Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of the novel Th17 cytokine IL-26 in intestinal inflammation

Background and aims: Interleukin 26 (IL-26), a novel IL-10-like cytokine without a murine homologue, is expressed in T helper 1 (Th1) and Th17 cells. Currently, its function in human disease is completely unknown. The aim of this study was to analyse its role in intestinal inflammation. Methods: Expression studies were performed by reverse transcription-PCR (RT-PCR), quantitative PCR, western blot and immunohistochemistry. Signal transduction was analysed by western blot experiments and ELISA. Cell proliferation was measured by MTS (3-(4,5-dimethylthiazol-2-yl)-5-(carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assay. IL-26 serum levels were determined by an immunoluminometric assay (ILMA). Results: All examined intestinal epithelial cell (IEC) lines express both IL-26 receptor subunits IL-20R1 and IL-10R2. IL-26 activates extracellular signal-related kinase (ERK)-1/2 and stress-activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) mitogen-activated protein (MAP) kinases, Akt and signal transducers and activators of transcription (STAT) 1/3. IL-26 stimulation increases the mRNA expression of proinflammatory cytokines but decreases cell proliferation. In inflamed colonic lesions of patients with Crohn’s disease, an elevated IL-26 mRNA expression was found that correlated highly with the IL-8 and IL-22 expression. Immunohistochemical analysis demonstrated IL-26 protein expression in colonic T cells including Th17 cells expressing the orphan nuclear receptor RORγt, with an increased number of colonic IL-26-expressing cells in active Crohn’s disease. Conclusion: Intestinal cells express the functional IL-26 receptor complex. IL-26 modulates IEC proliferation and proinflammatory gene expression and its expression is upregulated in active Crohn’s disease, indicating a role for this cytokine system in the innate host cell response during intestinal inflammation. For the first time, IL-26 expression is demonstrated in colonic RORγt-expressing Th17 cells in situ, supporting a role for this cell type in the pathogenesis of Crohn’s disease.
Model atmosphere analysis of the extreme DQ white dwarf GSC2U J131147.2+292348

A new model atmosphere analysis for the peculiar DQ white dwarf discovered by Carollo et al. (2002) is presented. The effective temperature and carbon abundance have been estimated by fitting both the photometric data (UBJVRFINJHK )a nd a low resolution spectrum (3500 <λ< 7500 A) with a new model grid for helium-rich white dwarfs with traces of carbon (DQ stars). We estimate Teff � 5120 ±200 K and log(C/He) �− 5.8 ±0.5, which make GSC2UJ131147.2+292348 the coolest DQ star ever observed. This result indicates that the hypothetical transition from C2 to C2H molecules around Teff =6000 K, which was inferred to explain the absence of DQ stars at lower temperatures, needs to be reconsidered.
Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria

Almost nothing is known about the mechanisms of dissimilatory metal reduction by Gram-positive bacteria, although they may be the dominant species in some environments. Thermincola potens strain JR was isolated from the anode of a microbial fuel cell inoculated with anaerobic digester sludge and operated at 55 °C. Preliminary characterization revealed that T. potens coupled acetate oxidation to the reduction of hydrous ferric oxides (HFO) or anthraquinone-2,6-disulfonate (AQDS), an analog of the redox active components of humic substances. The genome of T. potens was recently sequenced, and the abundance of multiheme c-type cytochromes (MHCs) is unusual for a Gram-positive bacterium. We present evidence from trypsin-shaving LC-MS/MS experiments and surface-enhanced Raman spectroscopy (SERS) that indicates the expression of a number of MHCs during T. potens growth on either HFO or AQDS, and that several MHCs are localized to the cell wall or cell surface. Furthermore, one of the MHCs can be extracted from cells with low pH or denaturants, suggesting a loose association with the cell wall or cell surface. Electron microscopy does not reveal an S-layer, and the precipitation of silver metal on the cell surface is inhibited by cyanide, supporting the involvement of surface-localized redox-active heme proteins in dissimilatory metal reduction. These results provide unique direct evidence for cell wall-associated cytochromes and support MHC involvement in conducting electrons across the cell envelope of a Gram-positive bacterium.
Evolution-guided optimization of biosynthetic pathways

Significance Microbes can be made to produce industrially valuable chemicals in high quantities by engineering their central metabolic pathways. This process may require evaluating billions of cells, each containing a unique pathway design, to identify the rare cells with high production phenotypes. We mutated targeted locations across the genome to modify several genes identified as key players. We used sensory proteins responsive to a number of target chemicals to couple the concentration of the target chemical in each cell to individual cell fitness. This coupling of chemical production to fitness allows us to harness evolution to progressively enrich superior pathway designs. Through iterations of genetic diversification and selection, we increased the production of naringenin and glucaric acid 36- and 22-fold, respectively. Engineering biosynthetic pathways for chemical production requires extensive optimization of the host cellular metabolic machinery. Because it is challenging to specify a priori an optimal design, metabolic engineers often need to construct and evaluate a large number of variants of the pathway. We report a general strategy that combines targeted genome-wide mutagenesis to generate pathway variants with evolution to enrich for rare high producers. We convert the intracellular presence of the target chemical into a fitness advantage for the cell by using a sensor domain responsive to the chemical to control a reporter gene necessary for survival under selective conditions. Because artificial selection tends to amplify unproductive cheaters, we devised a negative selection scheme to eliminate cheaters while preserving library diversity. This scheme allows us to perform multiple rounds of evolution (addressing ∼109 cells per round) with minimal carryover of cheaters after each round. Based on candidate genes identified by flux balance analysis, we used targeted genome-wide mutagenesis to vary the expression of pathway genes involved in the production of naringenin and glucaric acid. Through up to four rounds of evolution, we increased production of naringenin and glucaric acid by 36- and 22-fold, respectively. Naringenin production (61 mg/L) from glucose was more than double the previous highest titer reported. Whole-genome sequencing of evolved strains revealed additional untargeted mutations that likely benefit production, suggesting new routes for optimization.
Palmprint authentication using fusion of wavelet based representations

Wavelets are widely used to extract the texture features for pattern recognition applications including biometric authentication. This can be attributed to the discriminating capability of wavelet features and the availability of fast algorithms for implementing discrete wavelet transform (DWT). In most of the wavelet based palmprint applications, distribution of energies in space-frequency domain are treated as features to classify the palmprints. Although wavelet energies are good discriminating features, they fail to characterize the palmprints sufficiently. In order to enhance the discriminating capability and the palmprint recognition accuracy, we extract the intramodal palmprint line and energy features from the same wavelet decomposition of palmprint. The score level (product rule and sum rule) fusion of these features improves the recognition accuracy significantly. We empirically found 39.38% relative improvement (RI) with an overall equal error rate (EER) of 1.37%, on PolyU online palmprint database (left hand palmprints). The computational burden on feature extraction is very less, and the EER is superior to other state of the art approaches. The comparison of the results with the state of the art wavelet and fusion based palmprint recognition approaches demonstrates the effectiveness of the proposed approach in classifying palmprints.
EXTINCTION OF FLEMING-VIOT-TYPE PARTICLE SYSTEMS WITH STRONG DRIFT

We consider a Fleming-Viot-type particle system consisting of independently moving particles that are killed on the boundary of a domain. At the time of death of a particle, another particle branches. If there are only two particles and the underlying motion is a Bessel process on $(0,\infty)$, both particles converge to 0 at a finite time if and only if the dimension of the Bessel process is less than 0. If the underlying diffusion is Brownian motion with a drift stronger than (but arbitrarily close to, in a suitable sense) the drift of a Bessel process, all particles converge to 0 at a finite time, for any number of particles.
Chemical Constituents of the Root of Jasminum giraldii

abstract: Two new compounds, ethylconiferin (1) and (−)-lariciresinol 4-(6'''-O-cinnamyl-β-D-glucopyranoside) (2), along with the three known compounds (+)-pinoresinol (3), (+)-cycloolivil (4), nobiletin (5), were isolated from the root of Jasminum girialdii. All these compounds were isolated for the first time from this source. Their structures were elucidated on the basis of extensive spectroscopic analysis and chemical methods. In addition, the in vitro cytotoxic activity of these compounds was evaluated. The results showed that none of the compounds had any significant inhibitory activities on the proliferation of HCT-116 and SW-620 cells.
Diurnal rhythms of serum total, free and bioavailable testosterone and of SHBG in middle‐aged men compared with those in young men

background Conflicting views are reported on the association between advancing age and gradually diminishing concentrations of serum total testosterone in men. The putative loss of diurnal rhythm in serum total testosterone in older men is reported to be in part due to low concentrations in the morning when compared to concentrations found in young men. We have measured total, free and bioavailable testosterone along with SHBG in samples taken every 30 min throughout a 24‐h period in 10 young and eight middle‐aged men.
Formation of the Interphase of a Cured Epoxy Resin Near a Metal Surface: Reactive Coarse-Grained Molecular Dynamics Simulations

Mesoscale molecular dynamics simulations are performed to analyze the curing process of an epoxy resin with polyfunctional amines on a generic surface. The coarse grained potentials were derived from all-atomistic molecular dynamics simulations using iterative Boltzmann inversion. The reactive scheme incorporates cross-linking between an epoxy resin and an amine, as well as amine adsorption on the surface. The structure of the cured network is examined and compared with equilibrium properties of the uncured system. Special attention has been paid on the implications of the surface that is believed to play a crucial role in the performance of epoxy systems.
Benchmarking Multi- and Many-Objective Evolutionary Algorithms Under Two Optimization Scenarios

Recently, a large number of multi-objective evolutionary algorithms (MOEAs) for many-objective optimization problems have been proposed in the evolutionary computation community. However, an exhaustive benchmarking study has never been performed. As a result, the performance of the MOEAs has not been well understood yet. Moreover, in almost all previous studies, the performance of the MOEAs was evaluated based on nondominated solutions in the final population at the end of the search. Such traditional benchmarking methodology has several critical issues. In this paper, we exhaustively investigate the anytime performance of 21 MOEAs using an unbounded external archive (UEA), which stores all nondominated solutions found during the search process. Each MOEA is evaluated under two optimization scenarios called UEA and reduced UEA in addition to the standard final population scenario. These two scenarios are more practical in real-world applications than the final population scenario. Experimental results obtained under the two scenarios are significantly different from the previously reported results under the final population scenario. For example, results on the Walking Fish Group test problems with up to six objectives indicate that some recently proposed MOEAs are outperformed by some classical MOEAs. We also analyze the reason why some classical MOEAs work well under the UEA and the reduced UEA scenarios.
Expressed emotion and the prediction of outcome in adolescent eating disorders.

OBJECTIVE This study examines whether parental Expressed Emotion (EE) ratings, based on the Camberwell Family Interview (CFI), are predictive of the course of illness in a sample of Dutch families with an adolescent eating disorder patient. Levels of EE at first assessment and at the termination of treatment are reported. METHOD The study was designed as a prospective follow-up study and involved 49 adolescent eating disorder patients (DSM-III-R) and their parents. Patient and family assessments were conducted at intake (T1), at the termination of treatment (T2), and at follow-up (T3) 1 year later. The Morgan-Russell Outcome Assessment Schedule, which was adjusted to accommodate bulimics, yielded the average outcome score (AOS) which served as our outcome measure. RESULTS The levels of parental EE at first assessment were low. During the treatment period the levels decreased further. We used a stepwise multiple regression analysis, with the parental EE variables as independent variables, to predict the AOS at T2 and T3. This way we showed that the mothers' Critical Comments (CC) rating explained 28 to 34% of the outcome variance. The mothers' CC rating was also the best predictor of outcome when compared to other possible predictor variables. DISCUSSION The results underscore the importance of involving the family in the treatment of adolescent eating disorders. Specific attention should be given to the mother's thoughts, feelings, and behavior concerning her ill daughter. Helping the mother and daughter to differentiate and separate through a constructive noncritical approach to the presenting problems may be a crucial factor in breaking through the perpetuating cycle of criticism and illness.
On the case of Goryachev-Chaplygin and new examples of integrable conservative systems on S^2

The aim of this paper is to describe a class of conservative systems on $S^2$ possessing an integral cubic in momenta. We prove that this class of systems consists off the case of Goryachev-Chaplygin, the one-parameter family of systems which has been found by the author in the previous paper (dg-ga/9711005) and a new two-parameter family of conservative systems on $S^2$ possessing an integral cubic in momenta.
Phylogeography of Supralittoral Rocky Intertidal Ligia Isopods in the Pacific Region from Central California to Central Mexico

Background Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region. Methodology/Principal Findings We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland. Conclusions/Significance Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.
Knowledge, Attitudes and Practices Related to Visceral Leishmaniasis in Rural Communities of Amhara State: A Longitudinal Study in Northwest Ethiopia

Background In the northwest of Ethiopia, at the South Gondar region, there was a visceral leishmaniasis (VL) outbreak in 2005, making the disease a public health concern for the regional health authorities ever since. The knowledge on how the population perceives the disease is essential in order to propose successful control strategies. Methodology/Principal findings Two surveys on VL knowledge, attitudes and practices were conducted at the beginning (May 2009) and at the end (February 2011) of a VL longitudinal study carried out in rural communities of Libo Kemkem and Fogera, two districts of the Amhara Regional State. Results showed that VL global knowledge was very low in the area, and that it improved substantially in the period studied. Specifically, from 2009 to 2011, the frequency of proper knowledge regarding VL signs and symptoms increased from 47% to 71% (p<0.0001), knowledge of VL causes increased from 8% to 25% (p<0.0001), and knowledge on VL protection measures from 16% to 55% (p<0.0001). Moreover, the improvement observed in VL knowledge was more marked among the families with no previous history of VL case. Finally, in 2011 more than 90% of the households owned at least an impregnated bed net and had been sprayed, and attitudes towards these and other protective measures were very positive (over 94% acceptance for all of them). Conclusions/Significance In 2009 the level of knowledge regarding VL was very low among the rural population of this area, although it improved substantially in the study period, probably due to the contribution of many actors in the area. VL patients and relatives should be appropriately informed and trained as they may act as successful health community agents. VL risk behavioural patterns are subject to change as attitudes towards protective measures were very positive overall.
Character Networks and Book Genre Classification

We compared the social character networks of biographical, legendary and fictional texts in search for marks of genre differentiation. We examined the degree distribution of character appearance and found a power-law-like distribution that does not depend on the literary genre. We also analyzed local and global complex network measures, in particular, correlation plots between the recently introduced Lobby index and degree, betweenness and closeness centralities. Assortativity plots, which previous literature claims to separate fictional from real social networks, were also studied. We found no relevant differences among genres for the books studied when applying these network measures and we provide an explanation why the previous assortativity result is not correct.
The cell biology of leukocyte‐mediated proteolysis

Leukocyte‐derived proteinases have the capacity to degrade every component of the extracellular matrix, and thereby play fundamental roles in physiological processes. However, if the activity of these proteinases is uncontrolled or dysregulated, they have the capacity to contribute to tissue injury that potentially affects every organ in the body. Although there is a substantial literature on structure and activity of these proteinases when they are free in solution, until recently there has been little information about the cell biology of proteinases and their inhibitors. Recent studies, however, have identified several mechanisms by which inflammatory cells can degrade extracellular proteins in a milieu that contains high‐affinity proteinase inhibitors. J. Leukoc. Biol. 65: 137–150; 1999.
Provider perceptions of stigma and discrimination experienced by adolescents and young adults with pHiV while accessing sexual and reproductive health care

ABSTRACT Historically, children with perinatally-acquired HIV (PHIV) were viewed as the “innocent victims” as their HIV infection was not acquired through sexual/drug related means. Today, adolescents with PHIV are surviving into young adulthood and are engaging in developmentally expected behaviors such as establishing intimate, sexual relationships. Like other youth, those living with PHIV often need to access sexual and reproductive health (SRH) services. Previous research has documented stigma and discrimination experienced by adult women living with HIV as they try to access SRH care. However, little is known about the experiences of stigma and discrimination encountered by the maturing adolescents and young adults (AYA) with PHIV when accessing services. HIV health care providers (HHCPs) who frequently care for this population are in a unique position to learn about and understand the stigma and discrimination experienced by their patients in formal service settings. HHCPs (n = 57, 28 medical and 29 social service providers) were recruited using snowball sampling, and completed an online survey based on patient-shared experiences of stigma and discrimination when accessing SRH-related health care and social services. Thirty-eight percent (22/57) of providers reported that their patients with PHIV had shared encounters of stigma or discrimination when accessing SRH services. Coded open-ended provider comments indicated that AYA patients experienced challenges with providers who were unfamiliar with PHIV and expressed surprise that someone with PHIV was still alive. Analyses also revealed prejudicial attitudes towards women with HIV. Patients reported being counseled to terminate their pregnancy and lectured about their “poor choices. ” As AYA with PHIV transition out of pediatric and adolescent care, it is important for providers to simultaneously help them navigate care in other health settings, as well as educate adult health care providers about possible misconceptions of caring for individuals with PHIV.