gebhart/patrepeval huggingface dataset:
Differential Recognition of Influenza A Viruses by M1<sub>58–66</sub>Epitope-Specific CD8<sup>+</sup>T Cells Is Determined by Extraepitopic Amino Acid Residues (2015)

Influenza viruses are an important cause of acute respiratory tract infections. Natural influenza A virus infections elicit both humoral and cellular immunity. CD8(+) cytotoxic T lymphocytes (CTLs) are directed predominantly against conserved internal proteins and confer cross-protection, even against influenza A viruses of various subtypes. In some CTL epitopes, mutations occur that allow influenza A viruses to evade recognition by CTLs. However, the immunodominant HLA-A*0201-restricted M158-66 epitope does not tolerate mutations without loss of viral fitness. Here, we describe naturally occurring variations in amino acid residues outside the M158-66 epitope that influence the recognition of the epitope. These results provide novel insights into the epidemiology of influenza A viruses and their pathogenicity and may aid rational design of vaccines that aim at the induction of CTL responses.
A Boltzmann Machine Implementation for the D-Wave (2015)

The D-Wave is an adiabatic quantum computer. It is an understatement to say that it is not a traditional computer. It can be viewed as a computational accelerator or more precisely a computational oracle, where one asks it a relevant question and it returns a useful answer. The question is how do you ask a relevant question and how do you use the answer it returns. This paper addresses these issues in a way that is pertinent to machine learning. A Boltzmann machine is implemented with the D-Wave since the D-Wave is merely a hardware instantiation of a partially connected Boltzmann machine. This paper presents a prototype implementation of a 3-layered neural network where the D-Wave is used as the middle (hidden) layer of the neural network. This paper also explains how the D-Wave can be utilized in a multi-layer neural network (more than 3 layers) and one in which each layer may be multiple times the size of the D-Wave being used.
Program integration for languages with procedure calls (1995)

Given a program Base and two variants, A and B, each created by modifying separate copies of Base, the goal of program integration is to determine whether the modifications interfere, and if they do not, to create an integrated program that incorporates both sets of changes as well as the portions of Base preserved in both variants. Text-based integration techniques, such as the one used by the Unix diff3 utility, are obviously unsatisfactory because one has no guarantees about how the execution behavior of the integrated program relates to the behaviors of Base, A, and B. The first program integration algorithm to provide such guarantees was developed by Horwitz, Prins, and Reps. However, a limitation of that algorithm is that it only applied to programs written in a restricted language—in particular, the algorithm does not handle programs with procedures. This article describes a generalization of the Horwitz-Prins-Reps algorithm that handles programs that consist of multiple (and possibly mutually recursive) procedures. We show that two straightforward generalizations of the Horwitz-Prins-Reps algorithm yield unsatisfactory results. The key issue in developing a satisfactory algorithm is how to take into account different calling contexts when determining what has changed in the variants A and B. Our solution to this problem involves identifying two different kinds of affected components of A and B: those affected regardless of how the procedure is called, and those affected by a changed or new calling context. The algorithm makes use of interprocedural program slicing to identify these components, as well as components in Base, A, and B with the same behavior.
Psychedelics and Personality (2018)

In the past decade, an increasing number of clinical trials are reporting evidence that psychedelics or serotonergic hallucinogens (such as lysergic acid diethylamide, psilocybin, and ayahuasca/dimethyltryptamine) could be effective in the treatment of mood, anxiety, and substance use disorders. The mechanisms responsible for these effects are not fully understood but seem to involve changes in bran dynamics in areas rich in serotonergic 5-HT<sub>2A</sub> receptors and in personality. In the present text, we present a brief and critical overview of the current research in this field, pointing out both promises and limitations of these studies.
Angiotensin Type 2 Receptors Are Reexpressed by Cardiac Fibroblasts From Failing Myopathic Hamster Hearts and Inhibit Cell Growth and Fibrillar Collagen Metabolism (1997)

These findings demonstrate that AT2-R is re-expressed by cardiac fibroblasts present in fibrous regions in failing CM hearts and that the increased AT2-R exerts an anti-AT1-R action on the progression of interstitial fibrosis during cardiac remodeling by inhibiting both fibrillar collagen metabolism and growth of cardiac fibroblasts.
Expression of CD56 by human papillomavirus E7-specific CD8+ cytotoxic T lymphocytes correlates with increased intracellular perforin expression and enhanced cytotoxicity against HLA-A2-matched cervical tumor cells. (2001)

Human papillomavirus (HPV) infection represents the most important risk factor for developing cervical cancer. In this study, we examine the potential of full-length E7-pulsed autologous dendritic cells (DCs) to induce antigen-specific CTL responses from the peripheral blood of healthy individuals against HLA-A2-matched HPV-16 and HPV-18-positive tumor target cells in vitro. We show that DCs pulsed with E7 oncoprotein can consistently stimulate antigen-specific CTL responses that recognize and lyse HPV-16 or HPV-18-positive naturally infected cervical cancer cell lines. HPV-negative, EBV-transformed lymphoblastoid cell lines (LCLs) sharing the HLA haplotype of the target tumor cells, as well as autologous donor LCLs, were not significantly killed by E7-specific CTLs. Cytotoxicity against HLA-A2-matched HPV-16 and HPV-18 tumor target cells could be significantly inhibited by anti-HLA class I and by anti-HLA-A2 monoclonal antibodies. CD8+ CTLs expressed variable levels of CD56 and showed a strongly polarized Type 1 cytokine profile. Sorting of the CD8+ T cells on the basis of CD56 expression demonstrated that the most highly cytotoxic CTLs were CD56+ and expressed higher levels of perforin and IFN-gamma, compared with the CD8+/CD56- population. Taken together, these data demonstrate that full-length, E7-pulsed DCs can consistently induce E7-specific CD8+ CTL responses in healthy individuals that are able to kill naturally HPV-16 and HPV-18-infected cancer cells, and that CD56 expression defines a subset of CD8+ CTLs with high cytolytic activity against tumor cells.
High-resolution Computer Graphics Using C (1990)

Following the author's successful Practical Introduction to Computer Graphics, this new comprehensive textbook of computer graphics exploits the full range of techniques and effects that recent advanc
An adaptive approach to data placement (2002)

Programming distributed-memory machines requires careful placement of data to balance the computational load among the nodes and minimize excess data movement between the nodes. Most current approaches to data placement require the programmer or compiler to place data initially and then possibly to move it explicitly during a computation. This paper describes a new, adaptive approach. It is implemented in the Adapt system, which takes an initial data placement, efficiently monitors how well it performs and changes the placement whenever the monitoring indicates that a different placement would perform better. Adapt frees the programmer from having to specify data placements, and it can use run-time information to find better placements than compilers. Moreover, Adapt automatically supports a "variable block" placement, which is especially useful for applications with nearest-neighbor communication but an imbalanced workload. For applications in which the best data placement varies dynamically, using Adapt can lead to better performance than using any statically determined data placement.
Caries protection after orthodontic band cementation with glass ionomer. (1994)

This study evaluated the resistance of the enamel to an artificial caries challenge after removing orthodontic bands cemented with a glass ionomer cement (GIC). Ten extracted caries-free molars were cleaned with a slurry of pumice and randomly divided into 2 groups of 5 teeth each: Group 1: Cementation with GIC (Fuji) and Group 2: Cementation with a zinc phosphate cement (Mizzy). Both cements were handled according to manufacturer's instructions. Before cementing the bands, an area of S x S mm was masked with adhesive tape on the lingual surfaces of all teeth. The orthodontic bands were cemented over this adhesive tape. After band cementation, the occlusal and gingival margins of the band were delineated with a bur on the tooth surface. The teeth were thermocycled (200 cycles, 5-55 degrees C, 30-second dwell time) and stored in distilled water for 24 hours. Then, the bands and adhesive tape were removed and the teeth again stored in distilled water for a week, changing the water daily. The teeth were then varnished with the exception of a 5 x 5 mm window (including previously exposed and covered areas) on the buccal and lingual surfaces. All teeth were then placed in an acidified gel (pH 4.5) for 5 weeks to produce artificial caries. At least three sections from the exposed and covered areas were made from the buccal and lingual challenged areas. Sections were ground to approximately 100 microns. Polarized microscopy and image analysis were used to analyze the results.(ABSTRACT TRUNCATED AT 250 WORDS)
Fabricating nanometer-scale Co dot and line arrays on Cu(100) surfaces (2000)

We have templated Cu(100) surfaces with self-assembled arrays of atomic nitrogen islands and then used these islands as masks for Co growth. This method of nanolithography enables the creation of Co dot arrays with dot densities 4×1012 cm−2 (27 teradots/in.2). Adjusting the nitrogen coverage also enabled the creation of arrays of Co lines spaced 10 nm (0.01 μm) apart.
Improvement of Fountain-code Decoding (2011)

Fountain code,due to its rateless properties,could effectively transfer information over erasure channel with unknown erasure rates.However,traditional Fountain code(principally LT code and Raptor code)implements no processing on the discrepant information in the decoding process,thus resulting in certain loss of useful information.This paper describes a new decoding methods for Fountain code,which processes the discrepant information by eliminating the check symbol with a degree of 2.Simulation results show that this method could maintain the rateless properties of Fountain code while raise the utility of information and the efficiency of decoding.
Thermally Tailored Gradient Topography Surface on Elastomeric Thin Films (2014)

We report a simple method for creating a nanopatterned surface with continuous variation in feature height on an elastomeric thin film. The technique is based on imprinting the surface of a film of thermo-curable elastomer (Sylgard 184), which has continuous variation in cross-linking density introduced by means of differential heating. This results in variation of viscoelasticity across the length of the surface and the film exhibits differential partial relaxation after imprinting with a flexible stamp and subjecting it to an externally applied stress for a transient duration. An intrinsic perfect negative replica of the stamp pattern is initially created over the entire film surface as long as the external force remains active. After the external force is withdrawn, there is partial relaxation of the applied stresses, which is manifested as reduction in amplitude of the imprinted features. Due to the spatial viscoelasticity gradient, the extent of stress relaxation induced feature height reduction varies across the length of the film (L), resulting in a surface with a gradient topography with progressively varying feature heights (hF). The steepness of the gradient can be controlled by varying the temperature gradient as well as the duration of precuring of the film prior to imprinting. The method has also been utilized for fabricating wettability gradient surfaces using a high aspect ratio biomimetic stamp. The use of a flexible stamp allows the technique to be extended for creating a gradient topography on nonplanar surfaces as well. We also show that the gradient surfaces with regular structures can be used in combinatorial studies related to pattern directed dewetting.
Carrier multiplication in a PbSe nanocrystal and P3HT/PCBM tandem cell (2008)

Photoactivation of multiple carrier charge extraction in a tandem cell configuration is demonstrated. An all-solution-processed tandem photovoltaic structure, consisting of a hydrazine treated PbSe nanocrystal film and a P3HT/PCBM bulk-heterojunction solar cell, was fabricated. The PbSe nanocrystal film was used as the top cell to predominantly absorb short wavelength light (UV/blue). The lower P3HT/PCBM cell absorbed the remaining solar energy and supplied photocurrent as well as an electric field that extracts the photogenerated charge from the PbSe layer. Carrier multiplication from excitation of the PbSe film with high energy photons was quantified by selective light bias activation measurements.
Rate Constants for Reactions of Alkyl Radicals with Water and Methanol Complexes of Triethylborane (2007)

Reactions of secondary alkyl radicals with triethylborane and several of its complexes were studied. The H-atom transfer reactions from Et3B−OH2 and Et3B−OD2 were suppressed by addition of pyridine to the reaction mixture. Rate constants for reactions of secondary alkyl radicals with triethylborane and its complexes with water, deuterium oxide, methanol, and THF at ambient temperature were determined by radical clock methods. Cyclization of the 1-undecyl-5-hexenyl radical and ring opening of the 1-cyclobutyldodecyl radical were evaluated as clock reactions. The cyclobutylcarbinyl radical ring opening had the appropriate velocity for relatively precise determinations of the ratios of rate constants for H-atom transfer trapping and rearrangement, and these ratios combined with an estimated rate constant for the cyclobutylcarbinyl radical ring opening gave absolute values for the rate constants for the H-atom transfer reactions. For example, the triethylborane−water complex reacts with a secondary alkyl radical in benzene at 20 °C with a rate constant of 2 × 104 M-1 s-1. Variable temperature studies with the Et3B−CH3OH complex in toluene indicate that the hydrogen atom transfer reaction has unusually high entropic demand, which results in substantially more efficient hydrogen atom transfer trapping reactions in competition with radical ring opening and cyclization reactions at reduced temperatures.
VHDL Simulation of Magnetic Domain Wall Logic (2006)

The VHSIC hardware description language (VHDL) simulation of domain wall logic allows to validate magnetic circuits functionality early in the design stage. In this paper, we present two VHDL simulation techniques for domain wall (DW) logic. The first one, closer to the physics, uses models of components described at the behavioral level. It allows to study the basic functions and reveals the specificities of DW logic. The second one, closer to the logic, models components with logic gates and delays and it allows very fast simulation of complex circuits
ChemInform Abstract: SPECTROSCOPY OF COBALT‐ETHYLENEDIAMINE‐OXYGEN ADDUCTS IN THE SUPERCAGES OF ZEOLITES (1981)

Abstract Der Komplex (Ia) wird durch Adsorption von gasförmigem Ethylendi ‐ amin in den großen Hohlräumenvon Zeolithen des Faujasit‐Typs gebildet.
Pump to signal RIN transfer in Raman fiber amplifiers (2001)

We present an analytical model and measurements of the pump to signal relative intensity noise (RIN) transfer characteristics of copumped and counterpumped Raman amplifiers. We give a quantitative analysis of noise averaging from chromatic dispersion in copumped systems and from different propagation directions in counterpumped systems. It is shown that nondispersion-shifted fibers and other fibers with high dispersion between the signal and pump wavelengths give a greater potential for use in copumped Raman amplified systems.
Interleukin-10 Gene Expression in Acute Virus-induced Asthma (2005)

Asthma exacerbation triggered by respiratory virus infection is characterized by increased IL-10 gene expression that may explain the suppressed eosinophil influx in acute asthma. Airway neutrophilia due to respiratory virus infection is associated with chemokine gene expression involving RANTES and macrophage inflammatory protein-1alpha.
A logic and time nets for probabilistic inference (1991)

In this paper, we show a new approach for reasoning about time and probability that combines a formal declarative language with a graph representation of systems of random variables for making inferences. First, we provide a continuous-time logic for expressing knowledge about time and probability. Then, we introduce the time net, a kind of Bayesian network for supporting inference with statements in the logic. Time nets encode the probability of facts and events over time. We provide a simulation algorithm to compute probabilities for answering queries about a time net. Finally, we consider an incremental probabilistic temporal database based on the logic and time nets to support temporal reasoning and planning applications. The result is an approach that is semantically well-founded, expressive, and practical.
Radio in local loop for rural and sub-urban environments (2002)

The paper is focusing on various technologies for radio in the local loop (RLL). Special attention is paid to rural and sub-urban areas. Economical calculations are carried out for a digital cordless system (DECT) demonstrating the competitiveness of wireless solutions as compared to traditional copper wires. The calculations were done with the tools developed within RACE 2087/TITAN-project.
Mitochondrial dysfunction in some triple-negative breast cancer cell lines: role of mTOR pathway and therapeutic potential (2014)

Our study shows that TNBC cells have profound metabolic alterations characterized by decreased mitochondrial respiration and increased glycolysis. Due to their impaired mitochondrial function, TNBC cells are highly sensitive to glycolytic inhibition, suggesting that such metabolic intervention may be an effective therapeutic strategy for this subtype of breast cancer cells.
Formulation of intranasal mucoadhesive temperature-mediated<i>in situ</i>gel containing ropinirole and evaluation of brain targeting efficiency in rats (2009)

Mucoadhesive temperature-mediated in situ gel formulations using chitosan and hydroxyl propyl methyl cellulose were used to enhance intranasal (i.n.) delivery of the dopamine D2 agonist ropinirole to the brain. Formulations were tested for gelation time, thermosensitivity, mucoadhesion, in vitro release and permeation, in vitro cytotoxicity, nasal clearance, in vivo bioavailability and brain uptake. In vivo bioavailability and brain uptake of ropinirole were assessed in albino rats following intranasal administration of 99mTc-ropinirole in situ gel, intranasal ropinirole solution and intravenous (i.v.) ropinirole solution. Radiolabeled ropinirole uptake was calculated as a fraction of administered dose. The absolute bioavailabilty of ropinirole from the temperature-mediated in situ gelling nasal formulation was 82%. The AUC (0-480 min) in brain after nasal administration of ropinirole in situ gel was 8.5 times (869 +/- 250% x min/g versus 102 +/- 20% x min/g) that obtained following i.v. administration, this value was also considerably higher (869 +/- 250% x min/g versus 281 +/- 52% x min/g) than that achieved with intranasal ropinirole solution. High brain direct drug transport percentage (DTP; 90.36%) and drug targeting index (DTI) > 1 confirms direct nose to brain transport of the intranasal in situ gel formulation of ropinirole.
Mycological and Electron Microscopic Study of <i>Solanum chrysotrichum</i> Saponin SC-2 Antifungal Activity on <i>Candida</i> Species of Medical Significance (2007)

Solanum chrysotrichum is utilized in traditional Mexican medicine for the treatment of mycotic skin infections. Several microbiological studies have provided evidence of its antifungal activity against dermatophytes and yeasts. S. chrysotrichum saponins have been identified as a group of compounds with antifungal activity and saponin SC-2 has demonstrated to be the most active. Previous clinical studies have shown the therapeutic effectiveness of S. chrysotrichum-derived saponin-standardized herbal products in the treatment of Tinea pedis and Pityriasis capitis. There is no previous evidence of the activity of these saponins against Candida non-albicans species, or fluconazole- and ketoconazole-resistant Candida strains. The present study reports the biological activity of the SC-2 saponin (inhibitory concentration [IC (50)] and minimum fungicide concentration [MFC]), against 12 Candida strains of clinical significance ( C. albicans, five strains; C. glabrata and C. parapsilosis, two; C. krusei, C. lusitaniae and C. tropicalis, one), including some fluconazole (Fluco)- and ketoconazole (Keto)-resistant clinical isolates. In addition, SC-2-associated microstructural alterations were reported in four of the above-mentioned Candida species. Seven strains had IC (50) of 200 microg/mL for SC-2, 400 microg/mL was found in four strains, and 800 microg/mL for a sole C. glabrata strain. Susceptibility to SC-2 saponin was as follows: C. albicans = C. lusitaniae > C. krusei > C. glabrata. The MFC was 800 microg/mL for the majority of strains (nine), 400 microg/mL for C. albicans (two strains) and C. lusitaniae. The ultrastructural Candida changes originated by SC-2 included the following: 1) damage on cytoplasmic membrane and organelles; 2) changes in cell wall morphology and density, with separation of cytoplasmatic membrane from cell wall and disintegration of the latter; and 3) total degradation of cellular components and death. Changes were manifested from 6 h of incubation, reaching their maximum effect at 48 h. In conclusion, the saponin SC-2 possesses fungicide and fungistatic activity on different Candida albicans and non- albicans species (including some azole-resistant strains) with IC (50) values of 200 microg/mL (in Fluco-susceptible strains) and of 400 - 800 mug/mL (in Fluco-resistant strains). Additionally, we observed by transmission electron microscopy (TEM) that saponin SC-2 causes severe changes in all fungal cell membranes, and to a lesser degree on the cell wall.
An Election Algorithm for a Distributed Clock Synchronization Program (1985)

This paper describes the election algorithm that guarantees the reliability of TEMPO, a distributed clock synchronizer running on Berkeley UNIX 4.3BSD systems. TEMPO is a distributed program based on a master-slave scheme that is comprised of time daemon processes running on individual machines. The election algorithm chooses a new master from among the slaves after the crash of the machine on which the original master was running. When the master is working, it periodically resets an election timer in each slave. If the master disappears, the sl ave whose timer expires first will become a candidate for the new master. The election algorithm covers this normal case, as well as the infrequent case where there may be two or more simultaneous candidates. It also handles the case in which, due to a network partition that has been repaired, two masters are present at the same time.