Search results for "pac"
showing 10 items of 28794 documents
Induction of skeletal abnormalities and autophagy in Paracentrotus lividus sea urchin embryos exposed to gadolinium.
2017
Abstract Gadolinium (Gd) concentration is constantly increasing in the aquatic environment, becoming an emergent environmental pollutant. We investigated the effects of Gd on Paracentrotus lividus sea urchin embryos, focusing on skeletogenesis and autophagy. We observed a delay of biomineral deposition at 24 hours post fertilization (hpf), and a strong impairment of skeleton growth at 48 hpf, frequently displayed by an asymmetrical pattern. Skeleton growth was found partially resumed in recovery experiments. The mesodermal cells designated to biomineralization were found correctly migrated at 24 hpf, but not at 48 hpf. Western blot analysis showed an increase of the LC3-II autophagic marker…
Variable Ranking Feature Selection for the Identification of Nucleosome Related Sequences
2018
Several recent works have shown that K-mer sequence representation of a DNA sequence can be used for classification or identification of nucleosome positioning related sequences. This representation can be computationally expensive when k grows, making the complexity in spaces of exponential dimension. This issue effects significantly the classification task computed by a general machine learning algorithm used for the purpose of sequence classification. In this paper, we investigate the advantage offered by the so-called Variable Ranking Feature Selection method to select the most informative k − mers associated to a set of DNA sequences, for the final purpose of nucleosome/linker classifi…
PACAP38 and PAC1 receptor blockade: a new target for headache?
2018
Abstract Pituitary adenylate cyclase activating polypeptide-38 (PACAP38) is a widely distributed neuropeptide involved in neuroprotection, neurodevelopment, nociception and inflammation. Moreover, PACAP38 is a potent inducer of migraine-like attacks, but the mechanism behind this has not been fully elucidated. Migraine is a neurovascular disorder, recognized as the second most disabling disease. Nevertheless, the antibodies targeting calcitonin gene-related peptide (CGRP) or its receptor are the only prophylactic treatment developed specifically for migraine. These antibodies have displayed positive results in clinical trials, but are not effective for all patients; therefore, new pharmacol…
A multilevel statistical toolkit to study animal social networks: Animal Network Toolkit (ANT) R package
2018
AbstractHow animals interact and develop social relationships regarding, individual attributes, sociodemographic and ecological pressures is of great interest. New methodologies, in particular Social Network Analysis, allow us to elucidate these types of questions. However, the different methodologies developed to that end and the speed at which they emerge make their use difficult. Moreover, the lack of communication between the different software developed to provide an answer to the same/different research questions is a source of confusion. The R package Animal Network Toolkit (ANT) was developed with the aim of implementing in one package the many different social network analysis tech…
parSRA: A framework for the parallel execution of short read aligners on compute clusters
2018
The growth of next generation sequencing datasets poses as a challenge to the alignment of reads to reference genomes in terms of both accuracy and speed. In this work we present parSRA, a parallel framework to accelerate the execution of existing short read aligners on distributed-memory systems. parSRA can be used to parallelize a variety of short read alignment tools installed in the system without any modification to their source code. We show that our framework provides good scalability on a compute cluster for accelerating the popular BWA-MEM and Bowtie2 aligners. On average, it is able to accelerate sequence alignments on 16 64-core nodes (in total, 1024 cores) with speedup of 10.48 …
Variants associated with HHIP expression have sex-differential effects on lung function
2021
Background: Lung function is highly heritable and differs between the sexes throughout life. However, little is known about sex-differential genetic effects on lung function. We aimed to conduct the first genome-wide genotype-by-sex interaction study on lung function to identify genetic effects that differ between males and females. Methods: We tested for interactions between 7,745,864 variants and sex on spirometry-based measures of lung function in UK Biobank (N=303,612), and sought replication in 75,696 independent individuals from the SpiroMeta consortium. Results: Five independent single-nucleotide polymorphisms (SNPs) showed genome-wide significant (P<5x10-8) interactions with sex …
Inoculation of airborne conidia of Penicillium chrysogenum on the surface of a solid medium
2016
International audience; To reproduce a fungal contamination of food products by airborne conidia, a method to inoculate a few number (in the range 1-9) of conidia on the surface of agar media was developed. This technique would allow to determine accurately the time to detection of fungal colonies, then the mould free shelf-life of food products by using dry conidia. The method was based on dry-harvesting the conidia in the lid by gently taping the bottom of the dishes where sporulating mycelium was grown, retaining the conidia on glass beads, and, aseptically transferring the beads to successive Petri dishes to "dilute" the samples. Among the eleven factors tested by means of an experiment…
Quality characteristics and in vitro digestibility study of barley flour enriched ditalini pasta
2016
A ditalini pasta with a mixture of durum wheat and beta-glucan enriched barley flour (BF) (60/40%, w/w) was found to have a final content of 5% beta-glucan (BF-ditalini). Main quality parameters of BF-ditalini, water uptake and starch-protein texture, were comparable with those of 100% durum wheat ditalini (control). After in vitro simulated intestinal digestion, the content of beta-glucan in the post intestinal (PI) supernatant of BF-ditalini processed with its cooking water (soup) was six fold higher than that of pasta asciutta. BF-ditalini soup, but not pasta asciutta, strongly delayed the hydrolysis of the starch, without difference of viscosity between PI supernatant and control. PI su…
The latent geometry of the human protein interaction network
2017
Abstract Motivation A series of recently introduced algorithms and models advocates for the existence of a hyperbolic geometry underlying the network representation of complex systems. Since the human protein interaction network (hPIN) has a complex architecture, we hypothesized that uncovering its latent geometry could ease challenging problems in systems biology, translating them into measuring distances between proteins. Results We embedded the hPIN to hyperbolic space and found that the inferred coordinates of nodes capture biologically relevant features, like protein age, function and cellular localization. This means that the representation of the hPIN in the two-dimensional hyperboli…
A topological look at human trabecular bone tissue
2017
Bone quality is affected by trabecular architecture at microscopic level. Various abnormalities of bone tissue lead to altered strength and to an increased susceptibility to fracture, such as Osteoporosis and Osteoarthritis, two major health burdens of our society. These are two complex musculoskeletal diseases that mainly concern bone tissue. In the last twenty years, there has been a growing interest in finding an appropriate topological model for the micro-architecture of trabecular bone tissue. In particular, we prove that these models involve general topological spaces. The appropriate notion to deal with is that of CW-complex.