Miracle-dz/UniFAR-FTUs huggingface dataset:
4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy

Despite increasing insights in genome structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human genome, remains elusive. Facioscapulohumeral muscular dystrophy (FSHD) is associated with deletion of D4Z4 repeat array below 11 units at 4q35.2. It is known that the deletion alters chromatin structure in cis, leading to gene up-regulation. Here we show a genome-wide role of 4q-D4Z4 array in modulating gene expression via 3D nuclear contacts. We have developed an integrated strategy of 4q-D4Z4–specific 4C-seq and chromatin segmentation analyses, showing that 4q-D4Z4 3D interactome and chromatin states of interacting genes are impaired in FSHD1 condition; in particular, genes that have lost the 4q-D4Z4 interaction and with a more active chromatin state are enriched for muscle atrophy transcriptional signature. Expression level of these genes is restored by the interaction with an ectopic 4q-D4Z4 array, suggesting that the repeat directly modulates the transcription of contacted targets. Of note, the up-regulation of atrophic genes is a common feature of several FSHD1 and FSHD2 patients, indicating that we have identified a core set of deregulated genes involved in FSHD pathophysiology.
Subcellular Phenotyping: Using Proteomics to Quantitatively Link Subcellular Leaf Protein and Organelle Distribution Analyses of Pisum sativum Cultivars

Plant phenotyping to date typically comprises morphological and physiological profiling in a high-throughput manner. A powerful method that allows for subcellular characterization of organelle stoichiometric/functional characteristics is still missing. Organelle abundance and crosstalk in cell dynamics and signaling plays an important role for understanding crop growth and stress adaptations. However, microscopy cannot be considered a high-throughput technology. The aim of the present study was to develop an approach that enables the estimation of organelle functional stoichiometry and to determine differential subcellular dynamics within and across cultivars in a high-throughput manner. A combination of subcellular non-aqueous fractionation and liquid chromatography mass spectrometry was applied to assign membrane-marker proteins to cell compartmental abundances and functions of Pisum sativum leaves. Based on specific subcellular affiliation, proteotypic marker peptides of the chloroplast, mitochondria and vacuole membranes were selected and synthesized as heavy isotope labeled standards. The rapid and unbiased Mass Western approach for accurate stoichiometry and targeted absolute protein quantification allowed for a proportional organelle abundances measure linked to their functional properties. A 3D Confocal Laser Scanning Microscopy approach was developed to evaluate the Mass Western. Two P. sativum cultivars of varying morphology and physiology were compared. The Mass Western assay enabled a cultivar specific discrimination of the chloroplast to mitochondria to vacuole relations.
Impaired Skeletal Muscle Regeneration Induced by Macrophage Depletion Could Be Partly Ameliorated by MGF Injection

Skeletal muscle injury is one of the most common injuries in sports medicine. Our previous study found that macrophage depletion impairs muscle regeneration and that mechano growth factor (MGF) may play an important role in this process. However, whether injection of MGF protects against impaired muscle regeneration after macrophage depletion has not been explored. Therefore, we generated a muscle contusion and macrophage depletion mouse model and injected MGF into the damaged muscle. Comprehensive morphological and genetic analyses were performed on the injured skeletal muscle after macrophage depletion and MGF injection. The results showed that injection of MGF did not exert a protective effect on muscle fiber regeneration; however, it did decrease fibrosis in the contused skeletal muscle after macrophage depletion. Moreover, MGF injection decreased the expression of muscle inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and TGF-β), chemokines (CCL2, CCL5, and CXCR4), oxidative stress factors (gp91phox) and matrix metalloproteinases (MMP-1, MMP-2, MMP-9, MMP-10, and MMP-14). These results suggest that the impairment of skeletal muscle regeneration induced by macrophage depletion could be partly ameliorated by MGF injection and that inflammatory cytokines, oxidative stress factors, chemokines, and MMP may be involved in this process.
Comparative Analysis of C9orf72 and Sporadic Disease in a Large Multicenter ALS Population: The Effect of Male Sex on Survival of C9orf72 Positive Patients

We investigated whether the C9orf72 repeat expansion is associated with specific clinical features, comorbidities, and prognosis in patients with amyotrophic lateral sclerosis (ALS). A cohort of 1417 ALS patients, diagnosed between January 1, 2009 and December 31, 2013 by 13 Italian ALS Referral Centers, was screened for the C9orf72 repeat expansion, and the analyses were performed comparing patients carrying this expansion (ALS-C9Pos) to those negative for this and other explored ALS-related mutations (ALS without genetic mutations, ALSwoGM). Compared to the ALSwoGM group, ALS-C9Pos patients (n = 84) were younger at disease onset, at the first clinical observation and at diagnosis (p < 0.001). After correcting for these differences, we found that ALS-C9Pos patients had higher odds of bulbar onset, diagnosis of frontotemporal dementia (FTD) and family history of ALS, FTD, and Alzheimer's disease and had lower odds of spinal onset, non-invasive ventilation, hypertension and psychiatric diseases than ALSwoGM patients. Among these variables, those related to shorter survival time were: bulbar onset, presence of FTD, hypertension, psychiatric disease, and family history of ALS (p < 0.05). Cox proportional hazards regression multivariate analysis suggested that carrying the C9orf72 repeat expansion was an independent factor negatively impacting on survival time in men (HR 1.58, 95% CI 1.07–2.33, p = 0.021), but not in women (p > 0.05) as well as in the whole sample (p > 0.05). When compared to ALSwoGM, ALS-C9Pos showed an earlier disease onset, no significant diagnostic delay and a higher odds of bulbar onset, FTD and family history of ALS and dementia. Moreover, male sex drove the negative effect of expanded variant on survival, confirming the hypothesis that sex is likely to be a crucial factor in the biology of C9orf72-related disease.
The Stem Cell Marker Bcrp/ABCG2 Enhances Hypoxic Cell Survival through Interactions with Heme*

Our studies demonstrate that the ABC transporter and marker of stem and progenitor cells known as the breast cancer resistance protein (BCRP or ABCG2) confers a strong survival advantage under hypoxic conditions. We show that, under hypoxia, progenitor cells from Bcrp–/–mice have a reduced ability to form colonies as compared with progenitor cells from Bcrp+/+ mice. Blocking BCRP function in Bcrp+/+ progenitor cells markedly reduces survival under hypoxic conditions. However, blocking heme biosynthesis reverses the hypoxic susceptibility of Bcrp–/– progenitor cells, a finding that indicates that heme molecules (i.e. porphyrins) are detrimental to Bcrp–/– cells under hypoxia. BCRP specifically binds heme, and cells lacking BCRP accumulate porphyrins. Finally, Bcrp expression is up-regulated by hypoxia, and we demonstrate that this up-regulation involves the hypoxia-inducible transcription factor complex HIF-1. Collectively, our findings suggest that cells can, upon hypoxic demand, use BCRP to reduce heme or porphyrin accumulation, which can be detrimental to cells. Our findings have implications for the survival of stem cells and tumor cells in hypoxic environments.
Pilot‐Scale Evaluation of Separate‐Stage Nitrification Using an Attached‐Growth, Moving‐Bed Media Process

Submerged attached‐growth processes, both fixed and moving bed, are becoming more popular. These processes may or may not be used in combination with suspended‐growth treatment. The objective of this project was to evaluate a tertiary attached‐growth, moving‐bed media nitrification system based on the ammonia‐nitrogen removal rates and effluent concentrations that could be achieved. A pilot‐scale system for nitrification of secondary municipal wastewater effluent was operated for 142 days. The minimum aeration requirements for media mixing provided sufficient dissolved oxygen. The generation of biological solids from nitrification was insignificant. Design effluent ammonia‐nitrogen concentrations (<6 mg/L) were achieved at influent loading rates greater than design (1.18 g ammonia‐nitrogen/[m2·d]) coincident with detention times shorter than design conditions (4 hours). Empirical relationships for the ammonia‐nitrogen removal rate and effluent concentration as a function of influent ammonia‐nitrogen loading were developed. Detention time is believed to be an important parameter affecting these relationships.
An improved certificateless authenticated key agreement protocol

Recently, Mokhtarnameh, Ho, Muthuvelu proposed a certificateless key agreement protocol. In this paper, we show that their protocol is unsecured against a man-in-the-middle attack. In addition, the authors claimed that their scheme provides a binding long-term public key with a corresponding partial private key. In fact, their protocol does not achieve the binding. We propose an improved key agreement protocol based on the protocol proposed by Mokhtarnameh et al. The improved protocol can resist the man-in-the-middle attack as well as satisfy the desired security properties for key agreement. It truly achieves the one-to-one correspondence between the long-term public key and the partial private key of a user. Compared with the other related protocols, the protocol has advantages in both security and computational efficiency.
Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules

Pollinosis is sub-diagnosed and rarely studied in tropical countries. Cashew tree pollen has been reported as an allergen source although the knowledge of its immunoglobulin E (IgE)-reactive molecules is lacking. Therefore, this work aimed to identify IgE-reactive molecules and provide a proteomic profile of this pollen. From the 830 proteins identified by shotgun analysis, 163 were annotated to gene ontology, and a list of 39 proteins filtered for high confidence was submitted to the Allfam database where nine were assigned to allergenic families. Thus, 12 patients from the northeast of Brazil with persistent allergic rhinitis and aggravation of symptoms during cashew flowering season were selected. Using a 2D-based approach, we identified 20 IgE-reactive proteins, four already recognized as allergens, including a homolog of the birch isoflavone-reductase (Bet v 6). IgE-reactivity against the extract in native form was confirmed for five patients in ELISA, with three being positive for Bet v 6. Herein, we present a group of patients with rhinitis exposed to cashew tree pollen with the first description of IgE-binding proteins and a proteomic profile of the whole pollen. Cashew tree pollen is considered an important trigger of rhinitis symptoms in clinical practice in the northeast of Brazil, and the elucidation of its allergenic molecules can improve the diagnostics and treatment for allergic patients.
Emotion dysregulation and posttraumatic stress disorder: a test of the incremental role of difficulties regulating positive emotions

ABSTRACT Background and Objectives: Literature provides support for the role of emotion dysregulation in the development and course of posttraumatic stress disorder (PTSD) among women victims of intimate partner violence (IPV). However, a dearth of studies have examined the contribution of emotion dysregulation stemming from positive emotions to PTSD. Extending research, the current study examined (1) the bivariate association of difficulties regulating positive emotions to PTSD symptom severity, and (2) the incremental role of difficulties regulating positive emotions in PTSD symptom severity beyond difficulties regulating negative emotions. Design: Participants were 210 women victims of IPV involved in the criminal justice system because of their partners’ arrest (M age = 36.14, 48.6% African American). Methods: Participants completed empirically-supported self-report measures assessing difficulties regulating positive and negative emotions and PTSD symptom severity. Results: Difficulties regulating positive and negative emotions (overall and across each of the specific dimensions) were significantly positively associated with PTSD symptom severity. Moreover, difficulties regulating positive emotions demonstrated an incremental relation to PTSD symptom severity beyond the variance accounted for by difficulties regulating negative emotions. Conclusions: Our findings suggest the potential utility of targeting difficulties regulating positive emotions in interventions for PTSD among women victims of IPV.
Incorporating heterogeneous parent–child environmental effects in biometrical genetic models

Heritability is an important index used to measure genetic effects in epidemiologic studies. For estimating heritability, researchers have proposed various statistical models to accommodate different study settings. These models include the ACE or ADE models for classical twin studies and the ACDE model for extended twin family studies. Researchers have shown that the ACDE model is less biased in heritability estimation, because of the utilization of the data of two generations. However, this model simply assumes that all family members, including twins and their parents, are exposed to the same environmental factors. This assumption may not be reasonable in many cases. In this paper, we propose a novel biometrical genetic model that can incorporate heterogeneous parent–child environmental effects. This model enables us to identify the heterogeneity of heritability, if it exists, between the two generations. This advantage is numerically demonstrated in our simulation studies. We apply our proposed model to the anterior chamber depth data from the Guangzhou Twin Eye Study in China. The analysis result reveals significant heterogeneity of heritability between the twin cohort and the parent cohort. Copyright © 2013 John Wiley & Sons, Ltd.
Draft Genome Sequence of Enterococcus faecalis Strain CECT7121, a Corn Silage Isolate with Antibacterial Activity against Gram-Positive Pathogens

Enterococcus faecalis CECT7121 is a corn silage probiotic bacterium that shows antibacterial activity against Gram-positive pathogens from different origins. Its genome sequence is 2.9 Mb long with a G+C content of 37.3%. ABSTRACT Enterococcus faecalis CECT7121 is a corn silage probiotic bacterium that shows antibacterial activity against Gram-positive pathogens from different origins. Its genome sequence is 2.9 Mb long with a G+C content of 37.3%. Genome annotation identified three bacteriocin gene clusters in the genome.
Nitric Oxide Reductase Gene Expression and Nitrous Oxide Production in Nitrate-Grown Pseudomonas mandelii

ABSTRACT Pure cultures of Pseudomonas mandelii were incubated with or without nitrate, which acts as a substrate and an electron acceptor for denitrification. Nitric oxide reductase (cnorB) gene expression was measured using a quantitative reverse transcription-PCR, and nitrous oxide emissions were measured by gas chromatography. P. mandelii cells in either the presence or absence of nitrate demonstrated an increase in cnorB gene expression during the first 3 h of growth. The level of expression of cnorB in nitrate-amended cells remained high (average, 2.06 × 108 transcripts/μg of RNA), while in untreated cells it decreased to an average of 3.63 × 106 transcripts/μg of RNA from 4 to 6 h. Nitrous oxide accumulation in the headspace was detected at 2 h, and cumulative emissions continued to increase over a 24-h period to 101 μmol in nitrate-amended cells. P. mandelii cnorB gene expression was not detected under aerobic conditions. These results demonstrate that P. mandelii cnorB gene expression was induced 203-fold at 4 h when nitrate was present in the medium. Accumulations of N2O indicated that the cNorB enzyme was synthesized and active.
Looking for alternative treatments for bovine and caprine mastitis: Evaluation of the potential of Calliandra surinamensis leaf pinnulae lectin (CasuL), both alone and in combination with antibiotics

This work aimed to evaluate the effects of CasuL on growth and viability of 15 mastitis isolates from cows and goats, to determine the synergistic potential between CasuL and antibiotics, and to investigate the effects on bacterial ultrastructure and antibiofilm activity. The lectin inhibited the growth of Staphylococcus isolates from either bovine (Ssp6PD and Sa) or caprine (Ssp5D and Ssp01) mastitis. The minimal inhibitory concentrations were ranged from 3.75 to 15 µg/ml. Synergistic effect was observed for CasuL‐tetracycline against Sa and Ssp6PD and CasuL‐ampicillin against Ssp01. No structural damage was observed under the scanning electron microscope in CasuL treatments. Flow cytometry analysis using thiazol orange and propidium iodide demonstrated that CasuL was unable to reduce the cell viability of the isolates tested. At sub‐inhibitory concentrations, CasuL reduced biofilm formation by the isolates Sa and Ssp5D. However, CasuL‐tetracycline and CasuL‐ampicillin combinations inhibited biofilm formation by Ssp6PD and Ssp01, respectively. In conclusion, CasuL is a bacteriostatic and antibiofilm agent against some mastitis isolates and displayed a synergistic potential when used in combination with either ampicillin (against one isolate) or tetracycline (against two isolates). The results stimulate the evaluation of CasuL for the treatment of mastitis, particularly when used in conjunction with antibiotics.
Draft Genome Sequence of a Novel Marine Anaerobic Ammonium-Oxidizing Bacterium, “Candidatus Scalindua sp.”

A novel anaerobic ammonium-oxidizing (anammox) bacterium was detected in an upflow column reactor treating synthetic nitrogen-rich saline solution. Here, we assembled a 4.59-Mb draft genome sequence of this bacterium, identified as a member of the genus “Candidatus Scalindua,” that has 84% nucleotide-level genomic similarity with the closest related anammox bacterium (“Candidatus Scalindua rubra”). ABSTRACT A novel anaerobic ammonium-oxidizing (anammox) bacterium was detected in an upflow column reactor treating synthetic nitrogen-rich saline solution. Here, we assembled a 4.59-Mb draft genome sequence of this bacterium, identified as a member of the genus “Candidatus Scalindua,” that has 84% nucleotide-level genomic similarity with the closest related anammox bacterium (“Candidatus Scalindua rubra”).
Rationale and Design of the VITALITY-HFpEF Trial.

Background The VITALITY-HFpEF trial (Evaluate the Efficacy and Safety of the Oral sGC Stimulator Vericiguat to Improve Physical Functioning in Daily Living Activities of Patients With Heart Failure and Preserved Ejection Fraction) is designed to determine the efficacy and safety of a novel oral soluble guanylate cyclase stimulator, vericiguat, on quality of life and exercise tolerance in heart failure patients with preserved ejection fraction (HFpEF). Impaired physical functioning reduces the quality of life in patients with HFpEF. The primary goal of HF treatment along with improving survival is to improve function, reduce symptoms, and maximize quality of life. Abnormal cyclic guanosine monophosphate signaling may contribute to physical limitations in patients with HFpEF via central and peripheral mechanisms. Exploratory post hoc analyses from a prior trial showed that vericiguat can improve patient-relevant domains of the Kansas City Cardiomyopathy Questionnaire, especially the physical limitation score. Methods and Results VITALITY-HFpEF is a placebo-controlled, double-blind, multi-center, phase IIb trial of ≈735 patients, ≥45 years with HFpEF and ejection fraction ≥45% who will be randomized 1:1:1 to placebo, 10 mg, or 15 mg vericiguat. The primary end point is change in Kansas City Cardiomyopathy Questionnaire physical limitation score from baseline to week 24 and change in 6-minute walk test from baseline to week 24 is the secondary end point. Conclusions VITALITY-HFpEF is the first trial designed to assess the efficacy of vericiguat in patients with HFpEF using the Kansas City Cardiomyopathy Questionnaire physical limitation score as a novel primary end point. This study will also extend the prior dosing experience with vericiguat in HF by studying the safety and efficacy of a 15 mg dose. Clinical Trial Registration URL: https://www.clinicaltrials. gov . Unique identifier: NCT03547583.
New Trends in Food Allergens Detection: Toward Biosensing Strategies

Food allergens are a real threat to sensitized individuals. Although food labeling is crucial to provide information to consumers with food allergies, accidental exposure to allergenic proteins may result from undeclared allergenic substances by means of food adulteration, fraud or uncontrolled cross-contamination. Allergens detection in foodstuffs can be a very hard task, due to their presence usually in trace amounts, together with the natural interference of the matrix. Methods for allergens analysis can be mainly divided in two large groups: the immunological assays and the DNA-based ones. Mass spectrometry has also been used as a confirmatory tool. Recently, biosensors appeared as innovative, sensitive, selective, environmentally friendly, cheaper and fast techniques (especially when automated and/or miniaturized), able to effectively replace the classical methodologies. In this review, we present the advances in the field of food allergens detection toward the biosensing strategies and discuss the challenges and future perspectives of this technology.
Smaddening Complexity: The Role of Smad3 in Epithelial-Myofibroblast Transition

Epithelial-mesenchymal transition (EMT) has emerged as a major mechanism in the pathogenesis of organ fibrosis. The epithelium has been proposed to be a significant source of matrix-producing fibroblasts and of myofibroblasts (MFs), a motile and contractile cell type hallmarked by the expression of α-smooth muscle actin (SMA). Importantly, tissue accumulation of MFs shows strong correlation with the severity and progression of fibrotic diseases. The pleiotropic cytokine transforming growth factor-β1 has been long known as the chief inducer of fibrosis, EMT and MF generation. Accordingly, receptor Smads (Smad2 and particularly Smad3), the direct targets of the activated transforming growth factor-β receptor have been implicated as critical mediators in fibrogenesis and EMT. However, evidence is accumulating that the role of Smad3 is complex and apparently controversial; in fact, Smad3 may differentially affect the various components of EMT, including the loss of epithelial markers (de-epithelialization), the production of extracellular matrix (fibrogenesis) and the expression of SMA (myogenic program). In this review, we revisit the role of Smad3 in epithelial-myofibroblast transition (EMyT). We first summarize the evidence supporting the thesis that Smad3 is a key mediator of EMT and MF generation; next, we present evidence supporting the antithesis that Smad3 is in fact a negative regulator of SMA expression and the activation of the myogenic program in the epithelium; finally, we propose a synthesis, which depicts Smad3 as a timekeeper and context-dependent modulator of EMyT. We suggest that EMyT is composed of an early, mesenchymal, Smad3-promoted phase and a late, myogenic, Smad3-inhibitable phase.