Miracle-dz/UniFAR-FTUs huggingface dataset:
CSCI 699 Project : Detecting software component relationships Literature Survey

My project proposal is to apply information extraction techniques to capture compatibility relationships between software components that exists in the form of unstructured text on online forums. My goal is to focus on the Stack Overflow Q&A site. Therefore, related work here is presented in the context of information extraction techniques with a focus on the Software Engineering domain. In section 2, relevant work related to mining software engineering knowledge is presented. Specifically, work related to extracting information from Stack Overflow is reviewed. In section 3, work related to applications of relation extraction is discussed. First, relation extraction in the Biomedical domain is presented since it is a well known research area for application of relation extraction techniques. Secondly, relation extraction in the context of ontology construction in software engineering is presented. Work pertaining to Software Engineering relation extraction from Stack Overflow is then discussed. Section 4 provides a summary and lists the challenges that need to be solved.
An Amphipathic Helical Region of the N-terminal Barrel of Phospholipid Transfer Protein Is Critical for ABCA1-dependent Cholesterol Efflux*

Phospholipid lipid transfer protein (PLTP) mimics high-density lipoprotein apolipoproteins in removing cholesterol and phospholipids from cells through the ATP-binding cassette transporter A1 (ABCA1). Because amphipathic α-helices are the structural determinants for ABCA1 interactions, we examined the ability of synthetic peptides corresponding to helices in PLTP to remove cellular cholesterol by the ABCA1 pathway. Of the seven helices tested, only one containing PLTP residues 144–163 (p144), located at the tip of the N-terminal barrel, promoted ABCA1-dependent cholesterol efflux and stabilized ABCA1 protein. Mutating methionine 159 (Met-159) in this helix in PLTP to aspartate (M159D) or glutamate (M159E) nearly abolished the ability of PLTP to remove cellular cholesterol and dramatically reduced PLTP binding to phospholipid vesicles and its phospholipid transfer activity. These mutations impaired PLTP binding to ABCA1-generated lipid domains and PLTP-mediated stabilization of ABCA1 but increased PLTP binding to ABCA1. PLTP interactions with ABCA1 also mimicked apolipoproteins in activating Janus kinase 2; however, the M159D/E mutants were also able to activate this kinase. Structural analyses showed that the M159D/E mutations had only minor effects on PLTP conformation. These findings indicate that PLTP helix 144–163 is critical for removing lipid domains formed by ABCA1, stabilizing ABCA1 protein, interacting with phospholipids, and promoting phospholipid transfer. Direct interactions with ABCA1 and activation of signaling pathways likely involve other structural determinants of PLTP.
Attachment of radon progeny to cigarette-smoke aerosols

The daughter products of radon gas are now recognized as a significant contributor to radiation exposure to the general public. It is also suspected that a synergistic effect exists with the combination cigarette smoking and radon exposure. We have conducted an experimental investigation to determine the physical nature of radon progeny interactions with cigarette smoke aerosols. The size distributions of the aerosols are characterized and attachment rates of radon progeny to cigarette-smoke aerosols are determined. Both the mainstream and sidestream portions of the smoke aerosol are investigated. Unattached radon progeny are very mobile and, in the presence of aerosols, readily attach to the particle surfaces. In this study, an aerosol chamber is used to contain the radon gas, progeny and aerosol mixture while allowing the attachment process to occur. The rate of attachment is dependent on the size distribution, or diffusion coefficient, of the radon progeny as well as the aerosol size distribution. The size distribution of the radon daughter products is monitored using a graded-screen diffusion battery. The diffusion battery also enables separation of the unattached radon progeny from those attached to the aerosol particles. Analysis of the radon decay products is accomplished using alpha spectrometry. The aerosols of interest are size fractionated with the aid of a differential mobility analyzer and cascade impactor. The measured attachment rates of progeny to the cigarette smoke are compared to those found in similar experiments using an ambient aerosol. The lowest attachment coefficients observed, {approximately}10{sup {minus}6} cm{sup 3}/s, occurred for the ambient aerosol. The sidestream and mainstream smoke aerosols exhibited higher attachment rates in that order. The results compared favorably with theories describing the coagulation process of aerosols.
STUDIES ON THE CHARACTERIZATION OF THE SnO2 NANOWIRES GROWTH

ABSTRACT In this paper, tin dioxide (SnO2) nanowires were synthesized on silicon substrate (111) using a direct gas reaction route on a large scale at 700°C∼ 1000°C. These SnO2 nanowires were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Raman-scattering spectroscopy. XRD, SEM and TEM indicated that the products were tetragonal SnO2 nanowires with lattice parameters of a = 4.73 Å, c = 3.17 Å. Three vibrational modes were observed in Raman spectra of the samples. According to the current-voltage (I-V) measurements, Tin dioxide nanowires can be used as a sensor.
The minor allele of the missense polymorphism Ser251Pro in perilipin 2 (PLIN2) disrupts an α‐helix, affects lipolysis, and is associated with reduced plasma triglyceride concentration in humans

Perilipin 2 (PLIN2) is the most abundant lipid droplet (LD)‐associated protein in nonadipose tissue, and its expression correlates with intracellular lipid accumulation. Here we identified a missense polymorphism, Ser251Pro, that has major effect on protein structure and function, along with an influence on human plasma triglyceride concentration. The evolutionarily conserved Ser251Pro polymorphism was identified with the ClustalW program. Structure modeling using 3D‐JigSaw and the Chimera package revealed that the Pro251 allele disrupts a predicted α‐helix in PLIN2. Analyses of macrophages from individuals carrying Ser251Pro variants and human embryonic kidney 293 (HEK293) cells stably transfected with either of the alleles demonstrated that the Pro251 variant causes increased lipid accumulation and decreased lipolysis. Analysis of LD size distribution in stably transfected cells showed that the minor Pro251 allele resulted in an increased number of small LDs per cell and increased perilipin 3 protein expression levels as compared with cells carrying the major Ser251 allele. Genotyping of 2113 individuals indicated that the Pro251 variant is associated with decreased plasma triglyceride and very low‐density lipoprotein concentrations. Altogether, these data provide the first evidence of a polymorphism in PLIN2 that affects PLIN2 function and may influence the development of metabolic and cardiovascular diseases. —Magné, J., Aminoff, A. , Perman Sundelin, J., Mannila, M. N. , Gustafsson, P., Hultenby, K. , Wernerson, A. , Bauer, G. , Listenberger, L. , Neville, M. J., Karpe, F. , Borén, J., Ehrenborg, E. , The minor allele of the missense polymorphism Ser251Pro in perilipin 2 (PLIN2) disrupts an α‐helix, affects lipolysis, and is associated with reduced plasma triglyceride concentration in humans. FASEB J. 27, 3090–3099 (2013). www.fasebj. org
DeepPerfusion: Camera-based Blood Volume Pulse Extraction Using a 3D Convolutional Neural Network

Imaging photoplethysmography (iPPG) is a camera-based approach for the remote extraction of the blood volume pulse (BVP) most commonly applied to facial video recordings. The major challenges of this promising technique are the low amplitude of BVP signals and their superposition with artifacts as well as physiological and non-physiological movement induced distortions. We addressed this complexity with a 3D convolutional neural network, which we called DeepPerfusion, to improve BVP extraction from iPPG. Our approach is based on the idea of enabling DeepPerfusion to learn the extraction of the BVP from videos by understanding their relation to the ground truth signals. First results show that DeepPer-fusion outperforms state-of-the-art algorithms for remote BVP extraction demonstrating a mean absolute error of 0.66 beats per minute (up to 60 % improvement) regarding the BVP based pulse rate estimation for 21 randomly chosen held out test subjects of the UBFC dataset.
Two, three, and four body interactions in model water interactions

Dimer energy surfaces for three models of the water-water interaction are examined and compared with high level ab initio SCF calculations for two important sections. All three models studied (ST2, MCY, and PE(Q) show significant differences which would be expected to be important in full liquid state simulation; the inclusion of an additional dipole-octupole term in PE appears sufficient to reproduce the energy-angle variations shown in the SCF calculations. ST2 distinguishes too strongly between the lone pairs on the acceptor water molecule, while MCY shows little sign at all of lone pair separation. All three models disagree with the rotational barrier heights given by the SCF calculations; these differences we would expect to have structural consequences in a room temperature liquid ensemble. Although there are insufficient experimental and numerical data available to fully test the three-body (and higher) interactions of the PE model, good agreement is obtained with experimental enhanced dipole momen.
Phénols et flavonoïdes totaux dans les extraits secs des feuilles des bouleaux argentés bulgares (Betula pendula )

La quantite de phenols et de flavonoides totaux dans les extraits secs des feuilles des bouleaux argentes bulgares ( Betula pendula ) a ete evaluee par la methode de Folin-Ciocalteu et par la methode colorimetrique de chlorite d’aluminium. L’interet pour des supplements alimentaires issus des differentes plantes a augmente recemment et il a ete montre que les extraits secs des feuilles des bouleaux argentes bulgares ( Betula pendula ) possedent des proprietes benefiques pour la sante. Le present article montre les resultats obtenus pour les teneurs en phenols et en flavonoides totaux dans les extraits secs des feuilles des bouleaux argentes bulgares ( Betula pendula ) pour la periode 2005-2008.
Measurements of stratospheric ClO over Antarctica in 1996–2000 and implications for ClO dimer chemistry

Measurements of ClO over Antarctica during the 1996 to 2000 ozone holes are compared with predictions of the SLIMCAT model. The model captures all of the major features of the measurements, including the rapid rise in August, the drop in mid or late September due to the arrival of warmer, ClOx poor air overhead, and the deactivation of ClOx into the reservoir species, HCl and ClONO2 in the ozone poor air. The model uses the standard JPL rates for the photolysis of the ClO dimer (j) and for the forward reaction forming the dimer (kf). The predicted ClO mixing ratios and columns are in excellent agreement with the measurements. A comparison of the model and data for all 5 years leads to a value of the ratio (j/kf) consistent with the standard value, namely 1.06 ± 0.30(j/kf)JPL.
Occurrence and separation of Cryptosporidium oocysts in drinking water treatment

The presence of Cryptosporidium sp. in Czech drinking water sources was monitored. High numbers of Cryptosporidium oocysts were found in the Slezska Harta reservoir after 1997 summer floods. The influence of iron (III) coagulant dose, mixing conditions and preozonation on the removal efficiency of Cryptosporidium oocysts was studied. Low mixing intensity produced flocs with poor settling features. The efficiency of sedimentation expressed as residual iron after sedimentation was proportional to removal efficiency of oocysts. Both underdosing or overdosing of iron (III) coagulant resulted in decrease of COD, turbidity and oocyst removal. Preozonation positively influenced removal efficiency of oocysts in the conventional drinking water treatment train studied.
Dense YMn2O5 Ceramics Prepared by Spark Plasma Sintering

Dense multiferroic YMn2O5 ceramics with a single orthorhombic phase are quite difficult to prepare because the orthorhombic phase decomposes at about 1180°C. In this study, spark plasma sintering (SPS) was investigated to synthesize YMn2O5 ceramics. The sample sintered at 900°C for 5 min by SPS consisted of the main orthorhombic YMn2O5 phase and a small amount of hexagonal YMnO3 phase and Mn3O4. After heat treatment at 1100°C for 9 h, YMn2O5 ceramics in a single orthorhombic phase with a relative density of 94% were obtained. The results suggested that SPS is a promising process for preparing ceramics whose optimal sintering temperatures are higher than their decomposition temperatures.
Pathogenesis of heparin-induced thrombocytopenia

Heparin-induced thrombocytopenia (HIT), is a unique model of immune-mediated disorder due to the development of antibodies (mainly IgG) specific to platelet factor 4 (PF4). PF4 is a C-X-C chemokine present in platelet alpha granules and released in plasma as tetramers that exposed an electropositive ring critical for the binding of heparin, a negatively-charged molecule. PF4-heparin interactions induce the expression of neoepitopes involving several aminoacids (including P37, R49, L55 and K61) and responsible for the humoral immune response associated with HIT that requires helper T-cells and immunoglobulin class switching. Thrombocytopenia and thrombotic complications are likely to result from a multicellular activation involving platelets, endothelial cells, and monocytes. Platelet activation is mediated by the binding of HIT-IgG present within large multimolecular immune complexes to FcgammaRIIa receptors. This interaction leads to platelet activation, granule release and the generation of procoagulant phospholipid-rich microparticles. HIT antibodies might also activate endothelium by interacting with PF4-heparan sulfate complexes. Recently, a PF4-dependent binding of HIT IgG to monocytes inducing a tissue factor synthesis was also demonstrated and this mechanism likely contributes to the generation of thrombin associated with HIT and resulting thrombotic events. The treatment of HIT depending on this physiopathology is based on the replacement of heparin by drugs (danaparoid sodium or hirudin) that poorly or does not crossreact with antibodies to PF4. The risk of HIT is higher in conditions associated with a strong platelet activation such as cardiopulmonary bypass and in patients who are treated by unfractionated heparin, mixture of glycosaminoglycans containing large amounts of chains exceeding ten monosaccharides with a high degree of sulfation. The risk of HIT is therefore lower with low-molecular weight heparins and might be further reduced in the future with the use of synthetic pentasaccharide.
Thermoelectric Behavior of Nickel Oxide

Measurements have been made on the thermoelectric power of several nickel oxide samples containing foreign ions. Using an energy model recently proposed for nickel oxide, the effect of the nature and concentration of additions on the Fermi level, hole concentration, and mobility is derived and discussed. For most of the samples hole concentration can be related to chemical composition. A case of change in valence of the addition induced upon introduction into the matrix is found. The use of the thermoelectric effect to determine impurity in nickel oxide is discussed. The energy scheme of nickel oxide which emerges from this work and that of Morin is emphasized as a drastic departure from the classical model of an electrical semiconductor.
Multi-year Assessment of Airborne Metals in Fallon, Nevada, Using Leaf-surface Chemistry

1.1 Fallon, Nevada Spatial patterns of airborne metals are described from leaf-surface chemistry of trees in Fallon, Nevada (Fig. 1a), where a cluster of childhood leukemia began in 1997. Officially, 16 cases of childhood leukemia were diagnosed from 1997 to 2002 inclusive (Expert Panel, 2004), and one additional case was reported in December 2004 (Nevada State Health Division, 2004). Although the cluster is thought to have abated (Reno Gazette-Journal, 11 October 2008), at least one additional case of childhood leukemia has occurred in Fallon since 2004 (Lahontan Valley News, 15 October 2010). Given Fallon’s pediatric population of about 2500 children up to 19 years in age (U.S. Census, 2000) and a national expected rate of childhood leukemia of 4.1 cases per 100,000 children up to 19 years in age per year (U.S. NCI, 2003), the expected rate of childhood leukemia for Fallon should be only one case every ten years. This cluster, deemed "one of the most unique ever reported" (Steinmaus et al., 2004; Steinmaus et al., 2005), prompted multiple investigations to determine if an environmental cause might have been responsible. Research focused on drinking water (Moore et al. 2002; Shaw et al., 2005; Walker & Fosbury 2009; Walker et al., 2006), jet fuel (U.S. ATSDR, 2002), pesticides (Rubin et al., 2007; U.S. CDC, 2003), surface water (U.S. ATSDR, 2003a), outdoor air (U.S. ATSDR, 2003b), surface soil and indoor dust (U.S. ATSDR, 2003c), potential lingering effects of underground nuclear bomb testing in the area (Seiler, 2004), and groundwater (Seiler et al., 2005). A non-environmental hypothesis–population mixing–was also considered (Kinlen & Doll, 2004; Wakeford, 2004]. Few definitive conclusions emerged from these studies, prompting an interpretation that Fallon had been given a “clean bill of health” by the US Agency for Toxic Substances and Disease Registry and the US Centers for Disease Control (Lahontan Valley News, 8 August 2007). However, this interpretation is questionable (Pleil et al., in press), and the need to monitor the environment of Fallon continues to exist. To monitor the environment of Fallon, we have employed multiple techniques, all of which have shown notable patterns of airborne tungsten and cobalt. Elevated tungsten and cobalt was identified in airborne particulates of Fallon relative to comparison towns (Sheppard et al., 2006a) and in lichens within Fallon compared to outlying desert areas (Sheppard et al.,
Using GAC to Remove VOCs From Air Stripper Off-Gas

This article focuses on the technical and economic feasibility of treating air stripper off-gas with granular activated carbon (GAC). For dichloroethene and trichloroethene, air stripping followed by off-gas GAC treatment was shown to be very effective and economical compared with aqueous-phase GAC treatment, with GAC usage rates for gas-phase adsorption being less than one half those for aqueous-phase adsorption. Also, because gas-phase adsorption kinetics are much faster than liquid-phase kinetics, the required bed depth and diameter are much smaller for gas-phase beds. Steam regeneration was found to be ineffective for regeneration gas-phase GAC at low concentrations.
An Optimization Study on the Ultrasonic Treatments for Saccharomyces cerevisiae Inactivation in Red Grape Juice with Maintaining Critical Quality Attributes

This study was conducted to decrease Saccharomyces cerevisiae cell count and to maximize levels of quality characteristics in red grape juice during ultrasound process using response surface methodology (RSM). The effects of three process parameters (considered as independent variables), namely temperature (25–50C), time (20–40 min) and frequency (0–135 Hz), on the yeast inactivation, total anthocyanin content (TAC), total color difference (TCD), antioxidant activity (AA), polymeric color content (PCC), pH, total titratable acidity (TTA) and total soluble solids (TSS) (considered as dependent variables) were studied based on RSM. The optimum operating conditions for the maximum yeast inactivation and the optimal juice quality characteristics were found to be frequency of 135.0 kHz, temperature of 30.9C and time of 40.0 min. In these conditions, the yeast inactivation, TAC, PCC, AA, TCD, pH, TTA and TSS were 1 cfu/mL, 808.0 mg/g, 67.85%, 0.94 mmol/L, 1.64, 3.47, 977.4 mg citric acid/100 mL and 20.04, respectively. Practical Applications In recent years, emerging nonthermal methods, such as ultrasound (US), for inactivating microorganisms have been developed in food industries to manufacture natural products. Red grape juice, due to the presence of anthocyanins and flavonoids, has many health-promoting effects. As the nutritive and organoleptic characteristics of grapes decrease during storage and ripening periods because of their high susceptibility to pathogenic infection and physiological deterioration, the use of US method as a potential technology can inactive foodborne spoilage or pathogenic microorganisms and produce juices with organoleptic and nutritional qualities. Moreover, the optimization of US conditions enabled us to shorten the process duration and to reduce the production costs while maintaining the quality at a relatively high level.
Prediction of whole-tree basic density and pulp yield using wood core samples in Eucalyptus nitens

The potential for predicting whole-tree basic density and pulp yield from core samples of 12-year-old Eucalyptus nitens was evaluated using trees from three sites in Tasmania. A total of 55 trees were used to examine longitudinal patterns of variation for basic density and to determine the relationship between whole tree values and core samples. Twenty-five trees from one site were tested to determine the relationship between whole-tree pulp yield, and cellulose and extractives contents of core samples. A subset of these trees was used to determine longitudinal patterns of variation for cellulose and extractives content and to calculate relationships between cores and whole tree values. Equations were developed to predict whole tree values for both basic density and kraft pulp yield. Whole tree values for basic density, cellulose content and kraft pulp yield were all reliably predicted by core samples from 0.9 m above ground. For basic density, the core samples explained between 85 and 92% of variation in whole-tree density whilst for cellulose content 89% of variation was explained. Cellulose content of a core was also a very good predictor of kraft pulp yield of the whole tree, with potentially 86% of variation in pulp yield at Kappa 18 accounted for by the core sample. The relationship between extractives content and pulp yield was significant and negative but not sufficiently strong to be used as a predictive tool.
Environmental Chemistry of Soils

This introduction to modern soil chemistry describes chemical processes in soils in terms of established principles of inorganic, organic, and physical chemistry. The text provides an understanding of the structure of the solid mineral and organic materials from which soils are formed, and explains such important processes as cation exchange, chemisorption and physical absorption of organic and inorganic ions and molecules, soil acidification and weathering, oxidation-reduction reactions, and development of soil alkalinity and swelling properties. Environmental rather than agricultural topics are emphasized, with individual chapters on such pollutants as heavy metals, trace elements, and inorganic chemicals.