Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Aryl Hydrocarbon Receptor as a Putative Wnt/β-Catenin Pathway Target Gene in Prostate Cancer Cells

Recent genetic and functional analyses have implicated the wnt/β-catenin signaling pathway in prostate cancer (CaP) pathogenesis. Thus, there is much interest in understanding the consequences of wnt signaling in CaP; target gene expression is one important area of inquiry and is the focus of this report. Adenoviral-mediated overexpression of a mutant, hyperactive form of β-catenin in CWR22-Rv1 CaP cells led to increased aryl hydrocarbon receptor (AhR, or dioxin receptor) and transmembrane protein 2 RNA transcript expression, as detected by cDNA-microarray analyses. Validating these results, reverse transcription-PCR assays demonstrated that in CWR22-Rv1 cells as well as in LAPC-4 CaP cells, increased putative target gene RNA expression occurs with transient overexpression of mutant β-catenin, treatment of cells with lithium chloride, or with wnt3a-conditioned medium, three distinct modes of experimental wnt/β-catenin pathway activation. This β-catenin-associated expression of AhR and transmembrane protein 2 does not require de novo protein synthesis and may only involve a certain subset of CaP cell lines. Western and immunofluorescence analyses were undertaken to assess the relationship between the wnt/β-catenin-stimulated increase in AhR transcripts and AhR protein expression; we provide evidence that an association exists whereby up-regulation of AhR RNA by wnt or β-catenin is coupled with augmented AhR protein levels. Intriguingly, these studies also demonstrated that nuclear β-catenin staining may not be a sole deciding factor when predicting the status of wnt/β-catenin signaling in CaP cells. Finally, the extent to which wnt signaling may synergize with an environmental agonist of AhR (2,3,7,8-tetrachlorodibenzo-p-dioxin) to potentiate AhR transcriptional activity was examined. Considering previous work linking AhR to processes of development and carcinogenesis, our data may highlight one particular role for wnt/β-catenin signaling in prostate tumor biology.
Binge Eating Disorder Mediates Links between Symptoms of Depression, Anxiety, and Caloric Intake in Overweight and Obese Women

Despite considerable comorbidity between mood disorders, binge eating disorder (BED), and obesity, the underlying mechanisms remain unresolved. Therefore, the purpose of this study was to examine models by which internalizing behaviors of depression and anxiety influence food intake in overweight/obese women. Thirty-two women (15 BED, 17 controls) participated in a laboratory eating-episode and completed questionnaires assessing symptoms of anxiety and depression. Path analysis was used to test mediation and moderation models to determine the mechanisms by which internalizing symptoms influenced kilocalorie (kcal) intake. The BED group endorsed significantly more symptoms of depression (10.1 versus 4.8, P = 0.005 ) and anxiety (8.5 versus 2.7, P = 0.003). Linear regression indicated that BED diagnosis and internalizing symptoms accounted for 30% of the variance in kcal intake. Results from path analysis suggested that BED mediates the influence of internalizing symptoms on total kcal intake (empirical P < 0.001 ). The associations between internalizing symptoms and food intake are best described as operating indirectly through a BED diagnosis. This suggests that symptoms of depression and anxiety influence whether one engages in binge eating, which influences kcal intake. Greater understanding of the mechanisms underlying the associations between mood, binge eating, and food intake will facilitate the development of more effective prevention and treatment strategies for both BED and obesity.
The cognitive neuroscience of autism

The non-motor manifestations of essential tremor may be important The paper in this issue by Chatterjee et al (page 958)1 is the first large cross sectional study of personality in people with essential tremor compared with a control group. This careful study showed higher scores in the essential tremor group on the transdimensional personality questionnaire (TPQ) in the domain of harm avoidance—implying a personality with increased levels of pessimism, fearfulness, shyness, and anxiety, and easy fatigability. Essential tremor is the commonest movement disorder seen in clinical practice and has hitherto been considered a pure motor disorder without evidence of neuronal degeneration or widespread changes in the central nervous system. The age specific prevalence is reported to be between 1% and 3% of the general population. It is often given the prefix “benign,” which is unfortunate as many affected individuals have physical, social, and psychological handicaps, and some are totally disabled.2 As with essential tremor, the …
Continuum percolation in two dimensions: Monte Carlo tests of scaling and universality for non-interacting discs

Detailed results are reported for the connectivity properties of a system of discs of unit radius free to be situated anywhere within a square of area 2L2. Ordinary lattke percolation would correspond to the discs being situated on the vertices of a J2L x J2L lattice. Computer simulations are carried out for a sequence of increasing system sizes ranging from L = 20 to L = 1000; for each value of L a large number of realisations are generated for 25 values of the disc concentration x. We calculate a variety of estimates for the threshold parameter x,, as well as the critical exponents p, y, T and v. Our exponent estimates are in close agreement with accepted values for ordinary lattice percolation; therefore, this continuum system appears to be in the same 'universality class' as lattice percolation.
Down-regulation of Cholesterol 7α-Hydroxylase (CYP7A1) Gene Expression by Bile Acids in Primary Rat Hepatocytes Is Mediated by the c-Jun N-terminal Kinase Pathway*

Cholesterol 7α-hydroxylase (CYP7A1), the rate-limiting enzyme in the neutral pathway of bile acid biosynthesis, is feedback-inhibited at the transcriptional level by hydrophobic bile acids. Recent studies show that bile acids are physiological ligands for farnesoid X receptor (FXR). Activated FXR indirectly repressesCYP7A1 transcription through induction of small heterodimer protein (SHP-1). In this study, we provide evidence that bile acids rapidly down-regulate CYP7A1 transcription via activation of the JNK/c-Jun pathway. Furthermore, we demonstrate that SHP-1 is also a direct target of activated c-Jun. In primary rat hepatocyte cultures, taurocholate (TCA) strongly activated JNK in a time- and concentration-dependent manner. Tumor necrosis factor-α, a potent activator of JNK, also rapidly activated JNK and down-regulated CYP7A1 mRNA levels. Overexpression of dominant-negative JNK1 or a transactivating domain mutant of c-Jun significantly blocked the ability of TCA to down-regulateCYP7A1 mRNA. In contrast, overexpression of wild-type c-Jun (c-Junwt) enhanced the repression ofCYP7A1 by TCA. Moreover, overexpression of c-Junwt resulted in increased SHP-1 promoter activity. Mutation of a putative AP-1 (c-Jun) element suppressed c-Jun-mediated activation of the SHP-1 promoter construct. These results indicate that the bile acid-activated JNK pathway plays a pivotal role in regulatingCYP7A1 levels in primary rat hepatocytes.
Auditory speech recognition and visual text recognition in younger and older adults: similarities and differences between modalities and the effects of presentation rate.

PURPOSE To examine age-related differences in auditory speech recognition and visual text recognition performance for parallel sets of stimulus materials in the auditory and visual modalities. In addition, the effects of variation in rate of presentation of stimuli in each modality were investigated in each age group. METHOD A mixed-model design was used in which 3 independent groups (13 young adults with normal hearing, 10 elderly adults with normal hearing, and 16 elderly hearing-impaired adults) listened to auditory speech tests (a sentence-in-noise task, time-compressed monosyllables, and a speeded-spelling task) and viewed visual text-based analogs of the auditory tests. All auditory speech materials were presented so that the amplitude of the speech signal was at least 15 dB above threshold through 4000 Hz. RESULTS Analyses of the group data revealed that when baseline levels of performance were used as covariates in the group analyses the only significant group difference was that both elderly groups performed worse than the young group on the auditory speeded-speech tasks. Analysis of individual data, using correlations, factor analysis, and linear regression, was generally consistent with the group data and revealed significant, moderate correlations of performance for similar tasks across modalities, but stronger correlations across tasks within a modality. This suggests that performance on these tasks was mediated both by a common underlying factor, such as cognitive processing, as well as modality-specific processing. CONCLUSION Performance on measures of auditory processing of speech examined here was closely associated with performance on parallel measures of the visual processing of text obtained from the same participants. Young and older adults demonstrated comparable abilities in the use of contextual information in each modality, but older adults, regardless of hearing status, had more difficulty with fast presentation of auditory speech stimuli than young adults. There were no differences among the 3 groups with regard to the effects of presentation rate for the visual recognition of text, at least for the rates of presentation used here.
Pesticide use and adult-onset asthma among male farmers in the Agricultural Health Study

Although specific pesticides have been associated with wheeze in farmers, little is known about pesticides and asthma. Data from 19,704 male farmers in the Agricultural Health Study were used to evaluate lifetime use of 48 pesticides and prevalent adult-onset asthma, defined as doctor-diagnosed asthma after the age of 20 yrs. Asthma cases were categorised as allergic (n = 127) and nonallergic (n = 314) based on their history of eczema or hay fever. Polytomous logistic regression, controlling for age, state, smoking and body mass, was used to assess pesticide associations. High pesticide exposure events were associated with a doubling of both allergic and nonallergic asthma. For ever-use, 12 individual pesticides were associated with allergic asthma and four with nonallergic asthma. For allergic asthma, coumaphos (OR 2.34; 95% CI 1.49–3.70), heptachlor (OR 2.01; 95% CI 1.30–3.11), parathion (OR 2.05; 95% CI 1.21–3.46), 80/20 mix (carbon tetrachloride/carbon disulfide) (OR 2.15; 95% CI 1.23–3.76) and ethylene dibromide (OR 2.07; 95% CI 1.02–4.20) all showed ORs of >2.0 and significant exposure–response trends. For nonallergic asthma, DDT (dichlorodiphenyltrichloroethane) showed the strongest association (OR 1.41; 95% CI 1.09–1.84), but with little evidence of increasing asthma with increasing use. Current animal handling and farm activities did not confound these results. There was little evidence that allergy alone was driving these associations. In conclusion, pesticides may be an overlooked contributor to asthma risk among farmers.
Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells

Spatially distinct gene expression profiles in neural stem cells (NSCs) are a prerequisite to the formation of neuronal diversity, but how these arise from the regulatory interactions between chromatin accessibility and transcription factor activity has remained unclear. Here, we demonstrate that, despite their distinct gene expression profiles, NSCs of the mouse cortex and spinal cord share the majority of their DNase I hypersensitive sites (DHSs). Regardless of this similarity, domain-specific gene expression is highly correlated with the relative accessibility of associated DHSs, as determined by sequence read density. Notably, the binding pattern of the general NSC transcription factor SOX2 is also largely cell type specific and coincides with an enrichment of LHX2 motifs in the cortex and HOXA9 motifs in the spinal cord. Interestingly, in a zebrafish reporter gene system, these motifs were critical determinants of patterned gene expression along the rostral-caudal axis. Our findings establish a predictive model for patterned NSC gene expression, whereby domain-specific expression of LHX2 and HOX proteins act on their target motifs within commonly accessible cis-regulatory regions to specify SOX2 binding. In turn, this binding correlates strongly with these DHSs relative accessibility—a robust predictor of neighboring gene expression.
The Mannose Receptor Mediates the Uptake of Diverse Native Allergens by Dendritic Cells and Determines Allergen-Induced T Cell Polarization through Modulation of IDO Activity

The mannose receptor (MR) is a C-type lectin expressed by dendritic cells (DCs). We have investigated the ability of MR to recognize glycosylated allergens. Using a gene silencing strategy, we have specifically inhibited the expression of MR on human monocyte-derived DCs. We show that MR mediates internalization of diverse allergens from mite (Der p 1 and Der p 2), dog (Can f 1), cockroach (Bla g 2), and peanut (Ara h 1) through their carbohydrate moieties. All of these allergens bind to the C-type lectin-like carbohydrate recognition domains 4–7 of MR. We have also assessed the contribution of MR to T cell polarization after allergen exposure. We show that silencing MR expression on monocyte-derived DCs reverses the Th2 cell polarization bias, driven by Der p 1 allergen exposure, through upregulation of IDO activity. In conclusion, our work demonstrates a major role for MR in glycoallergen recognition and in the development of Th2 responses.
Validation and verification of simulation models

This paper discusses validation and verification of simulation models. The different approaches to deciding model validity are presented; how model validation and verification relate to the model development process are discussed; various validation techniques are defined; conceptual model validity, model verification, operational validity, and data validity are described; ways to document results are given; and a recommended procedure is presented.
Antibacterial Activity of Some Selected Seaweeds from Pudumadam Coastal Regions

The antibacterial activities of four important seaweeds namely Ulva lactuca, Padina gymnospora, Sargassum wightii and Gracilaria edulis were screened against human bacterial pathogens Staphylococcus aureus, Vibrio cholerae, Shigella dysentriae, Shigella bodii, Salmonella paratyphi, Pseudomonas aeruginosa and Klebsiella pneumonia. The maximum activity (8.8 mm) was recorded from the extract of G. edulis against S. aureus and minimum (1.2 mm) by U. lactuca against P. aeruginosa. The H-NMR analysis 1 revealed the presence of signals corresponding to poly unsaturated esters in Sargassum wightii and Gracilaria edulis and poly saturated alcohols in Padina gymnospora.
Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level.
A Survey of Glove-Based Systems and Their Applications

Hand movement data acquisition is used in many engineering applications ranging from the analysis of gestures to the biomedical sciences. Glove-based systems represent one of the most important efforts aimed at acquiring hand movement data. While they have been around for over three decades, they keep attracting the interest of researchers from increasingly diverse fields. This paper surveys such glove systems and their applications. It also analyzes the characteristics of the devices, provides a road map of the evolution of the technology, and discusses limitations of current technology and trends at the frontiers of research. A foremost goal of this paper is to provide readers who are new to the area with a basis for understanding glove systems technology and how it can be applied, while offering specialists an updated picture of the breadth of applications in several engineering and biomedical sciences areas.
Simultaneous recordings of oesophageal acid exposure with conventional pH monitoring and a wireless system (Bravo)

Objectives: Oesophageal pH monitoring is a useful test for the diagnosis of gastro-oesophageal reflux disease (GORD) but has some limitations related to the nasopharyngeal electrode. Recently, a telemetric catheter free system (CFS) (Bravo; Medtronic) was developed. The aim of this study was to determine the concordance of data between the conventional pH measurement system (CPHMS) and the CFS Bravo. Methods: Forty patients with symptoms suggestive of GORD underwent 24 hour oesophageal pH monitoring using the CPHMS with a nasopharyngeal electrode and the Bravo CFS simultaneously. The sensitive tips of both electrodes were positioned at the same level under fluoroscopy. In addition to automatic analysis, each reflux episode was checked visually and characterised. Results: There was a significant correlation (r = 0.87, p<0.0001) between the 24 hour oesophageal acid exposures recorded by the CPHMS and the CFS. Twenty four hour oesophageal acid exposure was significantly lower with the CFS than with the CPHMS (2.4 (0.4–8.7) v 3.6 (0.7–8.6); p< 0.0001). Consequently, with the CFS, the cut off level for the diagnosis of GORD, as calculated from the regression equation, was 2.9% (for the 4.2% cut off determined in controls with the CPHMS). After this adjustment, concordance of the diagnosis of GORD was 88% (kappa 0.760). Diagnosis of GORD was established in more patients with the CFS 48 hour results than with the 24 hour results. Conclusions: Despite strong correlations between oesophageal acid exposure recorded with the two devices, the Bravo CFS significantly under recorded acid exposure compared with the CPHMS. Provided some correcting factors are used, the Bravo CFS can improve the sensitivity of pHmetry for the diagnosis of GORD by allowing more prolonged recordings.
Vacua of M theory and string theory

We argue that supersymmetric higher-dimension operators in the effective actions of M theory and type IIB string theory do not affect the maximally supersymmetric vacua: AdS{sub 4}{times}S{sup 7} and AdS{sub 7}{times}S{sup 4} in M theory and AdS{sub 5}{times}S{sup 5} in type IIB string theory. All these vacua are described in superspace by a fixed point with all components of supertorsion and supercurvature being supercovariantly constant. This follows from 32 unbroken supersymmetries and allows us to prove that such vacua are exact. {copyright} {ital 1998} {ital The American Physical Society}
Comparison of Apical Extrusion of Debris by Using Single-File, Full-Sequence Rotary and Reciprocating Systems

Objectives: During root canal preparation, apical extrusion of debris can cause inflammation, flare-ups, and delayed healing. Therefore, instrumentation techniques that cause the least extrusion of debris are desirable. This study aimed to compare apical extrusion of debris by five single-file, full-sequence rotary and reciprocating systems. Materials and Methods: One hundred twenty human mandibular premolars with similar root lengths, apical diameters, and canal curvatures were selected and randomly assigned to six groups (n=20): Reciproc R25 (25, 0.08), WaveOne Primary (25, 0.08), OneShape (25, 0.06), F360 (25, 0.04), Neoniti A1 (25, 0.08), and ProTaper Universal. Instrumentation of the root canals was performed in accordance with the manufacturers’ instructions. Each tooth's debris was collected in a pre-weighed vial. After drying the debris in an incubator, the mass was measured three times consecutively; the mean was then calculated. The preparation time by each system was also measured. For data analysis, one-way ANOVA and Games-Howell post hoc test were used. Results: The mean masses (±standard deviation) of the apical debris were as follows: 2.071±1.38mg (ProTaper Universal), 1.702±1.306mg (Neoniti A1), 1.295±0.839mg (OneShape), 1.109±0.676mg (WaveOne), 0.976±0.478mg (Reciproc) and 0.797±0.531mg (F360). Compared to ProTaper Universal, F360 generated significantly less debris (P=0.02). The ProTaper system required the longest preparation time (mean=88.6 seconds); the Reciproc (P=0.008), OneShape (P=0.006), and F360 (P=0.001) required significantly less time (P<0.05). Conclusions: All instruments caused extrusion of debris through the apex. The F360 produced significantly less debris than did the ProTaper Universal.
Enumerating exceptional collections of line bundles on some surfaces of general type

We use constructions of surfaces as abelian covers to write down exceptional collections of line bundles of maximal length for every surface X in certain families of surfaces of general type with pg = 0 and K 2 = 3,4,5,6,8. We also compute the algebra of derived endomorphisms for an appropriately chosen exceptional collection, and the Hochschild cohomology of the corresponding quasiphantom category. As a consequence, we see that the subcategory generated by the exceptional collection does not vary in the family of surfaces. Fi- nally, we describe the semigroup of effective divisors on each surface, answering a question of Alexeev.