Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying fault prone modules: an empirical study in telecommunication system

Telecommunication systems are becoming more dependent on software-intensive products and systems. Poor software quality can threaten safety, risk a company's business, or alienate potential customers. It is no longer acceptable to ignore software quality until just prior to a product's release. This study identifies troublesome modules in a large telecommunication system. For this, we propose the software metrics of the CHILL language, which are used to develop the telecommunication software. We present the identification method of fault-prone software modules of telecommunication software using neural networks. We investigate the relationship between the proposed metrics and the change request frequency of software modules which are found during the development phase. Using the neural network model, we classify software modules as either fault prone or not fault prone based on the proposed metrics. We obtained the experimental results that the total fitting rate of 52 testing data sets was 96.2%. Therefore, for newly added software modules, we can predict whether the software module is fault prone or not.
Spectral Alignment of Networks

Network alignment refers to the problem of nding a bijective mapping across vertices of two graphs to maximize the number of overlapping edges and/or to minimize the number of mismatched interactions across networks. This problem arises in many elds such as computational biology, social sciences and computer vision and is often cast as an expensive quadratic assignment problem (QAP). Although spectral methods have received signicant attention in dierent network science problems such as network clustering, the use of spectral techniques in the network alignment problem has been limited partially owing to the lack of principled connections between spectral methods and relaxations of the network alignment optimization. In this paper, we propose a network alignment framework that uses an orthogonal relaxation of the underlying QAP in a maximum weight bipartite matching optimization. Our method takes into account the ellipsoidal level sets of the quadratic objective function by exploiting eigenvalues and eigenvectors of (transformations of) adjacency graphs. Our framework not only can be employed to provide a theoretical justication for existing heuristic spectral network alignment methods, but it also leads to a new scalable network alignment algorithm which outperforms existing ones over various synthetic and real networks. Moreover, we generalize the objective function of the network alignment problem to consider both matched and mismatched interactions in a standard QAP formulation. This can be critical in applications where networks have low similarity and therefore we expect more mismatches than matches. We assess the eectiveness of our proposed method theoretically for certain classes of networks, through simulations over various synthetic network models, and in two real-data applications; in comparative analysis of gene regulatory networks across human, y and worm, and in user de-anonymization over twitter follower subgraphs.
Analysis of mutations in adeno-associated virus Rep protein in vivo and in vitro

The adeno-associated virus (AAV) Rep protein is required for both viral DNA replication and transactivation of the AAV promoters. Here we report the effects of mutations in the rep gene on transcription and replication in vivo and terminal repeat binding and terminal resolution site (trs) endonuclease activities in vitro. In all, we examined 10 in-frame deletions and 14 amino acid substitution mutations at eight positions. The point mutations were targeted to regions that are highly conserved among the parvovirus nonstructural proteins and include the extended ATPase domain of the AAV Rep protein. The mutations identify at least two noncontiguous regions of Rep which are essential for terminal repeat binding (amino acids 134 to 242 and amino acids 415 to 490). Mutations in either region render the protein inactive for both DNA replication and transactivation. In addition, mutations within a putative ATPase region also cause defects in replication and transactivation in vivo as well as in the ATP-dependent trs endonuclease activity in vitro. These results suggest that Rep transactivates via a novel mechanism which may require both DNA binding and an enzymatic activity, namely, ATPase or DNA helicase activity.
Geochemical evidence for active tropical serpentinization in the Santa Elena Ophiolite, Costa Rica: An analog of a humid early Earth?

Serpentinization is a planetary process that has important consequences on geochemical cycles, supporting microbial activity through the formation of H2 and CH4 and having the potential to sequester atmospheric CO2. We present geochemical evidence of active serpentinization in the Santa Elena Ophiolite, Costa Rica which is sustained by peridotites with a degree of serpentinization less than 50% with no evidence of an internal heat source. Average spring water temperatures are 29.1°C. Two hyperalkaline spring systems were discovered, with a spring fluid pH up to 11.18. The fluids are characterized by low Mg (1.0–5.9 mg/L) and K (1.0–5.5 mg/L) and relative high Ca (29–167 mg/L), Na (16–27 mg/L), Cl (26–29 mg/L), hydroxide (41–63 mg/L), and carbonate (31–49 mg/L). Active CH4 (24.3% v/v) vents coupled with carbonate deposits ( δ13CCO2 =−27 to −14‰ ; δ18OCO2 =−17 to − 6‰ ) also provide evidence for active serpentinization and carbonation. Isotope ratios of the alkaline fluids (δ18O = −7.9‰, δ2H = −51.4‰) and groundwater (δ18O = −7.6‰; δ2H = −48.0‰) suggests that, during base flow recession, springs are fed by groundwater circulation. Methanogenic Archaea, which comprises a relatively high percentage of the 16S rRNA gene tag sequences, suggests that biological methanogenesis may play a significant role in the system. Santa Elena's extreme varying weather results in a scenario that could be of significant importance for (a) improving the knowledge of conditions on a humid early Earth or Mars that had periodic changes in water supply, (b) revealing new insights on serpentinizing solute transport, and (c) modeling hydrogeochemical responses as a function of recharge.
Argatroban for anticoagulation in continuous renal replacement therapy*

Objective:Argatroban, a direct thrombin inhibitor, was evaluated for anticoagulation in continuous renal replacement therapy (CRRT) in critically ill patients with heparin-induced thrombocytopenia type II and acute renal failure. The investigation focused on predictors for the maintenance doses of argatroban with efficacy and safety of argatroban being secondary outcomes. Design:Prospective, dose finding study. Setting:Two intensive care units (medical and surgical) of a university hospital. Patients:Medical and surgical patients (n = 30) with acute or histories of heparin-induced thrombocytopenia type II and acute renal failure with necessity for CRRT. Intervention:CRRT with argatroban for anticoagulation. Measurements and Main Results:Critical illness severity scores Acute Physiology and Chronic Health Evaluation (APACHE)-II, Simplified Acute Physiology Score (SAPS) II, and the indocyanine green plasma disappearance rate (ICG-PDR) were correlated to the argatroban maintenance doses. These diagnostic tools can help to identify patients with the necessity for decreased argatroban doses. The following recommendations for argatroban dosing during CRRT could be determined: a loading dose of 100 &mgr;g/kg followed by a maintenance infusion rate (&mgr;g/kg/min), which can be calculated from the scores as follows: for APACHE II: 2.15–0.06 × APACHE II (r = −.81, p < 0.001); for SAPS II: 2.06–0.03 × SAPS II (r = −.8, p < 0.001); and for ICG-PDR: −0.35 + 0.08 × ICG-PDR (r = .89, p < 0.001). The efficacy and safety of anticoagulation during CRRT were determined by the steady state of blood urea nitrogen (32.16 ± 18.02 mg/dL), mean filter patency at 24 hrs (98%), and the rate of bleeding episodes. Only two patients developed minor bleeding; no patient developed severe bleeding episodes. Conclusion:In critically ill patients with heparin-induced thrombocytopenia type II and necessity for CRRT critical illness scores (APACHE II, SAPS II) or ICG-PDR can help to predict the required argatroban maintenance dose for anticoagulation. These predictors identify decreased argatroban dosing requirements resulting in effective and safe CRRT.
N‐glycan maturation mutants in Lotus japonicus for basic and applied glycoprotein research

Studies of protein N-glycosylation are important for answering fundamental questions on the diverse functions of glycoproteins in plant growth and development. Here we generated and characterised a comprehensive collection of Lotus japonicusLORE1 insertion mutants, each lacking the activity of one of the 12 enzymes required for normal N-glycan maturation in the glycosylation machinery. The inactivation of the individual genes resulted in altered N-glycan patterns as documented using mass spectrometry and glycan-recognising antibodies, indicating successful identification of null mutations in the target glyco-genes. For example, both mass spectrometry and immunoblotting experiments suggest that proteins derived from the α1,3-fucosyltransferase (Lj3fuct) mutant completely lacked α1,3-core fucosylation. Mass spectrometry also suggested that the Lotus japonicus convicilin 2 was one of the main glycoproteins undergoing differential expression/N-glycosylation in the mutants. Demonstrating the functional importance of glycosylation, reduced growth and seed production phenotypes were observed for the mutant plants lacking functional mannosidase I, N-acetylglucosaminyltransferase I, and α1,3-fucosyltransferase, even though the relative protein composition and abundance appeared unaffected. The strength of our N-glycosylation mutant platform is the broad spectrum of resulting glycoprotein profiles and altered physiological phenotypes that can be produced from single, double, triple and quadruple mutants. This platform will serve as a valuable tool for elucidating the functional role of protein N-glycosylation in plants. Furthermore, this technology can be used to generate stable plant mutant lines for biopharmaceutical production of glycoproteins displaying relative homogeneous and mammalian-like N-glycosylation features.
Inhibitory Networks of Fast-Spiking Interneurons Generate Slow Population Activities due to Excitatory Fluctuations and Network Multistability

Slow population activities (SPAs) exist in the brain and have frequencies below ∼5 Hz. Despite SPAs being prominent in several cortical areas and serving many putative functions, their mechanisms are not well understood. We studied a specific type of in vitro GABAergic, inhibition-based SPA exhibited by C57BL/6 murine hippocampus. We used a multipronged approach consisting of experiment, simulation, and mathematical analyses to uncover mechanisms responsible for hippocampal SPAs. Our results show that hippocampal SPAs are an emergent phenomenon in which the “slowness” of the network is due to interactions between synaptic and cellular characteristics of individual fast-spiking, inhibitory interneurons. Our simulations quantify characteristics underlying hippocampal SPAs. In particular, for hippocampal SPAs to occur, we predict that individual fast-spiking interneurons should have frequency–current (f–I) curves that exhibit a suitably sized kink where the slope of the curve decreases more abruptly in the gamma frequency range with increasing current. We also predict that these interneurons should be well connected with one another. Our mathematical analyses show that the combination of synaptic and intrinsic conditions, as predicted by our simulations, promotes network multistability. Population slow timescales occur when excitatory fluctuations drive the network between different stable network firing states. Since many of the parameters we use are extracted from experiments and subsequent measurements of experimental f–I curves of fast-spiking interneurons exhibit characteristics as predicted, we propose that our network models capture a fundamental operating mechanism in biological hippocampal networks.
The use and origin of antimonate colorants in early Egyptian glass

The origin of the colorants in Egyptian glass of the second millennium BC has been the subject of much research and debate. Several colorants including lead antimonate yellow and calcium antimonate white appear in the archaeological record apparently concurrently with the introduction of glass, and it is possible that their origins are in some way linked. This paper examines the use of the antimonate colorants and uses analytical and experimental techniques to deduce possible technologies of production. Trace element data derived from a pilot study by LA-ICPMS gives additional indications of a possible source in the Caucasus for the antimony of these glasses.
Gamma Interferon Expression in CD8+ T Cells Is a Marker for Circulating Cytotoxic T Lymphocytes That Recognize an HLA A2-Restricted Epitope of Human Cytomegalovirus Phosphoprotein pp65

ABSTRACT Antigen-specific CD8+ T cells with cytotoxic activity are often critical in immune responses to infectious pathogens. To determine whether gamma interferon (IFN-γ) expression is a surrogate marker for cytotoxic T lymphocytes (CTL), human cytomegalovirus-specific CTL responses were correlated with CD8+ T-cell IFN-γ expression determined by cytokine flow cytometry. A strong positive correlation was observed between specific lysis of peptide-pulsed targets in a 51Cr release assay and frequencies of peptide-activated CD8+ T cells expressing IFN-γ at 6 h (r2 = 0.72) or 7 days (r2 = 0.91). Enumeration of responding cells expressing perforin, another marker associated with CTL, did not improve this correlation. These results demonstrate that IFN-γ expression can be a functional surrogate for identification of CTL precursor cells.
Effects of dehydroepiandrosterone and quinapril on nephropathy in obese Zucker rats.

BACKGROUND The obese Zucker rat exhibits insulin resistance, develops nephropathy at an early age, and may be a model of diabetic nephropathy. Dehydroepiandrosterone (DHEA) may ameliorate many of the factors that contribute to diabetic nephropathy, while angiotensin-converting enzyme inhibitors are known to be effective. One marker of nephropathy is the expression of alpha-smooth muscle actin. METHODS We studied the effect of DHEA on the expression of alpha-smooth muscle actin in obese Zucker rats and compared the changes with those in a control group, a group given quinapril, and a group on a low-calorie diet. DHEA (0.6%) added to plain chow, quinapril (0.3 mg/kg) added to drinking water, and a low-calorie diet based on pair-feeding were administered to obese rats from age 4 to 20 weeks. Immunohistochemical expression of alpha-smooth muscle actin, a marker of interstitial and glomerular fibrosis and an early indicator of nephropathy, was measured semiquantitatively in glomeruli, cortical interstitium, and medullary interstitium on a scale of 0 to 4 and was reported as mean +/- SEM. RESULTS When compared with the obese control group, quinapril exhibited a marked reduction in alpha-smooth muscle actin staining in glomeruli, cortical interstitium, and medullary interstitium (P < 0.0005); DHEA reduced alpha-smooth muscle actin staining in cortical interstitium and medullary interstitium (P < 0. 005), and a low-calorie diet reduced alpha-smooth muscle actin staining in cortical and medullary interstitium (P < 0.005), which was similar to the effects of DHEA. CONCLUSIONS DHEA was similar to a low-calorie diet in reducing the immunohistochemical staining of alpha-smooth muscle actin in obese Zucker rats. However, quinapril exerted a marked protective effect on the development of fibrosis, as indicated by alpha-smooth muscle actin staining, which was significantly less than that of DHEA at the doses studied.
Improving Test Suites Maintainability with the Page Object Pattern: An Industrial Case Study

The page object pattern is used in the context of web testing for abstracting the application's web pages in order to reduce the coupling between test cases and application under test. This paper reports on an industrial case study in a small Italian company (eXact learning solutions S.p.A.) investigating the potential benefits of adopting the page object pattern to improve the maintainability of Selenium WebDriver test cases. After a maintenance/evolution activity performed on the application under test, we compared two equivalent test suites, one built using the page object pattern and one without it. The results of our case study indicate a strong reduction in terms of time required (by a factor of about three) and number of modified LOCs (by a factor of about eight) to repair the test suite when the page object pattern is used.
An experimental study on the image-based atmospheric correction method for high resolution multispectral data

The atmospheric correction is prerequisite to derive both land and ocean surface properties from satellite remote sensing data. It also improves the satellite image quality and the performance of value-added image processing. The purpose of this study is to develop an image-based atmospheric correction method for the forthcoming Korea Multi-Purpose SATellite-2 (KOMPSAT-2) multi-spectral camera (MSC) data. For this purpose, we have first tested the several atmospheric correction models using the Landsat Enhanced Thermal Mapper Plus (ETM+) data that have quite similar spectral characteristics to the KOMPSAT-2 MSC data, and the in-situ measured surface reflectance data during the satellite overflight. Subsequently, we have applied the selected models to the IKONOS data with off-nadir viewing corrections because most passes of KOMPSAT-2 are subject to such viewing conditions. This presentation discusses the results of the above tests.
Image thresholding based on Adjusted Rand Index

This paper proposes a new image thresholding method by integrating Multi-scale Gradient Multiplication (MGM) transformation and Adjusted Rand Index (ARI). The proposed method evaluates the optimal threshold by computing the accumulation similarity between two image collections from the perspective of global spatial attributes of images. One of the image collections are obtained by binarizing the original gray level image with each possible gray level. The others are the reference images, produced by binarizing MGM image. The MGM image is the result of applying MGM transformation to the original image. ARI is a similarity measurement in statistics, particularly in data clustering, which can be readily computed based on two image matrices. To be more accurate, the optimal threshold is determined by maximizing the accumulation similarity of ARI. Comparisons with three well established thresholding methods are depicted for numbers of real-world images. Experiment results demonstrate the effectiveness and robustness of the proposed method.
Octupole magnet for soft X ray magnetic dichroism experiments: Design and performance

An octupole magnet endstation for soft x-ray magnetic dichroism measurements has been developed at the Advanced Light Source. The system consists of an eight pole electromagnet that surrounds a small vacuum chamber. The magnet provides fields up to 0.9 T that can be applied in any direction relative to the incoming x-ray beam. High precision magnetic circular and linear dichroism spectra can be obtained reversing the magnetic field for each photon energy in an energy scan. Moreover, the field dependence of all components of the magnetization vector can be studied in detail by choosing various angles of x-ray incidence while keeping the relative orientation of magnetic field and sample fixed.
Exploring the Plant Transcriptome through Phylogenetic Profiling1[w]

Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species- and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.
An Approximation Scheme for RNA Folding Structure Prediction Including Pseudoknots

The paper further investigates the computational problem and complexity of predicting Ribonucleic Acid structure. In order to find a way to optimize the Ribonucleic Acid pseudoknotted structure, we investigate the Ribonucleic Acid pseudoknotted structure based on thermal dynamic model, computational methods, minimum free energy are adopted to predict Ribonucleic Acid structure. The contribution of this paper is to obtain an efficient Approximation algorithm for finding RNA pseudoknotted structure, compared with other algorithms, the algorithm takes O(n3) time and O(n2) space. The experimental test in PseudoBase shows that the algorithm is more effective and exact than other algorithms, and the algorithm can predict arbitrary pseudoknots. And we also give a proof of existing 1+e (e>0) Polynomial Time Approximation Scheme(PTAS) in Searching Maximum Number of Stackings.