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17:37 EDT 21st July 2018 | BioPortfolio

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Showing "Biosciences" PubMed Articles 1–25 of 106


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Optimizing the utility of the individual development plan for trainees in the biosciences.

Biobanking Genetic Material for Agricultural Animal Species.

Biobanking animal germplasm and tissues is a major component of conserving genetic resources. Effectively constructing such gene banks requires an understanding and evaluation of genetic resources, the ability to conserve various tissues through cryopreservation, and a robust information technology infrastructure to allow managers and potential users to fully understand and make use of the collection. Progress has been made internationally in developing national genetic resource collections. As these collec...

Weird Animals, Sex, and Genome Evolution.

Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide ...

Long-read sequencing of the human cytomegalovirus transcriptome with the Pacific Biosciences RSII platform.

Long-read RNA sequencing allows for the precise characterization of full-length transcripts, which makes it an indispensable tool in transcriptomics. The human cytomegalovirus (HCMV) genome has been first sequenced in 1989 and although short-read sequencing studies have uncovered much of the complexity of its transcriptome, only few of its transcripts have been fully annotated. We hereby present a long-read RNA sequencing dataset of HCMV infected human lung fibroblast cells sequenced by the Pacific Bioscien...

Lessons from the Barn to the Operating Suite: A Comprehensive Review of Animal Models for Fetal Surgery.

The International Fetal Medicine and Surgery Society was created in 1982 and proposed guidelines for fetal interventions that required demonstrations of the safety and feasibility of intended interventions in animal models prior to application in humans. Because of their short gestation and low cost, small animal models are useful in early investigation of fetal strategies. However, owing to the anatomic and physiologic differences between small animals and humans, repeated studies in large animal models ar...

Metabolic and Endocrine Role of Adipose Tissue During Lactation.

The adipose tissue serves an essential role for survival and reproduction in mammals, especially females. It serves primarily as an energy storage organ and is directly linked to the reproductive success of mammals. In wild animals, adipose tissue function is linked to seasonality of the food supply to support fetal growth and milk production. Adipose tissue depots in ruminants and non-ruminants can secrete many signal molecules (adipokines) that act as hormones and as pro- and anti-inflammatory cytokines. ...

NanoPack: visualizing and processing long read sequencing data.

Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.

Chemical composition and antifungal activity of essential oils from four Asteraceae plants grown in Egypt.

The objective of the present paper was the assessment of the chemical composition of the essential oils from four Asteraceae species with a considerable food, medicinal, and agricultural value, collected in Egypt, together with their in vitro inhibitory activity against molds and yeasts. The essential oil of Launaea cornuta flowers was also evaluated for the first time, but because of its very low yield (

Gaussian process approximations for fast inference from infectious disease data.

We present a flexible framework for deriving and quantifying the accuracy of Gaussian process approximations to non-linear stochastic individual-based models of epidemics. We develop this for the SIR and SEIR models, and show how it can be used to perform quick maximum likelihood inference for the underlying parameters given population estimates of the number of infecteds or cases at given time points. We also show how the unobserved processes can be inferred at the same time as the underlying parameters.

Final size of a multi-group SIR epidemic model: Irreducible and non-irreducible modes of transmission.

A model of an epidemic outbreak incorporating multiple subgroups of susceptible and infected individuals is investigated. The asymptotic behavior of the model is analyzed and it is proved that the infected classes all converge to 0. A computational algorithm is developed for the cumulative final size of infected individuals over the course of the epidemic. The results are applied to the SARS epidemic in Singapore in 2003, where it is shown that the two-peak evolution of the infected population can be attrib...

How to choose biomarkers in view of parameter estimation.

In numerous applications in biophysics, physiology and medicine, the system of interest is studied by monitoring quantities, called biomarkers, extracted from measurements. These biomarkers convey some information about relevant hidden quantities, which can be seen as parameters of an underlying model. In this paper we propose a strategy to automatically design biomarkers to estimate a given parameter. Such biomarkers are chosen as the solution of a sparse optimization problem given a user-supplied dictiona...

Critical patch-size for two-sex populations.

As environments become increasingly degraded, mainly due to human activities, species are often subject to isolated habitats surrounded by unfavorable regions. Since the pioneering work by [25] mathematical models have provided useful insights into the population persistence in such cases. Most of these models, however, neglect the sex structure of populations and the differences between males and females. In this work we investigate, through a reaction-diffusion system, the dynamics of a sex-structured pop...

Mathematical modeling of cancer-immune system, considering the role of antibodies.

A mathematical model for the quantitative analysis of cancer-immune interaction, considering the role of antibodies has been proposed in this paper. The model is based on the clinical evidence, which states that antibodies can directly kill cancerous cells (Ivano et al. in J Clin Investig 119(8):2143-2159, 2009). The existence of transcritical bifurcation, which has been proved using Sotomayor theorem, provides strong biological implications. Through numerical simulations, it has been illustrated that under...

Antimicrobial and antioxidant activities of two polyketides from lichen-endophytic fungus Preussia sp.

Two compounds, compounds 1 and 2, were isolated from Preussia sp. The molecular structures of both compounds were elucidated by analyzing one-dimensional (1D) and 2D nuclear magnetic resonance data along with high-resolution mass spectrometry data. Compound 1 was obtained as novel in structure, and compound 2 was recently reported elsewhere. Compound 1 did not show antioxidant and antimicrobial activities and brine shrimp toxicity, while compound 2 showed strong antioxidant activity (DPPH reduction capacity...

IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.

In the past years, the long read (LR) sequencing technologies, such as Pacific Biosciences and Oxford Nanopore Technologies, have been demonstrated to substantially improve the quality of genome assembly and transcriptome characterization. Compared to the high cost of genome assembly by LR sequencing, it is more affordable to generate LRs for transcriptome characterization. That is, when informative transcriptome LR data are available without a high-quality genome, a method for de novo transcriptome assembl...

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