Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of celiac disease in adult patients with refractory functional dyspepsia: value of routine duodenal biopsy.

AIM To investigate the prevalence of celiac disease (CD) in adult patients referred to an open access gastroenterology clinic in the south of Italy and submitted to esophago-gastro-duodenoscopy (EGD) for evaluation of refractory functional dyspepsia. METHODS Seven hundred and twenty six consecutive dyspeptic patients (282 male, 444 female; mean age 39.6 years, range 18-75 years) with unexplained prolonged dyspepsia were prospectively enrolled. Duodenal biopsies were taken and processed by standard staining. Histological evaluation was carried out according to the Marsh-Oberhuber criteria. RESULTS The endoscopic findings were: normal in 61.2%, peptic lesions in 20.5%, malignancies in 0.5%, miscellaneous in 16.7%. CD was endoscopically diagnosed in 8 patients (1.1%), histologically in 15 patients (2%). The endoscopic features alone showed a sensitivity of 34.8% and specificity of 100%, with a positive predictive value (PPV) of 100% and a negative predictive value (NPP) of 97.9%. CONCLUSION This prospective study showed that CD has a high prevalence (1:48) in adult dyspeptic patients and suggests the routine use of duodenal biopsy in this type of patient undergoing EGD.
Complete Nucleotide Sequence of the pCTX-M3 Plasmid and Its Involvement in Spread of the Extended-Spectrum β-Lactamase Gene blaCTX-M-3

ABSTRACT Here we report the nucleotide sequence of pCTX-M3, a highly conjugative plasmid that is responsible for the extensive spread of the gene coding for the CTX-M-3 extended-spectrum β-lactamase in clinical populations of the family Enterobacteriaceae in Poland. The plasmid belongs to the IncL/M incompatibility group, is 89,468 bp in size, and carries 103 putative genes. Besides blaCTX-M-3, it also bears the blaTEM-1, aacC2, and armA genes, as well as integronic aadA2, dfrA12, and sul1, which altogether confer resistance to the majority of β-lactams and aminoglycosides and to trimethoprim-sulfamethoxazole. The conjugal transfer genes are organized in two blocks, tra and trb, separated by a spacer sequence where almost all antibiotic resistance genes and multiple mobile genetic elements are located. Only blaCTX-M-3, accompanied by an ISEcp1 element, is placed separately, in a DNA fragment previously identified as a fragment of the Kluyvera ascorbata chromosome. On the basis of sequence analysis, we speculate that pCTX-M3 might have arisen from plasmid pEL60 from plant pathogen Erwinia amylovora by acquiring mobile elements with resistance genes. This suggests that plasmids of environmental bacterial strains could be the source of those plasmids now observed in bacteria pathogenic for humans.
HIV-1 Proteins Preferentially Activate Anti-Inflammatory M2-Type Macrophages

HIV-1 proteins, including Tat, gp120, and Nef, activate macrophages (MΦ), which is consistent with the fact that HIV-1 infection is characterized by sustained immune activation. Meanwhile, MΦ are functionally classified into two types: proinflammatory M1-MΦ and anti-inflammatory M2-MΦ. We show that HIV-1 proteins, particularly Nef, preferentially activate M2-MΦ. Extracellular Tat, gp120, and Nef activated MAPK and NF-κB pathways in human peripheral blood monocyte-derived MΦ. However, the activation was marked in M-CSF–derived M2-MΦ but not GM-CSF–derived M1-MΦ. Nef was the most potent activator, and its signaling activation was comparable to that by TNF-α. Indeed, Nef was internalized more rapidly by M2-MΦ than by M1-MΦ. The myristoylation and proline-rich motif of Nef were responsible for the observed signaling activation. Consistent with the activation of MAPK/NF-κB pathways, Nef stimulated the production of a number of proinflammatory cytokines/chemokines by M2-MΦ. However, Nef reduced the expression of CD163 and phagocytosis, the characteristic markers of M2-MΦ, indicating that Nef drives an M2-like to M1-like phenotypic shift. Because the differentiation of most tissue MΦ depends on M-CSF and its receptor, which is the essential axis for the anti-inflammatory M2-MΦ phenotype, the current study reveals an efficient mechanism by which HIV-1 proteins, such as Nef, induce the proinflammatory MΦ.
Gender Differences in African American Adolescents' Personal, Educational, and Occupational Expectations and Perceptions of Neighborhood Quality

This study was conducted in an effort to generate information toward fostering academic outcomes among African American adolescents. Gender differences in African American adolescents' personal, educational, and occupational expectations were examined in relation to perceptions of neighborhood quality. Participants included 352 African American adolescents residing in an urban area. Measures were self-reported expectations and perceptions of neighborhood quality. Regression analyses indicated that (a) expectations were positively associated with perceptions of neighborhood quality, (b) female adolescents reported more positive expectations than male adolescents, and (c) the association between expectations and perceptions of neighborhood quality depended on gender, with male adolescents who rated their neighborhood higher in quality reporting higher personal and educational expectations than male adolescents who rated their neighborhood poorer in quality. Implications of this study for programs and research that focus on academic outcomes and neighborhoods of African American adolescents are discussed.
Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice.

AIM Favipiravir and oseltamivir are antiviral compounds used for the treatment of influenza infections. We have aimed to investigate the efficacy of the compounds in combination to treat influenza H1N1 virus infections in mice. MATERIALS & METHODS Mice infected with pandemic influenza A/California/04/2009 (H1N1pdm) virus or an oseltamivir-resistant (H275Y neuraminidase mutation) influenza A/Mississippi/ 3/2001 (H1N1) virus were treated orally with inhibitors twice a day for 5 days starting 4 h after infection. RESULTS Complete protection from death was afforded by favipiravir treatments of 100 mg/kg/day, but lower doses were less effective. Combinations of oseltamivir (1 and 3 mg/kg/day) with favipiravir (3, 10 and 30 mg/kg/day) resulted in a synergistic improvement in survival rates against H1N1pdm infections. Significant reductions in lung virus titers also occurred. Against the H275Y virus infection, oseltamivir alone was only 30% protective from death at 100 mg/kg/day, but combinations of the two compounds produced a synergistic improvement in survival rate. CONCLUSION The utility of treating H1N1 influenza virus infections with oseltamivir and favipiravir in combination has been established.
MACHINED SURFACE ROUGHNESS PREDICTION USING ADAPTIVE NEUROFUZZY INFERENCE SYSTEM

This work considers the effect of the depth of cut, feed, and number of revolutions on the roughness of the machined surface. The results obtained by experimentally investigating the workpiece “diving manifold” were used to model the input/output data plan for the adaptive neurofuzzy inference system (ANFIS). Those data were used to generate a fuzzy inference system that made it possible to predict the output (surface roughness) based on the given inputs (feed, number of revolutions, and depth of cut). The surface roughness results obtained by the fuzzy inference system (FIS) were compared with the surface roughness results obtained by neural networks, moving linear least square method and moving linear least absolute deviation method on the same set of experimental data. These methods and systems for prediction of surface roughness are helpful when solving practical technological problems in a manufacturing process, first by determining the cutting parameter values that will add to the demanded quality of a product, and later when optimizing the technological process.
Adaptive Multivariable Integral TSMC of a Hypersonic Gliding Vehicle With Actuator Faults and Model Uncertainties

This paper presents a fault-tolerant control (FTC) strategy for a hypersonic gliding vehicle (HGV) subject to actuator malfunctions and model uncertainties. The control-oriented model of the HGV is established according to the HGV kinematic and aerodynamic models. A composite-loop design for HGV FTC under actuator faults is subsequently developed, where newly developed multivariable integral terminal sliding-mode control (TSMC) and adaptive techniques are integrated. The multivariable integral TSMC is capable of ensuring the finite-time stability of the closed-loop system in the presence of actuator malfunctions and model uncertainties, while the adaptive laws are employed to tune the control parameters in response to the HGV status. Simulation studies based on a six-degree-of-freedom nonlinear model of the HGV are illustrated to highlight the effectiveness of the developed FTC scheme.
The Contribution of Group Supervision Processes to the Formation of Professional Identity among Novice Psychotherapists

ABSTRACT Group supervision is a commonly employed method in graduate psychology training. The present study examines the role of group processes in the formation of professional identity among 129 Israeli graduate students following the conclusion of their supervision process. The following three identity statuses were identified: achievement, diffusion, and moratorium. Working alliance and group engagement were significantly higher for achievement students and differentiated between achievement and moratorium students. Cohesion was significantly lower for moratorium students than for students at each of the other two identity statuses. All differences were maintained when controlling for anxiety. Finally, working alliance was found to be the dominant process in predicting committed professional identity status. The findings stress the links between group processes in group supervision and a committed professional identity.
Beverage intake and obesity in early childhood: evidence form primary health care clients in Northwest Argentina

Sugar sweetened beverages (SSB) are thought to play an important role in weight gain. We examined the relationship between the intake of caloric and noncaloric beverages (SSB and water) and the nutritional status of children. In 2014, we randomly selected 16 public health clinics in four cities of Northwest Argentina and conducted a survey among mothers of children 0–6 years of age. Children’s beverage intake was ascertained by 24-h dietary recall provided by the mothers. Children’s weight and height measures were obtained from clinic’s registries. We calculated the body mass index using the International Obesity Task Force standards. The analysis included 562 children 25 months to 6 years of age with normal or above normal nutritional status. Children’s beverage consumption was as follows, water 81.8%, carbonated soft drinks (CSD) 49.7%, coffee/tea/cocoa 44.0%, artificial fruit drinks 35.6%, flavored water 17.9%, natural fruit juice 14.5%. In multivariate logistic regression models the likelihood of being obese v. being overweight or having normal weight doubled with an intake of one to five glasses of CSD (OR=2.2) and increased by more than three-fold with an intake of more than five glasses (OR=3.5). Drinking more than five glasses of water decreased the likelihood of being obese by less than half (OR=0.3). The percentage of children drinking more than five glasses of other beverages was low (3.3–0.9%) and regression models did not yield significant results. The study contributed evidence for reducing children’s CSD intake and for promoting water consumption, together with the implementation of comprehensive regulatory public health policies.
The Effect of Sodium Chloride on the Two–Step Kinetics of the Nitrifying Process

Sodium chloride affects the transformation rate of several compounds in bioreactors. Most authors report a decrease in microorganism activity at increasing salt concentrations. In this work, a kinetic model that relates sodium chloride concentration with the rates of each step of the nitrification process is proposed; thus, the effect of sodium chloride concentration (0 to 60 g/L) on the nitritation and nitratation rates was separately studied. To carry out the independent study of each step, a combination of the respirometric method with sodium azide, an inhibitor of the nitratation step, was performed. The dot–blot hybridization technique with 16S rRNA–targeted probes was used to determine the ammoniaoxidizing and nitrite–oxidizing bacterial fraction, then it was possible to relate the culture's function with its biological composition. Rates of both steps were linearly reduced at increasing salt concentrations; the nitratation rate was more affected than the nitritation rate. Simulations carried out in a nitrifying sequencing batch reactor indicate that nitrite might accumulate at high salt concentrations. Sodium chloride exerts a reversible inhibition on ammonia oxidation and nitrite oxidation.
Viscoelastic frictionless contact problems with adhesion

We consider two quasistatic frictionless contact problems for viscoelastic bodies with long memory. In the first problem the contact is modelled with Signorini's conditions and in the second one is modelled with normal compliance. In both problems the adhesion of the contact surfaces is taken into account and is modelled with a surface variable, the bonding field. We provide variational formulations for the mechanical problems and prove the existence of a unique weak solution to each model. The proofs are based on arguments of time-dependent variational inequalities, differential equations, and a fixed point theorem. Moreover, we prove that the solution of the Signorini contact problem can be obtained as the limit of the solutions of the contact problem with normal compliance as the stiffness coefficient of the foundation converges to infinity.
CNS live imaging reveals a new mechanism of myelination: The liquid croissant model

The overall morphology and with it associated the formation of myelin is generally thought to be resolved. Based on electron microscopic findings more than half a century ago, the current model of myelination describes all myelin membranes to run in parallel with the longitudinal axis of the axon and to form a smooth surface, reminiscent of a rolled up carpet. However, different studies in the past demonstrated a distinct myelin morphology with an uneven myelin surface contour that challenges the established concept. Even though the current model of myelination has since been recognized as insufficient, CNS myelin formation has not yet been investigated in real‐time with the requisite technique and resolution. We therefore traced myelin growth in murine organotypic cerebellar slice cultures using high‐resolution confocal live imaging, light and electron microscopy and assessed myelin morphology in young and adult mice by confocal microscopy. Our data verify that the myelin surface is indeed not smooth but runs in a bidirectional, regularly spaced coil along the axon in both young and adult mice. Time‐lapse imaging revealed that the growth of coiled myelin turns emerges during myelin formation. We therefore propose the “liquid croissant” model as a new concept of myelination that overcomes not only some of the incongruences of previous myelination theories, but potentially also explains the development of certain myelin pathologies observed in remyelination and axonopathies. © 2011 Wiley‐Liss, Inc.
Measuring Motivational Characteristics of Courses: Applying Keller's Instructional Materials Motivation Survey to a Web-Based Course

Purpose The Instructional Materials Motivation Survey (IMMS) purports to assess the motivational characteristics of instructional materials or courses using the Attention, Relevance, Confidence, and Satisfaction (ARCS) model of motivation. The IMMS has received little use or study in medical education. The authors sought to evaluate the validity of IMMS scores and compare scores between standard and adaptive Web-based learning modules. Method During the 2005–2006 academic year, 124 internal medicine residents at the Mayo School of Graduate Medical Education (Rochester, Minnesota) were asked to complete the IMMS for two Web-based learning modules. Participants were randomly assigned to use one module that adapted to their prior knowledge of the topic, and one module using a nonadaptive design. IMMS internal structure was evaluated using Cronbach alpha and interdimension score correlations. Relations to other variables were explored through correlation with global module satisfaction and regression with knowledge scores. Results Of the 124 eligible participants, 79 (64%) completed the IMMS at least once. Cronbach alpha was ≥0.75 for scores from all IMMS dimensions. Interdimension score correlations ranged 0.40 to 0.80, whereas correlations between IMMS scores and global satisfaction ratings ranged 0.40 to 0.63 (P < .001). Knowledge scores were associated with Attention and Relevance subscores (P = .033 and .01, respectively) but not with other IMMS dimensions (P ≥ .07). IMMS scores were similar between module designs (on a five-point scale, differences ranged from 0.0 to 0.15, P ≥ .33). Conclusions These limited data generally support the validity of IMMS scores. Adaptive and standard Web-based instructional designs were similarly motivating. Cautious use and further study of the IMMS are warranted.
Population variation in VKORC1 haplotype structure

Recently, improved prediction of maintenance warfarin dose has been linked to single nucleotide polymorphisms (SNPs) in the vitamin K epoxide reductase complex subunit 1 gene (VKORC1) [1–3]. In addition to the individual SNPs, haplotype-dependent predictions for warfarin dosing have been described [1]. The high-dose and low-dose haplotypes can be identified in patients by screening a small number of polymorphisms (haplotype tag SNPs) [1]. Previously, factors such as CYP2C9 genotype have also been described as predictors for warfarin dose [4,5]. VKORC1 haplotype accounts for 21–25% of the variation in warfarin dose, and adding CYP2C9*2 and *3 genotypes improved the prediction model to 31% [4]. As warfarin has a narrow therapeutic index, and overor under-dosing can be lifethreatening, screening of VKORC1 and CYP2C9 prior to initiating therapy are likely to provide essential information for improving dose selection and more cost effective monitoring strategies. Population differences of VKORC1 haplotype and CYP2C9 genotype frequencies have also been suggested from initial studies [1,4,6]. We identified the frequency of genotype combinations across world populations of the four haplotype tag SNPs for VKORC1 described by Reider et al. [1] (861, 5808, 6853, and 9041) and CYP2C9 (*2 and *3) using Pyrosequencing [1,4] in 556 unrelated healthy individuals from the following populations: European–American, African, African–American, Hispanic (Mexican and Peruvian) and Asian (Table 1). Using previously defined criteria to determine high and low dose VKORC1 haplotype groups [1] and incorporating dose-limiting CYP2C9 genetic variation [4], Asian and Caucasian populations had the highest incidence (86% and 55%, respectively) of low dose individuals from either VKORC1 or CYP2C9 variants (from at least one VKORC1 haplotype A or CYP2C9 variant allele). Eighteen percent of the Caucasian population had a combination of at least one VKORC1 haplotype A and at least one CYP2C9 variant, whereas CYP2C9 variant alleles were rare in other populations. In addition, haplotypes of unknown function were prominent in populations of African origin (up to 28%; Table 1). Assessment of the functional consequence of haplotypes not belonging to groups A or B in African populations is warranted. These data are consistent with the observations that Asian patients require a lower average maintenance warfarin dose, and African–Americans a higher average dose to obtain a therapeutic international normalized ratio (INR). However, the low dose requirements for Hispanic patients compared with Caucasian patients are not explained by these variants [7]. With the current focus on utilizing the individual patient’s genetic profile for treatment selection [1–4], care should be taken to identify the predictive SNPs and/or haplotypes in all populations when proposing pharmacogenetic-based dosing regimens for initiation of oral anticoagulation therapy with warfarin.
The Transcriptional Response of Candida albicans to Weak Organic Acids, Carbon Source, and MIG1 Inactivation Unveils a Role for HGT16 in Mediating the Fungistatic Effect of Acetic Acid

Candida albicans is a resident fungus of the human intestinal microflora. Commonly isolated at low abundance in healthy people, C. albicans outcompetes local microbiota during candidiasis episodes. Under normal conditions, members of the human gastrointestinal (GI) microbiota were shown to keep C. albicans colonization under control. By releasing weak organic acids (WOAs), bacteria are able to moderate yeast growth. This mechanism displays a synergistic effect in vitro with the absence of glucose in medium of culture, which underlines the complex interactions that C. albicans faces in its natural environment. Inactivation of the transcriptional regulator MIG1 in C. albicans results in a lack of sensitivity to this synergistic outcome. To decipher C. albicans transcriptional responses to glucose, WOAs, and the role of MIG1, we performed RNA sequencing (RNA-seq) on four biological replicates exposed to combinations of these three parameters. We were able to characterize the (i) glucose response, (ii) response to acetic and butyric acid, (iii) MIG1 regulation of C. albicans, and (iv) genes responsible for WOA resistance. We identified a group of six genes linked to WOA sensitivity in a glucose-MIG1-dependent manner and inactivated one of these genes, the putative glucose transporter HGT16, in a SC5314 wild-type background. As expected, the mutant displayed a partial complementation to WOA resistance in the absence of glucose. This result points toward a mechanism of WOA sensitivity in C. albicans involving membrane transporters, which could be exploited to control yeast colonization in human body niches.
The evolution of animal genitalia: distinguishing between hypotheses by single species studies

Rapid evolution of genitalia is one of the most general patterns of morphological diversification in animals. Despite its generality, the causes of this evolutionary trend remain obscure. Several alternative hypotheses have been suggested to account for the evolution of genitalia (notably the lock-and-key, pleiotropism, and sexual selection hypotheses). Here, I argue that thorough intraspecific studies are the key to gaining insight into the patterns and processes of genitalic evolution. Critical assumptions and predictions that may be used to distinguish between the different hypotheses are identified and discussed. However, current knowledge of selection on genitalia, or even of the degree of phenotypic and genotypic variability of genital morphology, is highly limited, allowing only a very tentative assessment of the various hypotheses. In-depth single species studies of current patterns and processes of selection on genitalia are badly needed, and a single species research program is briefly outlined.