdam study (N=465). Associations between fasting serum metabolites and EAT volume were assessed using cross‐sectional linear regression of individual‐level data in MESA and validated in Rotterdam. Results A total of 23 571 metabolomic spectral variables were evaluated. In MESA, after adjustment for age, sex, and race and ethnicity, 38 metabolites were positively and 19 metabolites negatively associated with EAT at a false discovery rate P<0.01. Several metabolites were replicated in Rotterdam, including 1,5‐anhydrosorbitol and N‐acetyl (glycoproteins) that were positively associated with EAT and trimethylamine (phospholipids) that were inversely associated with EAT. Branched‐chain amino acids (leucine, isoleucine, and valine) and 3‐hydroxybutyrate were also associated with EAT in the Rotterdam study. In MESA, apolipoprotein B and very‐low‐density and intermediate‐density lipoprotein fractions were positively associated with EAT and the majority of high‐density lipoprotein subclasses were inversely associated with EAT. Associations were partially attenuated in MESA and fully attenuated in Rotterdam after further adjustment for health and socioeconomic factors. Conclusions From >20 000 metabolomic features, 1,5‐anhydrosorbitol, glycoproteins, phospholipids, and atherogenic dyslipidemia markers emerged as significant markers of EAT. Further investigation is warranted to determine whether nuclear magnetic resonance–based metabolic profiling can improve EAT detection with implications for cardiometabolic health.
Diseases of the circulatory (Cardiovascular) system
Abdelrahman Saeed, Omar Saeed, Munia Rajabi
et al.
Abstract Background The female condom is a type of barrier contraception with a wide range of benefits. These benefits include significantly reducing the risk of sexually transmitted diseases and the number of unintentional pregnancies; however, their failure rates and functional performance have not been studied thoroughly. Objectives This study aimed to compare the functional performance and practical use of different types of female condoms. Methods We conducted a systematic review and network meta-analysis following the Preferred Reporting Items for Systematic reviews and Meta-analysis for Network Meta-Analyses (PRISMA-NMA) statement. We included randomized clinical trials assessing the types of female condoms in the sexually active female population using the PubMed, Scopus, and Web of Science databases. We assessed the risk of bias (RoB) in the included studies using the Cochrane risk of bias (ROB-1) tool. Results Through our literature search, 649 articles were identified, and only 11 randomized clinical trials were included. When assessing total clinical failure, Cupid condoms demonstrated noninferiority when compared to FC2 (NMA estimate: 0.79, 95% CI: − 1.09 to 2.73, p = 0.40). Regarding total condom failure, the analysis indicated no significant difference between the Cupid condom and others like V-Amour (NMA estimate: − 0.17, 95% CI: − 0.57 to 1.76, p = 0.32) or Velvet (NMA estimate: 0.69, 95% CI: − 1.62, 0.52, p = 0.32). Similarly, comparisons between Cupid and other types, such as Velvet or WC, regarding the incidence of slippage yielded nonsignificant results. These findings suggest generally consistent performance in terms of slippage across different types of condoms. Conclusion This systematic review and network meta-analysis showed the noninferiority of different types of female condoms compared to FC2 regarding their failure rates and functional performance. Our results show that female condoms are a reliable form of contraception, with minimal complications and adverse events.
We consider an SEIR epidemic model on a network also allowing random contacts, where recovered individuals could either recover naturally or be diagnosed. Upon diagnosis, manual contact tracing is triggered such that each infected network contact is reported, tested and isolated with some probability and after a random delay. Additionally, digital tracing (based on a tracing app) is triggered if the diagnosed individual is an app-user, and then all of its app-using infectees are immediately notified and isolated. The early phase of the epidemic with manual and/or digital tracing is approximated by different multi-type branching processes, and three respective reproduction numbers are derived. The effectiveness of both contact tracing mechanisms is numerically quantified through the reduction of the reproduction number. This shows that app-using fraction plays an essential role in the overall effectiveness of contact tracing. The relative effectiveness of manual tracing compared to digital tracing increases if: more of the transmission occurs on the network, when the tracing delay is shortened, and when the network degree distribution is heavy-tailed. For realistic values, the combined tracing case can reduce $R_0$ by $20-30\%$, so other preventive measures are needed to reduce the reproduction number down to $1.2-1.4$ for contact tracing to make it successful in avoiding big outbreaks.
The initial phase of an epidemic is often characterized by an exponential increase in the number of infected individuals. In this paper, we predict the exponential spreading rate of an epidemic on a complex network. We first find an expression of the reproduction number for a network, based on the degree distribution, the network assortativity, and the level of clustering. We then connect this reproduction number and the disease infectiousness to the spreading rate. Our result holds for a broad range of networks, apart from networks with very broad degree distribution, where no clear exponential regime is present. Our theory bridges the gap between classic epidemiology and the theory of complex networks, with broad implications for model inference and policy making.
Analysing the Stata regression commands from 4,420 reproduction packages of leading economic journals, we find that, among the 40,571 regressions specifying heteroskedasticity-robust standard errors, 98.1% adhere to Stata's default HC1 specification. We then compare several heteroskedasticity-robust inference methods with a large-scale Monte Carlo study based on regressions from 155 reproduction packages. Our results show that t-tests based on HC1 or HC2 with default degrees of freedom exhibit substantial over-rejection. Inference methods with customized degrees of freedom, as proposed by Bell and McCaffrey (2002), Hansen (2024), and a novel approach based on partial leverages, perform best. Additionally, we provide deeper insights into the role of leverages and partial leverages across different inference methods.
As part of the process of resolving issues submitted by users via bug reports, Android developers attempt to reproduce and observe the failures described by the bug report. Due to the low-quality of bug reports and the complexity of modern apps, the reproduction process is non-trivial and time-consuming. Therefore, automatic approaches that can help reproduce Android bug reports are in great need. However, current approaches to help developers automatically reproduce bug reports are only able to handle limited forms of natural language text and struggle to successfully reproduce failures for which the initial bug report had missing or imprecise steps. In this paper, we introduce a new fully automated Android bug report reproduction approach that addresses these limitations. Our approach accomplishes this by leveraging natural language process techniques to more holistically and accurately analyze the natural language in Android bug reports and designing new techniques, based on reinforcement learning, to guide the search for successful reproducing steps. We conducted an empirical evaluation of our approach on 77 real world bug reports. Our approach achieved 67% precision and 77% recall in accurately extracting reproduction steps from bug reports, and reproduced 74% of the bug reports, significantly outperforming state of the art techniques.
In this paper, we replicated a Bayesian educational research project, which explores the association between broadband access and online course enrollment in the US. We summarized key findings from our replication and compared them with the original project. Based on my replication experience, we aim to demonstrate the challenges of research reproduction, even when codes and data are shared openly and the quality of the materials on GitHub are high. Moreover, we investigate the implicit presumptions of the researchers' level of knowledge and discuss how such presumptions may add difficulty to the reproduction of scientific research. Finally, we hope this article sheds light on the design of reproducibility criterion and opens up a space to explore what should be taught in undergraduate statistics education.
Mixed lipid micelles were proposed to facilitate life through their documented growth dynamics and catalytic properties. Our previous research predicted that micellar self-reproduction involves catalyzed accretion of lipid molecules by the residing lipids, leading to compositional homeostasis. Here, we employ atomistic Molecular Dynamics simulations, beginning with 54 lipid monomers, tracking an entire course of micellar accretion. This was done to examine the self-assembly of variegated lipid clusters, allowing us to measure entry and exit rates of monomeric lipids into pre-micelles with different compositions and sizes. We observe considerable rate-modifications that depend on the assembly composition and scrutinize the underlying mechanisms as well as the energy contributions. Lastly, we describe the measured potential for compositional homeostasis in our simulated mixed micelles. This affirms the basis for micellar self-reproduction, with implications for the study of the origin of life.
Evans K. Cheruiyot, Mekonnen Haile-Mariam, Benjamin G. Cocks
et al.
Abstract Background Heat tolerance is a trait of economic importance in the context of warm climates and the effects of global warming on livestock production, reproduction, health, and well-being. This study investigated the improvement in prediction accuracy for heat tolerance when selected sets of sequence variants from a large genome-wide association study (GWAS) were combined with a standard 50k single nucleotide polymorphism (SNP) panel used by the dairy industry. Methods Over 40,000 dairy cattle with genotype and phenotype data were analysed. The phenotypes used to measure an individual’s heat tolerance were defined as the rate of decline in milk production traits with rising temperature and humidity. We used Holstein and Jersey cows to select sequence variants linked to heat tolerance. The prioritised sequence variants were the most significant SNPs passing a GWAS p-value threshold selected based on sliding 100-kb windows along each chromosome. We used a bull reference set to develop the genomic prediction equations, which were then validated in an independent set of Holstein, Jersey, and crossbred cows. Prediction analyses were performed using the BayesR, BayesRC, and GBLUP methods. Results The accuracy of genomic prediction for heat tolerance improved by up to 0.07, 0.05, and 0.10 units in Holstein, Jersey, and crossbred cows, respectively, when sets of selected sequence markers from Holstein cows were added to the 50k SNP panel. However, in some scenarios, the prediction accuracy decreased unexpectedly with the largest drop of − 0.10 units for the heat tolerance fat yield trait observed in Jersey cows when 50k plus pre-selected SNPs from Holstein cows were used. Using pre-selected SNPs discovered on a combined set of Holstein and Jersey cows generally improved the accuracy, especially in the Jersey validation. In addition, combining Holstein and Jersey bulls in the reference set generally improved prediction accuracy in most scenarios compared to using only Holstein bulls as the reference set. Conclusions Informative sequence markers can be prioritised to improve the genomic prediction of heat tolerance in different breeds. In addition to providing biological insight, these variants could also have a direct application for developing customized SNP arrays or can be used via imputation in current industry SNP panels.
A model of population growth and dispersal is considered where the spatial habitat is a lattice and reproduction occurs generationally. The resulting discrete dynamical systems exhibits velocity locking, where rational speed invasion fronts are observed to persist as parameters are varied. In this article, we construct locked fronts for a particular piecewise linear reproduction function. These fronts are shown to be linear combinations of exponentially decaying solutions to the linear system near the unstable state. Based upon these front solutions, we then derive expressions for the boundary of locking regions in parameter space. We obtain leading order expansions for the locking regions in the limit as the migration parameter tends to zero. Strict spectral stability in exponentially weighted spaces is also established.
We study the asymptotic behavior of solutions of the Cauchy problem associated to a quantitative genetics model with a sexual mode of reproduction. It combines trait-dependent mortality and a nonlinear integral reproduction operator "the infinitesimal model" with a parameter describing the standard deviation between the offspring and the mean parental traits. We show that under mild assumptions upon the mortality rate m, when the deviations are small, the solutions stay close to a Gaussian profile with small variance, uniformly in time. Moreover we characterize accurately the dynamics of the mean trait in the population. Our study extends previous results on the existence and uniqueness of stationary solutions for the model. It relies on perturbative analysis techniques together with a sharp description of the correction measuring the departure from the Gaussian profile.
Vincenzo Zaccà, Pablo Martinez-Nuevo, Martin Møller
et al.
Accurate sound field reproduction in rooms is often limited by the lack of knowledge of the room characteristics. Information about the room shape or nearby reflecting boundaries can, in principle, be used to improve the accuracy of the reproduction. In this paper, we propose a method to infer the location of nearby reflecting boundaries from measurements on a microphone array. As opposed to traditional methods, we explicitly exploit the loudspeaker directivity model (beyond omnidirectional radiation) and the microphone array geometry. This approach does not require noiseless timing information of the echoes as input, nor a tailored loudspeaker-wall-microphone measurement step. Simulations show the proposed model outperforms current methods that disregard directivity in reverberant environments.
We propose an epidemiological model using an adaptive dynamic three compartment (with four states) SIR(D) model. Our approach is similar to non-parametric curve fitting in spirit and automatically adapts to key external factors, such as interventions, while retaining the parsimonious nature of the standard SIR(D) model. Initial dynamic temporal estimates of the model parameters are obtained by minimising the aggregate residual sum of squares across the number of infections, recoveries, and fatalities, over a chosen lag period. Then a geometric smoother is applied to obtain the final time series of estimates. These estimates are used to obtain dynamic temporal robust estimates of the key feature of this pandemic, namely the "reproduction number". We illustrate our method on the Indian COVID-19 data for the period March 14 - August 31, 2020. The time series data plots of the 36 states and union territories shows a clear presence of inter-regional variation in the prognosis of the epidemic. This is also bourne out by the estimates of the underlying parameters, including the reproduction numbers for the 36 regions. Due to this, an SIR(D) model, dynamic or otherwise, on the national aggregate data is not suited for robust local predictions. The time series of estimates of the model enables us to carry out daily, weekly and also long term predictions, including construction of predictive bands. We obtain an excellent agreement between the actual data and the model predicted data at the regional level. Our estimates of the current reproduction number turn out to be more than 2 in three regions (Andhra Pradesh, Maharashtra and Uttar Pradesh) and between 1.5 and 2 in 13 regions. Each of these regions have experienced an individual trajectory, which typically involves initial phase of shock(s) followed by a relatively steady lower level of the reproduction number.