gebhart/patrepeval huggingface dataset:
Automatic structuring and retrieval of large text files (1994)

article Free Access Share on Automatic structuring and retrieval of large text files Authors: Gerard Salton Cornell Univ., Ithaca, NY Cornell Univ., Ithaca, NYView Profile , James Allan Cornell Univ., Ithaca, NY Cornell Univ., Ithaca, NYView Profile , Chris Buckley Cornell Univ., Ithaca, NY Cornell Univ., Ithaca, NYView Profile Authors Info & Claims Communications of the ACMVolume 37Issue 2Feb. 1994pp 97–108https://doi.org/10.1145/175235.175243Published:01 February 1994Publication History 142citation1,383DownloadsMetricsTotal Citations142Total Downloads1,383Last 12 Months39Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Identification of conserved T cell receptor CDR3 residues contacting known exposed peptide side chains from a major histocompatibility complex class I‐bound determinant (1993)

We have analyzed the T cell receptor (TCR) repertoire found in the major histocompatibility complex class I-restricted cytotoxic T lymphocyte (CTL) response to the protein ovalbumin (OVA). Despite skewing towards the expression of V beta 5.2+TCR by OVA-specific CTL from C57BL/6 mice, we found a relatively high degree of diversity in V(D)J usage in both TCR alpha- and beta-chains. Closer examination showed that the majority of these sequences encoded negatively and positively charged residues at their respective TCR alpha- and beta-chain VJ or VDJ junctions. These junctions form the third complementarity-determining regions (CDR3) of the TCR polypeptides involved in the direct interaction with the class I-bound peptide. Crystallographic analyses of Kb-peptide complexes predict that the major determinant from OVA, peptide OVA257-264 (SIINFEKL), contains two exposed charged side chains which can contact the TCR. These are the negatively charged glutamic acid at determinant position 6 (P6) and the positively charged lysine at P7. To examine whether the TCR alpha-chain makes contact with P7 lysine, we established a single chain TCR transgenic C57BL/6 mouse line where all T cells express a TCR beta-chain derived from the V beta 5.2+ clone B3. OVA-specific T cells derived from in vivo primed transgenic mice preferentially expressed TCR alpha-chains that also contained negatively charged junctional residues despite some further variation in V alpha and J alpha sequences. Stimulation of naive TCR beta-chain transgenic T cells with a P7 substitution peptide analogue induced a T cell response that was no longer cross-reactive with the wild-type OVA257-264 determinant, suggesting that the TCR alpha-chain from the T cell clone B3 can determine the specificity for this residue. Consequently, these results reveal the existence of conserved residues in the CDR3 of TCR alpha- and beta-chains specific for OVA257-264 and identify their possible orientation over the peptide-class I complex.
Molecular cloning of human cardiac troponin I using polymerase chain reaction (1990)

We have used the polymerase chain reaction (PCR) to synthesise a cDNA encoding part of human cardiac troponin I. Amplification was achieved using fully degenerate sets of oligonucleotides corresponding to conserved regions of amino acid sequence identified in other troponin I isoforms. The cloned PCR fragment was subsequently used to isolate full-length cDNAs from a cardiac cDNA library. We describe the approach, as a general cloning strategy starting from limited amino-acid sequence data and report the cloning, and complete amino acid sequence of human cardiac troponin I. Analysis of human development using these clones demonstrates early expression of this gene in the heart.
Human class I alcohol dehydrogenases catalyze the oxidation of glycols in the metabolism of norepinephrine. (1985)

Investigations of the function of human liver alcohol dehydrogenase (ADH) in norepinephrine metabolism have revealed that class I ADH catalyzes the oxidation of the intermediary alcohols 4-hydroxy-3-methoxyphenyl glycol (HMPG) and 3,4-dihydroxyphenyl glycol (DHPG) in vitro. The kcat/Km values for the individual homogeneous class I isozymes are generally in the range from 2.0 to 10 mM-1 X min-1, slightly lower than those obtained for ethanol oxidation, 16-66 mM-1 X min-1, but considerably higher than those obtained for ethylene glycol oxidation, 0.23-1.5 mM-1 X min-1. Importantly, HMPG and DHPG are not substrates for the class II or class III ADHs. 4-Methylpyrazole and 1,10-phenanthroline inhibit the class I ADH-catalyzed oxidation of HMPG, DHPG, and ethanol with inhibition constants of 75-90 nM and 19-22 microM, respectively, indicating that these substrates interact at the same catalytic site of ADH. Moreover, ethanol inhibits the oxidation of HMPG. The competition of ethanol with HMPG for ADH provides a basis for the in vivo changes observed in norepinephrine metabolism after acute ethanol intake. Any assessment of norepinephrine function through the study of metabolites in peripheral body fluid must include monitoring the oxidation of HMPG by ADH.
Pooled‐matrix protein interaction screens using Barcode Fusion Genetics (2016)

High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods.
A new yeast display vector permitting free scFv amino termini can augment ligand binding affinities (2005)

Yeast surface display and sorting by flow cytometry are now widely used to direct the evolution of protein binding such as single-chain antibodies or scFvs. The available commercial yeast display vector pYD1 (Invitrogen) displays the protein of interest flanked on the N-terminus by Aga2, the disulfide of which binds the myristylated surface membrane protein Aga1. We have noted that two anti-CD3epsilon scFvs expressed as fusion proteins suffer a 30- to 100-fold loss of affinity when placed NH(2) terminal to either truncated toxins or human serum albumin. In the course of affinity maturing one of these scFv (FN18) using pYD1 we noted that the affinity towards the ectodomain of monkey CD3epsilongamma was too low to measure. Consequently we rebuilt pYD1 tethering the scFv off the NH(2) terminus of Aga2. This display vector, pYD5, now gave a positive signal displaying FN18 scFv with its ligand, monkey CD3epsilongamma. The apparent equilibrium association constant of the higher affinity scFv directed at human CD3epsilongamma increased approximately 3-fold when displayed on pYD5 compared with pYD1. These data show that for certain yeast-displayed scFvs a carboxy-tethered scFv can result in increased ligand-scFv equilibrium association constants and thereby extend the low range of affinity maturation measurements.
Requirement of leucine-rich repeats of glycoprotein (GP) Ibα for shear-dependent and static binding of von Willebrand factor to the platelet membrane GP Ib–IX-V complex (2000)

The platelet glycoprotein (GP) Ib-IX-V complex mediates adhesion to von Willebrand factor (vWf) in (patho)physiologic thrombus formation. The vWf-binding site on GP Ib-IX-V is within the N-terminal 282 residues of GP Ibalpha, which consist of an N-terminal flanking sequence (His-1-Ile-35), 7 leucine-rich repeats (Leu-36-Ala-200), a C-terminal flank (Phe-201-Gly-268), and a sulfated tyrosine sequence (Asp-269-Glu-282). We have used mammalian cell expression of canine-human chimeras of GP Ibalpha, corresponding to precise structural boundaries, to demonstrate the first specific requirement for individual leucine-rich repeats for binding of vWf either induced by a modulator, ristocetin, or under hydrodynamic flow. Implicit in this approach was that the GP Ibalpha chimeras retained a functional conformation, a supposition confirmed by analyzing restoration of function to reversed human-canine chimeras and demonstrating that all chimeras bound vWf activated by botrocetin, a modulator that is indiscriminate between species. Leucine-rich repeats 2, 3, and 4 of GP Ibalpha were identified as being critical for vWf adhesion to GP Ib-IX-V.
Efficient piecewise training of deep structured models for semantic segmentation (2015)

Recent advances in semantic image segmentation have mostly been achieved by training deep convolutional neural networks (CNNs). We show how to improve semantic segmentation through the use of contextual information; specifically, we explore `patch-patch' context between image regions, and `patch-background' context. For learning from the patch-patch context, we formulate Conditional Random Fields (CRFs) with CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied to avoid repeated expensive CRF inference for back propagation. For capturing the patch-background context, we show that a network design with traditional multi-scale image input and sliding pyramid pooling is effective for improving performance. Our experimental results set new state-of-the-art performance on a number of popular semantic segmentation datasets, including NYUDv2, PASCAL VOC 2012, PASCAL-Context, and SIFT-flow. In particular, we achieve an intersection-over-union score of 78.0 on the challenging PASCAL VOC 2012 dataset.
Dnd knockout ablates germ cells and demonstrates germ cell independent sex differentiation in Atlantic salmon (2016)

Introgression of farmed salmon escapees into wild stocks is a major threat to the genetic integrity of wild populations. Using germ cell-free fish in aquaculture may mitigate this problem. Our study investigated whether it is possible to produce germ cell-free salmon in F0 by using CRISPR-Cas9 to knock out dnd, a factor required for germ cell survival in vertebrates. To avoid studying mosaic animals, sgRNA targeting alb was simultaneously used as a visual tracer since the phenotype of alb KO is complete loss of pigmentation. Induced mutations for the tracer (alb) and the target (dnd) genes were highly correlated and produced germ cell-less fish lacking pigmentation, underlining the suitability of alb KO to serve as tracer for targeted double allelic mutations in F0 animals in species with prohibitively long generation times. This is also the first report describing dnd knockout in any fish species. Analyzing gene expression and histology of dnd KO fish revealed that sex differentiation of the somatic compartment does not depend on the presence of germ cells. However, the organization of the ovarian somatic compartment seems compromised in mutant fish.
Factor X Frankfurt I (1998)

A family with hereditary factor X deficiency is presented. One member, a 25-year-old man, showed a mild bleeding tendency. His factor X activity (extrinsic: 56%; intrinsic: 55%; Russell's viper venom: 57%) and his level of circulating factor X antigen (55% of normal) were markedly reduced. Analysis of his factor X gene revealed a single point mutation within exon II resulting in the substitution of +25 Gla (GAA) by Lys (AAA). The mutation was determined by gene analysis to be heterozygous in this patient, his mother and one of his brothers. Clotting assays of factor X purified from the plasma of the index patient revealed an activity of 89% of normal upon activation with Russell's viper venom, 77% of normal in the intrinsic and 81% of normal in the extrinsic coagulation pathway. The mutation responsible for the substitution of Lys for Gla+25 was introduced into an expression plasmid containing a wild type factor X cDNA and expressed in a mammalian cell line. Factor X antigen levels in the cell lysates and in the supernatant were identical in the mutant and wild type constructs. The specific activity of the factor X expressed from the mutant construct was 3% compared with the wild type construct. These data demonstrate that the substitution of Lys for Gla+25 results not only in a reduced level of factor X in the affected family members, but also in a substantial loss of specific factor X activity.
Strategies and Applications of in Vitro Mutagenesis (1985)

The many mutagenesis strategies made possible by the availability of cloned genes have been outlined in the context of how each strategy lends itself to the answering of different kinds of biological questions.
Extended-release opioids for the management of chronic non-malignant pain (2006)

Recent clinical trials have documented the use of extended-release (ER) opioids in the management of chronic non-malignant pain. This manuscript reviews the clinical pharmacology of investigational and current marketed ER opioids. Recent randomised clinical trials of ER opioids that document the efficacy and safety of opioid therapy for chronic pain are reviewed. Finally, the abuse liability of ER opioids is discussed. Current technologies aimed at defeating the abuse of ER opioids will also be presented.
Rituximab in indolent lymphoma: the single-agent pivotal trial. (1999)

Rituximab (Rituxan; IDEC Pharmaceuticals, San Diego, CA, and Genentech, Inc, San Francisco, CA) is a chimeric anti-CD20 monoclonal antibody that targets mature B cells and most B-cell malignancies. Rituximab was the first monoclonal antibody to be approved for therapeutic use for any malignancy. Its approval was based on a single-agent pivotal trial in patients with indolent B-cell lymphoma, in which 166 patients were enrolled from 31 centers in the United States and Canada. The overall results of the trial have been previously reported; additional aspects of the trial (eg, pharmacokinetics) have been reported separately as well. The current report includes an update, expansion, and synthesis of data from the single-agent pivotal trial of rituximab.
Optimal Higher Order Ambisonics Encoding With Predefined Constraints (2011)

In this paper, we propose a design method for 3-D higher order ambisonics (3-D HOA) encoding matrices which offers the possibility to impose spatial stop-bands in the directivity patterns of all the spherical-harmonic audio channels while keeping the transformed audio channels still compatible with the 3-D HOA reproduction sound format. This might be useful as an encoding technique which suppresses interfering signals from specific directions in a 3-D HOA recording, or in other situations where certain spatial areas should be suppressed. The design method is adapted from recent work on the optimization of spherical microphone array beamforming. Using the proposed optimization method and the spherical harmonics mathematics framework, the relationship between several design factors, e.g., distortions in the desired response, the dynamic range of matrix coefficients, can be analyzed and illustrated as function of frequency. Based on the proposed optimization formulation, additional constraints can also be easily included and solved. In some of the formulations, the processing can be applied as a matrix multiplication to recorded spherical harmonics coefficients, that is, already encoded 3-D HOA format signals. The modified signals can be of the same or a lower spherical harmonics order. For a full optimization that gives a globally optimal solution, on the other hand, the processing must be applied to the microphone signals themselves. Numerical and experimental results validate the proposed method.
In Vivo Analysis of Schwann Cell Programmed Cell Death in the Embryonic Chick: Regulation by Axons and Glial Growth Factor (2002)

The present study uses the embryonic chick to examine in vivo the mechanisms and regulation of Schwann cell programmed cell death (PCD) in spinal and cranial peripheral nerves. Schwann cells are highly dependent on the presence of axons for survival because the in ovo administration of NMDA, which excitotoxically eliminates motoneurons and their axons by necrosis, results in a significant increase in apoptotic Schwann cell death. Additionally, pharmacological and surgical manipulation of axon numbers also affects the relative amounts of Schwann cell PCD. Schwann cells undergoing both normal and induced PCD display an apoptotic-like cell death, using a caspase-dependent pathway. Furthermore, axon elimination results in upregulation of the p75 and platelet-derived growth factor receptors in mature Schwann cells within the degenerating ventral root. During early development, Schwann cells are also dependent on axon-derived mitogens; the loss of axons results in a decrease in Schwann cell proliferation. Axon removal during late embryonic stages, however, elicits an increase in proliferation, as is expected from these more differentiated Schwann cells. In rodents, Schwann cell survival is regulated by glial growth factor (GGF), a member of the neuregulin family of growth factors. GGF administration to chick embryos selectively rescued Schwann cells during both normal PCD and after the loss of axons, whereas other trophic factors tested had no effect on Schwann cell survival. In conclusion, avian Schwann cells exhibit many similarities to mammalian Schwann cells in terms of their dependence on axon-derived signals during early and later stages of development.
[Chaperone proteins--essential proteins for cellular activity]. (2000)

Molecular chaperones are an ubiquitous, abundant and highly conserved group of proteins which bind and stabilize proteins at intermediate stages of folding, assembly, translocation across membranes and degradation. They first came to attention because of their specific induction during the cellular response of all organisms to heat shock, but are now known to be constitutively and abundantly expressed in the absence of any stress. Despite the obvious importance of stress responses, only recently has scrutiny focused on the role of heat shock proteins in the control of disease pathology. Knowledge about Hsp functions in bacteria is much further advanced than in eukaryotes, but already some hints of Hsp involvement in mammalian diseases have emerged.
High-dose RHAMM-R3 peptide vaccination for patients with acute myeloid leukemia, myelodysplastic syndrome and multiple myeloma (2010)

High-dose RHAMM-R3 peptide vaccination induced immunological responses and positive clinical effects. Therefore, RHAMM constitutes a promising structure for further targeted immunotherapies in patients with different hematologic malignancies. However, higher doses of peptide did not improve the frequency and intensity of immune responses in this trial.
Chemical Modification of an Antitumor Alkaloid Camptothecin: Synthesis and Antitumor Activity of 7-C-Substituted Camptothecins. (1991)

A radical substitution reaction of 20(S)-camptothecin (1) with methanol furnished 7-hydroxymethylcamptothecin (2). Reaction of 1 with primary alcohols higher than methanol gave 7-alkylcamptothecins (4), of which alkyl groups were one carbon less than the alcohols used and also 7-hydroxyalkylcamptothecins (5). For the preparation of 7-alkylcamptothecin (4), aldehydes were used as a radical source and several alkylated derivatives were synthesized. 7-Acyloxymethyl derivatives (6), 7-carbaldehyde (7), iminomethyl derivatives (10), acid (11), esters (12) and amides (13) were synthesized starting from 2. 7-Ethyl- (4b) and 7-propylcamptothecin (4c), acyloxymethyl compounds 6a, 6c and ethyl ester (12b) exhibited higher antitumor activity than 1 against L1210 in mice.
[Superoxide-scavenging activity of carnosine in the presence of copper and zinc ions]. (1987)

In the presence of Cu2+ and Zn2+ carnosine (beta-alanyl-L-histidine) possesses a superoxide-scavenging activity. The efficiency of scavenging as measured by the inhibition of tetrazolium nitroblue reduction in superoxide anion generation systems (phenazine methasulfate/NADH and xanthine/xanthine oxidase) is concentration-dependent and shows a maximum in the presence of millimolar concentrations of carnosine and equimolar concentrations of Cu2+ and Zn2+. In the presence of Cu2+ and Zn2+ histidine also exhibits a superoxide-scavenging activity. The feasible role of the superoxide-scavenging activity of histidine-containing dipeptide complexes with bivalent metal ions in the realization of physiological function of these dipeptides in skeletal muscles is discussed.
Optimization of a Type III Secretion System-Based Pseudomonas aeruginosa Live Vector for Antigen Delivery (2007)

During the last few years, the use of type III secretion system-based bacterial vectors for immunotherapy purposes has been assessed in various applications. We showed that a type III secretion-based Pseudomonas aeruginosa vector delivering the ovalbumin (OVA) antigen induced an efficient specific CD8+ T-lymphocyte immune response against OVA-expressing cells. Because of the intrinsic toxicity of the vector, further virulence attenuation was needed. Therefore, we explored the effects of the deletion of quorum-sensing genes and the aroA gene toward toxicity and efficiency of the vector strain. The aroA mutation in our strain (making the strain auxotrophic for aromatic amino acids) conferred a strikingly reduced toxicity, with the bacterial lethal dose being more than 100 times higher than that of the parental strain. The quorum-sensing gene mutation alone was associated with a slightly reduced toxicity. In a prophylactic OVA-expressing melanoma mouse model, an OVA-delivering aroA-deficient mutant was the most efficient at a low dose (10(5)), but dose enhancement was not associated with a greater immune response. The quorum-sensing-deficient strain was the most efficient at a mild dose (10(6)), but this dose was close to the toxic dose. Combination of both mutations conferred the highest efficiency at an elevated dose (10(7)), in agreement with the known negative effects of quorum-sensing molecules upon T-cell activation. In conclusion, we have obtained a promising immunotherapy vector regarding toxicity and efficiency for further developments in both antitumor and anti-infectious strategies.
<title>Image Motion Compensation For Step-Stare Systems By Focal Plane And Optics Manipulation</title> (1979)

The derivation of earth relative motion (or &quot;smear rate&quot;) in a step-stare spaceborne optical system is presented. Suggested methods of compensating for the smear by focal-plane manipulation are also given. The simulation results of smearing for a 4-hour orbit optical system operating in a step-stare mode (above 45Ã‚Â° North Latitude) are provided.