Miracle-dz/UniFAR-FTUs huggingface dataset:
Object Type and Reification in Oracle

Resource Description Framework (RDF) is a standard for representing information that can be identified using a Universal Resource Identifier. In particular, it is intended for representing metadata about Web resources. RDF is being used in numerous application areas, including Life Sciences, Digital Libraries, and Intelligence. The RDF data structure is a directed graph or network. Current solutions to managing RDF data utilize flat relational tables for database storage. This paper presents an alternative approach to managing RDF data in the database. We introduce a new Oracle object type for storing RDF data. The object type is built on top of the Oracle Spatial Network Data Model (NDM), which is Oracle’s network solution in the database. This exposes the NDM functionality to RDF data, allowing RDF data to be managed as objects and analysed as networks. Reification, a means of providing metadata for the RDF data, puts a strain on storage. We present a streamlined approach to representing reified RDF data for faster retrievals. An RDF object type and reification in Oracle provide the basic infrastructure for effective metadata management.
Teaching Clinical Psychology Trainees about Weight Bias

Abstract As an assistant professor who teaches clinical psychology trainees about social aspects of behavior, I devote one week to the topic of weight bias. In this class, I rely on the research literature to challenge common myths about “obesity,” demonstrate the pervasiveness and harm of weight bias, and offer recommendations to trainees to apply to their own professional and personal lives. I encourage trainees to shift focus from weight and weight loss to health and well-being and to engage in self-reflection on the role of weight bias in their interactions with others. Here, I describe my weight bias seminar and outline common questions and my responses to them (e.g., Do you actually believe that “obese” people can be healthy? ). Weight bias is a neglected topic in most clinical psychology training programs. Weight bias must be addressed in clinical psychology programs to produce culturally competent graduates who are aware of diversity issues.
Real-time illumination estimation from faces for coherent rendering

We present a method for estimating the real-world lighting conditions within a scene in real-time. The estimation is based on the visual appearance of a human face in the real scene captured in a single image of a monocular camera. In hardware setups featuring a user-facing camera, an image of the user's face can be acquired at any time. The limited range in variations between different human faces makes it possible to analyze their appearance offline, and to apply the results to new faces. Our approach uses radiance transfer functions - learned offline from a dataset of images of faces under different known illuminations - for particular points on the human face. Based on these functions, we recover the most plausible real-world lighting conditions for measured reflections in a face, represented by a function depending on incident light angle using Spherical Harmonics. The pose of the camera relative to the face is determined by means of optical tracking, and virtual 3D content is rendered and overlaid onto the real scene with a fixed spatial relationship to the face. By applying the estimated lighting conditions to the rendering of the virtual content, the augmented scene is shaded coherently with regard to the real and virtual parts of the scene. We show with different examples under a variety of lighting conditions, that our approach provides plausible results, which considerably enhance the visual realism in real-time Augmented Reality applications.
Dihydropyridine actions on calcium currents of frog sympathetic neurons

Dihydropyridines (DHPs) generally have little effect on whole-cell calcium currents of neurons, even at concentrations far higher than those effective on muscle. Either neuronal calcium currents are much less sensitive to DHPs, or only a small proportion of the current is DHP-sensitive. We find that DHP agonists and antagonists act at low concentration on calcium currents in frog sympathetic neurons but that the effects are small even at optimal concentrations. The half-maximal dose (EC50) of the agonist Bay K 8644 is approximately 50 nM, and the effect of Bay K 8644 is blocked by 50% at approximately 300 nM nifedipine, from a holding potential of -80 mV. Nifedipine is more effective from a holding potential of -50 mV. These results suggest the presence of an L-type calcium current, with DHP sensitivity similar to L-currents in cardiac muscle. The predominant (greater than 90%) calcium current in frog sympathetic neurons is a DHP-resistant N-type current. However, high concentrations of DHPs (10 microM) partially block N-type calcium current, as well as voltage-dependent sodium and potassium currents.
Design methodology of low-power microprocessors

Low power is one of the most important targets of embedded microprocessor design. To reduce the dynamic power and static power, several design technologies applied in real microprocessors. But the term "low power" is not simple in real application. According to the system low power, many varieties of low power features are required for microprocessors. For example, an application processor for cellular phone was designed using many low-power technologies. Both device / circuits level and architecture / logic level low power technologies are discussed.
Stability of Lur'e systems with piecewise linear sector bounds

We consider the stability problem of Lur'e systems composed by a dynamical linear time invariant system closed in feedback through a static mapping belonging to a region bounded by piecewise linear characteristics. By exploiting the complementarity framework a model of the region expressed through constrained relations is obtained. Classical conic sectors representations can be derived as a particular case of the proposed model. The region representation is exploited to prove absolute stability of the Lur'e system in terms of cone-constrained linear matrix inequalities.
Effects on 4080 rats of chronic ingestion of N-nitrosodiethylamine or N-nitrosodimethylamine: a detailed dose-response study.

Four thousand eighty inbred rats were maintained from weaning on various different concentrations of N-nitrosodiethylamine (NDEA) or N-nitrosodimethylamine (NDMA). The principal aim was to characterize the dose-response relationship for the effects of these agents on esophageal cancer (NDEA) or on various types of liver cancer (NDEA and NDMA), although NDEA also caused a few tumors of the nasopharynx and NDMA also caused a few tumors of the lung. The numbers of tumors of mesenchymal and Kupffer cells in the liver were too few to allow easy characterization of the dose-response relationships, and although NDMA induced large numbers of bile duct neoplasms, NDEA did not. Thus, the four principal dose-response relationships studied were of NDEA on esophageal or liver cells and of NDMA on bile duct or liver cells. At doses sufficiently high for the median time to death from the disease of interest to be estimated, relationships were observed of the general form (Dose rate) x (median)n = constant where n was about 2.3 for the first three relationships and about 1 for the last one (NDMA on liver cell tumors). By contrast, at doses sufficiently low for longevity to be nearly normal (median survival about 2.5 years), there remained no material dependence on the dose rate of the age distribution of the induced neoplasms. At these low dose rates, the number of liver (but not of esophageal) neoplasms induced by treatment was simply proportional to the dose rate. This finding is not surprising, since the background incidence of liver (but not of esophageal) neoplasms was appreciable. The linear relationship observed at low dose rates (below 1 ppm) suggests that under these experimental conditions, among rats allowed to liver their natural life span, a dose of 1 ppm of NDEA or NDMA in the drinking water will cause about 25% to develop a liver neoplasm, a dose of 0.1 ppm will cause about 2.5% to do so, and a dose of 0.01 ppm will cause about 0.25% to do so, etc., with no indication of any "threshold. " (At these low dose rates, the incidence of liver neoplasms appears likely to exceed greatly that of esophageal neoplasms.) In addition, even quite low dose rates of the test agents caused a variety of nonneoplastic liver abnormalities (e.g., hyperplastic nodules, or shrinkage of hepatocytes) at a frequency roughly proportional to the dose rate.
Studying Production Phase SourceForge Projects : An Exploratory Analysis Using cvs 2 mysql and SFRA +

A wealth of data can be extracted from the natural byproducts of software development processes and used in empirical studies of software engineering. However, the size and accuracy of such studies depend in large part on the availability of tools that facilitate the collection of data from individual projects and the combination of data from multiple projects. To demonstrate this point, we present our experience gathering and analyzing data from nearly 10,000 open source projects hosted on SourceForge. We describe the tools we developed to collect the data and the ways in which these tools and data may be used by other researchers. We also provide examples of statistics that we have calculated from these data to describe interesting authorand project-level behaviors of the SourceForge community.
Cooperatively securing network coding against pollution attacks with incentive mechanism

The availability of network system with network coding can suffer from malicious nodes intentionally corrupt the encoded packets. The situation will get even worse when there are selfish nodes that are unwilling to take the measure of security mechanism. In such situation, selfish nodes should be motivated to follow the protocol, and malicious nodes need to be detected. We integrate an efficient Homomorphic MAC with a lightweight non-repudiation transmission protocol which can not only detect the corrupted packets but also locate the malicious nodes. In order to deal with the selfish behavior, we propose an incentive scheme which can encourage the nodes to follow the protocol faithfully and detect the pollution attacks. In addition, we analyze the relationship between security and parameters of the protocol, which can help to choose the better parameters the system requires. From the evaluated results, we can see that our design can effectively defense against pollution attacks in the system with network coding with high security and good performance.
On the use of a modified optical flow algorithm for the correction of axial strain estimates in ultrasonic elastography in medical diagnosis

Summary: We present a new system for imaging the elastic properties of prostate tissue in vivo by estimating, correcting, and visualizing the tissue strain from local axial time shift estimates. We show that the image quality of the strain images can be significantly improved by the correction of lateral motion components using a modified optical flow algorithm. Phantom images and clinical in vivo data are presented which show the high potential of the system for early tumor detection.
Multichannel audio rendering using amplitude panning [DSP Applications]

Spatial audio is a field that investigates techniques to reproduce spatial attributes of sound (e.g., direction, distance, width of sound sources, and room envelopment) to the listener. Such attributes cannot be reproduced accurately with one loudspeaker, therefore two-channel stereophony was introduced, later extended to different surround formats having five to eight loudspeakers. An even more accurate reproduction of spatial attributes can be achieved with loudspeaker setups often found in theaters and in some public venues, which contain a large number of loudspeakers around listeners, possibly also above and/or below them.
Rhetorical Figure Detection: the Case of Chiasmus

We propose an approach to detecting the rhetorical figure called chiasmus, which involves the repetition of a pair of words in reverse order, as in “all for one, one for all”. Although repetitions of words are common in natural language, true instances of chiasmus are rare, and the question is therefore whether a computer can effectively distinguish a chiasmus from a random criss-cross pattern. We argue that chiasmus should be treated as a graded phenomenon, which leads to the design of an engine that extracts all criss-cross patterns and ranks them on a scale from prototypical chiasmi to less and less likely instances. Using an evaluation inspired by information retrieval, we demonstrate that our system achieves an average precision of 61%. As a by-product of the evaluation we also construct the first annotated corpus of chiasmi.
Development of a Novel Plasmid-based Gene Integration System for Lactobacillus reuteri for the Persistent Treatment of Celiac Disease

Development of a Novel Plasmid-based Gene Integration System for Lactobacillus reuteri for the Persistent Treatment of Celiac Disease Jeremy LaBarge Celiac disease (CD) is an autoimmune disorder that affects approximately 1% of the population [55]. CD is characterized by intestinal villus atrophy after consumption of gluten from wheat, barley, or rye. Patients with CD often experience abdominal pain, diarrhea, malnutrition, fatigue, and a failure to thrive. There is currently no treatment for CD. Patients must live on a strict lifelong exclusion of dietary gluten. Due to the high content of gluten in western diets and poor labeling of gluten content, adherence to a gluten free diet (GFD) is difficult [15]. Nearly all the enzymes that can digest the gluten peptide are sensitive to the stomach’s low pH . As a result, dietary supplementation with enzymes to digest gluten has yet to produce a viable alternative treatment to a GFD. We propose to use a resident microbe of the human intestinal tract to express a peptidase to digest the immunoreactive gluten fragments. The bacteria, L. reuteri, will colonize the host’s intestines and digest the gluten peptides before causing an autoimmune response. To accomplish this task, this thesis describes a food grade, plasmid based system to integrate genes into the genome of L. reuteri. The plasmid system utilizes an origin of replication that requires a protein, RepA, to propagate itself. A helper plasmid provides the RepA protein in trans to an integration plasmid that cannot provide RepA to itself. The integration plasmid carries a homologous region to the genome of L. reuteri allowing for targeted genomic integration. The integration plasmid will not replicate on its own, and will be integrated into the genome if the helper plasmid is absent. To select for these genomic integrants the integration plasmid expresses an erythromycin resistance marker. Using the Cre/Lox system the antibiotic resistance will be removed from the bacterial genome to re-establish the L. reuteri’s food grade status. This thesis describes the construction and verification of the above mentioned plasmid tool kit containing the helper, integration, and Cre expression plasmids to integrate genes into the L. reuteri genome.
Relationship Mining Among the Entities Associated with GPCRs

G-protein-coupled receptors (GPCRs) share a characteristic core composed of seven-transmembrane α-helices represent by far the largest family of cell-surface molecules involved in signal transmission, accounting for ≫2% of the total genes encoded by the human genome. At present, most data types supplied by databases of GPCRs and relative proteins are mainly protein structure data, ligand binding data, interaction data of interactions with G-proteins and effectors, mutation data, sequence-derived data and protein family list. However, interaction data describe relationships of GPCRs related drugs and diseases are rare. We construct a measurement of relationships between GPCRs relative information based on calculating distances between entities (genes, diseases and drugs) in sentences of abstracts which are selected by key words “human” and nomenclatures of G-protein-coupled receptor and its family members. By using integrated method of distance measurement and mutual rank for relationship extraction, we obtain 88165 relationships and evaluate the result by randomly selected 700 sentences with an F-score of 67.58% and recall of 62.82%.
Supervised Learning Through Neuronal Response Modulation

Neural networks that are trained to perform specific tasks must be developed through a supervised learning procedure. This normally takes the form of direct supervision of synaptic plasticity. We explore the idea that supervision takes place instead through the modulation of neuronal excitability. Such supervision can be done using conventional synaptic feedback pathways rather than requiring the hypothetical actions of unknown modulatory agents. During task learning, supervised response modulation guides Hebbian synaptic plasticity indirectly by establishing appropriate patterns of correlated network activity. This results in robust learning of function approximation tasks even when multiple output units representing different functions share large amounts of common input. Reward-based supervision is also studied, and a number of potential advantages of neuronal response modulation are identified.
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA

MOTIVATION Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. RESULTS We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. AVAILABILITY AND IMPLEMENTATION https://zhanglab.ccmb. med.umich. edu/RNA-align/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Polymorphisms in the Toll-Like Receptor and the IL-23/IL-17 Pathways Were Associated with Susceptibility to Inflammatory Bowel Disease in a Danish Cohort

Background The inflammatory bowel diseases (IBD), Crohn’s disease (CD) and ulcerative colitis (UC), result from the combined effects of susceptibility genes and environmental factors. Previous studies have shown that polymorphisms in the Toll-like receptor (TLR), the apoptosis, the IL-23/IL-17 and the interferon gamma (IFNG) pathways are associated with risk of both CD and UC. Methods Using a candidate gene approach, 21 functional single nucleotide polymorphisms (SNPs) in 15 genes were assessed in a clinical homogeneous group of severely diseased ethnic Danish patients consisting of 624 patients with CD, 411 patients with UC and 795 controls. The results were analysed using logistic regression. Results The polymorphisms TLR5 (rs5744174) and IL12B (rs6887695) were associated with risk of CD, and TLR1 (rs4833095) and IL18 (rs187238) were associated with risk of both CD and UC (p<0.05). After Bonferroni correction for multiple testing, the homozygous variant genotype of TLR1 743 T>C (rs4833095) was associated with increased risk CD (OR: 3.15, 95% CI: 1.59–6.26, p = 0.02) and CD and UC combined (OR: 2.96, 95% CI: 1.64–5.32, p = 0.005). Conclusion Our results suggest that genetically determined high activity of TLR1 and TLR5 was associated with increased risk of both CD and UC and CD, respectively. This supports that the host microbial composition or environmental factors in the gut are involved in risk of IBD. Furthermore, genetically determined high activity of the IL-23/IL-17 pathway was associated with increased risk of CD and UC. Overall, our results support that genetically determined high inflammatory response was associated with increased risk of both CD and UC.
Overview of the TREC 2010 Session Track

Research in Information Retrieval has traditionally focused on serving the best results for a single query. In practice however users often enter queries in sessions of reformulations. The Sessions Track at TREC 2010 implements an initial experiment to evaluate the eectiveness of retrieval systems over single query reformulations. nd what they are looking for: early studies on web search query logs showed that half of all Web users reformulated their initial query: 52% of the users in 1997 Excite data set, 45% of the users in the 2001 Excite dataset (13). A search engine may be able to better serve a user not by ranking the most relevant results to each query in the sequence, but by ranking results that help \point the way" to what the user is really looking for, or by complementing results from previous queries in the sequence with new results, or in other currently-unanticipated ways. The standard evaluation paradigm of controlled laboratory experiments is unable to assess the eectiveness of