gebhart/patrepeval huggingface dataset:
Major histocompatibility complex conformational epitopes are peptide specific. (1992)

Serologically distinct forms of H-2Kb are stabilized by loading cells expressing "empty" class I major histocompatibility complex (MHC) molecules with different H-2Kb binding peptides. The H-2Kb epitope recognized by monoclonal antibody (mAb) 28.8.6 was stabilized by ovalbumin (OVA) (257-264) and murine cytomegalovirus (MCMV) pp89 (168-176) peptides, but not by vesicular stomatic virus nucleoprotein (VSV NP) (52-59) and influenza NP (Y345-360) peptides. The H-2Kb epitope recognized by mAb 34.4.20 was stabilized by VSV NP (52-59) peptide but not by OVA (257-264), MCMV pp89 (168-176), or influenza NP (Y345-360) peptides. Immunoprecipitation of H-2Kb molecules from normal cells showed that 28.8.6 and 34.4.20 epitopes were only present on a subset of all conformationally reactive H-2Kb molecules. Using alanine-substituted derivatives of the VSV peptide, the 28.8.6 epitope was completely stabilized by substitution of the first residue and partially stabilized by substitution of the third or the fifth residues in the peptides. These results indicate that distinct conformational MHC epitopes are dependent on the specific peptide that occupies the antigenic peptide binding groove on individual MHC molecules. The changes in MHC epitopes observed may also be important in understanding the diversity of T cell receptors used in an immune response and the influence of peptides on development of the T cell repertoire.
Molecular Cloning and Functional Characterization of a Novel Human CC Chemokine Receptor (CCR5) for RANTES, MIP-1β, and MIP-1α (1996)

Chemokines affect leukocyte chemotactic and activation activities through specific G protein-coupled receptors. In an effort to map the closely linked CC chemokine receptor genes, we identified a novel chemokine receptor encoded 18 kilobase pairs downstream of the monocyte chemoattractant protein-1 (MCP-1) receptor (CCR2) gene on human chromosome 3p21. The deduced amino acid sequence of this novel receptor, designated CCR5, is most similar to CCR2B, sharing 71% identical residues. Transfected cells expressing the receptor bind RANTES (regulated on activation normal T cell expressed), MIP-1beta, and MIP-1alpha with high affinity and generate inositol phosphates in response to these chemokines. This same combination of chemokines has recently been shown to potently inhibit human immunodeficiency virus replication in human peripheral blood leukocytes (Cocchi, F., DeVico, A. L., Garzino-Demo, A., Arya, S. K., Gallo, R. C., and Lusso, P.(1995) Science 270, 1811-1815). CCR5 is expressed in lymphoid organs such as thymus and spleen, as well as in peripheral blood leukocytes, including macrophages and T cells, and is the first example of a human chemokine receptor that signals in response to MIP-1beta.
Vitamins, Trace Elements, and Antioxidant Status in Dementia Disorders (2001)

Antioxidants, such as vitamins C and E, have been proposed for the treatment of dementia disorders. Although other vitamins and trace elements may also have antioxidant-enhancing activities, it is not known whether the overall antioxidant status in dementia patients is associated with the intake level of these vitamins and trace elements. In this study, we assessed the levels of vitamins and trace elements in the diet of patients with Alzheimer's disease (AD), vascular dementia (VaD), and dementia with Lewy bodies (DLB) and a group of carers, along with blood levels of total antioxidant capacity (TAC). Results show that the dietary intake was decreased for most measured vitamins and trace elements in severe AD, but not in other dementia groups. In addition, we found no significant difference in the levels of TAC between any of the dementia groups. There was, however, a significant correlationbetween intake of vitamin B1, vitamin B12, zinc, and selenium and blood levels of TAC in the VaD group, but not in the AD and DLB groups. Furthermore, no association was observed in any of the dementia groups between zinc and copper intake and Cu/Zn superoxide dismutase activity, or between dietary selenium intake and glutathione peroxidase activity. The activities of these two endogenous antioxidant enzymes do not seem to be influenced by intake levels of relevant substances. The data indicate that the influence of dietary vitamins and metal ions on the overall antioxidant status is limited to VaD patients only. Clinical trials are needed to ascertain the value of antioxidant supplementation in VaD patients.
What is the set of images of an object under all possible lighting conditions? (1996)

The appearance of a particular object depends on both the viewpoint from which it is observed and the light sources by which it is illuminated. If the appearance of two objects is never identical for any pose or lighting conditions, then-in theory - the objects can always be distinguished or recognized. The question arises: What is the set of images of an object under all lighting conditions and pose? In this paper, we consider only the set of images of an object under variable illumination (including multiple, extended light sources and attached shadows). We prove that the set of n-pixel images of a convex object with a Lambertian reflectance function, illuminated by an arbitrary number of point light sources at infinity, forms a convex polyhedral cone in IR/sup n/ and that the dimension of this illumination cone equals the number of distinct surface normals. Furthermore, we show that the cone for a particular object can be constructed from three properly chosen images. Finally, we prove that the set of n-pixel images of an object of any shape and with an arbitrary reflectance function, seen under all possible illumination conditions, still forms a convex cone in IR/sup n/. These results immediately suggest certain approaches to object recognition. Throughout this paper, we offer results demonstrating the empirical validity of the illumination cone representation.
Interaction Techniques for Immersive Virtual Environments: Design, Evaluation, and Application (1998)

Immersive virtual environments (VEs) have potential in many application areas, but most successful VE systems exhibit little interactivity. This is largely due to a lack of consideration or understanding of 3D interaction tasks and techniques. This work proposes the systematic study of design, evaluation, and application of VE interaction techniques. Design and evaluation are based on a formal task analysis and categorization of techniques, using multiple performance measures. This methodology will be tested by applying the results to a complex VE application allowing users to modify the design of a space while immersed within it. 1 INTRODUCTION Virtual Environments (VEs) offer a new human-computer interaction paradigm in which users are no longer simply external observers of images on a computer screen but are active participants with a computergenerated three-dimensional virtual world. Proposed and developing applications include design, visualization, education, and both training ...
Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing (2017)

Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones. Alternatively, CDR3α and CDR3β sequences can be associated using their frequency of co-occurrence in independent samples, but this approach can be confounded by the sharing of CDR3α and CDR3β across clones, commonly observed within epitope-specific T cell populations. The accurate, exhaustive, and economical recovery of TCR sequences from such populations therefore remains a challenging problem. Here we describe an algorithm for performing frequency-based pairing (alphabetr) that accommodates CDR3α- and CDR3β-sharing, cells expressing two TCRα chains, and multiple forms of sequencing error. The algorithm also yields accurate estimates of clonal frequencies.
Quantitative variation of biofilms among strains in natural populations of Candida albicans (2003)

This study examined the quantitative variation of biofilm formation and its relationship to multilocus genotypes in 115 strains of the human pathogenic fungus Candida albicans. These strains were isolated from three sources: 47 from oral cavities of healthy volunteers, 31 from the environment and 37 from the vaginas of patients with candidiasis. For each strain, biofilm formation was quantified as the ability to adhere to and grow on polystyrene plastic surfaces. Confocal laser scanning microscopy was used to visualize and confirm biofilm formation. Two methods were used to quantify biofilm formation abilities: (i). the XTT reduction assay, and (ii). absorbance following staining by crystal violet dye. Results obtained by the two methods were significantly correlated. Furthermore, biofilm formation ability was positively correlated with cell surface hydrophobicity. The analyses indicated that strains from each of the three sources varied widely in biofilm formation abilities. However, little correlation was observed between biofilm formation and multilocus genotypes as determined by PCR-RFLP at 16 polymorphic loci, regardless of source of strain. Strains with the same or similar multilocus genotypes often showed very different biofilm formation abilities. The results demonstrated that natural clones and clonal lineages of C. albicans exhibited extensive quantitative variation in biofilm formation.
Liposome-based Systems for Anti-tumor Vaccination: Influence of Lipopeptide Adjuvants (2006)

We have developed liposome-based synthetic constructs incorporating peptide epitope(s) (ErbB2 p63-67 CTL which is overexpressed in many tumors and/or HA 307-319 T-helper) and lipopeptide adjuvants (Pam3CysSerSer, Pam3CysAlaGly) in order to elicit an anti-tumor immune response. The epitopes, derivatized with a linker containing a cysteine residue, were conjugated on preformed vesicles (dia. approximately 100 nm) containing lipopeptides functionalized with thiol reactive groups (maleimide or bromoacetyl). The therapeutic efficacy of these constructs was evaluated on a Balb/c mice tumor model inoculated with syngenic murine renal carcinoma (Renca) cells expressing human ErbB2 (Her2/neu) receptor. A successful therapeutic vaccination was obtained which was antigen specific. Furthermore, it appeared that the nature of the polar head group of the lipopeptide adjuvant and also its type of functionalization influence the efficacy of the construct. In our study, the best results were obtained with formulations containing a Pam3CSS anchor in association with the CTL and Th epitopes. Considering these promising results studies are in progress with a new generation of liposomes that incorporate a neutral lipid--lacking adjuvant properties--that serves as anchor of the peptide epitopes and new adjuvants synthesized in our laboratory, which are screened for their antitumour activity in a therapeutic setting.
Generic plan recognition for dialogue systems (1993)

We describe a general framework for encoding rich domain models and sophisticated plan reasoning capabilities. The approach uses graph-basedreasoning to address a wide range of tasks that typically arise in dialogue systems. The graphical plan representation is independent of but connected to the underlying representation of action and time. We describe types of plan recognition that are needed, illustrating these with examples from dialogues collected as part of the TRAINS project. The algorithms for the tasks are presented, and issues in the formalization of the reasoning processes are discussed.
Analysis of siRNA specificity on targets with double-nucleotide mismatches (2008)

Although RNA interference as a tool for gene knockdown is a great promise for future applications, the specificity of small interfering RNA (siRNA)-mediated gene silencing needs to be thoroughly investigated. Most research regarding siRNA specificity has involved analysis of affected off-target genes instead of exploring the specificity of the siRNA itself. In this study we have developed an efficient method for generating a siRNA target library by combining a siRNA target validation vector with a nucleotide oligomix. We have used this library to perform an analysis of the silencing effects of a functional siRNA towards its target site with double-nucleotide mismatches. The results indicated that not only the positions of the mismatched base pair have an impact on silencing efficiency but also the identity of the mismatched nucleotide. Our data strengthen earlier observations of widespread siRNA off-target effects and shows that approximately 35% of the double-mutated target sites still causes knockdown efficiency of >50%. We also provide evidence that there may be substantial differences in knockdown efficiency depending on whether the mutations are positioned within the siRNA itself or in the corresponding target site.
Cleavage of the CD11b extracellular domain by the leukocyte serprocidins is critical for neutrophil detachment during chemotaxis (2011)

The β(2)-integrin CD11b/CD18 mediates the firm adhesion of neutrophils (PMNs) to epithelial monolayers, a key step in PMN transepithelial migration. To complete the transmigration process, adherent PMNs must detach from epithelial monolayer surfaces to move forward. The mechanism that governs the detachment of adherent PMNs, however, is not clear. Here, we present evidence that cleavage of the CD11b extracellular domain containing the ligand-binding I-domain by 3 structural and functional related serine proteases (elastase, proteinase-3 and cathepsin G) serves as a novel mechanism for PMN detachment after the initial cell adhesion. Kinetic studies showed that the cleavage of CD11b is positively correlated with PMN detachment and subsequent transmigration. Moreover, the results demonstrated that elastase, proteinase-3 and cathepsin G all cleaved the purified, functionally active form of CD11b in a pattern similar to the CD11b shedding that occurs during PMN transmigration. Their cleavage sites on purified CD11b were located at (761)Thr-Ala(762) (elastase/proteinase-3) and (760)Phe-Thr(761) (cathepsin G), respectively. CD11b cleavage and PMN detachment and chemotaxis, were impaired in elastase/cathepsin G-deficient Beige mice; this defect could be restored by the addition of extracellular elastase. By illustrating CD11b shedding by elastase, proteinase-3 and cathepsin G as a novel mechanism for PMN detachment, our study provides novel therapeutic targets for controlling inflammation.
Current trends in polymer dispersed liquid crystals (2002)

A novel cholesteric liquid crystal/polymer gel dispersion has been constructed which can be operated either in normal mode or reverse mode. The normal-mode cell is opaque in a field-OFF condition and clear in a field-ON condition. The reverse-mode cell is clear in a field-OFF condition and opaque in a field-ON condition. In the clear state, both cells are haze-free for all viewing angles. The cholesteric liquid crystal/polymer gel dispersion can be used to make normal-mode and reverse-mode light shutters. The reverse-mode shutter has very good electrooptical characteristics, exhibiting a sharp transition, small hysteresis, and fast dynamic response.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tuberculosis in Patients with Human Immunodeficiency Virus Infection (1991)

THE number of cases of tuberculosis reported annually in the United States declined steadily from 84,304 in 1953 to 22,255 in 1984.1,2 In a dramatic reversal of this trend, the number rose by 3 percent in 1986, by 5 percent to 23,495 in 1989, and by a provisional 6 percent in 1990.1 2 3 4 This unprecedented resurgence of tuberculosis is largely related to the human immunodeficiency virus (HIV) epidemic.1 2 3 Among the diseases associated with HIV infection, tuberculosis is of particular importance because it is contagious by the respiratory route, readily treatable, and potentially preventable with chemoprophylaxis. Physicians must be familiar with the . . .
Identifying surface structural changes in layered Li-excess nickel manganese oxides in high voltage lithium ion batteries: A joint experimental and theoretical study (2011)

High voltage cathode materials Li-excess layered oxide compounds Li[NixLi1/3−2x/3Mn2/3−x/3]O2 (0 < x < 1/2) are investigated in a joint study combining both computational and experimental methods. The bulk and surface structures of pristine and cycled samples of Li[Ni1/5Li1/5Mn3/5]O2 are characterized by synchrotron X-Ray diffraction together with aberration corrected Scanning Transmission Electron Microscopy (a-S/TEM). Electron Energy Loss Spectroscopy (EELS) is carried out to investigate the surface changes of the samples before/after electrochemical cycling. Combining first principles computational investigation with our experimental observations, a detailed lithium de-intercalation mechanism is proposed for this family of Li-excess layered oxides. The most striking characteristics in these high voltage high energy density cathode materials are 1) formation of tetrahedral lithium ions at voltage less than 4.45 V and 2) the transition metal (TM) ions migration leading to phase transformation on the surface of the materials. We show clear evidence of a new spinel-like solid phase formed on the surface of the electrode materials after high-voltage cycling. It is proposed that such surface phase transformation is one of the factors contributing to the first cycle irreversible capacity and the main reason for the intrinsic poor rate capability of these materials.
Type 1A fibre Bragg grating photosensitivity and the development of optimum temperature invariant type I-type IA strain sensors (2004)

Type 1A fibre Bragg gratings (FBG) form only after the erasure of a standard grating in hydrogenated germanosilicate fibre, under prolonged UV exposure. They are distinct from other grating types as they exhibit a uniquely large increase in the mean index of the core, readily identifiable by a large red shift in the Bragg wavelength. Type 1A gratings can surpass the conventional mean index change by a factor of six with a typical red shift of up to 20nm, interpreted as a mean index increase of up to 1.9x10<sup>-2</sup>. Importantly, 1A gratings have been shown to exhibit the lowest temperature coefficient of all FBG, which makes them ideal for use as temperature compensated, dual grating sensors. We report on the formation of Type 1A gratings and the correlation between the mean index change of the grating and the growth of a loss band at close to 1400nm that is associated with the formation of OH centres within the fibre. We present annealing data comparing the decay of Type 1 and Type 1A gratings. Finally, we demonstrate a dual temperature compensated strain sensor system, based on two adjoining Type 1 and Type 1A gratings, which have been formed using a common phase mask, yet with central wavelengths many nm apart.
Betahistine metabolites, Aminoethylpyridine, and Hydroxyethylpyridine increase cochlear blood flow in guinea pigsin vivo (2014)

Aminoethylpyridine and hydroxyethylpyridine are, like betahistine, able to increase cochlear blood flow significantly. The effect of aminoethylpyridine was greatest. Pyridylacetic acid had no effect on cochlear microcirculation.
Microflow-Based Automated Chemistries:  Application to Protein Sequencing (2001)

We describe a microflow-based instrument, consisting of multiple rotary valves, capillary tubing, and miniaturized reaction vessels, for the purpose of performing automated chemical and biochemical reations on a very small scale (i.e. submicroliter volumes). The novelty is that close to 100% of the reaction end products are available in a minimal volume (< or = 5 microL) inside a pressurized microvial for subsequent analysis. This makes the system compatible with capillary HPLC and, in principle, with continuous-flow nanoelectrospray mass spectrometry. Total control of flow path combinations and directions, temperatures, and gas pressures enables precise execution of complex biochemical laboratory procedures. Instrument performance was convincingly demonstrated by partially sequencing 100 fmol of an intact protein using classical Edman chemistry in combination with capillary-bore liquid chromatography. To our knowledge, this is the smallest amount of protein ever reported to be successfully analyzed in this way. Additional applications that merge enzymatic and chemical procedures with high-sensitivity analytical devices can be envisioned in the future.
Three pathways for trehalose metabolism in Corynebacterium glutamicum ATCC13032 and their significance in response to osmotic stress (2003)

Genome scanning of Corynebacterium glutamicum ATCC13032 revealed the presence of five different genes encoding enzymes belonging to three putative trehalose biosynthesis pathways (OtsAB, TreYZ, TreS). The function of the different pathways and of trehalose as an osmoprotectant was studied by characterizing several strains defective for individual trehalose biosynthetic routes. Trehalose synthesis was shown to increase upon hyperosmotic conditions. Cytoplasmic trehalose levels varied considerably depending on kind and accessibility of carbon and nitrogen sources. In contrast to other organisms, osmoregulated trehalose synthesis in C. glutamicum is mediated by the TreYZ and not by the OtsAB pathway. Irrespective of their significance for the osmotic response, otsA and treS were upregulated at the transcriptional level after hyperosmotic shock. In vivo, TreS-mediated trehalose synthesis only occurred if maltose was used as the carbon source. In vitro, TreS catalysed the conversion of maltose into trehalose and, conversely, trehalose into maltose. As the reaction seems to be near equilibrium, TreS appears to be important for trehalose degradation rather than synthesis because a 1000-fold excess of trehalose to maltose was detected in the cytoplasm. Also, evidence is given that both the OtsAB and the TreYZ pathways are involved, but not essential, in supplying trehalose for mycolic acid biosynthesis.