Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of IL-4 gene VNTR variant with deep venous thrombosis in Behçet’s disease and its effect on ocular involvement

Purpose Behçet’s disease (BD) is a systemic vasculitis characterized by inflammatory lesions of the urogenital mucosa, eyes, skin, central nervous system, and joints. Vein thrombosis constitutes the most frequent vascular manifestation of the disease, and may cause such ocular vascular thrombotic events as central retinal vein and central retinal artery thrombosis. Thrombosis is a serious problem, and often leads to irreversible vision loss. Previous studies have shown that genetic factors predispose individuals to BD. Several cytokine genes might play crucial roles in host susceptibility to BD and to thrombophilia. Various polymorphic regions of the interleukin-4 (IL-4) gene (−1098G and 590T) are associated with BD in the Turkish population. This study was conducted in Turkish patients with BD to determine the frequency of the IL-4 gene 70 bp variable number of tandem repeats (VNTR) variant, and its association with clinical findings. Methods Genomic DNA obtained from 488 individuals (238 patients with Behçet’s disease and 250 healthy controls) was used in the study. Genomic DNA was isolated and genotyped using PCR assay for the IL-4 gene 70 bp VNTR polymorphism determined by using PCR with the specific primers. Results There was statistical significance between the groups regarding IL-4 genotype distribution (p<0.001, odds ratio: 2.55 [1.629–4.052], 95% confidence interval) and allele frequencies (p<0.0012.381[1.586–3.617], 95% confidence interval). When we examined IL-4 genotype frequencies according to the clinical characteristics, we observed a statistically significant association between the P2P2 genotype and deep venous thrombosis (p=0.01). Deep venous thrombosis was also associated with ocular involvement in our study group (p=0.014). Conclusions Our findings suggest that the IL-4 gene 70 bp VNTR polymorphism is associated with susceptibility to development of BD. Deep venous thrombosis is also associated with ocular involvement in BD. The IL-4 gene could be a genetic biomarker in Behçet’s disease in a Turkish study population.
The chemical composition of donors in AM CVn stars and ultracompact X-ray binaries: observational tests of their formation

We study the formation of ultra-compact binaries (AM CVn stars and ultra-compact X-ray binaries) with emphasis on the surface chemical abundances of the donors in these systems. Hydrogen is not convincingly detected in the spectra of any these systems. Three different proposed formation scenarios involve different donor stars, white dwarfs, helium stars or evolved main-sequence stars. Using detailed evolutionary calculations we show that the abundances of helium white dwarf donors and evolved main-sequence stars are close to equilibrium CNOprocessed material, and the detailed abundances correlate with the core temperature and thus mass of the main-sequenceprogenitors. Evolved main-sequence donors typically have traces of H left. For hybrid or carbon/oxygen white dwarf donors, the carbon and oxygen abundances depend on the temperature of the helium burning and thus on the helium core mass of the progenitors. For helium star donors in addition to their mass, t he abundances depend strongly on the amount of helium burnt before mass transfer starts and can range from unprocessed and thus almost equal to CNO-processed matter, to strongly processed and thus C/O rich and N-deficient. We briefly discuss the relative frequency of the se cases for helium star donors, based on population synthesis results. Finally we give diagnostics for applying our results to observed systems and find that the most important test is the N /C ratio, which can indicate the formation scenario as well as, in some cases, the mass of the progenitor of the donor. In addition, if observed, the N/O, O/He and O/C ratios can distinguish between helium star and white dwarf donors. Applied to the known systems we find evide nce for white dwarf donors in the AM CVn systems GP Com, CE 315 and SDSS J0804+16 and evide nce for hybrid white dwarf or very evolved helium star donors in the ultra-compact X-ray binaries 4U 1626-67 and 4U 0614+09.
A Graph-Theoretic Analysis of Information Value

We derive qualitative relationships about the informational relevance of variables in graphical decision models based on a consideration of the topology of the models. Specifically, we identify dominance relations for the expected value of information on chance variables in terms of their position and relationships in influence diagrams. The qualitative relationships can be harnessed to generate nonnumerical procedures for ordering uncertain variables in a decision model by their informational relevance.
Regulation of Na+ channel inactivation by the DIII and DIV voltage-sensing domains

Functional eukaryotic voltage-gated Na+ (NaV) channels comprise four domains (DI–DIV), each containing six membrane-spanning segments (S1–S6). Voltage sensing is accomplished by the first four membrane-spanning segments (S1–S4), which together form a voltage-sensing domain (VSD). A critical NaV channel gating process, inactivation, has previously been linked to activation of the VSDs in DIII and DIV. Here, we probe this interaction by using voltage-clamp fluorometry to observe VSD kinetics in the presence of mutations at locations that have been shown to impair NaV channel inactivation. These locations include the DIII–DIV linker, the DIII S4–S5 linker, and the DIV S4-S5 linker. Our results show that, within the 10-ms timeframe of fast inactivation, the DIV-VSD is the primary regulator of inactivation. However, after longer 100-ms pulses, the DIII–DIV linker slows DIII-VSD deactivation, and the rate of DIII deactivation correlates strongly with the rate of recovery from inactivation. Our results imply that, over the course of an action potential, DIV-VSDs regulate the onset of fast inactivation while DIII-VSDs determine its recovery.
Intratumoral Epiregulin Is a Marker of Advanced Disease in Non–Small Cell Lung Cancer Patients and Confers Invasive Properties on EGFR-Mutant Cells

Non–small cell lung cancer (NSCLC) cells with activating epidermal growth factor receptor (EGFR) somatic mutations have unique biological properties, including high expression of the ErbB ligand epiregulin; however, the biological role of epiregulin in these cells has not been elucidated. To examine its role, we used an immunohistochemical approach to detect epiregulin expression in NSCLC biopsy samples and pharmacologic and genetic approaches to inhibit epiregulin in cultured NSCLC cells. In NSCLC biopsy samples, epiregulin was detected in 237 of 366 (64.7%) tumors, which correlated with nodal metastasis and a shorter duration of survival. In EGFR-mutant NSCLC cell lines, treatment with a small-molecule EGFR tyrosine kinase inhibitor diminished mRNA levels of the gene encoding epiregulin (EREG). The ability of EGFR-mutant NSCLC cells to invade through Matrigel in vitro was inhibited by treatment with an anti-epiregulin neutralizing antibody or by transfection with an EREG short hairpin RNA. Collectively, these findings show that epiregulin expression correlated with advanced disease, was EGFR dependent, and conferred invasive properties on NSCLC cells. Additional studies are warranted in NSCLC patients to evaluate whether epiregulin expression predicts the metastatic potential of primary tumors and whether anti-epiregulin treatment strategies are efficacious in the prevention of metastasis.
3D Axon Structure Extraction and Analysis in Confocal Fluorescence Microscopy Images

The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects.
Many‐valued Logic in Multistate and Vague Stochastic Systems

The state of the art in coherent structure theory is driven by two assertions, both of which are limiting: (1) all units of a system can exist in one of two states, failed or functioning; and (2) at any point in time, each unit can exist in only one of the above states. In actuality, units can exist in more than two states, and it is possible that a unit can simultaneously exist in more than one state. This latter feature is a consequence of the view that it may not be possible to precisely define the subsets of a set of states; such subsets are called vague. The first limitation has been addressed via work labeled ‘multistate systems’; however, this work has not capitalized on the mathematics of many‐valued propositions in logic. Here, we invoke its truth tables to define the structure function of multistate systems and then harness our results in the context of vagueness. A key contribution of this paper is to argue that many‐valued logic is a common platform for studying both multistate and vague systems but, to do so, it is necessary to lean on several principles of statistical inference.
THE ENTRY OF GRANULE-ASSOCIATED PEROXIDASE INTO THE PHAGOCYTIC VACUOLES OF EOSINOPHILS

The ultrastructural localization of peroxidase was studied in guinea pig eosinophils which had phagocytized zymosan or Escherichia coli. After phagocytosis, the membrane of the granule was joined to the membrane of the phagocytic vacuole, and the enzyme, which is ordinarily restricted to the matrix of the granule, was seen in the vacuole surrounding the ingested particle.
Integrating online and offline community through facebook

This paper presents an interview study of how social network communication media, Facebook specifically, can facilitate and influence proximal communities. We investigated scenarios in which users integrated their online interactions with offline activities. We found that Facebook heightened the visibility of social identities, but that these identities are multifaceted and dynamically modulated by context. We found that Facebook broadly facilitated offline activities from proposing and planning through to report and commenting. We found that people use Facebook features differentially as they maintain strong and weak ties. Finally we discussed how social identities, social engagements, and social ties are mutually reinforcing and cultivating with the affordances of Facebook.
Stability in Cognition Across Early Childhood

Children confront the formidable task of assimilating information in the environment and accommodating their cognitive structures to that information. Developmental science is concerned equally with two distinctive features of these processes: children's group mean level of performance through time and the standing of individual children through time. Prevailing opinion since the inception of the mental-measurement movement has been that individual development is unstable—that individual children change unpredictably in their abilities. We report results of a large-scale controlled, multivariate, prospective, microgenetic, 4-year longitudinal study that reveals a statistically significant cascade of species-typical cognitive abilities from infancy to childhood. Infancy is a recognizable starting point of life; we find that to a small but significant degree, infancy also represents a setting point in the life of the individual.
Supervised Learning of Semantic Classes for Image Annotation and Retrieval

A probabilistic formulation for semantic image annotation and retrieval is proposed. Annotation and retrieval are posed as classification problems where each class is defined as the group of database images labeled with a common semantic label. It is shown that, by establishing this one-to-one correspondence between semantic labels and semantic classes, a minimum probability of error annotation and retrieval are feasible with algorithms that are 1) conceptually simple, 2) computationally efficient, and 3) do not require prior semantic segmentation of training images. In particular, images are represented as bags of localized feature vectors, a mixture density estimated for each image, and the mixtures associated with all images annotated with a common semantic label pooled into a density estimate for the corresponding semantic class. This pooling is justified by a multiple instance learning argument and performed efficiently with a hierarchical extension of expectation-maximization. The benefits of the supervised formulation over the more complex, and currently popular, joint modeling of semantic label and visual feature distributions are illustrated through theoretical arguments and extensive experiments. The supervised formulation is shown to achieve higher accuracy than various previously published methods at a fraction of their computational cost. Finally, the proposed method is shown to be fairly robust to parameter tuning
Language abilities of children who stutter: a meta-analytical review.

PURPOSE To identify, integrate, and summarize evidence from empirical studies of the language abilities of children who stutter (CWS) and children who do not stutter (CWNS). METHOD Candidate studies were identified through electronic databases, the tables of contents of speech-language journals, and reference lists of relevant articles and literature reviews. The 22 included studies met the following criteria: studied both children who did and did not stutter between ages 2;0 (years;months) and 8;0, and reported norm-referenced language measures and/or measures from spontaneous language samples amenable to effect size calculation. Data were extracted using a coding manual and were assessed by application of general and specialized analytical software. Mean difference effect size was estimated using Hedges's g (Hedges, 1982). RESULTS Findings indicated that CWS scored significantly lower than CWNS on norm-referenced measures of overall language (Hedges's g = -0.48), receptive (Hedges's g = -0.52) and expressive vocabulary (Hedges's g = -0.41), and mean length of utterance (Hedges's g = -0.23). CONCLUSIONS Present findings were taken to suggest that children's language abilities are potentially influential variables associated with childhood stuttering.
Current Status of Herbal Medicines in Chronic Liver Disease Therapy: The Biological Effects, Molecular Targets and Future Prospects

Chronic liver dysfunction or injury is a serious health problem worldwide. Chronic liver disease involves a wide range of liver pathologies that include fatty liver, hepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. The efficiency of current synthetic agents in treating chronic liver disease is not satisfactory and they have undesirable side effects. Thereby, numerous medicinal herbs and phytochemicals have been investigated as complementary and alternative treatments for chronic liver diseases. Since some herbal products have already been used for the management of liver diseases in some countries or regions, a systematic review on these herbal medicines for chronic liver disease is urgently needed. Herein, we conducted a review describing the potential role, pharmacological studies and molecular mechanisms of several commonly used medicinal herbs and phytochemicals for chronic liver diseases treatment. Their potential toxicity and side effects were also discussed. Several herbal formulae and their biological effects in chronic liver disease treatment as well as the underlying molecular mechanisms are also summarized in this paper. This review article is a comprehensive and systematic analysis of our current knowledge of the conventional medicinal herbs and phytochemicals in treating chronic liver diseases and on the potential pitfalls which need to be addressed in future study.
Adherence to Glyburide and Metformin and Associated Factors in Type 2 Diabetes in Isfahan, Iran

The purpose of this study was to determine the adherence to oral hypoglycemic medications and associated factors in type 2 Diabetes Mellitus patients who were referred to the Isfahan Endocrinology and Metabolism Research Centre (IEMRC). Convenience sampling was used to enroll 248 patients with type 2 diabetes in a prospective study at IEMRC from January 2007 to January 2008. Patients had to be on a stable dose of oral hypoglycemic medications (glyburide and metformin) or for 3 months prior to the study and willing to participate in consultation sessions with a pharmacist. Pill count and self report methods were used to measure the adherence. Mean (SD) of patients studied was 56.6 (8.9) years and 62% were females. The mean (SD) duration of diabetes in the study patients was 10.8 (6.1) years and 81.9% of them were literate with basic education. Non-adherence rates to metformin and glyburide were recorded in 39.7% and 35.3% of the study population respectively. Lower HbA1C levels and higher education were associated with higher adherence rates. Forgetfulness, confusion, fasting, adverse effects, complexity of medication regimen and disruption of routines were most commonly reported causes of non adherence. Prevalence of adherence to these two medications did not differ significantly between pill count (62.3%) and self report (62.8%), (p >0.05). Adherence rates did not vary by pill count and self report significantly. It was concluded that good adherence to medications was associated with a lower HbA1C profile; so it seems that pill count is a useful method in the clinical practice to identify non-adherent patients. Further studies are needed to find out efficient interventions to improve the patient’s adherence.
The Case for Data Visualization Management Systems

Most visualizations today are produced by retrieving data from a database and using a specialized visualization tool to render it. This decoupled approach results in significant duplication of functionality, such as aggregation and filters, and misses tremendous opportunities for cross-layer optimizations. In this paper, we present the case for an integrated Data Visualization Management System (DVMS) based on a declarative visualization language that fully compiles the end-to-end visualization pipeline into a set of relational algebra queries. Thus the DVMS can be both expressive via the visualization language, and performant by lever-aging traditional and visualization-specific optimizations to scale interactive visualizations to massive datasets.
Vocal tract normalization equals linear transformation in cepstral space

Vocal tract normalization (VTN) is a widely used speaker normalization technique which reduces the effect of different lengths of the human vocal tract and results in an improved recognition accuracy of automatic speech recognition systems. We show that VTN results in a linear transformation in the cepstral domain, which so far have been considered as independent approaches of speaker normalization. We are now able to compute the Jacobian determinant of the transformation matrix, which allows the normalization of the probability distributions used in speaker-normalization for automatic speech recognition. We show that VTN can be viewed as a special case of Maximum Likelihood Linear Regression (MLLR). Consequently, we can explain previous experimental results that improvements obtained by VTN and subsequent MLLR are not additive in some cases. For three typical warping functions the transformation matrix is calculated analytically and we show that the matrices are diagonal dominant and thus can be approximated by quindiagonal matrices.
Implementation of a High-Throughput Screen for Identifying Small Molecules to Activate the Keap1-Nrf2-ARE Pathway

Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor that induces a battery of cytoprotective genes involved in antioxidant defense through binding to Antioxidant Response Elements (ARE) located in the promoter regions of these genes. To identify Nrf2 activators for the treatment of oxidative/electrophilic stress-induced diseases, the present study developed a high-throughput assay to evaluate Nrf2 activation using AREc32 cells that contain a luciferase gene under the control of ARE promoters. Of the 47,000 compounds screened, 238 (top 0.5% hits) of the chemicals increased the luminescent signal more than 14.4-fold and were re-tested at eleven concentrations in a range of 0.01–30 µM. Of these 238 compounds, 231 (96%) increased the luminescence signal in a concentration-dependent manner. Chemical structure relationship analysis of these 231 compounds indicated enrichment of four chemical scaffolds (diaryl amides and diaryl ureas, oxazoles and thiazoles, pyranones and thiapyranones, and pyridinones and pyridazinones). In addition, 30 of these 231 compounds were highly effective and/or potent in activating Nrf2, with a greater than 80-fold increase in luminescence, or an EC50 lower than 1.6 µM. These top 30 compounds were also screened in Hepa1c1c7 cells for an increase in Nqo1 mRNA, the prototypical Nrf2-target gene. Of these 30 compounds, 17 increased Nqo1 mRNA in a concentration-dependent manner. In conclusion, the present study documents the development, implementation, and validation of a high-throughput screen to identify activators of the Keap1-Nrf2-ARE pathway. Results from this screening identified Nrf2 activators, and provide novel insights into chemical scaffolds that might prevent oxidative/electrophilic stress-induced toxicity and carcinogenesis.