Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerating cross-project knowledge collaboration using collaborative filtering and social networks

Vast numbers of free/open source software (F/OSS) development projects use hosting sites such as Java.net and Source-Forge.net. These sites provide each project with a variety of software repositories (e.g. repositories for source code sharing, bug tracking, discussions, etc.) as a media for communication and collaboration. They tend to focus on supporting rich collaboration among members in each project. However, a majority of hosted projects are relatively small projects consisting of few developers and often need more resources for solving problems. In order to support cross-project knowledge collaboration in F/OSS development, we have been developing tools to collect data of projects and developers at SourceForge, and to visualize the relationship among them using the techniques of collaborative filtering and social networks. The tools help a developer identify "who should I ask? " and "what can I ask? " and so on. In this paper, we report a case study of applying the tools to F/OSS projects data collected from SourceForge and how effective the tools can be used for helping cross-project knowledge collaboration.
Feasibility of T-cell receptor gamma (TCRgamma) gene rearrangement on formalin-fixed, paraffin-embedded tissues by PCR assays.

INTRODUCTION T- and B-lymphocytes are involved in recognition of foreign antigen by the specificity of their surface T-cell receptor and immunoglobulin, generated by gene rearrangement. Each T- and B-lymphocyte carries unique rearranged TCR or immunoglobulin gene, which has been applied to detect clonal from non-clonal T- and B-cell proliferation. METHODS Paraffin-embedded biopsy tissues of 85 T-, 24 B-cell non-Hodgkin's lymphomas (NHL) of various subtypes, and seven reactive lymphoid hyperplasia were retrieved from the archives for determining the feasibility of TCRgamma gene rearrangement analysis by PCR assays in our laboratory. DNA was extracted by Proteinase K digestion. The analyses were performed by five PCR assays, and analysed on polyacrylamide gel. RESULTS Clonal TCRgamma gene rearrangement was demonstrated in 69/85 (81.2%) of the cases. Selective rearrangement of specific Vgamma segment was observed, especially in peripheral T-cell lymphoma-unspecified and nasal NK/T-cell lymphoma. Clonal TCRgamma rearranged band was also demonstrated in 4/24 (16.7%) and 2/7 (28.6%) of B-NHL and reactive lymphoid tissues respectively. CONCLUSION PCR assays were able to demonstrate clonal TCRgamma gene rearrangement in a high proportion of T-NHL. However, the PCR results should be interpreted carefully. A neoplasm should only be considered as T-cell type if it does not express any B-cell marker because TCRgamma is not lineage specific as shown by the presence of clonal TCRgamma gene rearrangement in B-NHL. Hence, the results for TCR gene rearrangement should always be interpreted in conjunction with histology and immunophenotyping.
Increased role of peripheral vision in self-induced motion in patients with age-related macular degeneration.

PURPOSE The contribution of peripheral vision in inducing self-motion (vection) was investigated in people with bilateral age-related macular degeneration (AMD). METHODS Eleven patients with bilateral AMD and dense central scotomas with no islands of functional central retina and 12 age-matched control subjects were exposed to random-dot patterns projected on a large screen. The dots either moved from left to right, inducing linear vection, or rotated about the roll axis, inducing roll vection. Latency, total vection time, and objective and subjective measures of tilt were recorded. RESULTS The patients with AMD experienced shorter latencies than did the age-matched control participants, but the total vection time in both conditions and tilt during roll vection were the same in both groups. There was a positive correlation between objective tilt and subjective measures of tilt in the AMD, but not in the age-matched control group. There was a negative relationship between absolute scotoma size and latency. CONCLUSIONS Two main conclusions were drawn. First, the role of peripheral vision in inducing vection is enhanced in people with bilateral central vision loss. Second, people with bilateral AMD adapt successfully to a moving environment (they do not experience vection longer, nor do they tilt more) and are more aware of their postural position than are age-matched control subjects.
M-PPM noncoherent receivers for UWB applications

The paper investigates ultra-wideband receivers for applications in sensor and control networks, M-ary pulse position modulation is considered and the detector operates with no knowledge of the channel response. It is shown that the optimum decision rule consists of comparing the signal energies received in the M possible pulse positions in a symbol interval and deciding for that position corresponding to the maximum energy. Simple synchronization algorithms are proposed and their performance is assessed by simulation over realistic multipath channels. The algorithms are non-data-aided (blind) and have a feedback structure in which the error signal is based on energy measurements from the received waveform. The receiver performance degradations due to timing errors are found to be marginal
Diagnose breast cancer through mammograms, using image processing techniques and optimization techniques

Microcalcifications are one of the key symptoms facilitating early detection of breast cancer. In this paper, The textural features are extracted from the segmented mammogram image to classify the microcalcifications into benign, malignant or normal. The reduced features are selected from the extracted set of features using reduction algorithms. Initially the reduced features are normalized between zero and one. The normalized feature values are given as input to a three-layer BPN to classify the microcalcifications into benign, malignant or normal. The network is trained to produce the output value 0.9 for malignant, 0.5 for benign and 0.1 for normal images. The BPN classifier is validated using ten fold validation Method. A Receiver Operating Characteristics (ROC) analysis is performed to evaluate the classification performances of the proposed approaches. The area under the ROC curve is used as a measure of the classification performance and it is denoted by Az. A larger value of Az indicates better classification performance. The proposed system is tested on 161 pairs of digitized mammograms from the MIAS database to establish its competence
Organization of local horizontal functional interactions between neurons in the inferior temporal cortex of macaque monkeys.

Detailed knowledge of neuronal circuitry is necessary for understanding the mechanisms underlying information processing in the brain. We investigated the organization of horizontal functional interactions in the inferior temporal cortex of macaque monkeys, which plays important roles in visual object recognition. Neuronal activity was recorded from the inferior temporal cortex using an array of eight tetrodes, with spatial separation between paired neurons up to 1.4 mm. We evaluated functional interactions on a time scale of milliseconds using cross-correlation analysis of neuronal activity of the paired neurons. Visual response properties of neurons were evaluated using responses to a set of 100 visual stimuli. Adjacent neuron pairs tended to show strong functional interactions compared with more distant neuron pairs, and neurons with similar stimulus preferences tended to show stronger functional interactions than neurons with different stimulus preferences. Thus horizontal functional interactions in the inferior temporal cortex appear to be organized according to both cortical distances and similarity in stimulus preference between neurons. Furthermore, the relationship between strength of functional interactions and similarity in stimulus preference observed in distant neuron pairs was more prominent than in adjacent pairs. The results suggest that functional circuitry is specifically organized, depending on the horizontal distances between neurons. Such specificity endows each circuit with unique functions.
Cystathionine Beta-Synthase (CBS) Contributes to Advanced Ovarian Cancer Progression and Drug Resistance

Background Epithelial ovarian cancer is the leading cause of gynecologic cancer deaths. Most patients respond initially to platinum-based chemotherapy after surgical debulking, however relapse is very common and ultimately platinum resistance emerges. Understanding the mechanism of tumor growth, metastasis and drug resistant relapse will profoundly impact the therapeutic management of ovarian cancer. Methods/Principal Findings Using patient tissue microarray (TMA), in vitro and in vivo studies we report a role of of cystathionine-beta-synthase (CBS), a sulfur metabolism enzyme in ovarian carcinoma. We report here that the expression of cystathionine-beta-synthase (CBS), a sulfur metabolism enzyme, is common in primary serous ovarian carcinoma. The in vitro effects of CBS silencing can be reversed by exogenous supplementation with the GSH and H2S producing chemical Na2S. Silencing CBS in a cisplatin resistant orthotopic model in vivo by nanoliposomal delivery of CBS siRNA inhibits tumor growth, reduces nodule formation and sensitizes ovarian cancer cells to cisplatin. The effects were further corroborated by immunohistochemistry that demonstrates a reduction of H&E, Ki-67 and CD31 positive cells in si-RNA treated as compared to scrambled-RNA treated animals. Furthermore, CBS also regulates bioenergetics of ovarian cancer cells by regulating mitochondrial ROS production, oxygen consumption and ATP generation. This study reports an important role of CBS in promoting ovarian tumor growth and maintaining drug resistant phenotype by controlling cellular redox behavior and regulating mitochondrial bioenergetics. Conclusion The present investigation highlights CBS as a potential therapeutic target in relapsed and platinum resistant ovarian cancer.
A feasibility study of interstitial hyperthermia plus external beam radiotherapy in glioblastoma multiforme using the multi electrode current source (MECS) system

Purpose: Thermoradiotherapy has been shown in several randomized trials to increase local control compared to radiotherapy alone. The first randomized study of interstitial hyperthermia in glioblastoma multiforme showed a survival benefit for hyperthermia, though small. Improvement of the heating technique could lead to improved results. The purpose of this feasibility study is to present the clinical and thermal data of application of an improved interstitial hyperthermia system. Methods and materials: Six patients with a glioblastoma multiforme were treated with interstitial hyperthermia using the Multi Electrode Current Source Interstitial Hyperthermia (MECS-IHT) system. The MECS-IHT system has the capability of spatial monitoring of temperature and individually steering of heating electrodes. Three sessions were given aiming at a steady state temperature of 42°C for 1 h, with an interval of 3–4 days, during an external irradiation scheme of 60 Gy in 6 weeks. Hyperthermia was delivered with a mean of 10 catheters, 18 heating electrodes and 38 thermal probes per patient. Results: Sub-optimal temperatures were encountered in the first two patients leading to adjustments in technique thereafter with subsequent improvement of thermal data. With a catheter spacing of 11–12 mm, measurements yielded a mean T90, T50 and T10 of 39.9, 43.7 and 45.2°C, respectively, over three sessions in the last patient. The power per electrode to reach this temperature distribution varied from 25–100% of full power in each of the last four patients. Thermal data were reproducible over the three sessions. Acute toxicity was minimal. Conclusions: Despite the spatial steering capabilities of the MECS-IHT system, a large temperature heterogeneity was encountered. The heterogeneity was the reason to limit the catheter spacing to 11–12 mm, thus making only small tumour volumes feasible for interstitial heating.
Phosphorylated FTY720 promotes astrocyte migration through sphingosine‐1‐phosphate receptors

Sphingosine‐1‐phosphate (S1P) receptors are widely expressed in the central nervous system where they are thought to regulate glia cell function. The phosphorylated version of fingolimod/FTY720 (FTY720P) is active on a broad spectrum of S1P receptors and the parent compound is currently in phase III clinical trials for the treatment of multiple sclerosis. Here, we aimed to identify which cell type(s) and S1P receptor(s) of the central nervous system are targeted by FTY720P. Using calcium imaging in mixed cultures from embryonic rat cortex we show that astrocytes are the major cell type responsive to FTY720P in this assay. In enriched astrocyte cultures, we detect expression of S1P1 and S1P3 receptors and demonstrate that FTY720P activates Gi protein‐mediated signaling cascades. We also show that FTY720P as well as the S1P1‐selective agonist SEW2871 stimulate astrocyte migration. The data indicate that FTY720P exerts its effects on astrocytes predominantly via the activation of S1P1 receptors, whereas S1P signals through both S1P1 and S1P3 receptors. We suggest that this distinct pharmacological profile of FTY720P, compared with S1P, could play a role in the therapeutic effects of FTY720 in multiple sclerosis.
Eating Behavior and Gastric Emptying in Adults with Prader-Willi Syndrome

Background/Aims: Prader-Willi syndrome (PWS) is a complex genetic disorder characterized by distinctive physical, behavioral and psychiatric features. One cardinal symptom is excessive eating, often leading to extreme obesity. The etiology of the hyperphagia is unknown, but eating behaviors and gastrointestinal motility could play a pivotal role. In this pilot study, we therefore sought to give a closer description of the two. Methods: 12 PWS adults, 6 men and 6 women, 17–37 years of age with a median BMI of 34.9 were evaluated. Computerized monitoring of eating behavior and assessment of gastric emptying using paracetamol absorption were analyzed. Gastric emptying rate was compared to the rate in normal and obese controls. Results: Eating behavior pattern was nonhomogeneous in the PWS patients, but they experienced both hunger and satiation. In PWS gastric emptying was similar to lean subjects (p > 0.05), but longer than in obese subjects (p < 0.05). Conclusions: Despite obesity, this group of adults with PWS did not display overeating in the test situation and gastric emptying rate was normal. Numbers are small, but the results are important for the treatment of obesity in this special group of patients.
Multivariate examination of data from gait analysis of persons with stroke.

BACKGROUND AND PURPOSE Gait analyses yield redundant information that often is difficult to interpret. The purpose of this study was to show how principal-component analysis can provide insight into gait data obtained from persons with stroke. SUBJECTS Twenty male and 11 female adults who were ambulatory were studied (mean age = 60.5 years, SD = 11.8, range = 24-79; mean time since stroke = 11.4 months, SD = 15.4, range = 2.0-88.0). METHODS Spatial data were used in a 4-segment link-segment model to calculate the kinematic and kinetic variables of gait. Principal components were constructed on the averages for 40 variables. RESULTS The first principal component was related to speed and accounted for 40.8% of the variance. The second principal component was related to differences between the 2 limbs (symmetry) and accounted for 12.8% of the variance. The third principal component was related to adoption of a postural flexion bias and accounted for 10.2% of the variance. The fourth principal component, which was not interpretable, accounted for 6.8% of the variance. CONCLUSION AND DISCUSSION The principal-component analysis allowed clustering of related variables and simplified the complex picture presented by the large number of variables resulting from gait analysis. Examination of variables closely related to each principal component yielded insight into the nature of the strategies used in walking and their interrelationships. The method has potential for insight into similarities and differences in gait performances arising from different pathologies and for comparing the progress of individuals with similar pathologies.
Learning by appraising: an emotion-based approach to intrinsic reward design

In this paper, we investigate the use of emotional information in the learning process of autonomous agents. Inspired by four dimensions that are commonly postulated by appraisal theories of emotions, we construct a set of reward features to guide the learning process and behaviour of a reinforcement learning (RL) agent that inhabits an environment of which it has only limited perception. Much like what occurs in biological agents, each reward feature evaluates a particular aspect of the (history of) interaction of the agent history with the environment, thereby, in a sense, replicating some aspects of appraisal processes observed in humans and other animals. Our experiments in several foraging scenarios demonstrate that by optimising the relative contributions of each reward feature, the resulting “emotional” RL agents perform better than standard goal-oriented agents, particularly in consideration of their inherent perceptual limitations. Our results support the claim that biological evolutionary adaptive mechanisms such as emotions can provide crucial clues in creating robust, general-purpose reward mechanisms for autonomous artificial agents, thereby allowing them to overcome some of the challenges imposed by their inherent limitations.
Osseous reaction to implantation of two endodontic cements: Mineral trioxide aggregate (MTA) and calcium enriched mixture (CEM)

Aim: The aim of the present in vivo study was to determine bone tissue reaction to calcium enriched mixture (CEM) and mineral trioxide aggregate (MTA) using a rat femur model. Study Design: Sixty-three rats were selected and randomly divided into three groups of 21 each [experimental groups (n=15), control (n=6)]. Implantation cavities were prepared in each femoral bone and randomly filled with the biomaterials only in the experimental groups. The animals in three groups were sacrificed 1, 4, and 8 weeks postoperatively. Histologic evaluations comprising inflammation severity and new bone formation were blindly made on H&E-stained decalcified 6-µm sections. Results: At 1, 4, and 8 weeks after implantation number of inflammatory cells had decreased in the CEM, MTA and control groups, respectively, with no statistically significant differences. Conversely, new bone formation had increased in all the experimental and control groups, without statistically significant differences. Conclusion: The results suggest that biocompatibility of MTA, as gold standard, and CEM cement as a new endodontic biomaterial are comparable Key words:Endodontics, MTA,CEM, osseous reaction.
Analysis of multi-path routing

In connection-oriented networks, resource reservations must be made before data can be sent along a route. For short or bursty connections, a selected route must have the required resources to ensure appropriate communication with regard to desired quality-of-service (QoS). For example, in ATM networks, the route setup process considers only links with sufficient resources and reserves these resources while it advances toward the destination. The same concern for QoS routing appears in datagram networks such as the Internet, when applications with QoS requirements need to reserve resources along pinned routes. In this paper, we analyze the performance of multi-path routing algorithms and compare them to single-path reservation that might be persistent, i.e., retry after a failure. The analysis assumes that the routing process reserves resources while it advances toward the destination, thus there is a penalty associated with a reservation that cannot be used. Our analysis shows that while multi-path reservation algorithms perform comparably to single-path reservation algorithms, either persistent or not, the connection-establishment time for multi-path reservation is significantly lower. Thus, multi-path reservation becomes an attractive alternative for interactive applications such as World Wide Web browsing.
Screening of lactic acid bacteria from vacuum packaged beef for antimicrobial activity

The objective of this study was to isolate lactic acid bacteria (LAB) from vacuum packaged beef and to investigate their antagonist activity. LAB mean counts of 5.19 log cfu/cm2 were obtained from five samples of vacuum packaged beef. Two hundred isolates were selected and screened for the inhibitory effect on five ATCC reference Lactobacillus strains. Thirty six isolates showed activity in the agar spot test against at least two of the indicator strains. However, only six cell free supernatants (CFS) from these isolates exhibited activity against the indicator strains using the well-diffusion test and conditions that eliminated the effects of organic acids and hydrogen peroxide. L. acidophilus was the most sensitive indicator tested, whereas L. plantarum and L. fermentum were the most resistant ones. Identification by MIDI system indicated that these LAB isolates were Lactococcus lactis subsp. cremoris, Pediococcus acidilactici, Lactobacillus delbrueckii subsp. bulgaricus and Lactobacillus casei GC subgroup A. The antagonistic factors produced by most of these LAB against L. acidophilus were resistant to heat treatment (100°C for 10 min) and stable over a wide pH range (4.0 to 9.0). These data suggest that these isolates could be used as promising hurdles aiming increased safety and extended shelf life of meat products.
Multiscale approach including microfibril scale to assess elastic constants of cortical bone based on neural network computation and homogenization method

The complexity and heterogeneity of bone tissue require a multiscale modeling to understand its mechanical behavior and its remodeling mechanisms. In this paper, a novel multiscale hierarchical approach including microfibril scale based on hybrid neural network (NN) computation and homogenization equations was developed to link nanoscopic and macroscopic scales to estimate the elastic properties of human cortical bone. The multiscale model is divided into three main phases: (i) in step 0, the elastic constants of collagen‐water and mineral‐water composites are calculated by averaging the upper and lower Hill bounds; (ii) in step 1, the elastic properties of the collagen microfibril are computed using a trained NN simulation. Finite element calculation is performed at nanoscopic levels to provide a database to train an in‐house NN program; and (iii) in steps 2–10 from fibril to continuum cortical bone tissue, homogenization equations are used to perform the computation at the higher scales. The NN outputs (elastic properties of the microfibril) are used as inputs for the homogenization computation to determine the properties of mineralized collagen fibril. The mechanical and geometrical properties of bone constituents (mineral, collagen, and cross‐links) as well as the porosity were taken in consideration. This paper aims to predict analytically the effective elastic constants of cortical bone by modeling its elastic response at these different scales, ranging from the nanostructural to mesostructural levels. Our findings of the lowest scale's output were well integrated with the other higher levels and serve as inputs for the next higher scale modeling. Good agreement was obtained between our predicted results and literature data. Copyright © 2013 John Wiley & Sons, Ltd.