gebhart/patrepeval huggingface dataset:
Cooperation between Thrombospondin-1 Type 1 Repeat Peptides and αvβ3 Integrin Ligands to Promote Melanoma Cell Spreading and Focal Adhesion Kinase Phosphorylation (1999)

CD47-binding sequences from the carboxyl-terminal domain of thrombospondin-1 (TSP1) are known to regulate activity of the alpha(v)beta(3) integrin (Gao, G., Lindberg, F. P., Dimitry, J. M., Brown, E. J., and Frazier, W. A. (1996) J. Cell Biol. 135, 533-544). Here we show that peptides from the type 1 repeats of TSP1 also stimulate alpha(v)beta(3) integrin function in melanoma cells. Addition of soluble peptide 246 (KRFKQDGGWSHWSPWSS) enhances spreading of A2058 melanoma cells on several alpha(v)beta(3) integrin ligands, including vitronectin, recombinant TSP1 fragments containing the Arg-Gly-Asp sequence, and native TSP1. This activity requires the Trp residues and is independent of CD36-binding sequences in the type 1 repeats. Recombinant type 1 repeats expressed as a glutathione S-transferase fusion protein also enhance spreading on vitronectin and TSP1. Activation of alpha(v)beta(3) integrin by the soluble peptide 246 stimulates organization of F-actin and increases tyrosine phosphorylation of focal adhesion kinase. In contrast, direct adhesion of melanoma cells on immobilized peptide 246 inhibits tyrosine phosphorylation of focal adhesion kinase. Stimulation of alpha(v)beta(3) integrin function by the type 1 repeat peptide differs from that induced by CD47-binding TSP1 peptides in that heparan sulfate proteoglycans are required and pertussis toxin does not inhibit the former activity. Thus, the type 1 repeats contain a second sequence of TSP1 that can enhance alpha(v)beta(3) integrin signaling, and these two sequences stimulate recognition of both vitronectin and TSP1 by the alpha(v)beta(3) integrin.
Diversity and structure of human T-cell receptor beta-chain variable region genes. (1986)

The nucleotide sequences of 27 T-cell receptor beta cDNA clones isolated from a human peripheral lymphocyte library were determined and compared to five additional published sequences. These cDNA clones represent 22 distinct T-cell receptor beta-chain variable region (V beta) gene segment sequences, which fall into 15 different V beta gene subfamilies, each containing six or fewer members. From this analysis, we estimate that the repertoire of expressed human V beta genes is less than 59, apparently much smaller than the immunoglobulin heavy chain and light chain variable region (VH and VL) repertoires. Variability plots comparing these human V beta regions with each other and with published mouse V beta regions provide evidence for only four hypervariable regions homologous to those seen in comparisons of immunoglobulin V regions. Somatic hypermutation appears to be used infrequently, if at all, in these V beta genes.
Substituents on Quinone Methides Strongly Modulate Formation and Stability of Their Nucleophilic Adducts (2006)

Electronic perturbation of quinone methides (QM) greatly influences their stability and in turn alters the kinetics and product profile of QM reaction with deoxynucleosides. Consistent with the electron-deficient nature of this reactive intermediate, electron-donating substituents are stabilizing and electron-withdrawing substituents are destabilizing. For example, a dC N3-QM adduct is made stable over the course of observation (7 days) by the presence of an electron-withdrawing ester group that inhibits QM regeneration. Conversely, a related adduct with an electron-donating methyl group is very labile and regenerates its QM with a half-life of approximately 5 h. The generality of these effects is demonstrated with a series of alternative quinone methide precursors (QMP) containing a variety of substituents attached at different positions with respect to the exocyclic methylene. The rates of nucleophilic addition to substituted QMs measured by laser flash photolysis similarly span 5 orders of magnitude with electron-rich species reacting most slowly and electron-deficient species reacting most quickly. The reversibility of QM reaction can now be predictably adjusted for any desired application.
The Lymphoid Past of Mouse Plasmacytoid Cells and Thymic Dendritic Cells (2003)

There has been controversy over the possible lymphoid origin of certain dendritic cell (DC) subtypes. To resolve this issue, DC and plasmacytoid pre-DC isolated from normal mouse tissues were analyzed for transient (mRNA) and permanent (DNA rearrangement) markers of early stages of lymphoid development. About 27% of the DNA of CD8(+) DC from thymus, and 22-35% of the DNA of plasmacytoid pre-DC from spleen and thymus, was found to contain IgH gene D-J rearrangements, compared with 40% for T cells. However, the DC DNA did not contain IgH gene V-D-J rearrangements nor T cell Ag receptor beta gene D-J rearrangements. The same DC lineage populations containing IgH D-J rearrangements expressed mRNA for CD3 chains, and for pre-T alpha. In contrast, little of the DNA of the conventional DC derived from spleen, lymph nodes, or skin, whether CD8(+) or CD8(-), contained IgH D-J rearrangements and splenic conventional DC expressed very little CD3 epsilon or pre-T alpha mRNA. Therefore, many plasmacytoid pre-DC and thymic CD8(+) DC have shared early steps of development with the lymphoid lineages, and differ in origin from conventional peripheral DC.
Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease (2012)

Emerging influenza viruses are a serious threat to human health because of their pandemic potential. A promising target for the development of novel anti-influenza therapeutics is the PA protein, whose endonuclease activity is essential for viral replication. Translation of viral mRNAs by the host ribosome requires mRNA capping for recognition and binding, and the necessary mRNA caps are cleaved or "snatched" from host pre-mRNAs by the PA endonuclease. The structure-based development of inhibitors that target PA endonuclease is now possible with the recent crystal structure of the PA catalytic domain. In this study, we sought to understand the molecular mechanism of inhibition by several compounds that are known or predicted to block endonuclease-dependent polymerase activity. Using an in vitro endonuclease activity assay, we show that these compounds block the enzymatic activity of the isolated PA endonuclease domain. Using X-ray crystallography, we show how these inhibitors coordinate the two-metal endonuclease active site and engage the active site residues. Two structures also reveal an induced-fit mode of inhibitor binding. The structures allow a molecular understanding of the structure-activity relationship of several known influenza inhibitors and the mechanism of drug resistance by a PA mutation. Taken together, our data reveal new strategies for structure-based design and optimization of PA endonuclease inhibitors.
Restriction Endonuclease Analysis of Marek's Disease Virus DNA and Homology between Strains (1983)

The restriction endonuclease patterns of viral DNA obtained from serotypes 1 and 2 strains of Marek's disease virus have been compared and homology between the strains examined by hybridization. The results have shown that HPRS 16 (serotype 1) DNA has a structure similar to its attenuated variant HPRS 16/att except for a few fragments that are present only in the virulent strain. Evidence was obtained which suggested that these restriction fragments contained repeat sequences and that insertion of heterogeneous DNA occurred at these sites during attenuation of HPRS 16. The restriction enzyme patterns of HPRS 24 (serotype 2) differed substantially from those of HPRS 16 and HPRS 16/att and reassociation experiments showed that HPRS 24 shares less than 10% homology with either HPRS 16 or herpesvirus of turkeys (serotype 3).
Finding community structure in networks using the eigenvectors of matrices (2006)

We consider the problem of detecting communities or modules in networks, groups of vertices with a higher-than-average density of edges connecting them. Previous work indicates that a robust approach to this problem is the maximization of the benefit function known as "modularity" over possible divisions of a network. Here we show that this maximization process can be written in terms of the eigenspectrum of a matrix we call the modularity matrix, which plays a role in community detection similar to that played by the graph Laplacian in graph partitioning calculations. This result leads us to a number of possible algorithms for detecting community structure, as well as several other results, including a spectral measure of bipartite structure in networks and a centrality measure that identifies vertices that occupy central positions within the communities to which they belong. The algorithms and measures proposed are illustrated with applications to a variety of real-world complex networks.
A Concise Route to Benzofused Macrolactones via Ynolides:  Cycloproparadicicol (2003)

A new facile synthesis has been developed for nanomolar Hsp90 inhibitor, cycloproparadicicol (2). Our approach relied on cobalt-complexation promoted RCM, in combination with tandem Diels-Alder/retro-Diels-Alder reactions to assemble the resorcycinylic macrolactone.
Hypolipidemic Effect of Ethyl all-cis-5,8,11,14,17-Icosapentaenoate (EPA-E) in Rats (1992)

We examined the effect of ethyl all-cis-5,8,11,14,17-icosapentaenoate (EPA-E) with high purity on circulating lipids in rats under several experimental conditions. In normolipidemic rats, EPA-E decreased the lipids in a dose-dependent manner. Clofibrate (100 mg/kg/day) was more potent in lowering the lipids than EPA-E (1000 mg/kg/day). In high cholesterol diet-fed rats, EPA-E (300 mg/kg/day) decreased the total cholesterol. However, clofibrate (300 mg/kg/day) had little effect on the total cholesterol. In hypertriglycemic rats induced by corn oil, EPA-E (300 mg/kg/day) or clofibrate (100 mg/kg/day) reduced the rise of triglycerides. EPA-E (300 mg/kg/day), clinofibrate (100 mg/kg/day) or clofibrate (300 mg/kg/day) caused a significant reduction in the lipids induced by the injection of Triton WR-1339. Furthermore, EPA-E (300 mg/kg/day) or clinofibrate (100 mg/kg/day) decreased the elevation of lipids produced by feeding the rats a casein-rich diet. These results show that EPA-E possesses potent inhibitory activity on experimental hyperlipidemia induced either exogenously or endogenously.
Characterization of two novel Ly-6 genes. Protein sequence and potential structural similarity to alpha-bungarotoxin and other neurotoxins (1993)

Genomic clones cross-hybridizing with Ly-6A.2 cDNA were isolated and characterized for functional Ly-6-related genes. Two new Ly-6 genes, designated Ly-6F.1 and Ly-6G.1, were found to have high nucleotide homology (> or = 70%) and the characteristic four exon gene organization of Ly-6A/E and Ly-6C. By a PCR-based assay, Ly-6G.1 mRNA was readily found in bone marrow, whereas Ly-6F.1 mRNA was not detected in lymphoid tissues. Thus, Ly-6G.1 represents an additional Ly-6 gene with apparent selective expression in hematopoietic cells distinct from Ly-6A/E and Ly-6C. Using the available deduced protein sequence data for mature Ly-6 proteins, searches of the database uncovered an evolutionary relationship of Ly-6 proteins with neurotoxins isolated from snake venoms. The protein sequence conservation between the two groups was selective for, but not limited to, residues in neurotoxins that have been found to be important for their tertiary structures. From this relationship, we propose a neurotoxin-like structure for Ly-6 and Ly-6-related proteins, such as CD59.
Distribution patterns of type VII collagen in normal and malignant human tissues. (1991)

The distribution of basement membrane type VII collagen was detected immunohistochemically and compared in normal human organs and their neoplastic derivatives using monoclonal antibody LH7.2. In normal tissues, type VII collagen was found to be restricted to the basement membrane surrounding or underlying combined epithelia, such as those lining breast, prostate, and bronchus, which are composed of a basal and luminal cell layer, and stratified epithelia, such as larynx, esophagus, trachea, vagina, ectocervix, and epidermis. No type VII collagen was found in the "simple' epithelia lining the major part of the gastrointestinal tract (GI) tract, such as liver, stomach, and intestine, or around blood vessels, muscle, and nerve fibers, which are surrounded, however, by a basement membrane containing type IV collagen and laminin. When tested in benign and malignant local tumors, antibody LH7.2 showed staining patterns partly similar to those observed in the corresponding normal tissues. This resulted in a well-circumscribed positive reaction around ducts in carcinomas in situ of the breast, in benign prostate tumors, in pleomorphic adenomas, and in a negative reaction in tumors of the GI tract. Furthermore type VII collagen was predominantly seen in carcinomas with a squamous differentiation, such as squamous carcinomas of the lung, head and neck, vulva, and vagina. These results indicate that the presence of type VII collagen in malignant tumors is correlated with (squamous) differentiation rather than with the origin of the tumor. With tumor progression, an increased presence of type VII collagen, as compared with normal urinary bladder, was found in infiltrating transitional cell carcinomas. Thus, although in general invasive and metastatic tumors do not express extensively type VII collagen, exceptions to this rule exist in bladder cancer, squamous carcinomas of the lung, tumors of the head and neck region, female genital tract tumors, and in some adenocarcinomas of the breast.
Melanin-concentrating hormone 1 receptor-deficient mice are lean, hyperactive, and hyperphagic and have altered metabolism (2002)

Melanin-concentrating hormone (MCH) is a cyclic 19-aa hypothalamic neuropeptide derived from a larger prohormone precursor of MCH (Pmch), which also encodes neuropeptide EI (NEI) and neuropeptide GE (NGE). Pmch-deficient (Pmch-/-) mice are lean, hypophagic, and have an increased metabolic rate. Transgenic mice overexpressing Pmch are hyperphagic and develop mild obesity. Consequently, MCH has been implicated in the regulation of energy homeostasis. The MCH 1 receptor (MCH1R) is one of two recently identified G protein-coupled receptors believed to be responsible for the actions of MCH. We evaluated the physiological role of MCH1R by generating MCH1R-deficient (Mch1r-/-) mice. Mch1r-/- mice have normal body weights, yet are lean and have reduced fat mass. Surprisingly, Mch1r-/- mice are hyperphagic when maintained on regular chow, and their leanness is a consequence of hyperactivity and altered metabolism. Consistent with the hyperactivity, Mch1r-/- mice are less susceptible to diet-induced obesity. Importantly, chronic central infusions of MCH induce hyperphagia and mild obesity in wild-type mice, but not in Mch1r-/- mice. We conclude that MCH1R is a physiologically relevant MCH receptor in mice that plays a role in energy homeostasis through multiple actions on locomotor activity, metabolism, appetite, and neuroendocrine function.
Definition of the HLA-A29 peptide ligand motif allows prediction of potential T-cell epitopes from the retinal soluble antigen, a candidate autoantigen in birdshot retinopathy. (1996)

The peptide-binding motif of HLA-A29, the predisposing allele for birdshot retinopathy, was determined after acid-elution of endogenous peptides from purified HLA-A29 molecules. Individual and pooled HPLC fractions were sequenced by Edman degradation. Major anchor residues could be defined as glutamate at the second position of the peptide and as tyrosine at the carboxyl terminus. In vitro binding of polyglycine synthetic peptides to purified HLA-A29 molecules also revealed the need for an auxiliary anchor residue at the third position, preferably phenylalanine. By using this motif, we synthesized six peptides from the retinal soluble antigen, a candidate autoantigen in autoimmune uveoretinitis. Their in vitro binding was tested on HLA-A29 and also on HLA-B44 and HLA-B61, two alleles sharing close peptide-binding motifs. Two peptides derived from the carboxyl-terminal sequence of the human retinal soluble antigen bound efficiently to HLA-A29. This study could contribute to the prediction of T-cell epitopes from retinal autoantigens implicated in birdshot retinopathy.
EFFECTS OF VASOACTIVE INTESTINAL PEPTIDE ON HUMAN SPERM MOTILITY (1999)

Sperm flagellar activity is modulated by cAMP. In target tissues, vasoactive intestinal peptide (VIP) stimulates adenyl cyclase activity, which elevates intracellular cAMP levels and activates protein kinase activity. This study investigated the effects of VIP on motility of sperm from 17 subjects. Motile activities, monitored before (0 min, baseline) and for 40 min after incubation with VIP (0.2 microgram/mL cell suspension), were analyzed by computer-assisted semen analysis. The data (mean +/- SEM) are expressed as percentages of baseline values and changes were compared by trend analysis for interval level measures by repeated measures analysis of variance orthogonal polynominal contrasts. The addition of VIP significantly increased motile sperm concentration (110 +/- 17% [10 min], 132 +/- 15% [20 min], 152 +/- 18% [30 min], 125 +/- 18% [40 min]; p < .02) and sperm with rapid straight-line motility (V > 25 microns/s) (167 +/- 20%, 174 +/- 19%, 173 +/- 23%, 141 +/- 16%; p < .02). Mean track speed (micron/s) was increased (125 +/- 12%, 134 = 9%, 129 +/- 12% and 126 +/- 12%; p < .02), while mean progressive velocity, amplitude of head displacement, and beat frequency were not affected by VIP. These results indicate that VIP stimulates sperm motile activity by cAMP-mediated phosphorylation of axonemal proteins.
Resistance to neurotoxicity in cortical cultures from neuronal nitric oxide synthase-deficient mice (1996)

In addition to its functions as a neuronal messenger molecule, nitric oxide (NO) has also been implicated in playing a major role in ischemic damage and glutamate neurotoxicity. Using primary cortical cultures from transgenic neuronal NO synthase (NOS) null (nNOS-) mice, we definitively establish NO as a mediator of NMDA and hypoxic neurotoxicity. Neurotoxicity elicited by NMDA is markedly attenuated in nNOS- cortical cultures compared with wild-type cultures. The NOS inhibitor nitro-L-arginine is neuroprotective in wild-type but not nNOS-cultures, confirming the role of nNOS-derived NO in glutamate neurotoxicity. Confirming that the nNOS- cultures lack NMDA-stimulated nNOS activity, NMDA did not stimulate the formation of cGMP in nNOS- cultures, but markedly elevates cGMP in wild-type cultures. Both wild-type and nNOS- cultures are sensitive to toxicity induced by NO donors, indicating that pathways stimulated by NO that result in neuronal cell death are still intact in the transgenic mice. Superoxide dismutase is neuroprotective against NMDA and NO neurotoxicity in both wild-type and nNOS- cultures, highlighting the importance of superoxide anion in subsequent neuronal damage. The unknown cellular factors that endow differential resistance to NMDA neurotoxicity and differential susceptibility to quisqualate neurotoxicity remain intact in the nNOS- cultures, because the response of somatostatin-immunopositive neurons in nNOS- cultures to high-dose NMDA and low-dose quisqualate is identical to the response of NOS-immunopositive neurons in the wild-type cultures. There is no difference in susceptibility to kainate neurotoxicity between nNOS- and wild-type cultures and only a modest resistance to quisqualate neurotoxicity, confirming observations that NO-mediated neurotoxicity is associated primarily with activation of the NMDA receptor. The nNOS- cultures are markedly protected from 60 min of combined oxygen-glucose deprivation neurotoxicity compared with wild-type cultures. Wild-type cultures are protected from neuronal cell death by the NMDA receptor antagonist MK-801 and the NOS inhibitor L-nitroarginine methyl ester, but not its inactive stereoisomer D-nitroarginine methyl ester. nNOS- cultures were not additionally protected. These data confirm that activation of NMDA receptors and production of NO are primary mediators of neuronal damage after ischemic insult.
The pulmonary physician in critical care * 5: Acute lung injury and the acute respiratory distress syndrome: definitions and epidemiology (2002)

An understanding of the epidemiology of ALI/ARDS and the effects of treatment have been hampered by the lack of a uniform definition of the syndrome. Various definitions have been proposed, and these are reviewed with particular attention to how changes in definition have affected our understanding of the natural history and treatment options for the condition.
Towards a universal influenza vaccine: different approaches for one goal (2018)

Influenza virus infection is an ongoing health and economic burden causing epidemics with pandemic potential, affecting 5-30% of the global population annually, and is responsible for millions of hospitalizations and thousands of deaths each year. Annual influenza vaccination is the primary prophylactic countermeasure aimed at limiting influenza burden. However, the effectiveness of current influenza vaccines are limited because they only confer protective immunity when there is antigenic similarity between the selected vaccine strains and circulating influenza isolates. The major targets of the antibody response against influenza virus are the surface glycoprotein antigens hemagglutinin (HA) and neuraminidase (NA). Hypervariability of the amino acid sequences encoding HA and NA is largely responsible for epidemic and pandemic influenza outbreaks, and are the consequence of antigenic drift or shift, respectively. For this reason, if an antigenic mismatch exists between the current vaccine and circulating influenza isolates, vaccinated people may not be afforded complete protection. There is currently an unmet need to develop an effective "broadly-reactive" or "universal" influenza vaccine capable of conferring protection against both seasonal and newly emerging pre-pandemic strains. A number of novel influenza vaccine approaches are currently under evaluation. One approach is the elicitation of an immune response against the "Achille's heel" of the virus, i.e. conserved viral proteins or protein regions shared amongst seasonal and pre-pandemic strains. Alternatively, other approaches aim toward eliciting a broader immune response capable of conferring protection against the diversity of currently circulating seasonal influenza strains.In this review, the most promising under-development universal vaccine approaches are discussed with an emphasis on those targeting the HA glycoprotein. In particular, their strengths and potential short-comings are discussed. Ultimately, the upcoming clinical evaluation of these universal vaccine approaches will be fundamental to determine their effectiveness against preventing influenza virus infection and/or reducing transmission and disease severity.
Evolutionary Induction of Sparse Neural Trees (1997)

This paper is concerned with the automatic induction of parsimonious neural networks. In contrast to other program induction situations, network induction entails parametric learning as well as structural adaptation. We present a novel representation scheme called neural trees that allows efficient learning of both network architectures and parameters by genetic search. A hybrid evolutionary method is developed for neural tree induction that combines genetic programming and the breeder genetic algorithm under the unified framework of the minimum description length principle. The method is successfully applied to the induction of higher order neural trees while still keeping the resulting structures sparse to ensure good generalization performance. Empirical results are provided on two chaotic time series prediction problems of practical interest.