Miracle-dz/UniFAR-FTUs huggingface dataset:
A solvable model of the genesis of amino-acid sequences via coupled dynamics of folding and slow-genetic variation

We study the coupled dynamics of primary and secondary structures formation (i.e. slow-genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and long-range polarity-driven forces. Our solution is based on the diagonalization of replicated transfer matrices, and leads in the thermodynamic limit to explicit predictions regarding phase transitions and phase diagrams at genetic equilibrium. The predicted phenomenology allows for natural physical interpretations, and finds satisfactory support in numerical simulations.
Connectivity of the coset poset and the subgroup poset of a group

Abstract We study the connectivity of the coset poset and the subgroup poset of a group, focusing in particular on simple connectivity. The coset poset was recently introduced by K. S. Brown in connection with the probabilistic zeta function of a group. We take Brown’s study of the homotopy type of the coset poset further, and in particular generalize his results on direct products and classify direct products with simply connected coset posets. The homotopy type of the subgroup poset L(G ) has been examined previously by Kratzer, Thévenaz, and Shareshian. We generalize some results of Kratzer and Thévenaz, and determine π 1(L(G )) in nearly all cases.
Performance Assurance via Software Rejuvenation: Monitoring, Statistics and Algorithms

We present three algorithms for detecting the need for software rejuvenation by monitoring the changing values of a customer-affecting performance metric, such as response time. Applying these algorithms can improve the values of this customer-affecting metric by triggering rejuvenation before performance degradation becomes severe. The algorithms differ in the way they gather and use sample values to arrive at a rejuvenation decision. Their effectiveness is evaluated for different sets of control parameters, including sample size, using simulation. The results show that applying the algorithms with suitable choices of control parameters can significantly improve system performance as measured by the response time
Vitamin D deficiency and lower respiratory tract infections in children: a systematic review and meta-analysis of observational studies

Studies related to vitamin D deficiency and lower respiratory tract infections (LRTI) in children have inconsistent findings. The objective of this systematic review was to assess the prevalence of vitamin D deficiency in children with LRTI, and to evaluate the correlation between vitamin D levels and the incidence and severity of LRTI. A total of 12 studies enrolling 2279 participants were included in our analysis. Children with LRTI were found to have significantly lower mean vitamin D levels as compared to controls There was likewise a correlation between vitamin D levels and incidence and severity of LRTI. Large randomised controlled trials are needed to evaluate effect of vitamin D supplementation for LRTI.
Role of Memory T Cells in Allograft Rejection and Tolerance

Memory T cells are characterized by their low activation threshold, robust effector functions, and resistance to conventional immunosuppression and costimulation blockade. Unlike their naïve counterparts, memory T cells reside in and recirculate through peripheral non-lymphoid tissues. Alloreactive memory T cells are subdivided into different categories based on their origins, phenotypes, and functions. Recipients whose immune systems have been directly exposed to allogeneic major histocompatibility complex (MHC) molecules display high affinity alloreactive memory T cells. In the absence of any prior exposure to allogeneic MHC molecules, endogenous alloreactive memory T cells are regularly generated through microbial infections (heterologous immunity). Regardless of their origin, alloreactive memory T cells represent an essential element of the allograft rejection process and a major barrier to tolerance induction in clinical transplantation. This article describes the different subsets of alloreactive memory T cells involved in transplant rejection and examine their generation, functional properties, and mechanisms of action. In addition, we discuss strategies developed to target deleterious allospecific memory T cells in experimental animal models and clinical settings.
Resisting Suggestive Questions: Can Theory of Mind Help?

Abstract Children's credibility as witnesses in court cases has become an important issue in recent years. When testifying, younger children are considered to be more susceptible to suggestion than are older children. The present study examined the possibility that knowledge of an interviewer's mental states (intention and false belief, in this study) would influence the accuracy of young children's reporting of a recently witnessed event. Five-year-old children were shown a short video clip, after which they were asked to free recall as well as respond to a list of specific questions. Results showed that children who were given knowledge of an interviewer's intention resisted suggestive questioning, whereas children without mental-states knowledge were misled to report inaccurate information.
Host-Parasite Relationship in Cystic Echinococcosis: An Evolving Story

The larval stage of Echinococcus granulosus causes cystic echinococcosis, a neglected infectious disease that constitutes a major public health problem in developing countries. Despite being under constant barrage by the immune system, E. granulosus modulates antiparasite immune responses and persists in the human hosts with detectable humoral and cellular responses against the parasite. In vitro and in vivo immunological approaches, together with molecular biology and immunoproteomic technologies, provided us exciting insights into the mechanisms involved in the initiation of E. granulosus infection and the consequent induction and regulation of the immune response. Although the last decade has clarified many aspects of host-parasite relationship in human cystic echinococcosis, establishing the full mechanisms that cause the disease requires more studies. Here, we review some of the recent developments and discuss new avenues in this evolving story of E. granulosus infection in man.
Ectodomain Shedding of Epidermal Growth Factor Receptor Ligands Is Required for Keratinocyte Migration in Cutaneous Wound Healing

Keratinocyte proliferation and migration are essential to cutaneous wound healing and are, in part, mediated in an autocrine fashion by epidermal growth factor receptor (EGFR)–ligand interactions. EGFR ligands are initially synthesized as membrane-anchored forms, but can be processed and shed as soluble forms. We provide evidence here that wound stimuli induce keratinocyte shedding of EGFR ligands in vitro, particularly the ligand heparin-binding EGF-like growth factor (HB-EGF). The resulting soluble ligands stimulated transient activation of EGFR. OSU8-1, an inhibitor of EGFR ligand shedding, abrogated the wound-induced activation of EGFR and caused suppression of keratinocyte migration in vitro. Soluble EGFR–immunoglobulin G-Fcγ fusion protein, which is able to neutralize all EGFR ligands, also suppressed keratinocyte migration in vitro. The application of OSU8-1 to wound sites in mice greatly retarded reepithelialization as the result of a failure in keratinocyte migration, but this effect could be overcome if recombinant soluble HB-EGF was added along with OSU8-1. These findings indicate that the shedding of EGFR ligands represents a critical event in keratinocyte migration, and suggest their possible use as an effective clinical treatment in the early phases of wound healing.
Song2Guitar: A Difficulty-Aware Arrangement System for Generating Guitar Solo Covers from Polyphonic Audio of Popular Music

This paper describes Song2Guitar which automatically generates difficulty-aware guitar solo cover of popular music from its acoustic signals. Previous research has utilized hidden Markov models (HMMs) to generate playable guitar piece from music scores. Our Song2Guitar extends the framework by leveraging MIR technologies so that it can handle beats, chords and melodies extracted from polyphonic audio. Furthermore, since it is important to generate a guitar piece to meet the skill of a player, Song2Guitar generates guitar solo covers in consideration of playing difficulty. We conducted a data-driven investigation to find what factor makes a guitar piece difficult to play, and restricted Song2Guitar to use certain hand forms adaptively so that the player can play the piece without experiencing too much difficulty. The user interface of Song2Guitar is also implemented and is used to conduct user tests. The results indicated that Song2Guitar succeeded in generating guitar solo covers from polyphonic audio with various playing difficulties.
The Frequency of Optical Coherence Tomography Testing in Glaucoma at a Single Academic Medical Center

Purpose:To determine the frequency of optical coherence tomography (OCT) examinations compared with clinical examinations and visual field (VF) tests in patients with 5 types of glaucoma. Patients and Methods:A retrospective, longitudinal cohort study was conducted of 5154 patients treated between 2003 and 2010 at a single academic medical center. Patients were classified using billing records as having primary open-angle glaucoma, low-tension open-angle glaucoma (NTG), pigmentary open-angle glaucoma, chronic angle-closure glaucoma, or pseudoexfoliation glaucoma. Analysis of variance, &khgr;2 test, and exact &khgr;2 test were performed to identify associations between glaucoma type and test frequency. Results:Pigmentary open-angle glaucoma and NTG patients had a higher rate of undergoing at least 2 VFs (94.4%, 94.9%), and chronic angle-closure glaucoma patients had a lower rate of undergoing at least 2 OCTs (25.3%) than all other glaucoma types. NTG patients also had the highest rate of undergoing at least 2 OCTs and at least 2 VFs (36.6%). Overall, the rate of clinical examinations (2.68 examinations/y) exceeded the rates of OCTs (1.39 examinations/y), which exceeded the rate of VF tests (1.24 tests/y). There were no differences in OCT frequency between glaucoma types (0.91 to 1.63 OCTs/y). Within each glaucoma diagnosis, patients had clinical examinations more frequently than OCTs and clinical examinations more frequently than VFs. Primary open-angle glaucoma and pseudoexfoliation glaucoma patients also had OCTs more frequently than VFs. More patients had at least 2 VF tests than at least 2 OCTs (4481 vs. 1679). Conclusion:The relative use of clinical examinations, VF testing, and OCT imaging varies among glaucoma diagnoses.
O desempenho de falantes bilíngües: evidências advindas da investigação do VOT de oclusivas surdas do inglês e do português

Esta pesquisa investiga o tempo de ataque do vozeamento das oclusivas surdas produzidas por bilingues de infância falantes do portugues e ingles, com o intuito de detectar se as diferencas sutis na realizacao fonetica de um contraste fonologico que estao presentes na producao dos monolingues sao reproduzidas na fala desses bilingues. O corpus foi formado por 3 palavras do portugues e 3 do ingles gravadas em sentenca veiculo. As gravacoes foram submetidas a analise acustica usando-se o CSRE (Canadian Speech Research Environment). Os resultados obtidos indicam que bilingues de infância nao mantem seus codigos linguisticos separados. Sua competencia linguistica parece basear-se em um sistema reestruturado caracterizado por propriedades articulatorias e acusticas derivadas da interacao dos sistemas foneticos das linguas envolvidas e da interacao de outras variaveis tais como idade, background linguistico da familia e do ambiente social preponderante.
Diltiazem and exercise performance in patients with chronic atrial fibrillation.

To evaluate the influence of calcium entry blockade (diltiazem 60 mg qid) on exercise capacity in patients with chronic atrial fibrillation, nine men (mean age 65 years) with atrial fibrillation underwent maximal treadmill exercise on and off diltiazem therapy. Heart rate, blood pressure, and measured ventilatory parameters were assessed at a standard submaximal workload (3.0 mph/0% grade), the gas exchange anaerobic threshold (ATge), and maximal exercise. Significant reductions in heart rate at all stages of exercise were demonstrated: maximum heart rate decreased from 171 +/- 30 beats/min to 142 +/- 27 beats/min (17 percent, p less than .01) and submaximal exercise heart rate decreased from 123 +/- 22 beats/min to 96 +/- 16 beats/min (22 percent, p less than .01). However, there were no significant changes in blood pressure or gas exchange data, ie, oxygen uptake, minute ventilation, or respiratory exchange ratio at any of the exercise workloads. These data demonstrate that in patients with chronic atrial fibrillation, diltiazem controls the ventricular rate response throughout exercise without attenuating blood pressure or exercise capacity.
Adolescent napping behavior: Comparisons of school week versus weekend sleep patterns

Adolescents typically sleep in on weekends to catch up on their school-week sleep debt. This study explored adolescents’ napping behavior by comparing weekly sleep patterns with non-nappers. Older adolescents (n = 231) completed sleep questionnaires. Approximately 32% napped on average 4 times/week, typically around 16.00 hours. Nappers had a significantly delayed sleep timing compared to non-nappers (P < 0.0001). Although both nappers and non-nappers obtained more sleep on weekends by sleeping in (P < 0.0001), the data suggest that most nappers appear to catch up on school-week sleep debt by not only sleeping in on weekends, but by also napping during the school week.
Phase I/II Trial of the Pharmacokinetics, Safety, and Antiretroviral Activity of Tenofovir Disoproxil Fumarate in Human Immunodeficiency Virus-Infected Adults

ABSTRACT Tenofovir DF is an antiviral nucleotide with activity against human immunodeficiency virus type 1 (HIV-1). The pharmacokinetics, safety, and activity of oral tenofovir DF in HIV-1-infected adults were evaluated in a randomized, double-blind, placebo-controlled, escalating-dose study of four doses (75, 150, 300, and 600 mg given once daily). Subjects received a single dose of tenofovir DF or a placebo, followed by a 7-day washout period. Thereafter, subjects received their assigned study drug once daily for 28 days. Pharmacokinetic parameters were dose proportional and demonstrated no change with repeated dosing. Reductions in plasma HIV-1 RNA were dose related at tenofovir DF doses of 75 to 300 mg, but there was no increase in virus suppression between the 300- and 600-mg dose cohorts, despite dose-proportional increases in drug exposure. Grade III or IV adverse events were limited to laboratory abnormalities, including elevated creatine phosphokinase and liver function tests, which resolved with or without drug discontinuation and without sequelae. No patients developed detectable sequence changes in the reverse transcriptase gene.
Role of Activity of Gastrointestinal Microflora in Absorption of Calcium and Magnesium in Rats Fed β1-4 Linked Galactooligosaccharides

Rats fed a diet containing β1-4 linked galactooligosaccharides (GOS) (5 g/100 g of diet) absorbed calcium and magnesium more efficiently than those fed the control diet. However, the increment obtained through GOS-feeding was reduced by neomycin sulfate 0.67 g/100 g of diet). Since the decrease in cecal pH in rats fed GOS was suppressed by neomycin-feeding, bacterial action in the digestive tract was considered to be reduced by neomycin-feeding. Our findings suggest that the action of intestinal bacteria is necessary for the effects of GOS.
The Persistence of the Standardized Life Cycle

This article investigates to what degree the standardized life cycle has been replaced by an individualized life course, characterized by the absence of a strict sequence and timing of life's transitions. In order to measure the normative position of people, rather than the external conditions to which they are subject, the test is based on the ideal life course or life cycle as described by a purely random sample of 4666 inhabitants of Belgium, aged 18 to 36. The available evidence overwhelmingly points towards the persistence of a standardized ideal life cycle, characterized by a strict sequence and timing of the important transitions.
Alterations of miRNAs and Their Potential Roles in Arsenite-Induced Transformation of Human Bronchial Epithelial Cells

The alterations of micro RNAs (miRNAs) and their potential roles in arsenite-induced tumorigenesis are still poorly understood. In this study, miRNA Array was used to detect the expression level of miRNAs in human bronchial epithelial (HBE) cells that were transformed by 2.5 μM arsenite for 13 weeks. These cells exhibited a neoplastic phenotype manifested by increased levels of cellular proliferation and migration and clone formation. Subsequently, 191 dysregulated miRNAs were identified to be associated with arsenite-induced transformation by miRNA Array. Among them, six miRNAs were validated by their expression levels with quantitative real-time polymerase chain reaction (qPCR), and 17 miRNAs were further explored via their target genes as well as regulatory network. Three databases, TargetMiner, miRDB, and TarBase, were used to predict the target genes of the 17 miRNAs, and a total of 954 common genes were sorted. Results of Gene Ontology (GO) analyses showed that the 954 genes were involved in diverse terms of GO categories, such as positive regulation of macroautophagy, epithelial cell maturation, and synaptic vesicle clustering. Moreover, results of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that most of these target genes were enriched in various cancer-related pathways, including non-small cell lung cancer, Wnt signaling pathway, cell cycle, and p53 signaling pathway. The miRNA-gene regulatory network, which was constructed by cytoscape software with miRNAs and their target genes, showed that miR-15b-5p, miR-106b-5p, and miR-320d were the core hubs. Collectively, our results provide new insights into miRNA-mediated mechanisms underlying arsenite-induced transformation, although more experimental verification is still needed to prove these predictions.
Twice-Pruning Aided WASD Neuronet of Bernoulli-Polynomial Type with Extension to Robust Classification

This paper proposes a novel multi-input Bernoulli-polynomial neuronet (MIBPN) on the basis of function approximation theory. The MIBPN is trained by a weights-and-structure-determination (WASD) algorithm with twice pruning (TP). The WASD algorithm can obtain the optimal weights and structure for the MIBPN, and overcome the weaknesses of conventional BP (back-propagation) neuronets such as slow training speed and local minima. With the TP technique, the neurons of less importance in the MIBPN are pruned for less computational complexity. Furthermore, this MIBPN can be extended to a multiple input multiple output Bernoulli-polynomial neuronet (MIMOBPN), which can be applied as an important tool for classification. Numerical experiment results show that the MIBPN has outstanding performance in data approximation and generalization. Besides, experiment results based on the real-world classification data-sets substantiate the high accuracy and strong robustness of the MIMOBPN equipped with the proposed WASD algorithm for classification. Finally, the twice-pruning aided WASD neuronet of Bernoulli-polynomial type in the forms of MIBPN and MIMOBPN is established, together with the effective extension to robust classification.
Ethnicity and baseline symptomatology in patients with an At Risk Mental State for psychosis

Background Ethnicity has been associated with different incidence rates and different symptom profiles in young patients with psychotic-like disorders. No studies so far have examined the effect of ethnicity on symptoms in people with an At Risk Mental State (ARMS). Method In this cross-sectional study, we analysed the relationship between ethnicity and baseline data on the severity of psychopathology scores in 201 help-seeking patients who met the ARMS criteria and agreed to participate in the Dutch Early Detection and Intervention (EDIE-NL) trial. Eighty-seven of these patients had a non-Dutch ethnicity. We explored the possible mediating role of ethnic identity. Results Higher rates of negative symptoms, and of anhedonia in particular, were found in the ethnic minority group. This result could be attributed mainly to the Moroccan-Dutch and Turkish-Dutch subgroups, who also presented with more depression symptoms when the groups were examined separately. The ethnic minority group displayed a lower level of ethnic group identity compared to the immigrants of the International Comparative Study of Ethnocultural Youth (ICSEY). Ethnic identity was inversely related to symptoms in the Moroccan-Dutch patient group. Conclusions The prevalence of more severe negative symptoms and depression symptoms in ethnic minority groups deserves more attention, as the experience of attenuated positive symptoms when accompanied by negative symptoms or distress has proven to be predictive for transition to a first psychotic episode.
Sexual Dimorphism on Hypertension of Quantitative Trait Loci Entrapped in Dahl Congenic Rats

Although it is well-known that quantitative trait loci (QTLs) influence blood pressure (BP) in male Dahl salt-sensitive rats (DSS), few studies have been carried out to ascertain the BP effect of these QTLs in females. In the current work, we analyzed BP of seven selected congenic strains constructed in the DSS background. One QTL, C8QTL2, exhibited similar effects on systolic (SAP), diastolic (DAP), and mean arterial (MAP) pressures in females as previously shown in males. In contrast, six QTLs that previously demonstrated influences on SAP, DAP, and MAP in males did not have effects in females. These male-specific QTLs are likely regulated differently in males than in females and emphasize the necessity of identifying female-specific QTLs for diagnosing and treating hypertension in women. Current findings may have implications in genetic research of essential hypertension, and association and linkage analyses should be performed in separate genders. Men and women may possess distinctive as well as shared genetic determinants for SAP, DAP, and MAP. The data on a single gene or marker might be pooled from both genders only when evidence favors the sex-independence in a study.
Training and bradycardia in rats.

Bradycardia produced by training was investigated in 228 mature male rats belonging to normal, vagotomized, diencephalon-lesioned, immunological sympathectomized, and hypophysectomized groups. During a 70-day experimental period, resting heart rates of trained unanesthetized rats were significantly lower than those of non-trained rats at approximately 40 days after the training program had been initiated. Resting heart rates were correlated with body weight, wet and dry heart weight, percentage of solids, and the heart weight/body weight ratio (heart ratio). Several coefficients were statistically significant but the majority of the coefficients were below ±0.60 and exhibited a low relationship between the various parameters. Heart ratios for the trained vagotomized, diencephalon-lesioned, and immunological sympathectomized were significantly lower than the ratios from normal trained animals. Similar trends were observed with the nontrained subgroups when these ratios were compared with normal nontrained animals. The only exercising group that exhibited statistical evidence for cardiac hypertrophy was the normal trained group. It was concluded that other aspects beside the weight of the heart must be considered in any satisfactory explanation for this form of bradycardia.