gebhart/patrepeval huggingface dataset:
Information-theoretic software clustering (2005)

The majority of the algorithms in the software clustering literature utilize structural information to decompose large software systems. Approaches using other attributes, such as file names or ownership information, have also demonstrated merit. At the same time, existing algorithms commonly deem all attributes of the software artifacts being clustered as equally important, a rather simplistic assumption. Moreover, no method that can assess the usefulness of a particular attribute for clustering purposes has been presented in the literature. In this paper, we present an approach that applies information theoretic techniques in the context of software clustering. Our approach allows for weighting schemes that reflect the importance of various attributes to be applied. We introduce LIMBO, a scalable hierarchical clustering algorithm based on the minimization of information loss when clustering a software system. We also present a method that can assess the usefulness of any nonstructural attribute in a software clustering context. We applied LIMBO to three large software systems in a number of experiments. The results indicate that this approach produces clusterings that come close to decompositions prepared by system experts. Experimental results were also used to validate our usefulness assessment method. Finally, we experimented with well-established weighting schemes from information retrieval, Web search, and data clustering. We report results as to which weighting schemes show merit in the decomposition of software systems.
Role of vitamin D3-binding protein in activation of mouse macrophages (1996)

When mouse peritoneal nonadherent (lymphocytes) cells were treated with lysophosphatidylcholine (lyso-Pc) and cultured with adherent cells (macrophages) in 1% fetal calf serum (FCS)- or adult mouse serum (AMS)-supplemented medium for 3 h, markedly enhanced phagocytic and superoxide-generating capacities of macrophages were observed. Stepwise cultivation of lyso-Pc-treated B cells and untreated T cells with an FCS-supplemented medium generated a macrophage-activating factor (MAF), whereas cultivation of lyso-Pc-treated B cells alone in AMS-supplemented medium was sufficient to generate the MAF. The accumulated evidence suggests that lyso-Pc-inducible beta-galactosidase of B lymphocytes and the Neu-1 sialidase of T lymphocytes modified the bovine serum vitamin D3-binding protein (DBP) to yield the MAF, a protein with N-acetylgalactosamine as the remaining sugar. In contrast, the lyso-Pc-inducible beta-galactosidase of B cells alone modified mouse DBP to yield the MAF. These observations led us to conclude that bovine DBP carries a trisaccharide composed of N-acetylgalactosamine, galactose, and sialic acid, whereas mouse DBP carries a disaccharide composed of N-acetylgalactosamine and galactose. Thus, macrophages of a T-cell-deficient nude (BALB/c nu/nu) mouse and a T-cell Neu-1 sialidase-deficient SM/J mouse were efficiently activated by administration of lyso-Pc.
Learning the Irreducible Representations of Commutative Lie Groups (2014)

We present a new probabilistic model of compact commutative Lie groups that produces invariant-equivariant and disentangled representations of data. To define the notion of disentangling, we borrow a fundamental principle from physics that is used to derive the elementary particles of a system from its symmetries. Our model employs a newfound Bayesian conjugacy relation that enables fully tractable probabilistic inference over compact commutative Lie groups -- a class that includes the groups that describe the rotation and cyclic translation of images. We train the model on pairs of transformed image patches, and show that the learned invariant representation is highly effective for classification.
Effects of Some Antibiotics on Activity of Glucose-6-Phosphate Dehydrogenase from Human Erythrocytes In Vitro and Effect of Isepamicin Sulfate on Activities of Antioxidant Enzymes in Rat Erythrocytes (2005)

The purpose of this study was to investigate effects of some antibiotics on glucose-6-phosphate dehydrogenase (G6PD), antioxidant enzymes, and malondialdehyde (MDA). Initially, for in vitro studies, G6PD was purified from human erythrocyte, 9811-fold in a yield of 42.4% by using ammonium sulfate precipitation and 2',5' ADP-Sepharose 4B affinity gel. The purified enzyme showed a single band on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The effects of four different antibiotics (isepamicin sulfate, meropenem, chloramphenicol, and thiamphenicol glisinat hydrochloride) were investigated on the purified enzyme. K(i) value and type of inhibition were determined by means of Lineweaver-Burk graphs and regression analysis graphs. Isepamicin sulfate inhibited the enzyme activity (I(50) value, 2.1 mM; K(i) value, 1.7 mM), whereas thiamphenicol glisinat hydrochloride activated the G6PD dose dependently. Other drugs showed no inhibition and activation effect. In addition, the effects of isepamicin sulfate on the activities of G6PD, glutathione reductase (GR), superoxide dismutases (SOD), glutathione peroxidase (GPx), catalase (CAT), and glutathione S-transferase (GST) and MDA concentrations were examined in Sprague-Dawley rat erythrocytes in vivo. A marked alteration in the activities of these enzymes and MDA levels may be the result of oxidative stress in the rats receiving isepamicin sulfate.
Professional Topical Fluoride Applications— Clinical Efficacy and Mechanism of Action (1994)

All currently used topical fluoride agents deposit soluble fluoride as calcium fluoride on enamel or in lesions. Calcium fluoride serves as a source of fluoride for the formation of fluorapatite. The latter phase is formed when pH drops in plaque, not during topical application. The potential for calcium fluoride formation should probably be increased in topical fluoride agents. In countries with low caries prevalence, the clinical recommendations for topical fluoride need to be reconsidered. Toothpaste is the basic fluoride regimen recommended for everybody. The need for additional fluoride supplementation depends on caries activity. There is no distinct difference in the caries-preventive effects of concentrated fluoride solutions, gels, or varnishes. Thus, the choice of method depends on costs, convenience, patient acceptance, and safety. The use of fluoride varnishes has proven to be a feasible and safe method of fluoride application. With fluoride varnishes, the amounts of fluoride exposure can be better controlled, and less chair-time is required compared with conventional solutions and gels. No dose-response effect to concentrated fluoride agents is apparent, and the benefit of frequent application is not clearly established. In individuals with the most severe cariogenic challenge, combinations of fluoride and antimicrobials may give better clinical effects than fluoride alone.
Local Control over Filtered WWW Access (1995)

This paper describes a software system called Signet that provides local control over restricting access to resources on the World Wide Web (WWW). The strategy is to make it easy for a parent or teacher to rate WWW resources and place the tables of ratings into a proxy server designed to restrict Internet access according to the access permissions of the users. Ratings can be made dynamically as the rater browses, so that the rater can insert new ratings into the ratings database at any time. Ratings can also be shared by different raters or organizations so that rating of WWW materials can proceed in a distributed fashion.
Mn2+ Dopant‐Controlled Synthesis of NaYF4:Yb/Er Upconversion Nanoparticles for in vivo Imaging and Drug Delivery (2012)

Pure dark red emission (650-670 nm) of NaYF(4):Yb/Er upconversion nanoparticles (UCNPs) is achieved by manganese ions (Mn(2+)) doping. In addition, the Mn(2+)-doping can also control the crystalline phase and size of the resulting UCNPs simultaneously. Drug delivery studies suggest the promise of these UCNPs as drug carriers for intracellular drug delivery and eventually as a multifunctional nanoplatform for simultaneous diagnosis and therapy.
Susceptibility/resistance to mouse hepatitis virus strain 3 and macrophage procoagulant activity are genetically linked and controlled by two non-H-2-linked genes. (1986)

Abstract The mode of inheritance of susceptibility/resistance to mouse hepatitis strain 3 (MHV-3) was determined by typing the set of AXB/BXA recombinant inbred (RI) strains derived from resistant A/J (A) and susceptible C57BL/6J (B) progenitors for susceptibility to infection as determined by the severity of liver pathology. The strain distribution pattern for susceptibility showed a discontinuous variation: one strain was fully resistant (A-like), four strains were fully susceptible (B-like), and 16 strains showed an intermediate degree of susceptibility. The fully susceptible strains developed fulminant hepatitis and died; the fully resistant strain developed no liver disease, whereas a range of disease ranging from mild focal hepatitis to widespread hepatocellular necrosis was seen in the semisusceptible strains. This SDP best fits the two-recessive-gene model of inheritance, and neither of these two loci is linked to the H-2 complex. Macrophage procoagulant activity (PCA) segregated among the RI strains in a strain distribution pattern identical to that of susceptibility/resistance. PCA levels were greater than sevenfold elevated in fully susceptible RI mice and fourfold elevated in semisusceptible mice with no increase in resistant mice. These observations suggest genetic linkage of susceptibility/resistance to MHV-3 infection and macrophage PCA.
Infrared Thermographic Screening of Combinatorial Libraries of Heterogeneous Catalysts (1996)

A combinatorial library of catalyst candidates, each consisting of a different metal element supported on γ-alumina, is screened for hydrogen oxidation catalytic activity. Heat liberated on the surface of active catalysts by the catalyzed reaction is detected by noninvasive IR thermography. A 16-candidate library identifies four distinctly active pellets, which correspond to active formulations known from the literature. A higher density library shows similar results, but heat and mass transport effects influence the pellet temperatures. This method may be used to screen and optimize catalyst formulations more efficiently and quickly than current methods and may also be useful for study of operational lifetime, resistance to poisons, and regenerability.
Abstract 4491: AZD5363, a novel Akt inhibitor, delays prostate cancer progression by inhibiting androgen-receptor activity (2011)

Abstract Introduction and Objective: Despite initial response to androgen deprivation therapy, prostate cancer (PCa) inevitably progresses after 3 to 4 years to its castration-resistant state (CRPC). Consequently, there is an urgent need for novel therapeutic agents that can prevent or at least prolong the time to CRPC progression. The phosphoinositide 3-kinase (PI3K)/Akt pathway plays a key role in tumor progression and therefore is an attractive pharmacological target. In this study, we assessed the anti-cancer effects of the novel and selective Akt inhibitor, AZD5363, in vitro and in vivo in PCa. Methods: LNCaP and C4-2 cells were treated with AZD5363 and submitted to western blot, qRT-PCR and immunofluorescence analysis. AZD5363 was tested for its ability to modulate PSA transactivation by luciferase assay. Cell viability was assessed by crystal violet and cell cycle population by flow cytometry. For in vivo xenograft studies, LNCaP cells were inoculated s.c. in the flank region of athymic nude mice. Mice were castrated and randomly treated with AZD5363 or control by oral gavage. Tumor volume and serum prostate-specific antigen (PSA) were evaluated twice per week. Results: Here we report that AZD5363 inhibits cell growth in a dose-dependent manner (IC50 ± 200nM) in both LNCaP and C4-2, induces cell apoptosis as measured with PARP cleavage expression, Caspase 3 activity, and increases sub-G1 population (20.2% and 22.2% at 500nM for LNCaP and C4-2 cells, respectively). Interestingly, AZD5363 significantly abrogates androgen-induced PSA transactivation at concentrations &amp;gt; ∼100nM and down-regulates AR expression at concentrations &amp;gt; ∼1μM. These biologic events were accompanied by inhibition of downstream PI3K/Akt signaling. Most important, targeting the Akt-pathway in vivo significantly reduces tumor volume and serum PSA-levels and thereby delays progression to CRPC. Conclusions: This study reports as a preclinical proof-of-principle that targeting PI3K/Akt pathway with AZD5363 inhibits androgen-dependent PCa progression in vitro and in vivo, using the AR-axis as a pharmacodynamic tool. This work was supported by AstraZeneca, the Deutsche Forschungsgemeinschaft (German Research Foundation; Grant number: TH 1482/2-1), the Canadian Institutes of Health Research and l'Association pour la Recherche sur le Cancer (France). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4491. doi:10.1158/1538-7445.AM2011-4491
Neutrophil stimulation with Mycobacterium bovis bacillus Calmette-Guerin (BCG) results in the release of functional soluble TRAIL/Apo-2L (2005)

Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been used to treat bladder cancer for almost 30 years; however, the effector mechanism of the BCG-induced antitumor response remains enigmatic. Most BCG research has focused on the mononuclear-cell infiltrate, but growing evidence supports a role for neutrophils in the antitumor response. Previously, we demonstrated increased urinary tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL/Apo-2L) levels from BCG-responsive patients compared to nonresponders. Interestingly, neutrophils isolated from the urine expressed TRAIL/Apo-2L, leading us to investigate the neutrophil response to BCG. BCG-stimulated neutrophils expressed surface-bound and released functional soluble TRAIL/Apo-2L. Whereas neither interferon alpha (IFN-alpha) nor IFN-gamma directly induced TRAIL/Apo2L expression by neutrophils, IFN-alpha did stimulate TRAIL gene transcription, and IFN-primed neutrophils contained and released more TRAIL/Apo-2L after BCG stimulation than did unprimed neutrophils. In unstimulated neutrophils TRAIL/Apo-2L was present predominantly in the azurophilic granules and plasma-membrane-enriched/secretory-granule fraction. Finally, we observed that killed BCG, Toll-like receptor 2 (TLR2) and TLR4 agonists, and an M tuberculosis cell-wall fraction were each capable of inducing the release of soluble TRAIL/Apo-2L from neutrophils. These results further characterize the potential role neutrophils may play in initiating the antitumor response described with BCG treatment for superficial bladder cancer.
Distributed dynamic channel allocation for mobile computing (1995)

Efficient allocation of communication channels is critical for the performance of wireless mobile computing systems. The centralized channel allocation algorithms proposed in literature are neither robust, nor scalable. Distributed channel allocation schemes proposed in the past are complicated and require active participation of the mobile nodes. These algorithms are unable to dynamically adjust to spatial and temporal fluctuations in channel demand. We present a dynamic distributed channel allocation algorithm that can quickly adapt to changes in load distribution. The algorithm described in this paper requires minimal involvement of the mobile nodes, thus conserving their limited energy supply. The algorithm is proved to be deadlock free, starvation free and fair. It prevents co-channel interference and is scalable.
The Alteration Barrier in "Artificial Geothermal System" around a Repository of High-Level Radioactive Waste. (1996)

The multibarrier system for deep geologic disposal of high-level, long-lived and heat generating radioactive waste has been devised in order to keep them away from humanbeing. This system consists of engineering barrier and geological natural barrier. After burying the waste, an “artificial geothermal system” may be constructed because of heat from radioactive waste, and the artificial geothermal system would make some hydrothermal minerals and alteration zone, in host rocks.Hosokura ore deposits were made by an “old geothermal system”, and have impermeable zones developed along some ore veins. In some active geothermal area in Japan, geothermal alteration zones seem to play as caprocks. That is, a part of geothermal alteration zones sometimes work as hydraulic barrier (alteration barrier), which is very important for hydrology of that area. In this paper, the possibility about formation of the “artificial alteration zone” at geologic disposal is considered.Smectite, α-cristobalite, clinoptilolite, mordenite and stilbite are possibly formed by the interaction between neutral hot water and volcanic glass at temperatures below 100°C in an artificial geothermal system. These minerals have high adsorption capacity of radionuclides and low permeability. Because of these properties, the alterative minerals may form an “alteration barrier” which supports the multibarrier system.Nowadays, a large amount of bentonite is necessary for buffer and backfill material. Mixing volcanic glasses with bentonite may reduce the amount of bentonite, because volcanic glasses may change to smectite and form a part of alteration barrier in a long time.
β-Catenin Regulation during the Cell Cycle: Implications in G2/M and Apoptosis (2003)

Beta-catenin is a multifunctional protein involved in cell-cell adhesion and Wnt signal transduction. Beta-catenin signaling has been proposed to act as inducer of cell proliferation in different tumors. However, in some developmental contexts and cell systems beta-catenin also acts as a positive modulator of apoptosis. To get additional insights into the role of beta-catenin in the regulation of the cell cycle and apoptosis, we have analyzed the levels and subcellular localization of endogenous beta-catenin and its relation with adenomatous polyposis coli (APC) during the cell cycle in S-phase-synchronized epithelial cells. Beta-catenin levels increase in S phase, reaching maximum accumulation at late G2/M and then abruptly decreasing as the cells enter into a new G1 phase. In parallel, an increased cytoplasmic and nuclear localization of beta-catenin and APC is observed during S and G2 phases. In addition, strong colocalization of APC with centrosomes, but not beta-catenin, is detected in M phase. Interestingly, overexpression of a stable form of beta-catenin, or inhibition of endogenous beta-catenin degradation, in epidermal keratinocyte cells induces a G2 cell cycle arrest and leads to apoptosis. These results support a role for beta-catenin in the control of cell cycle and apoptosis at G2/M in normal and transformed epidermal keratinocytes.
Quantification of Mucosa oxygenation using three discrete spectral bands of visible light (2009)

Quantification of the mucosa oxygenation levels during Endoscopic imaging provides useful physiological/diagnostic information. In this work a method for non-contact quantification of the oxygen saturation index during Endoscopic imaging using three discrete spectral-band in the blue, the green, and the red parts of the spectrum (RGB bands) has been investigated. The oxygen saturation index (TOI_rgb) was calculated from the three discrete RGB spectral bands using diffusion approximation modeling and least-square analysis. A parametric study performed to identify the optimum band width for each of the three spectral bands. The quantification algorithm was applied to in vivo images of the endobronchial mucosa to calculate (TOI_rgb) from selected areas within the image view. The results were compared to that obtained from the full visible spectral (470-700 nm, 10 nm) measurements. The analysis showed that a band width of at least 20 nm in the blue and the green is required to obtain best results. The results showed that the method provides accurate estimation of the oxygenation levels with about 90% accuracy compared to that obtained using the full spectra. The results suggest the potential of quantifying the oxygen saturation levels from the three narrow RGB spectral bands/images.
Alignment-tolerant structures for ease of optoelectronic packaging (1999)

Expanded mode alignment tolerant optical structures will play an important role in low-cost, large-scale packaging of optoelectronic devices. In this paper, we present two expanded mode structures for operation at 1.55 micrometers . Our devices use single epitaxial growth and conventional fabrication schemes. High butt-coupling efficiencies (&gt; 40%) to a single mode fiber with relaxed alignment tolerances were achieved. The first of our devices uses adiabatic transformation over 500 micrometers . The second device uses resonant coupling over a much shorter region of 200 micrometers . The second scheme offers an interesting possibility for monolithic integration of active-passive components. We present the design and simulation results of such an integrated device.
Apolipoprotein E: A pathological chaperone protein in patients with cerebral and systemic amyloid (1992)

Many biochemically diverse proteins can give rise to amyloid fibrils; however, they are all accompanied by P component and glucosaminoglycans. With antibodies specific to apolipoprotein E (apo E) we used immunohistochemical techniques to test for the presence of this protein in both cerebral and systemic amyloid. We found apo E immunoreactivity in all tested types of cerebral and systemic amyloid. In amyloid deposits apo E P, component and glucosaminoglycans may be acting as 'pathological molecular chaperones'. The latter we define as a group of unrelated proteins that induce beta-pleated conformation in amyloidogenic polypeptides.