Biology subjects

Ha, L. M.

Publications and source records attributed to Ha, L. M..

3 recordsLinked to original sources

bioRxiv2025

denim: an R package for deterministic compartmental models with flexible dwell time distributions

O_LICompartmental models are widely used for dynamical systems where states are discrete such as in infectious diseases epidemiology with the so-called SIR or Susceptible-Infectious-Recovered framework. For mathematical simplicity, rates of transition between compartments are generally assumed to be independent of the dwell time (or secondary time scale in survival analysis): they are either constant or dependent on the epidemiological time (or primary time scale in survival analysis) only, either directly (e.g. environmental or behavioral forcings in epidemiological models) or indirectly through dependence on other variables of the system (e.g. the force of infection in epidemiological models). In some domains of application, this memoryless assumption leads to distributions of dwelling times that are incompatible with those observed on data which can lead to serious problems since the model predictions are highly sensitive on the exact shape of these distributions. C_LIO_LIHere we propose a deterministic, continuous-variable, numerical modelling approach that allows full flexibility on the dwell time distributions. The accompanying denim package provides a user-friendly interface to implement our proposed method through a dedicated language for model definition. C_LIO_LIThe package is open-source and available on CRAN. With more detailed data on the clinical process of infections becoming available, the denim package will be extremely useful for building more realistic epidemiological models providing more accurate projections. C_LI The denim package is publicly available for download on CRAN (https://cran.r-project.org/web/packages/denim/index.html) and GitHub (https://github.com/thinhong/denim). Additional documentation can be found on the denim webpage (https://drthinhong.com/denim/). Bug reports can be submitted via Github Issue.

bioinformatics↗

bioRxiv2024

Mitochondrial DNA analysis in ayu (Plecoglossus altivelis) raises an urgent conservation need for its southernmost population

The central-marginal hypothesis predicts that genetic diversity decreases and genetic differentiation increases toward the species distribution margin. We analyzed the mitochondrial DNA control region of ayu (Plecoglossus altivelis) collected from different localities, including central and marginal populations, to test the hypothesis. The results show that the ayu populations at southern marginal habitats (Tien Yen River in Vietnam and Yakugachi River in Amami-oshima Island) displayed low genetic diversity (Haplotype diversity, H = 0.52 and 0.67; Nucleotide diversity, Pi = 0.01 and 0.006, respectively) and significantly differed from the central populations (p < 0.001), consistent with the central-marginal hypothesis. However, ayu populations at the center of their distribution range (Shinano River in Honsyu and Hamoji River in Sado Island) and the northern marginal habitats (Yoichi River in Hokkaido and Aonae River in Okushiri Island) exhibited high genetic diversity (H = 1 for all rivers; Pi = 0.024-0.029). The genetic differences between the populations at the center and the northern marginal habitats were insignificant (p > 0.05). This study showed that in ayu, the central-marginal hypothesis is valid in the southern direction but not in the northern direction. Urgent conservation is needed for the genetically distinct population in the degraded southern habitat with severely low genetic diversity.

ecology↗

bioRxiv2018

Demographic features and mortality risks in smallholder poultry farms of the Mekong river delta region

This study describes the demographic structure and dynamics of small scale poultry farms of the Mekong river delta region, one of the worlds highest-risk regions for avian influenza outbreaks. Fifty farms were monitored over a 20-month period, with farm sizes, species, age, arrival/departure of poultry, and farm management practices recorded monthly. The history of poultry flocks in the sampled farms was recovered using a flock-matching algorithm. Median flock population sizes were 16 for chickens (IQR: 10 - 40), 32 for ducks (IQR: 18 - 101) and 11 for Muscovy ducks (IQR: 7 - 18); farm size distributions for the three species were heavily right-skewed. There was substantial flock overlap on almost all farms, with only one farm practicing an all-in-all-out management system. The rate of interspecific contacts was high, with two out of three farms housing at least two bird species. Among poultry species, demographic dynamics varied. Muscovy ducks were kept for long periods, in small numbers and outdoors, while chickens and ducks were farmed in larger numbers, indoors or in pens, with more rapid flock turnover. Most chicks were sold young to be fattened on other farms, and broiler and layer ducks had a short production period and higher degree of specialization. The rate of mortality due to disease did not differ much among species, with birds being less likely to die from disease at older ages, but frequency of disease symptoms differed by species. Time series of disease-associated mortality and population size were correlated for Muscovy ducks (Kendalls coefficient {tau} = 0.49, p value < 0.01).\n\nImpacts O_LIThe structure and dynamics of poultry populations kept in small scale farms in the Mekong river delta were accurately described.\nC_LIO_LIPoultry farms mix poultry of different species, ages, and production types, with multiple overlapping flocks present on a farm at all times. This promotes the persistence of pathogens.\nC_LIO_LIThe three main farmed poultry species of poultry (chickens, ducks and Muscovy ducks) are managed differently and have different demographic characteristics.\nC_LI

epidemiology↗