A global method for coupling transport with chemistry in heterogeneous porous media

Modeling reactive transport in porous media, using a local chemical equilibrium assumption, leads to a system of advection-diffusion PDE's coupled with algebraic equations. When solving this coupled system, the algebraic equations have to be solved at each grid point for each chemical species and at each time step. This leads to a coupled non-linear system. In this paper a global solution approach that enables to keep the software codes for transport and chemistry distinct is proposed. The method applies the Newton-Krylov framework to the formulation for reactive transport used in operator splitting. The method is formulated in terms of total mobile and total fixed concentrations and uses the chemical solver as a black box, as it only requires that on be able to solve chemical equilibrium problems (and compute derivatives), without having to know the solution method. An additional advantage of the Newton-Krylov method is that the Jacobian is only needed as an operator in a Jacobian matrix times vector product. The proposed method is tested on the MoMaS reactive transport benchmark.Comment: Computational Geosciences (2009) http://www.springerlink.com/content/933p55085742m203/?p=db14bb8c399b49979ba8389a3cae1b0f&pi=1

Natural Single-Nucleosome Epi-Polymorphisms in Yeast

Epigenomes commonly refer to the sequence of presence/absence of specific epigenetic marks along eukaryotic chromatin. Complete histone-borne epigenomes have now been described at single-nucleosome resolution from various organisms, tissues, developmental stages, or diseases, yet their intra-species natural variation has never been investigated. We describe here that the epigenomic sequence of histone H3 acetylation at Lysine 14 (H3K14ac) differs greatly between two unrelated strains of the yeast Saccharomyces cerevisiae. Using single-nucleosome chromatin immunoprecipitation and mapping, we interrogated 58,694 nucleosomes and found that 5,442 of them differed in their level of H3K14 acetylation, at a false discovery rate (FDR) of 0.0001. These Single Nucleosome Epi-Polymorphisms (SNEPs) were enriched at regulatory sites and conserved non-coding DNA sequences. Surprisingly, higher acetylation in one strain did not imply higher expression of the relevant gene. However, SNEPs were enriched in genes of high transcriptional variability and one SNEP was associated with the strength of gene activation upon stimulation. Our observations suggest a high level of inter-individual epigenomic variation in natural populations, with essential questions on the origin of this diversity and its relevance to gene x environment interactions

The Human Phenotype Ontology in 2024: phenotypes around the world

\ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

Effects of aging in multisensory integration: A systematic review

Multisensory integration (MSI) is the integration by the brain of environmental information acquired through more than one sense. Accurate MSI has been shown to be a key component of successful aging and to be crucial for processes underlying activities of daily living (ADLs). Problems in MSI could prevent older adults (OA) to age in place and live independently. However, there is a need to know how to assess changes in MSI in individuals. This systematic review provides an overview of tests assessing the effect of age on MSI in the healthy elderly population (aged 60 years and older). A literature search was done in Scopus. Articles from the earliest records available to January 20, 2016, were eligible for inclusion if assessing effects of aging on MSI in the healthy elderly population compared to younger adults (YA). These articles were rated for risk of bias with the Newcastle-Ottawa quality assessment. Out of 307 identified research articles, 49 articles were included for final review, describing 69 tests. The review indicated that OA maximize the use of multiple sources of information in comparison to YA (20 studies). In tasks that require more cognitive function, or when participants need to adapt rapidly to a situation, or when a dual task is added to the experiment, OA have problems selecting and integrating information properly as compared to YA (19 studies). Additionally, irrelevant or wrong information (i.e., distractors) has a greater impact on OA than on YA (21 studies). OA failing to weigh sensory information properly, has not been described in previous reviews. Anatomical changes (i.e., reduction of brain volume and differences of brain areas' recruitment) and information processing changes (i.e., general cognitive slowing, inverse effectiveness, larger time window of integration, deficits in attentional control and increased noise at baseline) can only partly explain the differences between OA and YA regarding MSI. Since we have an interest in successful aging and early detection of MSI issues in the elderly population, the identified tests form a good starting point to develop a clinically useful toolkit to assess MSI in healthy OA

Effects of aging on illusory target motion in a hitting task

Age-related changes in multisensory integration (MSI, brain integration of multiple unisensory signals) were investigated. Accurate MSI is a key component of successful aging and crucial to perform activities of daily living (ADLs). Previous research suggests that with aging, different sources of sensory information are not properly weighted anymore. Twenty healthy younger (YA, age 18-34) and twenty-four healthy older adults (OA, age 60-82) were asked to hit discs moving downwards on a screen with their index finger. Illusory direction of motion was included (moving a checkerboard-like background either to the left or right). The discs disappeared before the screen was reached. Experimental conditions were: sitting (baseline), standing on foam (balance task), and sitting while doing a cognitive dual task (counting task). Participants hit the disc more to the right for left background motion compared to right background motion, conforming the illusory effect. OA show a larger effect of the illusion compared to YA in the baseline and balance conditions (p=.036 and p=.047, respectively). The same tendency was shown in the counting condition. Overall, background motion had a greater influence on the counting condition compared to the other conditions (p=.005 for YA and p=.009 for OA). No significant differences were found for the summed reaction and movement time, and no correlations between hitting performance and results of clinical pretests were found. We conclude that OA are more affected by the background motion than YA, which supports the idea that OA do not weigh information properly. Our finding that a cognitive dual task increases the illusion effect in both groups of participants suggests that cognitive resources are required for proper weighting, which may be a problem for OA. Future research will include OA with ADLs difficulties in order to develop a toolkit for early detection of MSI problems in the elderly population