Miracle-dz/UniFAR-FTUs huggingface dataset:
Relation of Brachial and Digital Measures of Vascular Function in the Community: The Framingham Heart Study

Impaired vascular function contributes to the development of clinical cardiovascular disease. The relation between vasodilator function assessed noninvasively in the brachial and digital arteries remains incompletely defined. In the Framingham Offspring, Third Generation and Omni Cohorts, we measured flow-mediated dilation (FMD; n=7031; age 48±13 years; age range, 19 to 88 years; 54% women) and peripheral arterial tonometry (PAT) ratio (n=4352; 55±16 years; age range, 19 to 90 years; 51% women). Abnormal vascular function for each measure was defined by the sex-specific fifth percentile in a reference group free of conventional cardiovascular risk factors. The prevalence of abnormal FMD but not abnormal PAT ratio was higher with advancing age. In multivariable models, higher body mass index was associated with a higher prevalence of both abnormal FMD and PAT ratio. Additional correlates of abnormal FMD included increasing age and higher systolic blood pressure. In contrast, correlates of abnormal PAT ratio included lower systolic blood pressure, increasing total/high-density lipoprotein cholesterol ratio, diabetes, smoking, and lipid-lowering medication. Whereas women had higher FMD and PAT ratios compared with men, using sex-specific reference values, women had a higher prevalence of abnormal brachial and digital vascular function. In participants who had concurrent testing (n=1843), PAT ratio was not significantly associated with FMD in multivariable models. In this large, community-based cohort, brachial and digital measures of vascular function had differing relations with cardiovascular risk factors and were nearly uncorrelated with each other. These results suggest that FMD and PAT provide distinct information regarding vascular function in conduit versus smaller digital vessels.
On Decoding Irregular Tanner Codes With Local-Optimality Guarantees

We consider decoding of binary linear Tanner codes using message-passing iterative decoding and linear-programming (LP) decoding in memoryless binary-input output-symmetric (MBIOS) channels. We present new certificates that are based on a combinatorial characterization for the local optimality of a codeword in irregular Tanner codes with respect to any MBIOS channel. This characterization is a generalization of (Arora , Proc. ACM Symp. Theory of Computing, 2009) and (Vontobel, Proc. Inf. Theory and Appl. Workshop, 2010) and is based on a conical combination of normalized weighted subtrees in the computation trees of the Tanner graph. These subtrees may have any finite height h (even equal or greater than half of the girth of the Tanner graph). In addition, the degrees of local-code nodes in these subtrees are not restricted to two (i.e., these subtrees are not restricted to skinny trees). We prove that local optimality in this new characterization implies maximum-likelihood (ML) optimality and LP optimality, and show that a certificate can be computed efficiently. We also present a new message-passing iterative decoding algorithm, called normalized weighted min-sum (NWMS). NWMS decoding is a belief-propagation (BP) type algorithm that applies to any irregular binary Tanner code with single parity-check local codes (e.g., low-density and high-density parity-check codes). We prove that if a locally optimal codeword with respect to height parameter h exists (whereby notably h is not limited by the girth of the Tanner graph), then NWMS decoding finds this codeword in h iterations. The decoding guarantee of the NWMS decoding algorithm applies whenever there exists a locally optimal codeword. Because local optimality of a codeword implies that it is the unique ML codeword, the decoding guarantee also provides an ML certificate for this codeword. Finally, we apply the new local-optimality characterization to regular Tanner codes, and prove lower bounds on the noise thresholds of LP decoding in MBIOS channels. When the noise is below these lower bounds, the probability that LP decoding fails to decode the transmitted codeword decays doubly exponentially in the girth of the Tanner graph.
Towards the introduction of the ‘Immunoscore’ in the classification of malignant tumours

The American Joint Committee on Cancer/Union Internationale Contre le Cancer (AJCC/UICC) TNM staging system provides the most reliable guidelines for the routine prognostication and treatment of colorectal carcinoma. This traditional tumour staging summarizes data on tumour burden (T), the presence of cancer cells in draining and regional lymph nodes (N) and evidence for distant metastases (M). However, it is now recognized that the clinical outcome can vary significantly among patients within the same stage. The current classification provides limited prognostic information and does not predict response to therapy. Multiple ways to classify cancer and to distinguish different subtypes of colorectal cancer have been proposed, including morphology, cell origin, molecular pathways, mutation status and gene expression‐based stratification. These parameters rely on tumour‐cell characteristics. Extensive literature has investigated the host immune response against cancer and demonstrated the prognostic impact of the in situ immune cell infiltrate in tumours. A methodology named ‘Immunoscore’ has been defined to quantify the in situ immune infiltrate. In colorectal cancer, the Immunoscore may add to the significance of the current AJCC/UICC TNM classification, since it has been demonstrated to be a prognostic factor superior to the AJCC/UICC TNM classification. An international consortium has been initiated to validate and promote the Immunoscore in routine clinical settings. The results of this international consortium may result in the implementation of the Immunoscore as a new component for the classification of cancer, designated TNM‐I (TNM‐Immune). © 2013 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
High prevalence of antimicrobial-resistant Escherichia coli from animals at slaughter: a food safety risk.

BACKGROUND There has been concern about the increase of antimicrobial resistant bacteria and protection of animal and public health, along with food safety. In the present study, we evaluate the incidence of antimicrobial resistance among 192 strains of Escherichia coli isolated from faecal samples of healthy food-producing animals at slaughter in Portugal. RESULTS Ninety-seven % of the pig isolates, 74% from sheep and 55% from cattle were resistant to one or more antimicrobial agents, with the resistances to ampicillin, streptomycin, tetracycline and trimethoprim-sulfamethoxazole the most common phenotype detected. Genes encoding resistance to antimicrobial agents were detected in most of the resistant isolates. Ninety-three % of the resistant isolates were included in the A or B1 phylogenetic groups, and the virulence gene fimA (alone or in association with papC or aer genes) was detected in 137 of the resistant isolates. Five isolates from pigs belonging to phylogroup B2 and D were resistant to five different antimicrobial agents. CONCLUSION Our data shows a high percentage of antibiotic resistance in E. coli isolates from food animals, and raises important questions in the potential impact of antibiotic use in animals and the possible transmission of resistant bacteria to humans through the food chain.
Nonequivalent effects of PKC activation by PMA on murine CD4 and CD8 cell‐surface expression

The membrane glycoproteins CD4 (L3T4) and CD8 (Lyt2) are expressed on distinct populations of mature murine T lymphocytes, and are thought to be receptors for monomorphic determinants expressed on MHC class II and class I molecules, respectively. Although they differ in their ligand specificity, it has been presumed that CD4 and CD8 perform equivalent functions in the T cells that bear them. Since activation of protein kinase C (PKC) is known to cause rapid down‐regulation of various receptors, including the T cell receptor complex (TcR complex), we treated cells with phorbol 12‐myristate 13‐acetate (PMA), a PKC activator, to determine whether cell‐surface expression of CD4 and CD8 would be similarly affected by this intracellular mediator. Brief or relatively prolonged treatment with PMA induced mature murine T cells to reduce their surface expression of the TcR complex and of CD4, but not of CD8. Similarly, PMA rapidly induced transfected L cells to down‐regulate surface CD4 expression, but had no effect on surface CD8 expression. Most significantly, PMA treatment induced CD4+CD8+ immature thymocytes to rapidly reduce their surface CD4 expression, but, again, it had no immediate effect on the surface expression of CD8. These results indicate that CD4 and TcR complex cell‐surface expression are both sensitive to PKC activation by brief treatment with PMA, whereas CD8 expression is not, and suggest that CD4 and CD8 surface expression levels are regulated by distinct intracellular mechanisms. — Kaldjian, E. ; McCarthy, S. A. ; Sharrow, S. O. ; Littman, D. R. ; Klausner, R. D. ; Singer, A. Nonequivalent effects of PKS activation by PMA on murine CD4 and CD8 cell surface expression. FASEB J. 2: 2801‐2806; 1988.
Minimally Invasive Endotracheal Tube Suctioning and Suction-Related Pain, Airway Clearance and Airway Trauma in Patients with Intubation: A Randomized Controlled Trial

Background: Due to the frequency and risks associated with endotracheal suctioning, there is a need to examine clinical practice critically and identify clinical research to guide practice. Correct technique and preparation by the clinicians can assist to reduce the risks of adverse events and the level of discomfort for the patients. Objectives: The current study aimed to investigate the effects of routine versus the minimally invasive endotracheal tube suctioning procedure on suction-related pain, airway clearance and airway trauma in patients who were intubated. Methods: In this randomized clinical trial, 64 patients with intubation in the intensive care units (ICUs) of Alzahra Hospital, Isfahan, Iran, were randomly allocated to minimally invasive endotracheal tube suctioning (MIETS) and routine endotracheal tube suctioning (RETS) groups. Pain intensity was assessed immediately before, immediately after and 10 minutes after endotracheal tube suctioning (ETS). Airway clearance was defined by numbers of suctioning and airway trauma noted after suctioning. The Chisquare test, independent T-test, and repeated measures analysis of variance were performed to analyze the data. Results: There was no significant difference in the number of suctions needed to effectively clear airway between the two groups. No significant differences were observed in the pain score changes during the three -time measurements in the MIETS group. However, in the RETS group the increase of pain scores were statistically significant during the threetime measurements. In addition, the number of airway traumatization was significantly higher in the RETS group. The number of medications used as a pain relief during 10 minutes after the ETS was significantly higher in the RETS group. Conclusions: The results of the study suggest that using MIETS instead of RETS caused a lower incidence of airway traumatization and lower suction-related pain intensity. In addition, MIETS was sufficiently effective, the same as RETS, to remove airway secretions. Hence, MIETS may be useful to reduce the complications of ETS as long as being effective to remove airway secretions.
Role of the Pre-S2 Domain of the Large Envelope Protein in Hepatitis B Virus Assembly and Infectivity

ABSTRACT Among the three viral proteins present in the hepatitis B virus (HBV) envelope, both the small and large polypeptides, but not the middle polypeptide, are necessary for the production of complete viral particles. Whereas it has been established that the C-terminal extremity of the pre-S1 region is required for HBV morphogenesis, whether the pre-S2 region of the large surface protein plays a critical role remains questionable. In the present study, we have analyzed the role of the large-polypeptide pre-S2 region in viral maturation and infectivity. For this purpose, mutants bearing contiguous deletions covering the entire pre-S2 domain were generated. First, the efficient expression of all the mutant large envelope proteins was verified and their ability to substitute for the wild-type form in virion secretion was tested. We found that distinct deletions covering the domain between amino acids 114 and 163 still allowed virion production. In contrast, the polypeptide lacking the first 5 amino acids of pre-S2 (amino acids 109 to 113) was unable to support viral secretion. This result shows that the domain of the large surface protein, required for this process, must be extended to the N-terminal extremity of pre-S2. We then demonstrated that all the mutants competent for virion release were able to infect normal human hepatocytes in primary culture. Taken together, these results indicate that only 10% of the large-protein pre-S2 region at its N-terminal extremity is essential for virion export and that the remaining part, dispensable for viral secretion, is also dispensable for infectivity.
Fitness consequences of social network position in a wild population of forked fungus beetles (Bolitotherus cornutus)

Social networks describe the pattern of intraspecific interactions within a population. An individual’s position in a social network often is expected to influence its fitness, but only a few studies have examined this relationship in natural populations. We investigated the fitness consequences of network position in a wild beetle population. Copulation success of male beetles positively covaried with strength (a measure of network centrality) and negatively covaried with clustering coefficient (CC) (a measure of cliquishness). Further analysis using mediation path models suggested that the activity level of individuals drove the relationships between strength and fitness almost entirely. In contrast, selection on CC was not explained by individual behaviours. Although our data suggest that social network position can experience strong sexual selection, it is also clear that the relationships between fitness and some network metrics merely reflect variation in individual‐level behaviours.
Update on the glutamatergic neurotransmitter system and the role of excitotoxicity in amyotrophic lateral sclerosis

Excitotoxicity may play a role in certain disorders of the motor system thought to be caused by environmentally acquired toxins, including lathyrism and domoic acid poisoning. Motor neurons appear to be particularly susceptible to toxicity mediated via α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole propionic acid (AMPA)–kainate receptors. There is a body of evidence implicating glutamatergic toxicity as a contributory factor in the selective neuronal injury occurring in amyotrophic lateral sclerosis (ALS). Interference with glutamate‐mediated toxicity is so far the only neuroprotective therapeutic strategy that has shown benefit in terms of slowing disease progression in ALS patients. Biochemical studies have shown decreased glutamate levels in central nervous system (CNS) tissue and increased levels in the cerebrospinal fluid (CSF) of ALS patients. CSF from ALS patients is toxic to neurons in culture, apparently via a mechanism involving AMPA receptor activation. There is evidence for altered expression and function of glial glutamate transporters in ALS, particularly excitatory amino acid transporter 2 (EAAT2). Abnormal splice variants of EAAT2 have been detected in human CNS. Mitochondrial dysfunction may contribute to excitotoxicity in ALS. Induction of neuronal nitric oxide synthase and cyclooxygenase 2 in ALS may also lead to significant interactions with regulation of the glutamate transmitter system. Certain features of motor neurons may predispose them to the neurodegenerative process in ALS, such as the cell size, mitochondrial activity, neurofilament content, and relative lack of certain calcium‐binding proteins and molecular chaperones. Motor neurons appear vulnerable to toxicity mediated by calcium‐permeable AMPA receptors. The relatively low expression of the glutamate receptor 2 (GluR2) AMPA receptor subunit and the high current density caused by the large number and density of cell surface AMPA receptors are potentially important factors that may predispose to such toxicity. © 2002 Wiley Periodicals, Inc. Muscle Nerve 26: 438–458, 2002
A Micro Hydro Pelton Turbine Prototype (Review of the effect of water debitand nozzle angle to rotation and pelton turbine power)

This research began when the writer conducted a field study to Curup Tenang Bedegung Waterfall, Tanjung Agung District, Muara Enim, South Sumatra. The CurupTenang Bedegung waterfall has the potential to build a micro-hydro Pelton turbine power plant. This study aims to see the flow rate andwater discharge. From this preliminary study, the researcher decided to carry out the design of a micro-hydro Pelton turbine prototype on a mini scale but has optimal rotation and power. In this study, the analyses of the effect of water dischargewere 20, 25, 30, 35, and 40 1/s and the nozzle angle was 50 °, 55 °, 60 ° and 65 ° toward rotation and Pelton turbine power. From the results obtained the higher the water discharge, the turbine rotation is increasing, the highest turbine rotation (691.3 rpm) achieved was at a water discharge of 40 l/s with nozzle angle of 50 °, the higher the water discharge will increase turbine power, the highest turbine power (15.89 watts) was obtained at a water discharge of 40 l/s with a 50 ° of nozzle angle.
Deficient recovery response and adaptive feedback potential in dynamic gait stability in unilateral peripheral vestibular disorder patients

Unilateral peripheral vestibular disorder (UPVD) causes deficient locomotor responses to novel environments due to a lack of accurate vestibular sensory information, increasing fall risk. This study aimed to examine recovery response (stability recovery actions) and adaptive feedback potential in dynamic stability of UPVD‐patients and healthy control subjects during perturbed walking. 17 UPVD‐patients (>6 months since onset) and 17 matched healthy control participants walked on a treadmill and were subjected to eight unexpected perturbations during the swing phase of the right leg. For each perturbation, the margin of stability (MS; state of body's centre of mass in relation to the base of support), was determined at touchdown of the perturbed leg and during the following six recovery steps. The first perturbation caused a reduced MS at touchdown for the perturbed leg compared to baseline, indicating an unstable position, with controls requiring five recovery steps to return to MS baseline and UPVD‐patients not returning to baseline level within the analyzed six recovery steps. By the eighth perturbation, control subjects needed two steps, and UPVD‐patients required three recovery steps, both thereby improving their recovery response with practice. However, MS at touchdown of the perturbed leg increased only for the controls after repeated perturbations, indicating adaptive feedback‐driven locomotor improvements for the controls, but not for the UPVD‐patients. We concluded that UPVD‐patients have a diminished ability to control dynamic gait stability during unexpected perturbations, increasing their fall risk, and that vestibular dysfunction may inhibit the neuromotor system adapting the reactive motor response to perturbations.
Global Metabolomic Profiling of Acute Myocarditis Caused by Trypanosoma cruzi Infection

Chagas disease is caused by Trypanosoma cruzi infection, being cardiomyopathy the more frequent manifestation. New chemotherapeutic drugs are needed but there are no good biomarkers for monitoring treatment efficacy. There is growing evidence linking immune response and metabolism in inflammatory processes and specifically in Chagas disease. Thus, some metabolites are able to enhance and/or inhibit the immune response. Metabolite levels found in the host during an ongoing infection could provide valuable information on the pathogenesis and/or identify deregulated metabolic pathway that can be potential candidates for treatment and being potential specific biomarkers of the disease. To gain more insight into those aspects in Chagas disease, we performed an unprecedented metabolomic analysis in heart and plasma of mice infected with T. cruzi. Many metabolic pathways were profoundly affected by T. cruzi infection, such as glucose uptake, sorbitol pathway, fatty acid and phospholipid synthesis that were increased in heart tissue but decreased in plasma. Tricarboxylic acid cycle was decreased in heart tissue and plasma whereas reactive oxygen species production and uric acid formation were also deeply increased in infected hearts suggesting a stressful condition in the heart. While specific metabolites allantoin, kynurenine and p-cresol sulfate, resulting from nucleotide, tryptophan and phenylalanine/tyrosine metabolism, respectively, were increased in heart tissue and also in plasma. These results provide new valuable information on the pathogenesis of acute Chagas disease, unravel several new metabolic pathways susceptible of clinical management and identify metabolites useful as potential specific biomarkers for monitoring treatment and clinical severity in patients.