Choreographing rhizosphere effect with agricultural practices for agroecology?

For sustainable agriculture, soil-plant interactions (i.e., the rhizosphere effect) is prominent focus, since they determine plant health and nutrition.

Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches.

Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S.

Omnibus testing approach for gene-based gene-gene interaction.

Genetic interaction is considered as one of the main heritable component of complex traits. With the emergence of genome-wide association studies (GWAS), a collection of statistical methods dedicated to the identification of interaction at the SNP level have been proposed. More recently, gene-based gene-gene interaction testing has emerged as an attractive alternative as they confer advantage in both statistical power and biological interpretation.

"Should I stay or should I go now?" Recovery time effect on walking capacity in symptomatic peripheral artery disease.

The objective of the study was to investigate the effect of recovery time on walking capacity (WC) throughout repeated maximal walking bouts in symptomatic lower-extremity peripheral artery disease (PAD). The effect of recovery time on WC (maximal walking time) was determined in 21 participants with PAD in three experimental conditions [recovery time from 0.5 to 9.

Comparison of Activity Monitors Accuracy in Assessing Intermittent Outdoor Walking.

Purpose: This study aimed to determine and compare the accuracy of different activity monitors in assessing intermittent outdoor walking in both healthy and clinical populations through the development and validation of processing methodologies.

Methods: In study 1, an automated algorithm was implemented and tested for the detection of short (≤1 min) walking and stopping bouts during prescribed walking protocols performed by healthy subjects in environments with low and high levels of obstruction. The following parameters obtained from activity monitors were tested, with different recording epochs0.

Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic digestion at the preterm newborn stage.

Holder pasteurization (62.5 °C, 30 min) of human milk denatures beneficial proteins. The present paper aimed to assess whether this can affect the kinetics of peptide release during digestion at the preterm stage.

Reduced Cerebrospinal Fluid Inflow to the Optic Nerve in Glaucoma.

Purpose: To determine whether cerebrospinal fluid (CSF) entry into the optic nerve is altered in glaucoma.

Methods: Fluorescent 10-kDa dextran tracer was injected into the CSF of 2-month-old (n = 9) and 10-month-old DBA/2J glaucoma mice (n = 8) and age-matched controls (C57Bl/6; n = 8 each group). Intraocular pressure (IOP) was measured in all mice before tracer injection into CSF.

Progressive loss of retinal blood vessels in a live model of retinitis pigmentosa.

Objective: To assess retinal blood vessels in a live retinitis pigmentosa (RP) model with rd1 mutation and green fluorescent protein (GFP) expressed in vascular endothelium.

Methods: Homozygous (hm) Tie2-GFP mice with rd1 mutation and known retinal degeneration were crossed with wild-type CD1 mice to generate control heterozygous (ht) Tie2-GFP mice. The retinas of 16 live hm mice were evaluated at 2 weeks and 3, 5, and 8 months of age, and compared with age-matched control ht and CD1 mice by optical coherence tomography (OCT) and confocal scanning laser ophthalmoscopy (cSLO).

Toward Haptic Communication: Tactile Alphabets Based on Fingertip Skin Stretch.

This paper studies the possibility to convey information using tactile stimulation on fingertips. We designed and evaluated three tactile alphabets which are rendered by stretching the skin of the index's fingertip: (1) a Morse-like alphabet, (2) a symbolic alphabet using two successive dashes, and (3) a display of Roman letters based on the Unistrokes alphabet. All three alphabets (26 letters each) were evaluated through a user study in terms of recognition rate, intuitiveness, and learnability.

Evidence for Cerebrospinal Fluid Entry Into the Optic Nerve via a Glymphatic Pathway.

Purpose: The purpose of this study was to determine whether cerebrospinal fluid (CSF) enters the optic nerve via a glymphatic pathway and whether this entry is size-dependent.

Methods: Fluorescent dextran tracers (fluorescein isothiocyanate [FITC]) of four different sizes (10, 40, 70, and 500 kDa) and FITC-ovalbumin (45 kDa) were injected into the CSF of 15 adult mice. Tracer distribution in the orbital optic nerve at 1 hour after injection was assessed in tissue sections with confocal microscopy.

Power comparison of Cochran-Armitage trend test against allelic and genotypic tests in large-scale case-control genetic association studies.

The Cochran-Armitage trend test (CA) has become a standard procedure for association testing in large-scale genome-wide association studies (GWAS). However, when the disease model is unknown, there is no consensus on the most powerful test to be used between CA, allelic, and genotypic tests. In this article, we tackle the question of whether CA is best suited to single-locus scanning in GWAS and propose a power comparison of CA against allelic and genotypic tests.

Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic term newborn digestion.

Holder pasteurization (62.5°C, 30 min) ensures sanitary quality of donor's human milk but also denatures beneficial proteins. Understanding whether this further impacts the kinetics of peptide release during gastrointestinal digestion of human milk was the aim of the present paper.

AGGrEGATOr: A Gene-based GEne-Gene interActTiOn test for case-control association studies.

Among the large of number of statistical methods that have been proposed to identify gene-gene interactions in case-control genome-wide association studies (GWAS), gene-based methods have recently grown in popularity as they confer advantage in both statistical power and biological interpretation. All of the gene-based methods jointly model the distribution of single nucleotide polymorphisms (SNPs) sets prior to the statistical test, leading to a limited power to detect sums of SNP-SNP signals. In this paper, we instead propose a gene-based method that first performs SNP-SNP interaction tests before aggregating the obtained p-values into a test at the gene level.

Power evaluation of asymptotic tests for comparing two binomial proportions to detect direct and indirect association in large-scale studies.

Asymptotic tests are commonly used for comparing two binomial proportions when the sample size is sufficiently large. However, there is no consensus on the most powerful test. In this paper, we clarify this issue by comparing the power functions of three popular asymptotic tests: the Pearson's χ test, the likelihood-ratio test and the odds-ratio based test.

In vivo imaging of lymphatic drainage of cerebrospinal fluid in mouse.

Background: Mouse models are commonly used to study central nervous system disorders, in which cerebrospinal fluid (CSF) drainage may be disturbed. However, mouse CSF drainage into lymphatics has not been thoroughly characterized. We aimed to image this using an in vivo approach that combined quantum dot fluorescent nanoparticles with hyperspectral imaging.

MetAmyl: a METa-predictor for AMYLoid proteins.

The aggregation of proteins or peptides in amyloid fibrils is associated with a number of clinical disorders, including Alzheimer's, Huntington's and prion diseases, medullary thyroid cancer, renal and cardiac amyloidosis. Despite extensive studies, the molecular mechanisms underlying the initiation of fibril formation remain largely unknown. Several lines of evidence revealed that short amino-acid segments (hot spots), located in amyloid precursor proteins act as seeds for fibril elongation.

Using biological networks to search for interacting loci in genome-wide association studies.

Genome-wide association studies have identified a large number of single-nucleotide polymorphisms (SNPs) that individually predispose to diseases. However, many genetic risk factors remain unaccounted for. Proteins coded by genes interact in the cell, and it is most likely that certain variants mainly affect the phenotype in combination with other variants, termed epistasis.

Risk assessment for hospital-acquired diseases: a risk-theory approach.

We introduce a new approach to hospital-acquired disease risk assessment from public health databases. In a spirit similar to actuarial risk theory, we define an adjustment coefficient that can quantify the risk associated with a hospital department, allowing comparisons of similar departments. The adjustment coefficient characterizes the tail of the distribution of the total patient length of stay in a department before the first disease event occurs.

A statistical approach to estimating the strength of cell-cell interactions under the differential adhesion hypothesis.

Background: The Differential Adhesion Hypothesis (DAH) is a theory of the organization of cells within a tissue which has been validated by several biological experiments and tested against several alternative computational models.

Results: In this study, a statistical approach was developed for the estimation of the strength of adhesion, incorporating earlier discrete lattice models into a continuous marked point process framework. This framework allows to describe an ergodic Markov Chain Monte Carlo algorithm that can simulate the model and reproduce empirical biological patterns.

Conditional coalescent trees with two mutation rates and their application to genomic instability.

Humans have invested several genes in DNA repair and fidelity replication. To account for the disparity between the rarity of mutations in normal cells and the large number of mutations present in cancer, an hypothesis is that cancer cells must exhibit a mutator phenotype (genomic instability) during tumor progression, with the initiation of abnormal mutation rates caused by the loss of mismatch repair. In this study we introduce a stochastic model of mutation in tumor cells with the aim of estimating the amount of genomic instability due to the alteration of DNA repair genes.