Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy Promotes Intracellular Degradation of Type I Collagen Induced by Transforming Growth Factor (TGF)-β1*

Background: Autophagy is a process that cells use to degrade and recycle cellular proteins, however, the role of autophagy in kidney fibrosis remains largely unknown. Results: Autophagy is responsible for the intracellular degradation of type I collagen. Conclusion: Autophagy negatively regulates and prevents excess collagen accumulation in the kidney. Significance: Our findings implicate a novel role of autophagy as a cytoprotective mechanism against renal fibrosis. Autophagy is a highly conserved cellular process regulating turnover of cytoplasmic proteins via a lysosome-dependent pathway. Here we show that kidneys from mice deficient in autophagic protein Beclin 1 exhibited profibrotic phenotype, with increased collagen deposition. Reduced Beclin 1 expression, through genetic disruption of beclin 1 or knockdown by specific siRNA in primary mouse mesangial cells (MMC), resulted in increased protein levels of type I collagen (Col-I). Inhibition of autolysosomal protein degradation by bafilomycin A1 also increased Col-I protein levels and colocalization of Col-I with LC3, an autophagy marker, or LAMP-1, a lysosome marker, whereas treatment with TFP, an inducer of autophagy, resulted in decreased Col-I protein levels induced by TGF-β1, without alterations in Col-I α1 mRNA. Heterozygous deletion of beclin 1 increased accumulation of aggregated Col-I under nonstimulated conditions, and stimulation with TGF-β1 further increased aggregated Col-I. These data indicate that Col-I and aggregated, insoluble procollagen I undergo intracellular degradation via autophagy. A cytoprotective role of autophagy is implicated in kidney injury, and we demonstrate that low-dose carbon monoxide, shown to exert cytoprotection against renal fibrosis, induces autophagy to suppress accumulation of Col-I induced by TGF-β1. We also show that TGF-β1 induces autophagy in MMC via TAK1-MKK3-p38 signaling pathway. The dual functions of TGF-β1, as both an inducer of Col-I synthesis and an inducer of autophagy and Col-I degradation, underscore the multifunctional nature of TGF-β1. Our findings suggest a novel role of autophagy as a cytoprotective mechanism to negatively regulate and prevent excess collagen accumulation in the kidney.
Semantic web application generation using Protégé tool

In this paper we give details about the role of ontologies in Semantic Web and tools required for constructing Semantic Web applications. The Protégé tool for ontology development and knowledge acquisition can be adapted for editing models in different Semantic Web languages. In recent experiments to prototype the Semantic Web, members of different communities with different backgrounds have created a multitudinous of languages for representing ontologies and instance data on the Web. Typically, a Semantic Web language for describing ontologies and instance data contains a hierarchical description of important conceptual thing in a domain. Individuals in the domain are instances of these classes, and properties of each classes describes the various features and attributes of the concept. Logical statements describe relations among concepts. Protégé adopt the new world of the Semantic Web reusing its user interface, internal representation, and framework also it is useful in conceptual modeling with the new Semantic Web languages.
High Efficiency Interface for Coupling Into Slotted Photonic Crystal Waveguides

We investigate the mechanism of coupling light into slotted photonic crystal waveguides. We identify two alternative approaches for improving the coupling efficiency, based on engineered mode dispersion and on resonant mechanisms. For the optimized geometry, we calculate a loss figure of 0.3 dB over 100-nm bandwidth per interface and demonstrate a corresponding experimental value of 1.5 dB over 78-nm bandwidth per interface.
Health insurance coverage among foreign-born US residents: the impact of race, ethnicity, and length of residence.

OBJECTIVES This study examined the health insurance status of the US foreign-born population and the influence of race, ethnicity, and length of residence on health insurance status. METHODS Data were obtained from the 1989 and 1990 National Health Interview Surveys, including the Insurance and Family Resource Supplements. RESULTS In 1989 and 1990, the foreign-born population was twice as likely as the US-born population to be uninsured (26.2% vs 13.0%). The highest rate of uninsured status, 40.8%, was found among foreign-born Hispanics. Persons who had lived in the United States for less than 15 years were 1.5 to 4.7 times more likely to be uninsured than were US-born Whites. CONCLUSIONS Foreign-born US residents-especially Hispanics and persons residing in the United States for less than 15 years-are vulnerable to not having health insurance, which may limit their access to medical services. The administrative criteria for public programs may explain the high rates of uninsured status among recent immigrants. Recently enacted federal legislation could substantially increase the number of uninsured among the US foreign-born population, with profound public health implications.
Clinical Efficiency of Diffusion Weighted Imaging with Background Body Signal Suppression in Magnetic Resonance Mammography — Choosing a Qualitative or a Quantitative Approach

Objectives: Diffusion Weighted Imaging with Background Body Signal Suppression (DWIBS) is a new and promising imaging technique designed to improve diagnostic performance of Dynamic Contrast-Enhanced-Magnetic Resonance Mammography (DCE-MRM). The aim of our study was to assess the diagnostic efficiency of both qualitative and quantitative DWIBS in a retrospective cohort study. Methods: We performed a registry-based study at the Department of Radiology, Lyon Sud Hospital. All consecutive MRM examinations from 02.2010 to 02.2011 were reviewed. DWIBS was interpreted blindly, both qualitatively (lesion characteristics and signal) and quantitatively (Apparent Diffusion Coefficient – ADC). The ADC cut-off value was determined using Receiver Operating Characteristics (ROC) curve analysis. Clinical efficiency indicators were calculated using either the pathological examination or the disease status after a minimum of 6 months follow-up as gold standard. Results: The lot consisted of 78 women, with a mean age of 50.3±14 years and a total of 112 breast lesions. Qualitative DWIBS found 73 suspicious and 39 non-suspicious lesions, while the gold standard (pathological diagnosis/follow-up) reported 56 benign and 56 malignant ones. The sensitivity and specificity values for qualitative DWIBS were 84% and 53.37%, respectively. ROC curve analysis revealed the best performance for quantitative DWIBS at an ADC of 1.1×10-3 mm2/s, resulting in a sensitivity of 71.4% and a specificity of 76.8%. Conclusion: DWIBS is a new and improved diffusion technique with a dual and efficient interpretation system applicable in clinical settings. Moreover, its use as a complement to DCE-MRM offers large potential for improving MRM efficiency in breast cancer diagnosis.
A bandpass sigma&#8211;delta demodulator for digital radio

This paper describes a bandpass Sigma-Delta A/D converter for use in digital radio receivers for conversion of the IF signal. The architecture used is efficient in terms of silicon area usage and has improved performance over previous bandpass converters, allowing the IF to be at a higher frequency than the modulator clock rate. A chopping scheme is used to shift signals from the passband to DC and a lowpass modulator running at a decimated clockrate performs the A/D conversion. Simulation results, along with test results from an IC implementation of the converter, are presented to show the operation of the circuit and its use in radio receivers.
Implicit active contours for N-dimensional biomedical image segmentation

The segmentation of shapes from biomedical images has a wide range of uses such as image based modelling and bioimage analysis. In this paper, an active contour model is proposed for the segmentation of N-dimensional biomedical images. The proposed model uses a curvature smoothing flow and an image attraction force derived from the interactions between the geometries of the active contour model and the image objects. The active contour model is formulated using the level set method so as to handle topological changes automatically. The magnitude and orientation of the image attraction force is based on the relative geometric configurations between the active contour model and the image object boundaries. The vector force field is therefore dynamic, and the active contour model can propagate through narrow structures to segment complex shapes efficiently. The proposed model utilizes pixel interactions across the image domain, which gives a coherent representation of the image object shapes. This allows the active contour model to be robust to image noise and weak object edges. The proposed model is compared against widely used active contour models in the segmentation of anatomical shapes from biomedical images. It is shown that the proposed model has several advantages over existing techniques and can be used for the segmentation of biomedical images efficiently.
Characterization of Regions within the N-Terminal 6-Kilodalton Domain of Phytochrome A That Modulate Its Biological Activity

Phytochrome A (phyA) is a red/far-red (FR) light photoreceptor responsible for initiating numerous light-mediated plant growth and developmental responses, especially in FR light-enriched environments. We previously showed that the first 70 amino acids of the polypeptide contain at least two regions with potentially opposite functions (E.T. Jordan, J.R. Cherry, J.M. Walker, R.D. Vierstra [1996] Plant J 9: 243–257). One region is required for activity and correct apoprotein/chromophore interactions, whereas the second appears to regulate phytochrome activity. We have further resolved these functional regions by analysis of N-terminal deletion and alanine-scanning mutants of oat (Avena sativa) phyA in transgenic tobacco (Nicotiana tabacum). The results indicate that the region involved in chromophore/apoprotein interactions contains two separate segments (residues 25–33 and 50–62) also required for biological activity. The region that regulates phyA activity requires only five adjacent serines (Sers) (residues 8–12). Removal or alteration of these Sers generates a photoreceptor that increases the sensitivity of transgenic seedlings to red and FR light more than intact phyA. Taken together, these data identify three distinct regions in the N-terminal domain necessary for photoreceptor activity, and further define the Ser-rich region as an important site for phyA regulation.
Progression from childhood overweight to adolescent obesity in a large contemporary cohort.

CONTEXT The overweight - as distinct from obese - child is a potential target for obesity prevention interventions, on the assumption that overweight often progresses to obesity. However, there is limited empirical evidence on the probability that overweight progresses to obesity in contemporary children. Aim. To quantify progression from overweight to obesity in a large contemporary cohort of children. METHODS Changes in weight status were studied longitudinally in 7-year-olds (n=5 175) participating in the Avon Longitudinal Study of Parents and Children (ALSPAC), over a 6-year period. Obesity was defined as BMI z-score ≥1.64 and overweight defined as BMI z-score ≥1.04 but <1.64. RESULTS Adjusted odds ratio for progression to obesity at age 13 for overweight at age 7 was 18.1 (95% CI 12.8-25.6), and 34% of overweight children at age 7 became obese by age 13 years. CONCLUSIONS The present study could inform judgements as to the value of monitoring changes in weight status in overweight children, and the extent to which the overweight state might be a useful target of future obesity prevention interventions.
Generation of EBV-Specific CD4+ Cytotoxic T Cells from Virus Naive Individuals1

Adoptive immunotherapy with EBV-specific CTL (EBV-CTL) effectively prevents and treats EBV-driven lymphoproliferation in immunocompromised hosts. EBV-seronegative solid organ transplant recipients are at high risk of EBV-driven lymphoproliferation because they lack EBV-specific memory T cells. For the same reason, standard techniques for generating EBV-CTL in vitro from EBV-naive individuals are unsuccessful. To overcome this problem, we compared several methods of expanding EBV-CTL from seronegative adults and children. First, the standard protocol, using EBV-transformed lymphoblastoid B cell lines (LCL) as the source of APC, was compared with protocols using EBV-Ag-loaded dendritic cells as APC. Surprisingly, the standard protocol effectively generated CTL from all seronegative adults. The additional finding of EBV-DNA in the peripheral blood of three of these four adults suggested that some individuals may develop cellular, but not humoral, immune responses to EBV. By contrast, LCL failed to reactivate EBV-CTL from any of the six EBV-seronegative children. EBV-Ag-loaded dendritic cells could expand EBV-CTL, but only in a minority of children. However, the selective expansion of CD25-expressing T cells, 9–11 days after activation with LCL alone, proved to be a simple and reliable method for generating EBV-CTL from all seronegative children. The majority of these CTL were CD4+ (71 ± 26%) and demonstrated HLA class II-restricted, EBV-specific killing. Our results suggest that a negative EBV serology does not accurately identify EBV-negative individuals. In addition, our method for selecting EBV-specific CTL from naive individuals by precursor cell enrichment may be applicable to the immunotherapy of cancer patients with a low frequency of tumor- or virus-specific CTL.
Methodology of High-Level Transaction Level Modeling Using 802.11 PHY Example

In the paper, we introduce TLM methodology focusing on IEEE 802.11 WLAN as a derivative system. Decomposing the entire system into several computation components, we analyzed the property of each transaction, resulting in the TLM. In the case of shared bus, the simulation results show the effect of communication architecture such as bus protocol and bus parameters on the system performance.
Paravertebral block: cervical, thoracic, lumbar, and sacral

Purpose of review This article outlines the new developments around all four types of paravertebral block: cervical, thoracic, lumbar, and sacral. Recent findings It is emphasized that paravertebral blocks are all performed on the level of the roots of the nerves or plexuses, which are surrounded by dura mater extending from the dura mater surrounding the spinal cord. Because of this, they are all performed with essentially the same technique and they all have the same characteristics and problems associated with them, although they are called by many different names: ‘cervical paravertebral’ vs. ‘posterior approach’, ‘psoas compartment’ vs. ‘lumbar plexus block’ vs. ‘lumbar paravertebral block’, and so on. The knowledge that the roots are surrounded by dura and root level blocks are done just outside the dura should afford all paravertebral blocks the same respect as spinal epidural blocks because the potential of devastating complications such as intrathecal or intramedullary injection, for example, is shared. The advances in ultrasound and other novel approaches are described, yet the value of these has not been established. Summary We discuss commonality and differences between the four types of paravertebral blocks, and newer indications and concerns, especially pertaining to nerve microanatomical differences, are highlighted.
Bayesian Model Averaging of Named Entity Extraction Algorithms

Automatic information extraction (IE) has emerged as a critical tool for commercial, industrial, and governmental applications that are confronted with an explosive growth of digital information. Within the framework of information extraction a hierarchy of objectives exists, many of which are heavily dependent upon the automatic recognition of people, places, and organizations—or, more specifically, named entities—in text documents. In this paper, we present a probabilistic approach to aggregating the results of multiple existing entity extraction technologies. The key achievements presented include: (i) the ability to quantify uncertainty in individual extractors and their parameter estimates, and (ii) increased robustness to the over-fitting commonly observed when individual extractors are trained and evaluated on data from different sources By utilizing Bayesian Model Averaging (BMA), we develop a coherent, data-driven approach for estimating posterior distributions over extracted entities. We demonstrate our approach on several data sets widely used in named entity extraction. The results compare favorably to existing offthe-shelf approaches in traditional settings, as well as in settings where training data are not representative of data encountered under operational conditions.
Solving the Hamilton-Jacobi equation for general relativity.

We demonstrate a systematic method for solving the Hamilton-Jacobi equation for general relativity with the inclusion of matter fields. The generating functional is expanded in a series of spatial gradients. Each term is manifestly invariant under reparametrizations of the spatial coordinates ("gauge invariant"). At each order we solve the Hamiltonian constraint using a conformal transformation of the three-metric as well as a line integral in superspace. This gives a recursion relation for the generating functional which then may be solved to arbitrary order simply by functionally differentiating previous orders. At fourth order in spatial gradients we demonstrate solutions for irrotational dust as well as for a scalar field. We explicitly evolve the three-metric to the same order. This method can be used to derive the Zel'dovich approximation for general relativity.
Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter

ABSTRACT Gluconacetobacter strains are prominent bacteria during traditional vinegar fermentation. Here, we report a draft genome sequence of Gluconacetobacter sp. strain SXCC-1. This strain was isolated from a fermentation starter (Daqu) used for commercial production of Shanxi vinegar, the best-known vinegar of China.
The quality of three decision-analytic diabetes models: a systematic health economic assessment

Aims: Diabetes mellitus has important economic impacts worldwide. Interventions to prevent diabetes-related complications are often analyzed using model-based cost–effectiveness analyses. As model results are usually influenced by structural assumptions and by the data used, decision-makers should be able to assess the quality of diabetes models. The aim of this study was to assess the quality of selected diabetes models and to determine if modeling recommendations by the American Diabetes Association are considered. Methods: The quality of three selected diabetes models (Archimedes Model, CDC Model and Center for Outcomes Research [CORE] Diabetes Model) was assessed using systematic methods. Results: This systematic approach to assess model quality proved to be feasible and highlighted two areas for improvement: the rationale for model structure and methods to identify parameter values, which should be presented more transparently. Conclusions: Overall, the need for a quality assessment of diabetes models is emphasized.
Impact of the residue of Deltamethrin and Endosulfan pesticides on biochemical toxicity and some neurotransmitter contents in different brain areas of male Albino mice

Evaluating the action of the residues of pesticides on non-target organisms has been of interest to many researchers. The present study aimed to evaluate the pesticides deltamethrin and endosulfan on biochemical toxicity and some neurotransmitter contents in different brain areas of male albino mice. The results showed that the daily oral administration of deltamethrin and endosulfan caused a significant decrease in neurotransmitter contents (NE, DA and GABA) in most of the tested brain areas (cerebellum, striatum, cerebral cortex, hypothalamus, brain stem and hippocampus). On the other hand a gradual significant reduction, ALT, AST and ALP enzyme activities, while the glucose level and acid phosphatase increase were observed in serum of mice treated with deltamethrin and endosulfan for two weeks. Also, this study has a significant inhibition in the activities of enzymes in liver tissues of treated mice including glutathione reductase. Meanwhile, the activity of lipid peroxide, glycolytic (PK, PFK and GPI) and gluconeogenic enzyme activities (F-1, 6-D-Pase) were significantly increased in liver tissues of treated mice in response to treatment. Additionally, total protein and glycogen content showed a significant reduction in liver tissues of mice treated with deltamethrin and endosulfan for two weeks. It was concluded that the pollution of the aquatic environment by deltamethrin and endosulfan pesticides, would adversely affect the metabolism of the mice.
A heuristic evaluation to support the instructional and enjoyment aspects of a math game

Purpose The purpose of this paper is to provide information about the design principles of educational games in the context of an educational math game example to educational game developers and instructors. Especially, it tries to demonstrate the importance of the academic content-fantasy integration and entertainment factors of educational games from the viewpoint of the experts. For this purpose, as a sample, an educational math game was examined to see how successful is the academic aspect, fantasy aspect, academic-fantasy aspects integration and enjoyment aspect of the game. Good aspects of the game and aspects need improvement were summarized for guidance to game developers while producing educational games. Design/methodology/approach In this study, heuristic evaluation method was used for evaluating the educational math game. In the scope of this study, an example of modern educational computer game was examined by experts in this study. The integration of academic-fantasy context and enjoyment aspects of the game were analyzed deeply by using qualitative and quantitative data collection methods together. Findings According to Relevance Embedding Translation Adaptation Immersion and Naturalization rubric results, embedding element received the highest mean score. It showed that the academic content is well coupled with the fantasy/story content. According to GameFlow criteria, clear goals and feedback sections got the highest scores; on the contrary immersion section got the lowest score. Immersion element of the game should be improved. According to the interview findings, more than half of the participants stated that, in terms of academic content of game, players can actively be involved in learning process during the game. The story of the game and elements used in the game have counterpart in daily life. Didactic elements do not affect learners’ flow in the game. It is easy to learn and feedbacks are enough and useful. Originality/value This study offered suggestions to designers for developing good educational games which are well balanced with academic and fantasy context.
Rheumatoid Arthritis and Risk of Malignant Lymphoma: Is the Risk Still Increased?

Patients with rheumatoid arthritis (RA) are at increased risk of malignant lymphomas with a strong correlation with RA disease severity. Given the changes in RA therapy over recent decades, this study was undertaken to assess whether lymphoma risk remains increased, and if so, to explore risk predictors and lymphoma subtypes.