Hasil untuk "Reproduction"

Bjarki Eldon

Recruitment dynamics, or the distribution of the number of offspring among individuals, is central for understanding ecology and evolution. Sweepstakes reproduction (heavy right-tailed offspring number distribution) is central for understanding the ecology and evolution of highly fecund natural populations. Sweepstakes reproduction can induce jumps in type frequencies and multiple mergers in gene genealogies of sampled gene copies. We take sweepstakes reproduction to be skewed offspring number distribution due to mechanisms not involving natural selection, such as in chance matching of broadcast spawning with favourable environmental conditions. Here, we consider population genetic models of sweepstakes reproduction in a diploid panmictic populations absent selfing and evolving in a random environment. Our main results are {\it (i)} continuous-time Beta and Poisson-Dirichlet coalescents, when combining the results the skewness parameter $α$ of the Beta-coalescent ranges from $0$ to $2$, and the Beta-coalescents may be incomplete due to an upper bound on the number of potential offspring produced by any pair of parents; {\it (ii)} in large populations time is measured in units proportional to either $N/\log N$ or $N$ generations (where $2N$ is the population size when constant); {\it (iii)} it follows that incorporating population size changes leads to time-changed coalescents with the time-change independent of $α$; {\it (iv)} using simulations we show that the ancestral process is not well approximated by the corresponding coalescent (as measured through certain functionals of the processes); {\it (v)} whenever the skewness of the offspring number distribution is increased the conditional (conditioned on the population ancestry) and the unconditional ancestral processes are not in good agreement.

Bin Liu, Yanjie Zhao, Zhenpeng Chen et al.

Automated vulnerability reproduction from CVE descriptions requires generating executable Proof-of-Concept (PoC) exploits and validating them in target environments. This process is critical in software security research and practice, yet remains time-consuming and demands specialized expertise when performed manually. While LLM agents show promise for automating this task, existing approaches often conflate exploring attack directions with fixing implementation details, which leads to unproductive debugging loops when reproduction fails. To address this, we propose CVE2PoC, an LLM-based dual-loop agent framework following a plan-execute-evaluate paradigm. The Strategic Planner analyzes vulnerability semantics and target code to produce structured attack plans. The Tactical Executor generates PoC code and validates it through progressive verification. The Adaptive Refiner evaluates execution results and routes failures to different loops: the Tactical Loop for code-level refinement, while the Strategic Loop for attack strategy replanning. This dual-loop design enables the framework to escape ineffective debugging by matching remediation to failure type. Evaluation on two benchmarks covering 617 real-world vulnerabilities demonstrates that CVE2PoC achieves 82.9% and 54.3% reproduction success rates on SecBench.js and PatchEval, respectively, outperforming the best baseline by 11.3% and 20.4%. Human evaluation confirms that generated PoCs achieve comparable code quality to human-written exploits in readability and reusability.

Bjarki Eldon

Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents where a random number of lineages merges at such times. We consider population genetic models of sweepstakes reproduction for haploid panmictic populations of both constant ($N$), and varying population size, and evolving in a random environment. We construct our models so that we can recover the observed number of new mutations in a given sample without requiring strong assumptions regarding the population size or the mutation rate. Our main results are {\it (i)} continuous-time coalescents that are either the Kingman coalescent or specific families of Beta- or Poisson-Dirichlet coalescents; when combining the results the parameter $α$ of the Beta-coalescent ranges from 0 to 2, and the Beta-coalescents may be incomplete due to an upper bound on the number of potential offspring an arbitrary individual may produce; {\it (ii)} in large populations we measure time in units proportional to either $ N/\log N$ or $N$ generations; {\it (iii)} incorporating fluctuations in population size leads to time-changed multiple-merger coalescents where the time-change does not depend on $α$; {\it (iv)} using simulations we show that in some cases approximations of functionals of a given coalescent do not match the ones of the ancestral process in the domain of attraction of the given coalescent; {\it (v)} approximations of functionals obtained by conditioning on the population ancestry (the ancestral relations of all gene copies at all times) are broadly similar (for the models considered here) to the approximations obtained without conditioning on the population ancestry.

Hongrong Yin, Jinhong Huang, Yao Li et al.

Mobile application development is a fast-paced process where maintaining high-quality user experiences is crucial. Bug reproduction, a key aspect of maintaining app quality, often faces significant challenges. Specifically, when descriptions in bug reports are ambiguous or difficult to comprehend, current approaches fail to extract accurate information. Moreover, modern applications exhibit inherent complexity with multiple pages and diverse functionalities, making it challenging for existing methods to map the relevant information in bug reports to the corresponding UI elements that need to be manipulated. To address these challenges, we propose BugRepro, a novel technique that integrates domain-specific knowledge to enhance the accuracy and efficiency of bug reproduction. BugRepro adopts a Retrieval-Augmented Generation (RAG) approach. It retrieves similar bug reports along with their corresponding steps to reproduce (S2R) entities from an example-rich RAG document. In addition, BugRepro explores the graphical user interface (GUI) of the app and extracts transition graphs from the user interface to incorporate app-specific knowledge to guide large language models (LLMs) in their exploration process. Our experiments demonstrate that BugRepro significantly outperforms two state-of-the-art methods (ReCDroid and AdbGPT). For S2R entity extraction accuracy, it achieves a 7.57 to 28.89 percentage point increase over prior methods. For the bug reproduction success rate, the improvement reaches 74.55% and 152.63%. In reproduction efficiency, the gains are 0.72% and 76.68%.

Hisashi Inaba, Shoko Konishi

We develop a linear one-sex dynamical model of human population reproduction through marriage. In our model, a woman may marry and divorce multiple times; however, only women who are currently married are assumed to bear children. The iterative marriage process is formulated as a three-state compartmental model, which is described by a system of McKendrick equations with a marital birth rate function that depends on the duration of marriage and the age at marriage. To examine the impact of changing nuptiality on fertility, we derive new formulas for the reproduction indices. In particular, the total fertility rate (TFR) is expressed as the product of the total marriage number and the average total marital fertility. Using Japanese vital statistics, we show that our model provides a reasonable estimate of the current TFR and its future trajectory.

Monireh Mahmoodi, Elham Shojafar, Maryam Dastjani-Farahani

The sperm freezing–thawing procedure is the most commonly used technique in clinics to preserve male fertility before any pathological destruction of the testis. Therefore, most studies are currently focused on optimizing this method to achieve high-quality semen after thawing. During cryopreservation, oxidative stress-induced damage affects sperm structures and decreases their fertility potential. The use of antioxidants in freezing media can protect sperm against oxidative damage. We designed this study to evaluate whether incubation of semen with human follicular fluid, which contains a wide variety of enzymatic and nonenzymatic antioxidants, can prevent the negative effects of freezing–thawing on human spermatozoa. Human semen was divided into three groups i) the 0-hour group (before freezing), ii) the control group (after freezing–thawing), and iii) the FF group (after freezing with 50% follicular fluid). The sperm motility, viability, integrity of the plasma membrane and DNA, mitochondrial membrane potential, malondialdehyde level, total antioxidant capacity, and catalase activity were assessed in these three groups. The findings showed a significant decrease in sperm motility, viability, plasma membrane and DNA integrity, mitochondrial membrane potential, total antioxidant capacity, and catalase activity and a significant increase in malondialdehyde level in the control group compared with the 0-hour group. The FF group displayed a considerable increase in sperm parameters, total antioxidant capacity, and catalase activity and a significant decrease in malondialdehyde level compared with the control group. Follicular fluid can be considered an effective supplement to improve antioxidant indices and sperm parameters during freezing–thawing.

Yalan Lin, Yingwei Ma, Rongyu Cao et al.

Reproducing buggy code is the first and crucially important step in issue resolving, as it aids in identifying the underlying problems and validating that generated patches resolve the problem. While numerous approaches have been proposed for this task, they primarily address common, widespread errors and struggle to adapt to unique, evolving errors specific to individual code repositories. To fill this gap, we propose EvoCoder, a multi-agent continuous learning framework for issue code reproduction. EvoCoder adopts a reflection mechanism that allows the LLM to continuously learn from previously resolved problems and dynamically refine its strategies to new emerging challenges. To prevent experience bloating, EvoCoder introduces a novel hierarchical experience pool that enables the model to adaptively update common and repo-specific experiences. Our experimental results show a 20\% improvement in issue reproduction rates over existing SOTA methods. Furthermore, integrating our reproduction mechanism significantly boosts the overall accuracy of the existing issue-resolving pipeline.

Yichen Han, Xiaona Lin

This narrative review explores the relationship between psychological stress and ovulatory disorders, focusing on the molecular mechanisms involved. Ovulation is regulated by the hypothalamus-pituitary-ovarian (HPO) axis, and disruptions in this axis can lead to ovulatory dysfunction. Chronic psychological stress affects the HPO axis, resulting in abnormalities in hypothalamus hormone secretion, pituitary hormone release, and ovarian function. These disruptions cause ovulation disorders and menstrual irregularities. The mechanisms by which psychological stress affects ovulation involve alterations in neuropeptides and hormones, activation of the hypothalamic-pituitary-adrenal (HPA) axis, impairment of follicular development, generation of oxidative stress, and the decline in ovarian reserve function. Understanding these mechanisms is crucial for developing interventions to restore reproductive health. Psychological interventions, such as cognitive-behavioral therapy, have shown promise in improving ovulation and pregnancy rates in women with ovulatory disorders. Further research is needed to explore the specific mechanisms of these interventions and optimize treatment strategies. Addressing psychological factors is essential in managing reproductive health and ovulatory disorders.

Simone De Reggi, Francesca Scarabel, Rossana Vermiglio

In this paper, we introduce a general numerical method to approximate the reproduction numbers of a large class of multi-group, age-structured, population models with a finite age span. To provide complete flexibility in the definition of the birth and transition processes, we propose an equivalent formulation for the age-integrated state within the extended space framework. Then, we discretize the birth and transition operators via pseudospectral collocation. We discuss applications to epidemic models with continuous and piecewise continuous rates, with different interpretations of the age variable (e.g., demographic age, infection age and disease age) and the transmission terms (e.g., horizontal and vertical transmission). The tests illustrate that the method can compute different reproduction numbers, including the basic and type reproduction numbers as special cases.

Carmelo Mario Vicario, Vito Scavone, Chiara Lucifora et al.

Evidence suggests that incidental modulation of affective states affects the ability to keep track of time. Alexithymia represents an ideal condition to further address the emotion-time processing link, as it refers to a trait characterized by a deficit of affective processing. 31 healthy participants completed an online version of the TAS-20 scale, which measures alexithymia, and a time reproduction task of visual stimuli related to positive (i.e., happiness) and negative (i.e., anger) facial expressions. Results documented a positive correlation between TAS-20 score and the variability in reproducing sub-second durations of the anger expression stimuli We also found an overestimation of sub-second durations of non-affective expressions in borderline/alexithymic participants. Finally, in line with the literature, we confirmed the overall tendency to overestimate the duration of anger expression stimuli. These findings, which can be interpreted in terms of abnormal scalar timing property in alexithymia, expand previous investigations linking this personality trait with abnormal processing of negative emotions. The evidence that alexithymia predicts the reproduction variability of sub-second durations of negative affective stimuli corroborates previous neuroimaging studies documenting cerebellar deficits in these individuals.

Isaac H. Goldstein, Jon Wakefield, Volodymyr M. Minin

Branching process inspired models are widely used to estimate the effective reproduction number -- a useful summary statistic describing an infectious disease outbreak -- using counts of new cases. Case data is a real-time indicator of changes in the reproduction number, but is challenging to work with because cases fluctuate due to factors unrelated to the number of new infections. We develop a new model that incorporates the number of diagnostic tests as a surveillance model covariate. Using simulated data and data from the SARS-CoV-2 pandemic in California, we demonstrate that incorporating tests leads to improved performance over the state-of-the-art.

Qiang Huang, Chaoliang Wen, Wei Yan et al.

Improving feed efficiency is one of the main goals of chicken breeding and production. The function of the digestive system, where feed is digested and nutrients are absorbed, is closely related to feed efficiency. However, the association between feed efficiency and the development of different digestive organs in chickens remains unclear. Here, we investigated the individual feed efficiency of 207 broilers during the fast-growing period with an electronic feeder and examined the characteristics of 8 organs of their digestive system (the liver, bile, proventriculus, gizzard, duodenum, jejunum, ileum, and cecum) at market age. Both the feed conversion ratio (FCR) and residual feed intake (RFI) were significantly negatively correlated with the gizzard weight (GW) and significantly positively correlated with the relative weight of the liver (RLW). Additionally, we found an obvious negative relationship between the FCR and cecal length (CL). A two-tailed t test further confirmed these correlation analysis results. Specifically, compared to birds with the lowest feed efficiencies, the GW of broilers with the highest feed efficiencies (the lowest FCR or RFI) was 22.74% and 17.97% higher, respectively. The RLW of chickens with the highest feed efficiencies was 10.82 to 13.73% less than that of chickens with the lowest feed efficiencies. In addition, we found that increased CL (5.42–12.09%) was significantly associated with better feed efficiency. Thus, our study showed that the feed efficiency of broilers was related to the development of the gizzard, liver, and cecum. These findings provide new insight into the genetic and physiological regulation of feed efficiency in broilers.

D. C. P. Jorge, J. F. Oliveira, J. G. V. Miranda et al.

The effective reproduction number, R(t), is a central point in the study of infectious diseases. It establishes in an explicit way the extent of an epidemic spread process in a population. The current estimation methods for the time evolution of R(t), using incidence data, rely on the generation interval distribution, g(τ), which is usually obtained from empirical data or already known distributions from the literature. However, there are systems, especially highly heterogeneous ones, in which there is a lack of data and an adequate methodology to obtain g(τ). In this work, we use mathematical models to bridge this gap. We present a general methodology for obtaining an explicit expression of the reproduction numbers and the generation interval distributions provided by an arbitrary compartmental model. Additionally, we present the appropriate expressions to evaluate those reproduction numbers using incidence data. To highlight the relevance of such methodology, we apply it to the spread of Covid-19 in municipalities of the state of Rio de janeiro, Brazil. Using two meta-population models, we estimate the reproduction numbers and the contributions of each municipality in the generation of cases in all others. Our results point out the importance of mathematical modelling to provide epidemiological meaning of the available data.

Mário Sousa, Jan Tesarik

Karim Karimi, A. Hossain Farid, Sean Myles et al.

Abstract Aleutian disease (AD) is the most significant health issue for farmed American mink. The objective of this study was to identify the genomic regions subjected to selection for response to infection with Aleutian mink disease virus (AMDV) in American mink using genotyping by sequencing (GBS) data. A total of 225 black mink were inoculated with AMDV and genotyped using a GBS assay based on the sequencing of ApeKI-digested libraries. Five AD-characterized phenotypes were used to assign animals to pairwise groups. Signatures of selection were detected using integrated measurement of fixation index (FST) and nucleotide diversity (θπ), that were validated by haplotype-based (hap-FLK) test. The total of 99 putatively selected regions harbouring 63 genes were detected in different groups. The gene ontology revealed numerous genes related to immune response (e.g. TRAF3IP2, WDR7, SWAP70, CBFB, and GPR65), liver development (e.g. SULF2, SRSF5) and reproduction process (e.g. FBXO5, CatSperβ, CATSPER4, and IGF2R). The hapFLK test supported two strongly selected regions that contained five candidate genes related to immune response, virus–host interaction, reproduction and liver regeneration. This study provided the first map of putative selection signals of response to AMDV infection in American mink, bringing new insights into genomic regions controlling the AD phenotypes.

Sahar Esfandyari, Ashraf Aleyasin, Zahra Noroozi et al.

Objective: Sulforaphane (SFN) is a natural free radical scavenger that can reduce oxidative stress (OS) through mediating nuclear factor (erythroid-derived 2)-like 2 (NF-E2-related factor 2 or NRF2)/antioxidant response element (ARE) signaling pathway and the downstream antioxidant enzymes. Here, we intended to study the role of SFN in OSinduced human granulosa cells (GCs) by investigating the intracellular levels of reactive oxygen species (ROS), cell death, and NRF2-ARE pathway. Materials and Methods: This experimental study was conducted on GCs of 12 healthy women who had normal menstrual cycles with no history of polycystic ovary syndrome (PCOS), endometriosis, menstrual disorders, hyperprolactinemia, or hormonal therapy. After isolation of GCs, the MTT assay was performed to explore GCs viability after treatment with SFN in the presence or absence of H2O2. Flow cytometry was utilized to determine the intracellular ROS production and the apoptosis rate. Evaluation of the mRNA and protein expression levels of NRF2 and phase II enzymes including superoxide dismutase (SOD) and catalase (CAT) was performed by quantitative real-time polymerase chain reaction (PCR) and western blotting. Finally, the data were analyzed by SPSS software using One-way ANOVA and the suitable post-hoc test. Significance level was considered as P<0.05. Results: Pretreatment of GCs with SFN attenuated intracellular ROS production and apoptosis rate in the H2O2-exposed cells. Moreover, SFN treatment increased the mRNA expression level of NRF2, SOD, and CAT. Higher expression of NRF2 and SOD was also observed at the protein level. Conclusion: Our study demonstrated that SFN protects human GCs against H2O2 induced-OS by reducing the intracellular ROS production and the following apoptosis through a mechanism by which NRF2 increases the antioxidant enzymes such as SOD and CAT. This result may have a potential application in assisted reproduction cycles by improving the quality of GCs and the embedded oocyte, especially in PCOS patients.

Mags Beksinska, Rodal Issema, Ivana Beesham et al.

Background: There is limited evidence on the impact of the use of progestin-only hormonal contraception (POC) on weight change. We conducted a secondary analysis of prospective weight change among women enrolled in the Evidence for Contraceptive options and HIV Outcomes (ECHO) trial. Methods: The ECHO trial was conducted at 12 sites in eSwatini, Kenya, South Africa and Zambia between December 2015 and October 2018. HIV negative, women aged 16–35 years, desiring contraception, were randomised (1:1:1) to either 3-monthly intramuscular depot medroxyprogesterone acetate (DMPA-IM), levonorgestrel (LNG) implant or copper intrauterine device (IUD). Follow-up was up to 18 months. Weight (kg) was measured at baseline and study exit. Analysis was performed as intention to treat (ITT) and time on continuous contraceptive use. The primary outcome of this secondary analysis is weight change from study enrolment to the final visit at study month 12–18. The ECHO trial is registered with ClinicalTrials.gov, NCT02550067. Findings: 7829 women were randomly assigned to DMPA-IM (n = 2609), copper IUD (n = 2607) or LNG implant (n = 2613). The ITT population included 7014 women 2293 DMPA-IM group, 2372 copper IUD group and 2349 LNG group) who were not lost to follow-up, pregnant on study, or missing weight data. The mean weight increased in all groups but was significantly different in magnitude: 3.5 kg (SD = 6.3), 2.4 kg (SD = 5.9) and 1.5 kg (SD = 5.7) in the DMPA-IM, LNG implant and copper IUD groups, respectively. Comparative differences between groups were (2.02 kg (95% CI, 1.68, 2.36, p < 0.001) for DMPA-IM versus copper IUD, 0.87 kg (0.53,1.20 p < 0.001) for LNG implant compared to copper IUD and 1.16 kg (0.82, 1.50, p < 0.001) for DMPA-IM compared with LNG implant. Results for continuous contraceptive use were similar. Interpretation: We found differences in weight gain between POC users compared to the non-hormonal copper IUD group over 12–18 months of use. Women using POCs should be counselled about this potential side effect when choosing a contraceptive method.

Sean Elliott, Christian Gourieroux

The aim of this paper is to understand the extreme variability on the estimated reproduction ratio $R_0$ observed in practice. For expository purpose we consider a discrete time stochastic version of the Susceptible-Infected-Recovered (SIR) model, and introduce different approximate maximum likelihood (AML) estimators of $R_0$. We carefully discuss the properties of these estimators and illustrate by a Monte-Carlo study the width of confidence intervals on $R_0$.

Tao Zhou, Quanhui Liu, Zimo Yang et al.

Objectives.--To estimate the basic reproduction number of the Wuhan novel coronavirus (2019-nCoV). Methods.--Based on the susceptible-exposed-infected-removed (SEIR) compartment model and the assumption that the infectious cases with symptoms occurred before January 25, 2020 are resulted from free propagation without intervention, we estimate the basic reproduction number of 2019-nCoV according to the reported confirmed cases and suspected cases, as well as the theoretical estimated number of infected cases by other research teams, together with some epidemiological determinants learned from the severe acute respiratory syndrome. Results The basic reproduction number falls between 2.8 to 3.3 by using the real-time reports on the number of 2019-nCoV infected cases from People's Daily in China, and falls between 3.2 and 3.9 on the basis of the predicted number of infected cases from colleagues. Conclusions.--The early transmission ability of 2019-nCoV is closed to or slightly higher than SARS. It is a controllable disease with moderate-high transmissibility. Timely and effective control measures are needed to suppress the further transmissions. Notes Added.--Using a newly reported epidemiological determinants for early 2019-nCoV, the estimated basic reproduction number is in the range [2.2,3.0].

Carrie A. Jones, Kelly S. Acharya, Chaitanya R. Acharya et al.

Abstract Background To evaluate the association of patient and IVF cycle characteristics with blastulation rate and formation of high-quality blastocysts Results We analyzed autologous blastocyst cycles from 2013 to 2017. Cycles were subdivided into low (< 33%), intermediate (33–66%), and high (> 66%) blastulation rates. Embryo quality was assigned by embryologists using Gardner Criteria. R statistical package was used, and the blastulation groups were compared using analysis of variance (ANOVA) for continuous variables and chi-squared tests for categorical variables. The Bonferroni correction was used to adjust for multiple comparisons. One hundred seventeen IVF cycles met our inclusion criteria. Of these, 20 (17.1%) had low, 74 (63.2%) had intermediate, and 23 (19.7%) had high blastulation rates. Low blastulation rate was associated with a lower number of blastocysts, including fewer high-quality blastocysts. The mean number of oocytes retrieved was highest (18.1) in the group with the lowest blastulation rate, and lowest (13.4) in those with the highest blastulation rate, although this did not reach statistical significance. There were no significant differences between blastulation rates and age, gravidity, prior live birth, anti-mullerian hormone, estradiol and progesterone levels on the day of ovulation trigger, follicle-stimulating hormone dose, or fertility diagnosis. Conclusions High blastulation rate is associated with a greater number of blastocysts, including a greater number of high-quality blastocysts. Higher oocyte yield, however, is not associated with improved blastulation rates. Blastulation rates, blastocyst number, and quality remain difficult to predict based on cycle characteristics alone, and oocyte yield may not be an accurate predictor of either outcome.