gebhart/patrepeval huggingface dataset:
Human T-cell clones to the 70-kilodalton heat shock protein of Mycobacterium leprae define mycobacterium-specific epitopes rather than shared epitopes (1997)

The mycobacterial 70-kDa heat shock protein (Hsp70) is a dominant antigen during the human T-cell response to mycobacterial infection despite the conserved sequence with the human homolog. To determine whether this response is pathogen specific, CD4+ T-cell clones were isolated from Mycobacterium leprae Hsp70-reactive individuals. The cytokine profile of the clones was mixed, with all of the clones releasing interferon gamma and half releasing interleukin-4 on stimulation, while six demonstrated cytolytic activity. Five clones reacted with the N-terminal half of the molecule, and the epitopes identified were mycobacterium specific. Residues 241 to 260 were identified by three clones, one of which was restricted by HLA-DR7 (DR7), while a DR1-restricted clone identified residues 71 to 90 and residues 261 to 280 were recognized in the context of DR3. The remaining five T-cell clones reacted with the C-terminal half of the molecule, and the precise position of these epitopes was mapped with 12-mer peptides overlapping by 11 residues. Two of these clones identified overlapping epitopes from residues 411 to 425 and 412 to 428, the latter restricted by DR3. Further epitopes were mapped to residues 298 to 313 restricted by DRw53, residues 388 to 406 restricted by DRw52 or DQ2, and residues 471 to 486 restricted by DR1. The sequences of three epitopes, residues 411 to 425, 412 to 428, and 471 to 486, showed significant identity with the equivalent regions of the prototype human Hsp70. However, when amino acid substitutions that made the sequence more like the human sequence were introduced, the changes were tolerated poorly as measured by proliferation, cytokine production, and cytotoxic potential. Therefore, T-cell recognition of the M. leprae Hsp70 antigen occurs in the context of multiple HLA-DR phenotypes and is exquisitely species specific.
Protein Structure Prediction and Structural Genomics (2001)

Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.
Privacy-enhanced electronic mail (1991)

(Revision 3). The security of electronic mail sent through the Internet may be described in exactly three words: there is none. The Privacy and Security Research Group has recommended implementing mechanisms designed to provide security enhancements. The first set of mechanisms provides a protocol to provide privacy, integrity, and authentication for electronic mail; the second provides a certificate-based key management infrastructure to support key distribution throughout the internet, to support the first set of mechanisms. This paper describes these mechanisms, as well as the reasons behind their selection and how these mechanisms can be used to provide some measure of securtiy in the exchange of electronic mail.
Role of a Streptococcus gordonii copper‐transport operon, copYAZ, in biofilm detachment (2004)

Streptococcus gordonii is a pioneer oral bacterium that is associated with the initiation of dental plaque development. Located downstream of the S. gordonii adc operon, which is involved in competence and biofilm formation, were three open reading frames, designated copY, copA and copZ. These open reading frames were homologous to the copYAZ genes in Streptococcus mutans that are involved in copper homeostasis and biofilm detachment. This study examined whether copYAZ genes play any role in the biofilm formation and detachment of S. gordonii. The copY gene encodes a 143-amino acid protein homologous to the negative transcriptional regulator of a copper-transport operon, copA encodes a 748-amino acid copper-transporting P-type ATPase, and copZ encodes a 69-amino acid putative metallochaperone protein in S. mutans. Each open reading frame in the copYAZ operon in S. gordonii was inactivated by insertional mutation and the growth, biofilm formation and detachment of each mutant were examined. S. gordonii copY::specR, copA::specR, and copZ::specR mutants were able to form biofilms on both polystyrene and glass surfaces. However, inactivation of copZ and to a lesser extent copY resulted in phenotypes that were defective in biofilm detachment, which is consistent with previous observations in S. mutans and suggests that the trace element copper might influence biofilm detachment of bacterial biofilms.
Holoprosencephaly: An update on cytogenetic abnormalities (2010)

Abstract Holoprosencephaly (HPE), the most common developmental defect of the forebrain and midface, is caused by a failure of midline cleavage early in gestation. Isolated HPE, which is highly genetically heterogeneous, can be due to major chromosomal abnormalities. Initially, karyotype approach led to the identification of several recurrent chromosomal anomalies predicting different HPE loci. Subsequently, several genes were isolated from these critical HPE regions, but point mutations and deletions in these genes were found only in 25% of the genetic cases. In order to identify other HPE genes, a more accurate investigation of the genome in HPE patients was necessary. To date, high‐resolution cytogenetic techniques such as subtelomeric multiplex ligation‐dependent probe amplification (MLPA) and microarray‐based comparative genomic hybridization (array CGH) have enhanced chromosomal aberration analysis. In this article, we have updated the cytogenetic anomalies associated with HPE in a map listing all the subtelomeric and interstitial deletions that have been characterized either by karyotype, MLPA, or array CGH. The accumulation of recurrent genomic imbalances will lead to the further delineation of minimal critical HPE loci, which is the first step to the identification of new HPE genes. © 2010 Wiley‐Liss, Inc.
Thin crystal film polarizers and retarders (2002)

We developed a new technology for thin crystal film (TCF) manufacturing based on water-soluble salts of aromatic polycyclic compounds. TCF is produced by coating and subsequent drying of an aqueous solution on plastic or glass surface into molecularly oriented 100-1000 nm thick crystal nano-film. First industrial application of nano-films is TCF polarizer for liquid crystal displays (LCD). TCF polarizers are made from modified organic dyes with relatively narrow spectral absorption band. Mixing various dyes allows covering broad spectral region. Blending provides variety of combinations of background and character colors that are necessary for applications. TCF made from dichroic dyes are highly anisotropic, biaxial extraordinary polarizers. Birefringence of TCF made from some materials reaches 1.0. Several highly birefringent TCFs show specific retardation characteristics. For example, 300 nm thick TCF based on dichroic dye with narrow absorption band at 450 nm and transparent in the long-wave region, has maximum birefringence of 0.85 in the wavelength region of 500-800 nm. TCF are available for industrial application in LCD as external, internal polarizers and retarders.
Nucleotide sequence of the Streptococcus mutans gtfD gene encoding the glucosyltransferase-S enzyme (1990)

The nucleotide sequence of the Streptococcus mutans GS-5 gtfD gene coding for the glucosyltransferase which synthesizes water-soluble glucan (GTF-S) has been determined. The complete gene contains 4293 base pairs and the unprocessed protein is composed of 1430 amino acids with a molecular mass of 159814 Da. The amino terminus of the unprocessed protein resembles the signal sequences of other extracellular proteins secreted by S. mutans and that of the GTF-I secreted by Streptococcus downei. In addition, the GTF-S protein exhibits high amino acid similarity with the strain GS-5 enzymes responsible for insoluble glucan synthesis (GTF-I, GTF-SI) previously isolated and sequenced in this laboratory. These results indicate that all three gtf genes evolved from a common ancestral gene.
Dissolution enhancement of flavonoids by solid dispersion in PVP and PEG matrixes: A comparative study (2006)

Abstract Polyvinylpyrrolidone (PVP) and poly(ethylene glycol) (PEG) solid dispersion systems with flavanone glycosides, naringin and hesperidin, and their aglycones, naringenin and hesperetin, were prepared, using solvent evaporation method, to enhance their dissolution rates that may affect their bioavailability. Drug release of both flavanone glycosides and their aglycones was directly affected by the physical state of solid dispersions. Powder‐XRD technique in combination with scanning and transmission electron microscopy revealed that PVP polymer formed amorphous nanodispersion systems with flavanone aglycones, while such systems could not be formed with their glycosides, which are bulkier molecules. Fourier transform infrared spectra suggest the presence of hydrogen bonds between PVP carbonyl groups and hydroxyl groups of both flavanone aglycones. These interactions prevent the crystallization of naringenin and hesperetin aglycones in PVP matrix. On the other hand, the ability of PEG carrier to form hydrogen bonds with flavanone glycosides or aglycones was limited, and as a result both flavanone glycosides and their aglycones remain in the crystalline form. For this reason, the solubility enhancement of PEG solid dispersions was lower than when PVP was used as drug carrier. At pH 6.8, the % release of naringenin and hesperetin from PVP/naringenin–hesperetin (80/20 w/w) solid dispersion was 100% while in PEG solid dispersions, it was not higher than 60–70%. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 460–471, 2006
Modularly Designed Organocatalytic Assemblies for Direct Nitro‐Michael Addition Reactions (2008)

It's so simple! Organocatalysts formed through the self-assembly of simple α-amino acids and alkaloid thiourea derivatives (see scheme) are used as highly efficient catalysts for the direct nitro-Michael addition of ketones and nitroalkenes, affording excellent ee values up to 99 %. Enantioselectivity may be tuned by changing components of the self-assembled catalyst. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z803236_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
G Protein-coupled Receptor Kinase 2 Regulator of G Protein Signaling Homology Domain Binds to Both Metabotropic Glutamate Receptor 1a and Gαq to Attenuate Signaling (2004)

Heterotrimeric guanine nucleotide-binding (G) protein-coupled receptor kinases (GRKs) are cytosolic proteins that contribute to the adaptation of G protein-coupled receptor signaling. The canonical model for GRK-dependent receptor desensitization involves GRK-mediated receptor phosphorylation to promote the binding of arrestin proteins that sterically block receptor coupling to G proteins. However, GRK-mediated desensitization, in the absence of phosphorylation and arrestin binding, has been reported for metabotropic glutamate receptor 1 (mGluR1) and gamma-aminobutyric acid B receptors. Here we show that GRK2 mutants impaired in Galphaq/11 binding (R106A, D110A, and M114A), bind effectively to mGluR1a, but do not mediate mGluR1a adaptation. Galphaq/11 is immunoprecipitated as a complex with mGluR1a in the absence of agonist, and either agonist treatment or GRK2 overexpression promotes the dissociation of the receptor/Galphaq/11 complex. However, these mGluR1a/Galphaq/11 interactions are not antagonized by the overexpression of either GRK2 mutants defective in Galphaq/11 binding or RGS4. We have also identified a GRK2-D527A mutant that binds Galphaq/11 in an AlF4(-)-dependent manner but is unable to either bind mGluR1a or attenuate mGluR1a signaling. We conclude that the mechanism underlying GRK2 phosphorylation-independent attenuation of mGluR1a signaling is RH domain-dependent, requiring the binding of GRK2 to both Galphaq/11 and mGluR1a. This serves to coordinate GRK2 interactions with Galphaq/11 and to disrupt receptor/Galphaq/11 complexes. Our findings indicate that GRK2 regulates receptor/G protein interactions, in addition to its traditional role as a receptor kinase.
Microprocessor control signal transmission through optical fiber (1992)

The authors describe an optical fiber control signal transmission system in which multiples frequency signals are used as an 8b control signal for a CPU control system consisting of Z80 data processors, motion control devices, and position sensors. Four control terminals are connected to the control center. Motion control devices are connected to the data processor installed in each control terminal. Frequencies at 100 kHz, 200 kHz, 300 kHz, and 400 kHz are used as series signals to specify the current operating states of the motion control devices, and the frequencies at 500 kHz, 600 kHz, 700 kHz, and 800 kHz are used as parallel signals to specify the four control terminals. The initial step in implementing the transmission system, including the function of the control bus and the configuration of the transmission system for the 8b parallel control signals, is discussed. >
Multitask learning (1998)

Multitask Learning is an approach to inductive transfer that improves learning for one task by using the information contained in the training signals of other related tasks. It does this by learning tasks in parallel while using a shared representation; what is learned for each task can help other tasks be learned better. In this thesis we demonstrate multitask learning for a dozen problems. We explain how multitask learning works and show that there are many opportunities for multitask learning in real domains. We show that in some cases features that would normally be used as inputs work better if used as multitask outputs instead. We present suggestions for how to get the most out of multitask learning in artificial neural nets, present an algorithm for multitask learning with case-based methods like k-nearest neighbor and kernel regression, and sketch an algorithm for multitask learning in decision trees. Multitask learning improves generalization performance, can be applied in many different kinds of domains, and can be used with different learning algorithms. We conjecture there will be many opportunities for its use on real-world problems.
CYTOGENETIC STUDIES INARABIDOPSIS THALIANA (1970)

The five primary trisomics and one telotrisomic of Arabidopsis have been established and identified with respect to known linkage groups. From diplotene preparations the chromosome complement was seen to comprise one long, three medium, and one short chromosome. All the trisomics except Fragilis were transmitted through the male (in frequencies up to 22%). There appears to be some selection against disomic eggs, only 21-30% recovery being observed from selfed trisomics. No tetrasomics were found.
소자약침(蘇子藥鍼)이 Type 1 Hypersensitivity에 미치는 영향 (2008)

Objectives: We studied anti-allergic effects of Cinnamomi Ramulus(CR) herbal acupuncture and Cinnamomi Ramulus extract. Methods: In vivo, animals were herbal-acupunctured with CR at both ST36s three times for 5 days. Then, we induced active systemic anaphylatic shock using compound 48/80 in ICR mice, and passive cutaneous anaphylaxis using anti-DNP IgE in Sprague Dawley rat. In vitro, we measured cell viability, β-hexosaminidase release and the expressions of IL-4, TNF-α and COX-2 mRNA in RBL-2H3 cells after treatment of various concentrations of CR extract. Results: In vivo, CR herbal acupuncture pretreatments at both ST36s inhibited compound 48/80-induced active systemic anaphylatic shock. Passive cutaneous anaphylaxis was inhibited by CR herbal acupuncture pretreatments at both ST36s and optional points. In vitro, CR extract treatments did not affect on cell viability and inhibited β-hexosaminidase release. CR extract treatments also decreased the expressions of IL-4, TNF-α and COX-2 mRNA in RBL-2H3 cells. Conclusions: These results suggest that CR herbal acupuncture and CR extract should be beneficial in the inhibition of allergic inflammatory response.
Azomethine Ylides in Organic Synthesis (2003)

This review will attempt to cover the literatures published from 1988 dealing with cyclic and acyclic azomethine ylides in which a part or the whole of the ylide conjugation is included in a conjugated heterocycle. Special emphasis will be given to the synthetic applications of these dipoles in the synthesis of complex structures as well as in key steps of total synthesis. Keywords: azomethine ylides, organic synthesis, ylide conjugation, conjugated heterocycle
Acupuncture for stable angina pectoris: a systematic review protocol (2018)

CRD42015016201.
Endoscopic treatment of non-variceal gastrointestinal bleeding:hemoclips and other hemostatic techniques (2000)

Although the number of hospitalizations for non-variceal gastrointestinal bleeding has decreased inrecent years,acute upper gastrointestinalhemorrhage continues to be a common reason forhospital admission,and peptic ulcers account for atleast fifty percent of all cases.Despite the fact thatbleeding from ulcers ceases spontaneously inapproximately 80% of patients,it is still a diagnosis
Enhanced kinetic extraction of parvovirus B19 structural proteins (2002)

Recombinant structural proteins (VP1 and VP2) of the human parvovirus B19 have been expressed simultaneously using the baculovirus expression system to form virus-like particles (VLPs) that have potential use as vaccines. In this study, we report optimization of extraction conditions to recover these VLPs from cell paste. Under hypotonic conditions with neutral pH these VLPs were poorly extracted (up to 3% extraction). Addition of reducing agents, detergents, salts, and sonication did not improve the extractability. While screening for conditions to improve the extractability of the VLPs, we discovered that a combination of higher pH and elevated processing temperature significantly increased the extraction. Whereas increasing pH alone increased extractability from 3% to 6% (pH increased from 8.0 to 9.5), the effect of elevated temperature was much more substantial. At 50 degrees C, we observed the extraction to be more than fivefold higher than that at room temperature (up to 25% extracted at pH 9.0). The kinetics of extraction at elevated temperatures showed a rapid initial rate of extraction (on the order of minutes) followed by a plateau. In addition, we compared the extraction of VP1 expressed alone. VP1 expressed alone is incapable of forming VLPs. We observed that non-VLP VP1 was easily extractable (up to 60% extracted) under conditions in which the VP1 + VP2 VLPs were not extractable. From these studies we conclude that parvovirus B19 structural proteins expressed to form VLPs have a hindered extractability as compared with non-VLP protein. This hindrance to extraction can be significantly reduced by processing at elevated temperatures and an increased pH, possibly due to the enhanced rates of solubilization and diffusion.
Least-square fitting a wave-front distortion estimate to an array of phase-difference measurements (1977)

The problem of fitting a wave-front distortion estimate to a (single-instant) set of phase-difference measurements has been formulated as an unweighted least-square problem. The least-square equations have been developed as a set of simultaneous equations for a square array of phase-difference sensors, with phase estimates at the corner of each measurement element. (This corresponds to the standard Hartmann configuration and to one version of a shearing interferometer of a predetection compensation wave-front sensor.) The noise dependence in the solution of the simultaneous equations is found to be expressible in terms of the solution to a particular version of the measurement inputs to the simultaneous equation, a sort of “Green’s-function” solution. The noise version of the simultaneous equations is solved using relaxation techniques for array sizes from 4 × 4 to 40 × 40 phase estimation points, and the mean-square wave-front error calculated as a function of the mean-square phase-difference measurement error. It is found that the results can be approximated within a fraction of a percent accuracy by 〈(δΦ)2〉=0.6558[1+0.2444 ln(N2)]σpd2, where 〈(δΦ)2〉 is the mean-square error (rad2) in the estimation of the wave-front distortion, for a square array consisting of N2 square subaperture elements over which two phase-difference measurements are made—one phase difference across the x dimension and the other difference across the y dimension. Here σpd2 is the mean-square error (rad2) in each phase-difference measurement.
Incremental loading of terrain textures (2013)

Graphic Processing Units (GPUs) are getting more powerful and are currently capable of displaying millions of polygons at a steady frame rate. The challenge is however, to display unique and interesting data while navigating in a 3D world. This task consists of both selecting which data to display, as well as storing all the required data.This thesis focuses on efficient methods for displaying portions of large terrain textures, by loading the textures incrementally, and thereby avoid some of the storage limitations of current graphics hardware and increase the detail level of the terrain rendered. These methods include algorithms for selecting the parts of the terrain to display, loading the data in time when it's needed and present the data in an appropriate quality while maintaining performance. How the camera behaves plays a key role in these algorithms.The process of displaying large terrains is divided into a multi step process, where coarser algorithms detect the active region of the terrain, then more accurate algorithms calculate which portions to load, and then the most precise algorithms aim to only display the necessary data. Camera movement is also taken into account in this process, and the algorithms attempt to fetch the necessary data in time before it's needed, which is a novel approach. The proposed implementation is compared to related approaches such as Virtual Texturing, a comparable methods which rely on feedback when required data is missing during rendering.