gebhart/patrepeval huggingface dataset:
Scan-Puf: Puf Elements Selection Methods for Viable IC Identification (2015)

The scan PUF, which is based-on the power-up states of scan flip-flops, had been proposed to overcome security issues of semiconductor ICs. IC identification, one of those security issues, requires decent uniqueness along with reliability and randomness. This paper presents two efficient PUF elements' selection methods for scan PUF: uniqueunanimous selection method and unique-majority selection method. These methods classify the scan cells according to their trend of power-up states and prioritize them to extract PUF elements. For experiments, enrollment and validation is performed on 15 chips, which are fabricated with 65nm CMOS process. A statistical analysis on experiments verifies the performance of proposed selection methods.
Accuracy in the localization of thoracic and abdominal tumors using respiratory displacement, velocity, and phase (2009)

This study illustrates that position of a tumor can be determined more accurately if displacement and velocity are used simultaneously as sorting parameters for 4D CT images or during treatment. A real-time displacement and velocity based 4D CT image sorting method may therefore produce fewer and smaller artifacts in 4D CT images than current retrospective sorting methods.
Cell culture propagation of foot-and-mouth disease virus: adaptive amino acid substitutions in structural proteins and their functional implications (2019)

Foot-and-mouth disease is endemic in livestock in large parts of Africa and Asia, where it is an important driver of food insecurity and a major obstacle to agricultural development and the international trade in animal products. Virtually all commercially available vaccines are inactivated whole-virus vaccines produced in cell culture, but the adaptation of a field isolate of the virus to growth in culture is laborious and time-consuming. This is of particular concern for the development of vaccines to newly emerging virus lineages, where long lead times from virus isolate to vaccine can delay the implementation of effective control programs. High antigen yields in production cells are also necessary to make vaccines affordable for less developed countries in endemic areas. Therefore, a rational approach to cell culture adaptation that combines prior knowledge of common adaptive mutations and reverse genetics techniques is urgently required. This review provides an overview of amino acid exchanges in the viral capsid proteins in the context of adaptation to cell culture.
Remaking the IT Management Curriculum: A 'Novel' Approach (2008)

We report on an experiment in redesign of curriculum for Information Technology (IT) management courses, a synthetic approach that attempts to combine the best features of explanation- and experience-based approaches. The IVK case series is a fictitious though realitybased story about the struggles of a newly appointed, not-technically-trained CIO in his first year on the job. The series constitutes a true-to-life novel, intended to involve students in an engaging story that simultaneously explores the nuances of major IT management issues. Three principles guided our development of this curriculum: 1) Emphasis on the business aspects of IT, independent of underlying technologies; 2) Student derivation of cumulative management frameworks arrived at via inductive in-class discussion; and 3) Identification of a set of core issues most vital in IT management practice, as a business discipline. We report results from using the curriculum with undergraduate and graduate students, and with executives at a multinational corporation.
Cancer biomarkers - current perspectives. (2010)

In the recent years, knowledge about cancer biomarkers has increased tremendously providing great opportunities for improving the management of cancer patients by enhancing the efficiency of detection and efficacy of treatment. Recent technological advancement has enabled the examination of many potential biomarkers and renewed interest in developing new biomarkers. Biomarkers of cancer could include a broad range of biochemical entities, such as nucleic acids, proteins, sugars, lipids, and small metabolites, cytogenetic and cytokinetic parameters as well as whole tumour cells found in the body fluid. A comprehensive understanding of the relevance of each biomarker will be very important not only for diagnosing the disease reliably, but also help in the choice of multiple therapeutic alternatives currently available that is likely to benefit the patients. This review provides a brief account on various biomarkers for diagnosis, prognosis and therapeutic purposes, which include markers already in clinical practice as well as various upcoming biomarkers.
Sustained Long-Term Engraftment and Transgene Expression of Peripheral Blood CD34+ Cells Transduced with Third-Generation Lentiviral Vectors (2008)

As mobilized peripheral blood (MPB) represents an attractive cell source for gene therapy, we investigated the ability of third-generation lentiviral vectors (LVs) to transfer the enhanced green fluorescent protein gene into MPB CD34(+) cells in culture conditions allowing expansion of transplantable human hematopoietic stem cells. To date, few studies have reported transduction of MPB cells with vesicular stomatitis virus G pseudotyped LVs. The critical issue remains whether primitive, hematopoietic repopulating cells have, indeed, been transduced. In vitro (5 weeks' culture in FLT3 ligand + thrombopoietin + stem cell factor + interleukin 6) and in vivo (serial transplantation in NOD/SCID mice) experiments show that MPB CD34(+) cells can be effectively long-term transduced by LV and maintain their proliferation, self-renewal, and multilineage differentiation potentials. We show that expansion following transduction improves the engraftment of transduced MPB CD34(+) (4.6-fold expansion of SCID repopulating cells by limiting dilution studies). We propose ex vivo expansion after transduction as an effective tool to improve gene therapy protocols with MPB. Disclosure of potential conflicts of interest is found at the end of this article.
Applications of pressure tolerant electronics (1977)

This paper begins with a brief background on Pressure Tolerant Electronics (PTE). Next is a section describing PTE systems that have been successfully used but are no longer in use, or have been in use for several years. Under this heading, five systems are described: (1) the control system for the two-manned, transparent-hulled submersible MAKAKAI, (2) the sonar used on the Navy's experimental submarine DOLPHIN (AGSS 555), (3) high current circuit breakers, (4) an acoustic line array telemetry system, and (5) a small preamplifier. Included in the discussion of each system is the rationale for using PTE in that system and available system performance and failure data. Next, five PTE systems currently in use are discussed. These are: (1) a pressure tolerant TV camera, (2) an acoustic imaging system, (3) a 70 mm still camera, (4) a digital compass, and (5) a submerged oil production system. Again, the rationale for using PTE in these systems and performance and failure data are included.
The Mixed-Network Former Effect in Phosphate Glasses: NMR and XPS Studies of the Connectivity Distribution in the Glass System (NaPO<sub>3</sub>)<sub>1−<i>x</i></sub>(B<sub>2</sub>O<sub>3</sub>)<sub><i>x</i></sub> (2008)

The structural organization of sodium borophosphate glasses with composition (NaPO3)1−x(B2O3)x (0.0 ≤ x ≤ 0.3) has been investigated by X-ray photoelectron spectroscopy (XPS), as well as single- and double-resonance 11B and 31P magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. O-1s XPS data provides a quantitative distinction between B−O−B, B−O−P, and P−O−P linkages as well as nonbridging oxygen atoms. 11B and 31P MAS NMR data indicate that within the compositional region 0 ≤ x ≤ 0.20 the entire boron inventory is present in the form of anionic BO4− units, resulting in the repolymerization of an equivalent fraction of the phosphate units (conversion of anionic metaphosphate (P(2)) into neutral branching groups (P(3)) species. Both XPS as well as 31P{11B} and 11B{31P} rotational echo double resonance (REDOR) NMR results reveal strong interactions between the two network formers boron oxide and phosphorus oxide, resulting in the dominant formation of B−O−P linkages. In addition, the shape of the REDOR curve reveals a certain tendency of these linkages to cluster, consistent with a preference of P(3) units to form more than one P−O−B linkage, even at low boron contents. The enhanced degree of network polymerization correlates with a significant increase of the glass transition temperature as a function of boron content.
Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A. (1988)

The protease encoded by the human immunodeficiency virus (HIV) processes the viral gag and gag-pol protein precursor by posttranslational cleavage. In this study we have demonstrated by site-specific mutagenesis (Asp----Thr) and by pepstatin A inhibition that the recombinant HIV protease is an aspartic-type protease. Furthermore, incubation of HIV-infected H9 cells with pepstatin A inhibited part of the intracellular processing of the HIV gag protein yet had no apparent toxicity on HIV-infected cells during 48 hr of incubation.
Corrosion Resistance of UV-Cured Urethane Acrylate Coatings Containing Dibutyl-Substituted Poly(3,4- propylenedioxythiophene) as a Corrosion Inhibitor (2015)

Photopolymerization of urethane acrylate (PUA) containing solution-processable dibutyl-substituted poly(3,4-propylenedioxythiophene) (Poly(ProDotBu2)) was applied on Q235 carbon steel. The corrosion resistance of as-prepared composite coatings with various contents of Poly(ProDotBu2) was studied by electrochemical techniques including open-circuit potential (OCP), potentiodynamic polarization curves and electrochemical impedance spectroscopy (EIS). It was observed that the PUA/Poly(ProDotBu2) composite coatings exhibited an excellent corrosion resistance and barrier properties in comparison with pure PUA coating.
Fuzzy Abduction Employing Implications with Composed Propositions in Their Antecedents : Solving Simultaneous Equations Consisting of Fuzzy Logical Products (1996)

原因と結果のあいまいな関係を利用し, 観測されたあいまいな事象からその原因を推論する方法として, ファジィ関係式の逆問題やファジィアブダクションがある。しかし, 複数の原因が同時に起こる時のみに生じる事象が含まれる問題にはこれまでに提案されている方法を適用することができない。そこで本稿では, そのような問題にもファジィアブダクションの適用を可能にする一方法を提案する。具体的にはまず, 複数の原因の論理積を前件に, それらの原因によって生じる事象を後件に持つ含意で因果関係を表現する。そして含意の前件にある合成命題を仮想的な1つの命題に置き換え, 従来のファジィアブダクションの問題を解く。これにより複数の合成命題に対する真理値が得られるため, 次にそれらの合成命題を構成する原因の真理値を求める問題を扱う。本稿ではこの後半の問題をファジィ論理積連立方程式と呼ぶ。そしてその解法, 解空間の構造, および解の存在と近似解の解法について議論する。最後に, 数値例を示し, 異常診断への応用について考察する。
Reasoning about functional dependencies generalized for semantic data models (1992)

We propose a more general form of functional dependency for semantic data models that derives from their common feature in which the separate notions of domain and relation in the relational model are combined into a single notion of class . This usually results in a richer terminological component for their query languages, whereby terms may navigate through any number of properties, including none. We prove the richer expressiveness of this more general functional dependency, and exhibit a sound and complete set of inference axioms. Although the general problem of decidability of their logical implication remains open at this time, we present decision procedures for cases in which the dependencies included in a schema correspond to keys, or in which the schema itself is acyclic. The theory is then extended to include a form of conjunctive query. Of particular significance is that the query becomes an additional source of functional dependency. Finally, we outline several applications of the theory to various problems in physical design and in query optimization. The applications derive from an ability to predict when a query can have at most one solution.
The Variable Discharge of Cortical Neurons: Implications for Connectivity, Computation, and Information Coding (1998)

Cortical neurons exhibit tremendous variability in the number and temporal distribution of spikes in their discharge patterns. Furthermore, this variability appears to be conserved over large regions of the cerebral cortex, suggesting that it is neither reduced nor expanded from stage to stage within a processing pathway. To investigate the principles underlying such statistical homogeneity, we have analyzed a model of synaptic integration incorporating a highly simplified integrate and fire mechanism with decay. We analyzed a "high-input regime" in which neurons receive hundreds of excitatory synaptic inputs during each interspike interval. To produce a graded response in this regime, the neuron must balance excitation with inhibition. We find that a simple integrate and fire mechanism with balanced excitation and inhibition produces a highly variable interspike interval, consistent with experimental data. Detailed information about the temporal pattern of synaptic inputs cannot be recovered from the pattern of output spikes, and we infer that cortical neurons are unlikely to transmit information in the temporal pattern of spike discharge. Rather, we suggest that quantities are represented as rate codes in ensembles of 50-100 neurons. These column-like ensembles tolerate large fractions of common synaptic input and yet covary only weakly in their spike discharge. We find that an ensemble of 100 neurons provides a reliable estimate of rate in just one interspike interval (10-50 msec). Finally, we derived an expression for the variance of the neural spike count that leads to a stable propagation of signal and noise in networks of neurons-that is, conditions that do not impose an accumulation or diminution of noise. The solution implies that single neurons perform simple algebra resembling averaging, and that more sophisticated computations arise by virtue of the anatomical convergence of novel combinations of inputs to the cortical column from external sources.
Functional and Physical Interactions of the Herpes Simplex Virus Type 1 UL20 Membrane Protein with Glycoprotein K (2008)

Herpes simplex virus type 1 glycoprotein K (gK) and the UL20 protein (UL20p) are coordinately transported to the trans-Golgi network (TGN) and cell surfaces and are required for cytoplasmic virion envelopment at the TGN. In addition, cell surface expression of gK and UL20p is required for virus-induced cell fusion. Previously, confocal microscopy colocalization and intracellular transport experiments strongly suggested direct protein-protein interactions between gK and UL20p. Direct protein-protein interactions between gK and UL20p were demonstrated through reciprocal coimmunoprecipitation experiments, as well as with glutathione S-transferase (GST) pull-down experiments. A fusion protein consisting of the amino-terminal 66 amino acids of UL20p fused in-frame with GST was expressed in Escherichia coli and purified via glutathione column chromatography. Precipitation of GST-UL20p from mixtures of GST-UL20p fusion protein with cellular extracts containing gK specifically coprecipitated gK but not other viral glycoproteins. The purified UL20p-GST fusion protein reacted with all gK-associated protein species. It was concluded that the amino terminus of UL20p, most likely, interacted with gK domain III, which is predicted to lie intracellularly. UL20p-gK domain-specific interactions must serve important functions in the coordinate transport of UL20p and gK to the TGN, because retention of UL20p in the endoplasmic reticulum (ER) via the addition of an ER retention signal at the carboxyl terminus of UL20p forced the ER retention of gK and drastically inhibited intracellular virion envelopment and virus-induced cell fusion.
Tuning hERG Out: Antitarget QSAR Models for Drug Development (2014)

Several non-cardiovascular drugs have been withdrawn from the market due to their inhibition of hERG K+ channels that can potentially lead to severe heart arrhythmia and death. As hERG safety testing is a mandatory FDArequired procedure, there is a considerable interest for developing predictive computational tools to identify and filter out potential hERG blockers early in the drug discovery process. In this study, we aimed to generate predictive and well-characterized quantitative structure-activity relationship (QSAR) models for hERG blockage using the largest publicly available dataset of 11,958 compounds from the ChEMBL database. The models have been developed and validated according to OECD guidelines using four types of descriptors and four different machine-learning techniques. The classification accuracies discriminating blockers from non-blockers were as high as 0.83-0.93 on external set. Model interpretation revealed several SAR rules, which can guide structural optimization of some hERG blockers into non-blockers. We have also applied the generated models for screening the World Drug Index (WDI) database and identify putative hERG blockers and non-blockers among currently marketed drugs. The developed models can reliably identify blockers and non-blockers, which could be useful for the scientific community. A freely accessible web server has been developed allowing users to identify putative hERG blockers and non-blockers in chemical libraries of their interest (http://labmol.farmacia.ufg.br/predherg).
Hepatic HIF-2 regulates erythropoietic responses to hypoxia in renal anemia (2010)

The kidney is the main physiologic source of erythropoietin (EPO) in the adult and responds to decreases in tissue oxygenation with increased EPO production. Although studies in mice with liver-specific or global gene inactivation have shown that hypoxia-inducible factor 2 (Hif-2) plays a major role in the regulation of Epo during infancy and in the adult, respectively, the contribution of renal HIF-2 signaling to systemic EPO homeostasis and the role of extrarenal HIF-2 in erythropoiesis, in the absence of kidney EPO, have not been examined directly. Here, we used Cre-loxP recombination to ablate Hif-2α in the kidney, whereas Hif-2-mediated hypoxia responses in the liver and other Epo-producing tissues remained intact. We found that the hypoxic induction of renal Epo is completely Hif-2 dependent and that, in the absence of renal Hif-2, hepatic Hif-2 takes over as the main regulator of serum Epo levels. Furthermore, we provide evidence that hepatocyte-derived Hif-2 is involved in the regulation of iron metabolism genes, supporting a role for HIF-2 in the coordination of EPO synthesis with iron homeostasis.
Unique Ecophysiology among U(VI)-Reducing Bacteria as Revealed by Evaluation of Oxygen Metabolism in <i>Anaeromyxobacter dehalogenans</i> Strain 2CP-C (2009)

Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2x10(7)+/-8.6x10(6) to 1.0x10(8)+/-2.2x10(7) cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3x10(4)+/-1.1x10(4) cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [micro=(-0.09xpO2)+0.051; R2=0.923] was observed between the instantaneous specific growth rate micro and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. dehalogenans from other known U(VI)-reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.
Localization and Significance of γ-Glutamyltranspeptidase in Normal and Neoplastic Mouse Skin (1978)

The suggestion that elevated γ-glutamyltranspeptidase (GGT) activity could be a marker for hepatic neoplasia has prompted us to investigate the role of this enzyme in normal and neoplastic mouse skin. In normal skin, as determined histochemically with N -(γ-l-glutamyl)-4-methoxy-2-naphthylamide as substrate, GGT was found only in the lower epithelium of growing hair follicles. GGT activity was never detected in the interfollicular epidermis of 1-day-old prenatal, newborn, or adult skin. Whole-skin enzyme activity measured biochemically, with l-γ-glutamyl- p -nitroanilide as substrate, was elevated about 9-fold during periods of hair growth. GGT activity rose and then fell abruptly as the mice progressed through the growing phase and then the resting phase of the hair growth cycle.

Skin tumors were induced by initiation with 7,12-dimethylbenz[ a ]anthracene followed by promotion with 12- O -tetradecanoylphorbol-13-acetate. Histochemically, GGT was not present in eight benign papillomas examined. However, single epithelial cells, islands of epithelial cells, and/or follicle-like structures were intensely GGT positive in seven of eight malignant squamous carcinomas examined. The association of GGT activity with normal hair growth and its presence in squamous carcinomas raises the following interesting possibilities: ( a ) aberrant gene activation in malignant interfollicular epidermis; ( b ) a recruitment of follicular cells by invasive malignant interfollicular epidermis; ( c ) a follicular origin for the GGT-positive carcinoma.
Imaging Time After Gd-DTPA Injection Is Critical in Using Delayed Enhancement to Determine Infarct Size Accurately With Magnetic Resonance Imaging (2001)

In reperfused acute MI, accurate determination of infarct size by delayed enhancement MRI requires imaging at specific times after Gd-DTPA injection, and this time varies with the duration of occlusion.