Miracle-dz/UniFAR-FTUs huggingface dataset:
Orion: A Software Project Search Engine with Integrated Diverse Software Artifacts

What projects contain more than 10, 000 lines of code developed by less than 10 people and are still actively maintained with a high bug-fixing rate? To address the challenges for answering such enquiries, we develop an integrated search engine architecture that combines information from different types of software repositories from multiple sources. Our search engine facilitates the construction and execution of complex search queries using a uniform interface that transparently correlates different artifacts of project development and maintenance, such as source code information, version control systems metadata, bug tracking systems elements, and metadata on developer activities and interactions extracted from hosting platforms. We have built an extensible system with an initial capability of over 100, 000 projects collected from the web, featuring various software development artifacts. Using scenarios, we illustrate the benefits of such a search engine for different kinds of project seekers.
Analysis of the Minimal Amyloid-forming Fragment of the Islet Amyloid Polypeptide

The development of type II diabetes was shown to be associated with the formation of amyloid fibrils consisted of the islet amyloid polypeptide (IAPP or amylin). Recently, a short functional hexapeptide fragment of IAPP (NH2-NFGAIL-COOH) was found to form fibrils that are very similar to those formed by the full-length polypeptide. To better understand the specific role of the residues that compose the fragment, we performed a systematic alanine scan of the IAPP “basic amyloidogenic units. ” Turbidity assay experiments demonstrated that the wild-type peptide and the Asn1 → Ala and Gly3 → Ala peptides had the highest rate of aggregate formation, whereas the Phe2 → Ala peptide did not form any detectable aggregates. Dynamic light-scattering experiments demonstrated that all peptides except the Phe2 → Ala form large multimeric structures. Electron microscopy and Congo red staining confirmed that the structures formed by the various peptides are indeed amyloid fibrils. Taken together, the results of our study provide clear experimental evidence for the key role of phenylalanine residue in amyloid formation by IAPP. In contrast, glycine, a residue that was suggested to facilitate amyloid formation in other systems, has only a minor role, if any, in this case. Our results are discussed in the context of the remarkable occurrence of aromatic residues in short functional fragments and potent inhibitors of amyloid-related polypeptides. We hypothesize that π-π interactions may play a significant role in the molecular recognition and self-assembly processes that lead to amyloid formation.
Real-Time Illumination Robust Maneuvering Target Tracking Based on Color Invariance

Illumination change is an important factor that affects the accuracy of tracking. In order to enhance the robustness against illumination changes in directions and intensities of the conventional tracking approaches, this paper proposes to apply color invariance theory to maneuvering target tracking. To depress the influence of the background, at the beginning of the process, we use expectation maximization algorithm based on Gaussian Mixture Model to extract the objects from the environment. Then, instead of using the gray space or RGB space, frames are transformed to color invariant space based on Kubelka-Munk model, followed by the implementation of conventional tracking approach such as mean shift or particle filtering to track the targets. Experimental results show that mean shift and improved particle filtering with color invariance can achieve 64.1 and 16.0 frames per second correspondingly, which is real-time, and the proposed approach improves the robustness of maneuvering targets tracking greatly.
The Impact of Questionnaire Design on Prevalence and Incidence Rates of Self-Reported Delinquency

Based on two samples of juveniles (total n = 1,629), this experimental study explores effects of modifying the design (not the wording) of a self-report questionnaire on prevalences and incidences of delinquency - the core instrument of the second International Self-Report Delinquency (ISRD-2) study. Research questions are: Do rates of self-reported delinquency differ by questionnaire design? Are there differences in item nonresponse? Do these effects differ by person characteristics, especially self-control? Do effect sizes of predictors of offending differ by questionnaire design? Omitting follow-up questions and reversing the response categories no/yes generates higher levels of self-reported delinquency as to minor offenses. Item nonresponse is affected by the design of filter questions and by person characteristics (e.g., low self-control) correlating with delinquency. Although the modifications reduce underreporting, effects of predictors on delinquency do not differ substantially. Nevertheless, more variance is explained using the modified version data.
Participants' Roles in the Context of a Video Club

This study examines the nature of teacher participation in the context of a video club. Video clubs are professional development meetings in which teachers watch and discuss excerpts of video from their classrooms. In this study, I adopt a situative perspective to examine how teachers develop in their participation to accomplish the goals of the video club. In particular, I examine the roles participants play and explore teachers' participation in four roles that correspond with key goals of the video club. Analysis revealed that teachers' participation shifted in qualitatively different ways over time, with the teachers coming to prompt the group to discuss student mathematical thinking, to propose a variety of interpretations of student ideas, to build on one another's ideas, and to challenge one another's thinking in order to advance the group's conversations. This analysis suggests that the group learned how to participate in roles central to accomplishing the goals of the video club. Studying teacher.
The use of ultrasonography in infantile hypertrophic pyloric stenosis: does the patient's age and weight affect pyloric size and pyloric ratio?

AIMS We aimed to obtain pyloric measurements of our patients with infantile hypertrophic pyloric stenosis (IHPS) using ultrasonography (US) and to evaluate the correlations between age, weight and pyloric size, pyloric ratio (PR). MATERIAL AND METHODS We designed a retrospective study including 20 term infants with surgically proven IHPS and studied the ultrasonographically obtained pyloric muscle thickness (PMT), pyloric diameter (width) (PD), pyloric length (PL) and PR (PMT/PD) to determine if there were statistically significant associations between patient age/weight and pyloric measurements. RESULTS The mean age of the infants was 38.7+/-17.3 days (range, 9-76 days) and their mean weight was 3688.5+/-772.7 g (range, 2810-6000 g), at referral. Mean PMT was 4.98+/-1.04 mm (range, 3.5-6.8 mm). Mean PD was 14.04+/-2.39 mm (range, 10-18 mm). Mean PL was 22.16+/-4.02 mm (range, 16-31.5 mm) and mean PR was 0.35+/-0.04 (range, 0.29-0.42). The correlation between age and PMT (r=0.654, p<0.05) and the correlation between age and PD (r=0.747, p <0.05) were significant. Age and weight were not significantly correlated with PR (p>0.05). CONCLUSIONS The PMT and PD are age dependent parameters. The PR is age and weight independent and therefore, when combined with PMT, PD and PL, it can be useful in the diagnosis of IHPS in infants with early onset disease and/or in those with a lower weight.
Efficacy and safety of colchicine for pericarditis prevention. Systematic review and meta-analysis

Objectives The purpose of this study was to investigate the efficacy and safety of colchicine for pericarditis prevention. Background Recurrent pericarditis prevention is a major management goal that may reduce morbidity and management costs. Although empiric anti-inflammatory therapy is considered the mainstay of treatment, no specific drug has been proven to be efficacious for prevention but colchicine. Methods Controlled clinical studies were searched in several databases and were included provided they focused on the pharmacologic primary or secondary prevention of pericarditis. We performed a meta-analysis including studies primary outcome, adverse events, and drug withdrawal. Results From the initial sample of 127 citations, five controlled clinical trials were finally included (795 patients): three studies were double-blind randomised controlled trials, and two studies were open-label randomised controlled trials. Trials followed patients for a mean of 13 months. Meta-analytic pooling showed that colchicine use was associated with a reduced risk of pericarditis during follow-up (RR=0.40, 95% CI 0.30 to 0.54, p for effect <0.001, p for heterogeneity = 0.95, I2=0%) either for primary or secondary prevention without a significant higher risk of adverse events compared with placebo (RR=1.22, 95% CI 0.71 to 2.10, p for effect 0.48, p for heterogeneity = 0.44, I2=0%), but more cases of drug withdrawals (RR=1.85, 95% CI 1.04 to 3.29, p for effect 0.04, p for heterogeneity = 0.42, I2=0%). Gastrointestinal intolerance is the most frequent side effect (mean incidence 8%), but no severe adverse events were recorded. Conclusions Available evidence suggests that colchicine is safe and efficacious for the primary and secondary prevention of pericarditis.
Nonparametric Function Estimation Using Overcomplete Dictionaries

We consider the problem of estimating an unknown function based on noisy data using nonparametric regression. One approach to this estimation problem is to represent the function in a series expansion using a linear combination of basis functions. Overcomplete dictionaries provide a larger, but redundant collection of generating elements than a basis, however, coefficients in the expansion are no longer unique. Despite the non-uniqueness, this has the potential to lead to sparser representations by using fewer non-zero coefficients. Compound Poisson random fields and their generalization to Lévy random fields are ideally suited for construction of priors on functions using these overcomplete representations for the general nonparametric regression problem, and provide a natural limiting generalization of priors for the finite dimensional version of the regression problem. While expressions for posterior modes or posterior distributions of quantities of interest are not available in closed form, the prior construction using Lévy random fields permits tractable posterior simulation via a reversible jump Markov chain Monte Carlo algorithm. Efficient computation is possible because updates based on adding/deleting or updating single dictionary elements bypass the need to invert large matrices. Furthermore, because dictionary elements are only computed as needed, memory requirements scale linearly with the sample size. In comparison with other methods, the Lévy random field priors provide excellent performance in terms of both mean squared error and coverage for out-of-sample predictions.
A Direct Interaction between the N Terminus of Adenylyl Cyclase AC8 and the Catalytic Subunit of Protein Phosphatase 2A

Although protein scaffolding complexes compartmentalize protein kinase A (PKA) and phosphodiesterases to optimize cAMP signaling, adenylyl cyclases, the sources of cAMP, have been implicated in very few direct protein interactions. The N termini of adenylyl cyclases are highly divergent, which hints at isoform-specific interactions. Indeed, the Ca2+-sensitive adenylyl cyclase 8 (AC8) contains a Ca2+/calmodulin binding site on the N terminus that is essential for stimulation of activity by the capacitative entry of Ca2+ in the intact cell. Here, we have used the N terminus of AC8 as a bait in a yeast two-hybrid screen of a human embryonic kidney (HEK) 293 cell cDNA library and identified the catalytic subunit of the serine/threonine protein phosphatase 2A (PP2AC) as a binding partner. Confirming the highly specific nature of this novel interaction, glutathione-S-transferase fusion proteins containing the full-length N terminus of AC8 affinity precipitated catalytically active PP2AC from both HEK293 and mouse forebrain membranes—the latter a normal source of AC8. The scaffolding subunit of PP2A (PP2AA; 65 kDa) was also precipitated by the N terminus of AC8, indicating that AC8 may occur in a complex with the PP2A core dimer. The interaction between the N terminus of AC8 and PP2AC was antagonized by Ca2+/calmodulin. However, PP2AC and Ca2+/calmodulin did not share identical binding specificities in the N terminus of AC8. PKA-mediated phosphorylation did not influence either calmodulin or PP2AC association with AC8. In addition, both PP2AC and AC8 occurred in lipid rafts. These findings are the first demonstration of an association between adenylyl cyclase and any downstream element of cAMP signaling.
Air-flow based multifunctional tactile display device with multi-jet integrated micro venturi nozzle array

In this paper, the first air-flow based multifunctional tactile display with 1-D mixed array of integrated air nozzles and multi-jet integrated micro venturi atomizers are presented. This device realizes simultaneous tactile presentation of “object surface shape” by distributed air-flow pressures and “sense of cold (cryesthesia)” by arrayed liquid mist injection. A new type venturi atomizer with multi jet structure was developed to control the mixture ratio of different liquids for temperature control. 2-D tactile display can be realized by simply stacking the 1-D array devices. Through the evaluations with fabricated devices, multifunctional and distributed tactile presentation has been successfully demonstrated for the first time.
A mammographic phantom image reconstruction through Monte Carlo techniques

Mammographic phantoms are employed during quality control test in breast screening locations and other health centres. These quality controls are performed to achieve the image quality required to detect breast abnormalities, ensuring the minimum risk to radiographied women. The aim of this study is the development of a methodology to reproduce the image of a mammogram during a routine exposure in a breast screening programme. In a first step, the CIRS 11A (MAMMO PHANTOM SP01) mammographic phantom has been simplified and modelled with the Monte Carlo transport code MCNP-4c2. Different tallies (F2 and F5) have been used to score the photon flux under the phantom, and a group of aluminium layers (99.9% purity) have been employed to reconstruct the characteristic curve, which transforms output air kerma in a grey-scale level. The code has been modified to produce photons in a semi-cone, allowing any polar and azimuthal angle. Furthermore, different tally bins have been introduced to count photons in each pixel of the final image, improving computer time simulations. The horizontal resolution target has been reproduced at different tube loadings and pixel pitches. The reconstructed images agree with the range of values, indicating that this method would be suitable for training purposes, phantom designing or dose calculations
Small-Cell Wireless Backhauling: A Non-Line-of-Sight Approach for Point-to-Point Microwave Links

In this paper we investigate the feasibility of using microwave frequencies for fixed non-line-of-sight wireless backhauling connecting small-cell radio base stations with an aggregation node in an outdoor urban environment, i.e. a typical heterogeneous network scenario. We study system level simulations for a point-to-point system where the wave propagation is based on diffraction over rooftops. We further investigate the effects of carrier frequency, interference, antenna height, rain, and tolerance to antenna alignment errors. It is found that the higher frequencies offer not only larger bandwidths but also higher antenna gains which would ideally work to their advantage. However, these advantages may be lost when taking antenna alignment errors and rain into account. Different frequencies simply have their different trade-offs.
Carbon Assimilation, Biomass Partitioning and Productivity in Grasses

Plant growth correlates with net carbon gain on a whole plant basis. Over the last several decades, the driving factors shaping plant morphology and performance have become increasingly clear. This review seeks to explore the importance of these factors for grass performance. Briefly, these fall into factors influencing photosynthetic rates directly, competition between plants in a canopy, and nutrient status and availability.
Combining Active Learning and Partial Annotation for Japanese Dependency Parsing

The machine learning-based approaches that dominate natural language processing research require massive amounts of labeled training data. Active learning has the potential to substantially reduce the human effort needed to prepare this data by allowing annotators to focus on only the most informative training examples. This paper shows how active learning can be used for domain adaptation of dependency parsers, and how entropy-based strategies can be used to select smaller units for annotation. We show how these strategies can be combined with partial annotation to annotate informative examples in the new domain without annotating full sentences. Research on active learning often uses simulations, but we measured the actual time needed by a human annotator for annotation work to better frame the results obtained in our simulations. We evaluate strategies based on both full and partial annotation in several domains, and find that they reduce the amount of in-domain training data needed for domain adaptation by up to 75% compared to random selection. While annotation speeds were similar for both, the proposed partial annotation strategy delivers better in-domain performance for the same amount of human effort.
The Acquisition of Simple and Complex Spatial Locatives in English: A Longitudinal Investigation

The emergence of simple and complex spatial locatives was investigated in six children learning English obtained from the CHILDES archives. We traced the emergence of 13 locative prepositions from the average age of 1;10 to 4;2. The locatives were as follows: (1) simple, in, on, into, onto, out of, off of, and (2) complex, across, along, around, through, deictic front, deictic back/behind, between. We determined the age of the initial occurrence and the age of the initial contrast with a related locative, e.g., into/onto and across/along. On average, the simple set emerged at 2;1 with minimal variability and maximal contrast, and the complex set at 3;4 with considerable variability and minimal contrast. The data were evaluated in the context of conceptual and linguistic factors.
Functional lung imaging using hyperpolarized gas MRI

The noninvasive assessment of lung function using imaging is increasingly of interest for the study of lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma. Hyperpolarized gas MRI (HP MRI) has demonstrated the ability to detect changes in ventilation, perfusion, and lung microstructure that appear to be associated with both normal lung development and disease progression. The physical characteristics of HP gases and their application to MRI are presented with an emphasis on current applications. Clinical investigations using HP MRI to study asthma, COPD, cystic fibrosis, pediatric chronic lung disease, and lung transplant are reviewed. Recent advances in polarization, pulse sequence development for imaging with Xe‐129, and prototype low magnetic field systems dedicated to lung imaging are highlighted as areas of future development for this rapidly evolving technology. J. Magn. Reson. Imaging 2007. © 2007 Wiley‐Liss, Inc.
Chlamydia pneumoniae Heat Shock Protein 60 Enhances Expression of ERK, TLR-4 and IL-8 in Atheromatous Plaques of Coronary Artery Disease Patients

Chlamydia pneumoniae heat shock protein (cHSP) 60 is produced during chronic chlamydial infection and activate innate immune and inflammatory responses thereby contributing to atherogenesis. However, to date there is no apparent signaling cascade delineated in human atherosclerotic plaques in C. pneumoniae positive coronary artery disease (CAD) patients. Atherosclerotic plaques were obtained from 40 CAD patients (28 men, 12 women) attending Department of Cardio Thoracic and Vascular Surgery Safdarjung Hospital, New Delhi. Atherosclerotic plaques were used for gene expression studies at RNA level by real-time PCR and to study expression of ERK1/2, JNK1/2, NF-kB, IkkB and MCP-1 at protein level by immunoblotting. Significantly higher (p < 0.001) RNA expression was found for IL-8, TLR-2/4, TGF-β, ICAM1, VCAM1 and MAPKinase genes, whereas significantly lower (p < 0.001) RNA expression for SMAD4, IkkB, BRCA1 and IL-10 was detected in cHSP60-positive atheromatous plaque of CAD patients. Moreover, at proteins level pERK1/2 (p = 0.05), NF-kB (p = 0.017), MCP-1 (p = 0.011) was higher and IkkB expression was lower (p = 0.038) in cHSP60-positive atheromatous plaque of CAD patients. This study by using human atheromatous plaques at RNA and protein levels demonstrated higher expression of TLR-2/4, IL-8, ICAM1, VCAM1, ERK1/2 and NF-kB in cHSP60-positive CAD patients.
A novel methodology for assignment of disulfide bond pairings in proteins

A novel methodology is described for the assignment of disulfide bonds in proteins of known sequence. The denatured protein is subjected to limited reduction by tris(2‐carboxyethyl)phosphine (TCEP) in pH 3.0 citrate buffer to produce a mixture of partially reduced protein isomers; the nascent sulfhydryls are immediately cyanylated by l‐cyano‐4‐dimethylamino‐pyridinium tetrafluoroborate (CDAP) under the same buffered conditions. The cyanylated protein isomers, separated by and collected from reversed‐phase HPLC, are subjected to cleavage of the peptide bonds on the N‐terminal side of cyanylated cysteines in aqueous ammonia to form truncated peptides that are still linked by residual disulfide bonds. The remaining disulfide bonds are then completely reduced to give a mixture of peptides that can be mass mapped by MALDI‐MS. The masses of the resulting peptide fragments are related to the location of the paired cysteines that had undergone reduction, cyanylation, and cleavage. A side reaction, β‐elimination, often accompanies cleavage and produces overlapped peptides that provide complementary confirmation for the assignment. This strategy minimizes disulfide bond scrambling and is simple, fast, and sensitive. The feasibility of the new approach is demonstrated in the analysis of model proteins that contain various disulfide bond linkages, including adjacent cysteines. Experimental conditions are optimized for protein partial reduction, sulfhydryl cyanylation, and chemical cleavage reactions.