gebhart/patrepeval huggingface dataset:
Frameshift-mutation-derived peptides as tumor-specific antigens in inherited and spontaneous colorectal cancer (2001)

The functional role and specificity of tumor infiltrating lymphocytes (TIL) is generally not well characterized. Prominent lymphocyte infiltration is the hallmark of the most common form of hereditary colon cancer, hereditary nonpolyposis colon cancer (HNPCC) and the corresponding spontaneous colon cancers with the microsatellite instability (MSI) phenotype. These cancers are caused by inherited or acquired defects in the DNA mismatch-repair machinery. The molecular mechanism behind the MSI phenotype provides a clue to understanding the lymphocyte reaction by allowing reliable prediction of potential T cell epitopes created by frameshift mutations in candidate genes carrying nucleotide repeat sequences, such as TGF beta RII and BAX. These tumors therefore represent an interesting human system for studying TIL and characterizing tumor-specific T cells. We here describe T cell reactivity against several T helper cell epitopes, representing a common frameshift mutation in TGF beta RII, in TIL and peripheral blood lymphocytes from patients with MSI(+) tumors. The peptide SLVRLSSCVPVALMSAMTTSSSQ was recognized by T cells from two of three patients with spontaneous MSI(+) colon cancers and from all three patients with HNPCC. Because such mutations are present in 90% of cancers within this patient group, these newly characterized epitopes provide attractive targets for cancer vaccines, including a prophylactic vaccine for individuals carrying a genetic disposition for developing HNPCC.
Economic mechanism design for computerized agents (1995)

. The field of economic mechanism design has been an active area of research in economics for at least 20 years. This field uses the tools of economics and game theory to design &amp;quot;rules of interaction&amp;quot; for economic transactions that will, in principle, yield some desired outcome. In this paper I will provide an overview of this subject for an audience interested in applications to electronic commerce and discuss some special problems that arise in this context. [This paper prepared for the USENIX Workshop on Electronic Commerce, July 11-12, 1995, New York, NY.] Keywords. electronic commerce, mechanism design, economics Address. Department of Economics, University of Michigan, Ann Arbor, MI 48109-1220. Voice: 313-764-2364. Fax: same as voice. E-mail: Hal.Varian@umich.edu. Homepage: http://gopher.econ.lsa.umich.edu Economic Mechanism Design for Computerized Agents Hal R. Varian As an example of mechanism design in action, let us consider the case of designing an auction to award an it...
The Rise of the New Racism (1996)

On December 7, 1995 two white soldiers from Fort Bragg went into nearby Fayetteville, North Carolina with semi-automatic weapons, "hunting for blacks." The two soldiers succeeded in their intended goal. They shot Michael James, age 36, and Jackie Burden, age 27, in the head at close range, killing them. In the soldiers' rooms the police found a Nazi flag, racist literature, a bombmaking book, and white supremacist paraphernalia.
CD96 is a leukemic stem cell-specific marker in human acute myeloid leukemia (2007)

Permanent cure of acute myeloid leukemia (AML) by chemotherapy alone remains elusive for most patients because of the inability to effectively eradicate leukemic stem cells (LSCs), the self-renewing component of the leukemia. To develop therapies that effectively target LSC, one potential strategy is to identify cell surface markers that can distinguish LSC from normal hematopoietic stem cells (HSCs). In this study, we employ a signal sequence trap strategy to isolate cell surface molecules expressed on human AML-LSC and find that CD96, which is a member of the Ig gene superfamily, is a promising candidate as an LSC-specific antigen. FACS analysis demonstrates that CD96 is expressed on the majority of CD34(+)CD38(-) AML cells in many cases (74.0 +/- 25.3% in 19 of 29 cases), whereas only a few (4.9 +/- 1.6%) cells in the normal HSC-enriched population (Lin(-)CD34(+)CD38(-)CD90(+)) expressed CD96 weakly. To examine whether CD96(+) AML cells are enriched for LSC activity, we separated AML cells into CD96(+) and CD96(-) fractions and transplanted them into irradiated newborn Rag2(-/-) gamma(c)(-/-) mice. In four of five samples, only CD96(+) cells showed significant levels of engraftment in bone marrow of the recipient mice. These results demonstrate that CD96 is a cell surface marker present on many AML-LSC and may serve as an LSC-specific therapeutic target.
Histologie Distribution and Biochemical Properties of α1‐Microglobulin in Human Placenta (1999)

The biochemical analysis indicates the presence in placenta of alpha 1-microglobulin forms not found in blood. The histochemical analysis supports the possibility that alpha 1-microglobulin may function as a local immunoregulator in the placenta.
TheLymnaeaCardioexcitatory Peptide (LyCEP) Receptor: A G-Protein–Coupled Receptor for a Novel Member of the RFamide Neuropeptide Family (1998)

A novel G-protein-coupled receptor (GRL106) resembling neuropeptide Y and tachykinin receptors was cloned from the mollusc Lymnaea stagnalis. Application of a peptide extract from the Lymnaea brain to Xenopus oocytes expressing GRL106 activated a calcium-dependent chloride channel. Using this response as a bioassay, we purified the ligand for GRL106, Lymnaea cardioexcitatory peptide (LyCEP), an RFamide-type decapeptide (TPHWRPQGRF-NH2) displaying significant similarity to the Achatina cardioexcitatory peptide (ACEP-1) as well as to the recently identified family of mammalian prolactin-releasing peptides. In the Lymnaea brain, the cells that produce egg-laying hormone are the predominant site of GRL106 gene expression and appear to be innervated by LyCEP-containing fibers. Indeed, LyCEP application transiently hyperpolarizes isolated egg-laying hormone cells. In the Lymnaea pericardium, LyCEP-containing fibers end blindly at the pericardial lumen, and the heart is stimulated by LyCEP in vitro. These data confirm that LyCEP is an RFamide ligand for GRL106.
Transfusion of Plasma, Platelets, and Red Blood Cells in a 1:1:1 vs a 1:1:2 Ratio and Mortality in Patients With Severe Trauma (2015)

clinicaltrials.gov Identifier: NCT01545232.
The high-foot implosion campaign on the National Ignition Facility (2014)

The “High-Foot” platform manipulates the laser pulse-shape coming from the National Ignition Facility laser to create an indirect drive 3-shock implosion that is significantly more robust against instability growth involving the ablator and also modestly reduces implosion convergence ratio. This strategy gives up on theoretical high-gain in an inertial confinement fusion implosion in order to obtain better control of the implosion and bring experimental performance in-line with calculated performance, yet keeps the absolute capsule performance relatively high. In this paper, we will cover the various experimental and theoretical motivations for the high-foot drive as well as cover the experimental results that have come out of the high-foot experimental campaign. At the time of this writing, the high-foot implosion has demonstrated record total deuterium-tritium yields (9.3×1015) with low levels of inferred mix, excellent agreement with implosion simulations, fuel energy gains exceeding unity, and evidence for the “bootstrapping” associated with alpha-particle self-heating.
Structure-activity relationship of quinazolinedione inhibitors of calcium-independent phosphodiesterase (1991)

A series of quinazolinediones and azaquinazolinediones is described which possess potent inhibitory activity toward the calcium-independent phosphodiesterase enzyme (CaIPDE). In vivo testing showed that this in vitro activity translates to animal models predictive of chronic diseases such as depression and inflammation. These results support the hypothesis that inhibition of CaIPDE may lead to useful activity in such chronic diseases.
Serotonin Receptor Subtypes: Implications for Psychopharmacology (1991)

Serotonin (5-HT) interacts with multiple brain 5-HT receptor subtypes to influence a wide range of behaviours. Three main families of 5-HT receptors (5-HT1, 5-HT2 and 5-HT3) have been described which differ in their binding affinity for selective ligands, their receptor-effector coupling mechanisms, and the behavioural processes they regulate. Nevertheless, manipulation of several different 5-HT receptor subtypes (5-HT1A, 5-HT1C, 5-HT2 and 5-HT3) may produce anxiolytic effects; 5-HT1A and 5-HT2 receptors may be involved in the aetiology of major depression and the therapeutic effects of antidepressant treatment; and 5-HT3 receptors have been linked to reward mechanisms and cognitive processes. These advances offer therapeutic possibilities, the value of which can only be satisfactorily assessed by controlled clinical trials.
Design and Analysis of Phase I Clinical Trials (1989)

The Phase I clinical trial is a study intended to estimate the so-called maximum tolerable dose (MTD) of a new drug. Although there exists more or less a standard type of design for such trials, its development has been largely ad hoc. As usually implemented, the trial design has no intrinsic property that provides a generally satisfactory basis for estimation of the MTD. In this paper, the standard design and several simple alternatives are compared with regard to the conservativeness of the design and with regard to point and interval estimation of an MTD (33rd percentile) with small sample sizes. Using a Markov chain representation, we found several designs to be nearly as conservative as the standard design in terms of the proportion of patients entered at higher dose levels. In Monte Carlo simulations, two two-stage designs are found to provide reduced bias in maximum likelihood estimation of the MTD in less than ideal dose-response settings. Of the three methods considered for determining confidence intervals--the delta method, a method based on Fieller's theorem, and a likelihood ratio method--none was able to provide both usefully narrow intervals and coverage probabilities close to nominal.
Primary structure of an amyloid prealbumin variant in familial polyneuropathy of Jewish origin. (1983)

The complete amino acid sequence of three related amyloid proteins (Mr 14,000, 10,000, and 5,000) derived from tissues of a Jewish patient who suffered from a variant of familial polyneuropathic amyloidosis was determined. The protein, which contains 127 residues, is identical to a human serum prealbumin subunit. Only one amino acid substitution, glycine for threonine, was detected at position 49, where enzymatic cleavage occurred, yielding Mr 5,000 and 10,000 fragments which represent the amino terminus (residues 1-48) and carboxyl terminus (residues 49-127) of the molecule, respectively. Thus, a prealbumin variant and its fragments constitute the amyloid fibrils in a heredofamilial amyloidosis syndrome of dominant inheritance.
Detrimental effect of a positive B lymphocyte crossmatch in renal transplantation. (1987)

Revue de 192 transplantations renales chez 182 receveurs. Les rejets sont significativement plus frequents dans les cas ou les lymphocytes B du receveur et du donneur donnent des reactions positives
Biomaterials for the central nervous system (2008)

Biomaterials are widely used to help treat neurological disorders and/or improve functional recovery in the central nervous system (CNS). This article reviews the application of biomaterials in (i) shunting systems for hydrocephalus, (ii) cortical neural prosthetics, (iii) drug delivery in the CNS, (iv) hydrogel scaffolds for CNS repair, and (v) neural stem cell encapsulation for neurotrauma. The biological and material requirements for the biomaterials in these applications are discussed. The difficulties that the biomaterials might face in each application and the possible solutions are also reviewed in this article.
Structural Basis for the Receptor Binding Specificity of Norwalk Virus (2008)

Noroviruses are positive-sense, single-stranded RNA viruses that cause acute gastroenteritis. They recognize human histo-blood group antigens as receptors in a strain-specific manner. The structures presented here were analyzed in order to elucidate the structural basis for differences in ligand recognition of noroviruses from different genogroups, the prototypic Norwalk virus (NV; GI-1) and VA387 (GII-4), which recognize the same A antigen but differ in that NV is unable to bind to the B antigen. Two forms of the receptor-binding domain of the norovirus coat protein, the P domain and the P polypeptide, that were previously shown to differ in receptor binding and P-particle formation properties were studied. Comparison of the structures of the NV P domain with and without A trisaccharide and the NV P polypeptide revealed no major ligand-induced changes. The 2.3-A cocrystal structure reveals that the A trisaccharide binds to the NV P domain through interactions with the residues Ser377, Asp327, His329, and Ser380 in a mode distinct from that previously reported for the VA387 P-domain-A-trisaccharide complex. Mutational analyses confirm the importance of these residues in NV P-particle binding to native A antigen. The alpha-GalNAc residue unique to the A trisaccharide is buried deeply in the NV binding pocket, unlike in the structures of A and B trisaccharides bound to VA387 P domain, where the alpha-fucose residue forms the most protein contacts. The A-trisaccharide binding mode seen in the NV P domain complex cannot be sterically accommodated in the VA387 P domain.
Diosgenin-bearing, molluscicidal saponins from Allium vineale: an NMR approach for the structural assignment of oligosaccharide units (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiosgenin-bearing, molluscicidal saponins from Allium vineale: an NMR approach for the structural assignment of oligosaccharide unitsShaoxing Chen and John K. SnyderCite this: J. Org. Chem. 1989, 54, 15, 3679–3689Publication Date (Print):July 1, 1989Publication History Published online1 May 2002Published inissue 1 July 1989https://pubs.acs.org/doi/10.1021/jo00276a033https://doi.org/10.1021/jo00276a033research-articleACS PublicationsRequest reuse permissionsArticle Views291Altmetric-Citations53LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Progesterone Increases Susceptibility and Decreases Immune Responses to Genital Herpes Infection (2003)

Depo-provera, a long-acting progestational formulation, is widely used to facilitate infection of sexually transmitted diseases in animal models. We have previously reported that hormone treatments change susceptibility and immune responses to genital tract infections. In this study we compared the changes in susceptibility of mice to genital herpes simplex virus type 2 (HSV-2) after Depo-provera or a saline suspension of progesterone (P-sal). We found that following Depo-provera-treatment, mice had prolonged diestrus that lasted more than 4 weeks. This coincided with a 100-fold increase in susceptibility to genital HSV-2 compared to that of untreated mice. Mice given P-sal were in diestrous stage for 4 to 6 days before returning to irregular reproductive cycles. When these mice were infected at diestrus they showed a 10-fold increase in susceptibility compared to that of normal, untreated mice. P-sal-treated mice infected at estrus were susceptible to HSV-2, depending on the infectious dose. Normal, untreated mice in estrus were not susceptible to HSV-2, even at a high infectious dose of 10(7) PFU. In addition to alterations in susceptibility, Depo-provera treatment had inhibitory effects on immune responses to HSV-2. Mice immunized with HSV-2 protein (gB) and treated with Depo-provera showed significant lowering of local HSV-2-specific immunoglobulin G (IgG) and IgA in their vaginal washes. Mice immunized with an attenuated strain of HSV-2 2 weeks after Depo-provera treatment failed to develop protection when challenged intravaginally with wild-type HSV-2. In contrast, mice given progesterone and immunized at diestrus or estrus were completely protected from intravaginal challenge. These studies show that Depo-provera treatment changes susceptibility and local immune responses to genital HSV-2 infection. Animal models and vaccine strategies for sexually transmitted diseases need to consider the effect of hormone treatments on susceptibility and immune responses.
Fundamentals of Human Lymphoid Cell Culture (1981)

Journal Article Fundamentals of Human Lymphoid Cell Culture Get access Fundamentals of Human Lymphoid Cell Culture By J. Leslie Glick. Pp. x+157, illustrated. Marcel Dekker, New York, Basle, 1980. Sw.Fr. 52.00. Postgraduate Medical Journal, Volume 57, Issue 665, March 1981, Page 205, https://doi.org/10.1136/pgmj.57.665.205-b Published: 01 March 1981
Failure mechanism of AlN nanocaps used to protect rare earth-implanted GaN during high temperature annealing (2006)

The structural properties of nanometric AlN caps, grown on GaN to prevent dissociation during high temperature annealing after Eu implantation, have been characterized by scanning electron microscopy and electron probe microanalysis. The caps provide good protection up to annealing temperatures of at least 1300°C, but show localized failure in the form of irregularly shaped holes with a lateral size of 1–2μm which extend through the cap into the GaN layer beneath. Compositional micrographs, obtained using wavelength dispersive x-ray analysis, suggest that these holes form when GaN dissociates and ejects through cracks already present in the as-grown AlN caps due to the large lattice mismatch between the two materials. Implantation damage enhances the formation of the holes during annealing. Simultaneous room temperature cathodoluminescence mapping showed that the Eu luminescence is reduced in N-poor regions. Hence, exposed GaN dissociates first by outdiffusion of nitrogen through AlN cracks, thereby opening a hole in the cap through which Ga subsequently evaporates.
Quantitative Footprinting Analysis of the Netropsin-DNA Interaction (1987)

The results of a series of quantitative footprinting experiments of the netropsin-DNA interaction as studied using two different DNA cleaving probes, the enzyme DNase I and a cationic manganese porphyrin complex, are described. Plots of the relative change in oligonucleotide concentration as a function of drug concentration, covering approximately 110 base pairs of a DNA restriction fragment, revealed netropsin induced changes in the cleavage rates of both probes. These appeared as inhibitions for the binding sites, enhancements where no binding took place, and enhancement/inhibitions for the weak binding sites. Determination of the concentration of drug necessary to reduce the amount of a particular oligomer to half of its initial value allowed a ranking of the affinities of the various binding sites on the fragment. In addition to uncovering the location of a number of overlapping netropsin binding sites, the data allowed additional insight on the manner in which both probes alter their DNA cleavage rates in the drug-footprinting experiment.
The Habit of Authority: Paternalism in British History (1967)

Find information about UTP Journals. University of Toronto Press is Canada’s leading academic publisher and one of the largest university presses in North America, with particular strengths in the social sciences, humanities, and business. The Book Publishing Division is widely recognized in Canada for its strength in history, political science, sociology, Indigenous studies, and cultural studies. Internationally, UTP is a leading publisher of medieval, Renaissance, Italian, Iberian, Slavic, and urban studies, as well as studies in book and print culture.
Electrophoretic Deposition of Carbon Nanotubes on Metallic Surfaces (2006)

A method based on electrophoretic deposition has been developed to produce uniform deposits of multi-walled carbon nanotubes on stainless steel substrates. Aqueous suspensions were used under constant voltage conditions in the range of 5 to 50 V, with deposition times ranging from 0.5 to 10 minutes. The thickness of the coatings was controlled by variation of voltage and deposition time during EPD. Coatings of up to 100μm thickness were achieved, which exhibit homogeneous microstructure. The EPD technique is fast, cost-effective, and it can be applied to complex shapes. Possible applications of CNT coatings are in heat extraction devices or porous nanostructured coatings for tissue engineering scaffolds.
Antibody–drug Conjugates: Using Monoclonal Antibodies for Delivery of Cytotoxic Payloads to Cancer Cells (2011)

One approach to improving activity of anticancer drugs is to conjugate them to antibodies that recognize tumor-associated, cell-surface antigens. The antibody-drug conjugate concept evolved following major advances, first, in the development of humanized and fully human antibodies; second, in the discoveries of highly cytotoxic compounds ('drugs) linkable to antibodies; and finally, in the optimization of linkers that couple the drug to the antibody and provide sufficient stability of the antibody-drug conjugate in the circulation, optimal activation of the drug in the tumor, and the ability of the activated drug to overcome multidrug resistance. In this article, we will review the considerations for selecting a target antigen, the design of the conjugate, and the pre-clinical and clinical experiences with the current generation of antibody-drug conjugates.
Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. (1992)

The substrate recognition regions in cytochrome P450 family 2 (CYP2) proteins were inferred by group-to-group alignment of CYP2 sequences and those of bacterial P450s, including Pseudomonas putida P450 101A (P450cam), whose substrate-binding residues have been definitely identified by x-ray crystallography of a substrate-bound form (Poulos T. L., Finzel, B. C., and Howard, A. J. (1987) J. Mol. Biol. 195, 687-700). The six putative substrate recognition sites, SRSs, thus identified are dispersively located along the primary structure and constitute about 16% of the total residues. All the reported point mutations and chimeric fragments that significantly affect the substrate specificities of the parental CYP2 enzymes fell within or overlapped some of the six SRSs. Analysis of nucleotide substitution patterns in closely related members in four subfamilies, CYP2A, 2B, 2C, and 2D, consistently indicated that the SRSs have accumulated more nonsynonymous (amino acid-changing) substitutions than the rest of the sequence. This observation supports the idea that diversification of duplicate genes of drug-metabolizing P450s occurs primarily in substrate recognition regions to cope with an increasing number of foreign compounds.