DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis

SREBP1 and 2, are cholesterol sensors able to modulate cholesterol-related gene expression responses. SREBPs binding sites are characterized by the presence of multiple target sequences as SRE, NFY and SP1, that can be arranged differently in different genes, so that it is not easy to identify the binding site on the basis of direct DNA sequence analysis. This paper presents a complete workflow based on a one-dimensional Convolutional Neural Network (CNN) model able to detect putative SREBPs binding sites irrespective of target elements arrangements. The strategy is based on the recognition of SRE linked (less than 250 bp) to NFY sequences according to chromosomal localization derived from TF Immunoprecipitation (TF ChIP) experiments. The CNN is trained with several 100 bp sequences containing both SRE and NF-Y. Once trained, the model is used to predict the presence of SRE-NFY in the first 500 bp of all the known gene promoters. Finally, genes are grouped according to biological process and the processes enriched in genes containing SRE-NFY in their promoters are analyzed in details. This workflow allowed to identify biological processes enriched in SRE containing genes not directly linked to cholesterol metabolism and possible novel DNA patterns able to fill in for missing classical SRE sequences

Storm-water infiltration and focused recharge modeling with finite-volume two-dimensional Richards equation: application to an experimental rain garden

Rain gardens are infiltration systems that provide volume and water quality control, recharge enhancement, as well as landscape, ecological, and economic benefits. A model for application to rain gardens based on Richards equation coupled to a surface water balance was developed, using a two-dimensional finite-volume code. It allows for alternating upper boundary conditions, including ponding and overflow, and can simulate heterogeneous soil-layering or more complex geometries to estimate infiltration and recharge. The algorithm is conservative, and exhibits good performance compared to standard models for several test cases (less than 0.1% absolute mass balance error); simulations were also performed for an experimental rain garden and comparisons to collected data are presented. The model accurately simulated the matrix flow, soil water distribution, as well as deep percolation (potential recharge) for a natural rainfall event in the controlled experimental setup. Read More: http://ascelibrary.org/doi/abs/10.1061/%28ASCE%29HY.1943-7900.0000111?prevSearch=authors%3A%28Dussaillant%2C%29&searchHistoryKey

Spatiotemporal dynamics of covert versus overt processing of happy, fearful and sad facial expressions

Behavioral and electrophysiological correlates of the influence of task demands on the processing of happy, sad, and fearful expressions were investigated in a within-subjects study that compared a perceptual distraction condition with task-irrelevant faces (e.g., covert emotion task) to an emotion task-relevant categorization condition (e.g., overt emotion task). A state-of-the-art non-parametric mass univariate analysis method was used to address the limitations of previous studies. Behaviorally, participants responded faster to overtly categorized happy faces and were slower and less accurate to categorize sad and fearful faces; there were no behavioral differences in the covert task. Event-related potential (ERP) responses to the emotional expressions included the N170 (140-180 ms), which was enhanced by emotion irrespective of task, with happy and sad expressions eliciting greater amplitudes than neutral expressions. EPN (200-400 ms) amplitude was modulated by task, with greater voltages in the overt condition, and by emotion, however, there was no interaction of emotion and task. ERP activity was modulated by emotion as a function of task only at a late processing stage, which included the LPP (500-800 ms), with fearful and sad faces showing greater amplitude enhancements than happy faces. This study reveals that affective content does not necessarily require attention in the early stages of face processing, supporting recent evidence that the core and extended parts of the face processing system act in parallel, rather than serially. The role of voluntary attention starts at an intermediate stage, and fully modulates the response to emotional content in the final stage of processing

Frequency and clinical aspects of neurological and psychiatric symptoms in patients with non-celiac wheat sensitivity

Background: Non-Celiac Wheat Sensitivity (NCWS) is characterized by both intestinal and extra-intestinal symptoms. The study aims to investigate the frequency of neuropsychiatric manifestations in NCWS patients and identify their clinical and demographic characteristics. Methods: 278 clinical records of NCWS patients, diagnosed by a double-blind placebo-controlled wheat challenge between 2006 and 2020, were retrospectively revised. Fifty-two patients with Celiac Disease (CD) and 54 patients with Irritable Bowel Syndrome (IBS) served as controls. Results: 87% of the NCWS patients had an IBS-like clinical presentation. The NCWS group showed a longer duration of symptoms, a higher frequency of positive serum anti-nuclear antibodies than CD and IBS patients, and a higher frequency of DQ2/DQ8 haplotypes and duodenal mucosa lymphocytosis than IBS controls. In addition, 50% of NCWS patients showed neuropsychiatric manifestations, while lower percentages were observed in CD (25%) and IBS (28%) controls. Neuropsychiatric symptoms in NCWS were more frequently associated with the male sex, longer duration of symptoms, and IBS-diarrhea-like clinical presentation. Conclusions: Our data suggest that in patients with IBS-like symptoms and neuropsychiatric manifestations of unknown cause, it could be useful to investigate a correlation of these symptoms with wheat ingestion to identify NCWS patients with this ‘atypical’ manifestation

RT-PCR and in situ hybridization analysis of apolipoprotein H expression in rat normal tissues

In this study, by using different techniques (i.e. Northern blot hybridization, RT-PCR and Southern blot hybridization) on various normal rat tissues, we were able to identify liver, kidney, heart, small intestine, brain, spleen, stomach and prostate as tissues in which the ApoH gene is transcribed. Moreover, for some of these tissues, by in situ hybridization, we found a specific localization of apoH transcripts. For instance epithelial cells of the bile ducts in liver and of the proximal tubules in kidney are the major sites of apoH synthesis. Our data suggest that some of the different physiological roles proposed for apoH could correlate with its direct expression, while others could correlate with its absorption from bloodstream or adjacent cells

Persistence of Nonceliac Wheat Sensitivity, Based on Long-term Follow-up

We investigated how many patients with a diagnosis of nonceliac wheat sensitivity (NCWS) still experienced wheat sensitivity after a median follow-up time of 99 months. We collected data from 200 participants from a previous study of NCWS, performed between July and December 2016 in Italy; 148 of these individuals were still on a strict wheat- free diet. In total, 175 patients (88%) improved (had fewer symptoms) after a diagnosis of NCWS; 145 of 148 patients who adhered strictly to a gluten-free diet (98%) had reduced symptoms, compared with 30 of 52 patients who did not adhere to a gluten-free diet (58%) (P < .0001). Of the 22 patients who repeated the double-blind, placebo- controlled challenge, 20 reacted to wheat. We conclude that NCWS is a persistent condition. Clinicaltrials.gov registration number: NCT02823522

Characterisation of the muon beams for the Muon Ionisation Cooling Experiment

A novel single-particle technique to measure emittance has been developed and used to characterise seventeen different muon beams for the Muon Ionisation Cooling Experiment (MICE). The muon beams, whose mean momenta vary from 171 to 281 MeV/c, have emittances of approximately 1.2–2.3 π mm-rad horizontally and 0.6–1.0 π mm-rad vertically, a horizontal dispersion of 90–190 mm and momentum spreads of about 25 MeV/c. There is reasonable agreement between the measured parameters of the beams and the results of simulations. The beams are found to meet the requirements of MICE