gebhart/patrepeval huggingface dataset:
Prediction of surface and interior regions in proteins--Part II: Predicting secondary structure in regions bound by surface exposed regions. (1992)

A new secondary structure prediction algorithm (SecondaryPlot) is described and has been developed for the IBM or compatible computer. This algorithm successfully predicts the boundaries of secondary structural regions by combining hydrophilicity, accessibility and flexibility parameters. Within the limits of these predicted structural regions, five algorithms (Chou and Fasman; Garnier, Osguthorpe and Robson; Delange and Roux; Barkovsky and Bandarin; and Lim) were used to predict helix and sheet regions. All of the algorithms correctly predicted 50-60% of the x-ray defined regions. Predictions were improved by combining the two most successful algorithms of Lim and Chou and Fasman. By combining the boundary predictions (hydrophilicity, accessibility, flexibility and linear polar tripeptide sequences) with secondary structure predictions (Lim, Chou and Fasman), approximately 80% of the x-ray defined structural regions were predicted correctly for 30 proteins (86% for the alpha-class, 79% for the beta-class and 82% for the alpha/beta class of proteins). In our hands, the best of the five algorithms studied to predict the state (helix or sheet) of these structural regions predicted 62% of helical regions and 64% of extended regions in a test set of fifteen proteins. However, SecondaryPlot predicted 78% of helical regions and 71% of extended regions for the same test. SecondaryPlot provides a significant improvement to structure prediction and is a necessary first step in the tertiary structure prediction of proteins.
NOD2/CARD15 disease associations other than Crohnʼs disease (2006)

At this moment, few confirmed associations between NOD2 mutations and diseases other than Crohn's disease (CD) and Blau syndrome (BS) have been reported, but research is ongoing in several fields where a genetic susceptibility factor and/or a role for the innate immune system is suspected. Whether the Crohn's-associated CARD15 mutations lead to a loss or gain of function of the NOD2 receptor is subject to controversy, and by which mechanisms this change in function might increase the susceptibility to CD is still under investigation. The possible involvement of NOD2/CARD15 in the pathogenesis of certain diseases with already (partially) unraveled pathophysiologic mechanisms might contribute to our further understanding of NOD2/CARD15 and its function in CD. We review studies on the association of CARD15 variants with diseases other than CD. The association of NOD2/CARD15 mutations with CD and BS, and possibly also early onset sarcoidosis, suggests a role for the gene in the development of granulomata and granulomatous diseases, possibly by inappropriate activation of the immune system. The data from the oncology field suggest that this inappropriate activation might even lead to uncontrolled proliferation of certain cell types. The studies in allergic diseases and atopy are the largest so far, and the association of NOD2/CARDI5 mutations with atopic phenotypes might be an indication that CARD15 also plays a role in the Th2 pathway. Finally, transplantation studies indicate that the genetic background of a patient should be taken into account when considering hematopoietic stem cell transplantation, given the increased risk of mortality and graft versus host disease observed. Whether NOD2 variants are also associated with an increased risk for infections and sepsis in patients receiving immunosuppressive therapies is unclear.
Pressure-induced structural phase transition in fullerides doped with rare-earth metals (2003)

Rare-earth-metal-doped fullerides with nominal composition of ${R}_{3}{\mathrm{C}}_{70}$ $(R=\mathrm{Sm},$ Eu) adopt a pseudomonoclinic structure in which ${\mathrm{C}}_{70}$ dimers glued with rare-earth ions are involved. High-pressure powder x-ray diffraction experiments revealed that these compounds undergo a reversible first-order structural phase transition at 1.5 GPa, associated with 2.7%--2.9% reduction of the unit cell volume. Structural analyses showed that the rare-earth ions, which are located close to the edge of tetrahedral sites at ambient pressure, move back to the center of the tetrahedral sites. Simultaneously, ${\mathrm{C}}_{70}$ molecules are realigned so that the fivefold (long) axes are perpendicular to the $(101\ifmmode\bar\else\textasciimacron\fi{})$ or $(111\ifmmode\bar\else\textasciimacron\fi{}{)}_{\mathrm{fcc}}$ plane at high pressure. The derived charge density map indicates that the transition is regarded as a structural change from dimers to three-dimensional polymers of fullerenes. These features are ascribed to the unique bonding nature in rare-earth ${\mathrm{C}}_{70}$ compounds.
LEUKOCYTE-DEPENDENT HISTAMINE RELEASE FROM RABBIT PLATELETS (1972)

We have studied the leukocyte-dependent mechanism of histamine release (LDHR) from rabbit platelets, a complement-independent mechanism which has been implicated in the deposition of immune complexes in acute serum sickness of rabbits. It was found by chromatography and passive transfer of serum from immunized rabbits that the antibody responsible for the LDHR was of IgE type. By electron microscope study of the reaction, the leukocyte involved in agglutination of platelets and release of their histamine content was identified as the basophil. Upon addition of antigen, basophils sensitized with IgE degranulated, released their histamine content and a platelet-activating factor (PAF) that caused aggregation of platelets and release of their histamine. Conditions of preparing and preserving PAF activity and some properties of this factor have been elucidated. LDHR must, therefore, be considered as an immediate hypersensitivity-type mechanism which may link allergic reactions with immunologic disease associated with severe structural injury.
Characterization of a rice gene showing organ-specific expression in response to salt stress and drought. (1990)

Protein changes induced by salinity stress were investigated in the roots of the salt-sensitive rice cultivar Taichung native 1. We found eight proteins to be induced and obtained partial sequences of one with a molecular mass of 15 kilodaltons and an isoelectric point of 5.5. Using an oligonucleotide probe based on this information, a cDNA clone, salT, was selected and found to contain an open reading frame coding for a protein of 145 amino acid residues. salT mRNA accumulates very rapidly in sheaths and roots from mature plants and seedlings upon treatment with Murashige and Skoog salts (1%), air drying, abscisic acid (20 microM), polyethylene glycol (5%), sodium chloride (1%), and potassium chloride (1%). Generally, no induction was seen in the leaf lamina even when the stress should affect all parts of the plant uniformly. The organ-specific response of salT is correlatable with the pattern of Na+ accumulation during salt stress.
Evaluation of antineoplastic action of 5-aza-2???-deoxycytidine (Dacogen) and docetaxel (Taxotere) on human breast, lung and prostate carcinoma cell lines (2004)

The antineoplastic activity of 5-aza-2'-deoxycytidine (5-AZA-CdR) and docetaxel (Taxotere, Taxo) alone or in combination against human MDA-MB-231 breast, Calu-6 lung and DU-145 prostate carcinoma cell lines was evaluated by clonogenic assay. We also investigated by RT-PCR the capacity of these agents to re-activate the expression of E-cadherin and maspin, two tumor suppressor genes that were silenced by DNA methylation. 5-AZA-CdR and Taxo in combination produced a greater loss of clonogenicity than either agent alone. In MDA-MB-231 breast carcinoma cells, Taxo did not interfere with the re-activation of E-cadherin and maspin genes by 5-AZA-CdR. These results provide a rationale for clinical trials on the combination of 5-AZA-CdR and Taxo in patients with advanced cancer.
Prolonged bile duct obstruction: a new experimental model for cirrhosis in the rat. (1984)

Hepatic morphological abnormalities were examined in rats whose bile ducts had been either cannulated and then obstructed or irreversibly ligated for 5, 10, 15 and 28 days or longer. Throughout the experiment most of the morphological changes observed in the cannulated group were comparable to those in the ligated group. Portal inflammation and marginal bile duct proliferation were noted with the same frequency in both groups. Biliary obstruction for 15 days or more led to cirrhosis. After 28 days obstruction, five out of six cannulated rats and four out of six ligated animals respectively developed cirrhosis. The development of cirrhosis was progressive and associated with ascites. It is concluded that in the rat the morphological sequelae of long term cholestasis induced by either cannulation and obstruction or ligation of bile ducts are similar and are accompanied by cirrhosis. The advantages of this experimental model for the study of human cirrhosis are discussed.
Stimulation of tumor-draining lymph node cells with superantigenic staphylococcal toxins leads to the generation of tumor-specific effector T cells. (1994)

In animal studies, lymph nodes (LN) draining progressive tumors contain immunologically sensitized but functionally deficient T cells. These preeffector cells can differentiate into mature effector cells on stimulation in vitro with anti-CD3 and IL-2. However, anti-CD3 react with all T cells and the activated cell population expressed a broad but normal distribution of V beta phenotypes. In this study, we examined the feasibility of using bacterial superantigens to stimulate tumor-draining LN cells. Because of their TCR V beta restriction, superantigen activation may afford a means to identify T cell subsets that are important in the antitumor immune response. Stimulation of draining LN cells with staphylococcal enterotoxins A (SEA) or B (SEB) followed by culture in IL-2 resulted in selective activation and expansion of V beta 3 and V beta 11 or V beta 3 and V beta 8 T cells, respectively. However, in adoptive immunotherapy, SEB- but not SEA-activated cells mediated the regression of established pulmonary metastases. To define the relative antitumor effects of V beta 3 and V beta 8 T cells, SEB-activated cells were depleted of either V beta 3 or V beta 8 T cells with mAb and magnetic beads. The antitumor effects were demonstratably diminished after V beta 8 cell depletion but enhanced after V beta 3 cell depletion. Using antigenically distinct MCA 205 and 207 sarcomas, tumor regression mediated by the activated cells was found to be immunologically specific for the tumor that stimulated the draining LN. Furthermore, the SEB-activated cells were virtually all T cells consisting of approximately equal proportions of CD4+ and CD8+ cells and the collaboration of the two T cell subsets was required for in vivo antitumor effects. However, the helper function of CD4+ cells could be facilitated by the administration of exogenous IL-2. Despite their in vivo antitumor reactivity, SEB-activated cells did not exhibit tumor cytotoxicity in the 4-h 51Cr release assay. However, they secreted IFN-gamma on specific stimulation with tumor cells. Taken together, these results provide for the first time clear evidence of the functional significance of superantigen interactions with immunologically committed T cells and suggest a preferential V beta use that might be associated with the T cell immune response to progressively growing tumors.
Chemotherapeutic Approaches for Targeting Cell Death Pathways (2006)

For several decades, apoptosis has taken center stage as the principal mechanism of programmed cell death in mammalian tissues. It also has been increasingly noted that conventional chemotherapeutic agents not only elicit apoptosis but other forms of nonapoptotic death such as necrosis, autophagy, mitotic catastrophe, and senescence. This review presents background on the signaling pathways involved in the different cell death outcomes. A re-examination of what we know about chemotherapy-induced death is vitally important in light of new understanding of nonapoptotic cell death signaling pathways. If we can precisely activate or inhibit molecules that mediate the diversity of cell death outcomes, perhaps we can succeed in more effective and less toxic chemotherapeutic regimens.
Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian genomic DNA. (1990)

Identification and recovery of transcribed sequences from cloned mammalian genomic DNA remains an important problem in isolating genes on the basis of their chromosomal location. We have developed a strategy that facilitates the recovery of exons from random pieces of cloned genomic DNA. The basis of this "exon trapping" strategy is that, during a retroviral life cycle, genomic sequences of nonviral origin are correctly spliced and may be recovered as a cDNA copy of the introduced segment. By using this genetic assay for cis-acting sequences required for RNA splicing, we have screened approximately 20 kilobase pairs of cloned genomic DNA and have recovered all four predicted exons.
Distributed Video Streaming with Forward Error Correction (2003)

With the explosive growth of video applications over the Internet, many approaches have been proposed to stream video effectively over packet switched, best-effort networks. Many use techniques from source and channel coding, or implement transport protocols, or modify system architectures in order to deal with delay, loss, and time-varying nature of the Internet. In our previous work, we proposed a framework with a receiver driven protocol to coordinate simultaneous video streaming from multiple senders to a single receiver in order to achieve higher throughput, and to increase tolerance to packet loss and delay due to network congestion. The receiver-driven protocol employs two algorithms: rate allocation and packet partition. The rate allocation algorithm determines the sending rate for each sender; the packet partition algorithm ensures no senders send the same packets, and at the same time, minimizes the probability of late packets. In this paper, we propose a novel rate allocation scheme to be used with Forward Error Correction (FEC) in order to minimize the probability of packet loss in bursty loss environments such as those caused by network congestion. Using both simulations and actual Internet experiments, we demonstrate the effectiveness of our rate allocation scheme in reducing packet loss, and hence, achieving higher visual quality for the streamed video. 1
Horizontal gene cluster transfer increased hallucinogenic mushroom diversity (2018)

Secondary metabolites are a heterogeneous class of chemicals that often mediate interactions between species. The tryptophan-derived secondary metabolite, psilocin, is a serotonin receptor agonist that induces altered states of consciousness. A phylogenetically disjunct group of mushroom-forming fungi in the Agaricales produce the psilocin prodrug, psilocybin. Spotty phylogenetic distributions of fungal compounds are sometimes explained by horizontal transfer of metabolic gene clusters among unrelated fungi with overlapping niches. We report the discovery of a psilocybin gene cluster in three hallucinogenic mushroom genomes, and evidence for its horizontal transfer between fungal lineages. Patterns of gene distribution and transmission suggest that synthesis of psilocybin may have provided a fitness advantage in the dung and late wood-decay fungal niches, which may serve as reservoirs of fungal indole-based metabolites that alter behavior of mycophagous and wood-eating invertebrates. These hallucinogenic mushroom genomes will serve as models in neurochemical ecology, advancing the (bio)prospecting and synthetic biology of novel neuropharmaceuticals.
Increasing importance of dry eye syndrome and the ideal artificial tear: consensus views from a roundtable discussion (2006)

The growing prevalence of dry eye syndrome demands increased attention. Further research, enhanced diagnostic tests, increased use of preservative-free artificial tear formulations as first-line therapy, greater patient-practitioner interaction, and patient education are warranted.
Disulfide exchange between insulin and its receptor. A possible post-binding step in insulin action. (1983)

A fraction of the insulin specifically bound to adipocytes undergoes a disulfide interchange with its receptor (Clark, S., and Harrison, L. C. (1982) J. Biol. Chem. 257, 12239-12244). In order to test the hypothesis that this covalent modification is a relevant step in insulin action, we have examined the relationship between disulfide binding of insulin and several insulin bioeffects, using sulfhydryl group blocking reagents as probes. The half-time of disappearance of disulfide linked insulin-receptor complexes (I-(S-S)-R) was rapid (4.5 min), consistent with their hypothesized role. A cell-impermeable reagent 5,5'-dithiobis(nitrobenzoic acid) (DTNB) had no effect on specific insulin binding but caused a dose-dependent decrease in both I-(S-S)-R and insulin-stimulated glucose transport. DTNB also inhibited the effect of insulin to stimulate glucose oxidation and to inhibit epinephrine-stimulated cyclic AMP production. In cultured IM-9 lymphocytes, insulin-induced down regulation of its receptor was decreased by 75% in the presence of 1 mM DTNB. Receptor antibodies stimulated adipocyte glucose transport maximally but their effect, unlike that of insulin, was not inhibited by DTNB. These findings suggest that receptor sulfhydryl groups are required for insulin action and support the notion that their interchange with insulin is a necessary step in activation of postreceptor pathways.
Discussion (2006)

New Haven, Conn. Received for publication April 8, 2005. J. Grant Thomson, M.D., M.Sc., Department of Surgery, Section of Plastic Surgery, Yale University School of Medicine, P.O. Box 208041, New Haven, Conn., [email protected]
Structural requirements of iodothyronines for the rapid inactivation and internalization of type II iodothyronine 5'-deiodinase in glial cells (1993)

3,3'5,5'-Tetraiodothyronine (T4), but not 3,3'5-triiodothyronine (T3), acutely regulates the activity of the plasma membrane-bound enzyme, type II iodothyronine 5'-deiodinase (5'D-II), by inducing internalization of the enzyme through an extranuclear, energy-dependent mechanism that requires an intact actin cytoskeleton. The affinity label, N-bromoacetyl-L-T4, binds to 5'D-II and irreversibly inhibits the enzyme but does not initiate internalization. To determine the structural elements of T4 which are required for enzyme internalization, T4 analogs were modified in the alanine side chain and were then evaluated for their ability to induce enzyme internalization, to inhibit enzyme activity, and to promote actin polymerization in hypothyroid cells. The analogs studied showed marked variability in their ability to inactivate 5'D-II. The rank order of potency for enzyme inactivation was T4 > COOH-blocked analogs > NH3 and COOH blocked analogs >> NH3 blocked analogs (EC50 values range from 1 to > 1000 nM). In contrast, all T4 analogs tested and T4 were excellent competitive inhibitors of 5'D-II with respect to substrate (Ki values ranged from 4 to 27 nM). The differential capability of iodothyronines to inactivate the enzyme was not related to their ability to enter the cell, since Ki values measured in intact glial cells were equivalent to those measured in cell sonicates. The power of the T4 analogs to inactivate 5'D-II was paralleled by their ability to polymerize actin in hypothyroid cells and to induce 5'D-II binding to F-actin. The data show that modification of the alanine side chain markedly alters the ability of T4 analogs to induce 5'D-II inactivation and actin polymerization. A net negative charge on the alanine side chain of T4 is detrimental for the hormone-dependent inactivation of 5'D-II and polymerization of actin, whereas uncharged or positively charged molecules retain significant activity.
Encapsulated PC 12 Cell Transplants into Hemiparkinsonian Monkeys: A Behavioral, Neuroanatomical, and Neurochemical Analysis (1995)

Four cynomolgus monkeys were trained on a hand reaching task and then rendered hemiparkinsonian with an intracarotid injection of n-methyl 4 phenyl 1,2,3,6, tetrahydropyridine (MPTP). Performance on this task with the limb contralateral to the MPTP injection was significantly impaired following the lesion. Three monkeys received implants of polymer-encapsulated containing PC12 cells into the caudate nucleus and putamen. One monkey received identical implants of empty capsules and served as a control. After a transient improvement, limb use in the control monkey dissipated and returned to post-MPTP disability. Two of the three PC12 cell grafted monkeys recovered performance on the hand reach task to near normal levels for up to 6.5 mo posttransplantation. Capsules retrieved from the monkeys who recovered limb function postimplantation contained numerous viable PC12 cells that continued to release levodopa, basal dopamine, and potassium evoked dopamine. In contrast, capsules retrieved from the PC12 cell-grafted monkey which did not recover limb use on the hand reach task contained few cells which secreted negligible or undetectable levels of levodopa and dopamine. Interestingly, functional disability was not reinstated following removal of the capsules. Neuroanatomical and neurochemical evaluation of the grafted striatum did not reveal a host-derived sprouting response of catecholaminergic or indolaminergic fibers. These data indicate that xenografts of PC12 cells can survive for up to 6.5 mo in nonimmunosuppressed monkeys when immunoisolated via polymer encapsulation. Moreover, these cells continue to secrete high levels of levodopa and dopamine and induce recovery of motor function in parkinsonian nonhuman primates.
Use of a Solids-free Viscous Carrying Fluid in Fracturing Applications: An Economic and Productivity Comparison in Shallow Completions (1995)

Abstract The paper presents the findings of 20 completions in both oil and gas wells. These completions were performed from the period of 1973 through 1994. The early completions employed sand control technology of the 1970's and 1980's with most requiring acid stimulation immediately after sand placement to assure the removal of completion damage. The 1994 completions involved fracturing combined with sand control (frac-packing) in the same reservoirs which had been gravel packed in the ‘70's and ‘80's. The unique aspect of this review is that these fracturing treatments were carried out using a solids-free viscoelastic surfactant fluid. The fluid system is discussed along with the reasons why this particular fluid was selected. The implications that this fluid has on the fracture placement as well as productivity are discussed. Laboratory testing indicates that the solids based polymer fluids actually exhibit "deep bed" filtration and plug the formation pore throats, the fracture packs, and perforations. This damage can require acid stimulation for optimized production. The completion results are compared by use of a productivity index (J), normalized J14, and bottom hole pressure build-up analysis.
General purpose telemetry for analog biomedical signals (1995)

The results presented show that the telemetry system described is convenient for transferring analog biomedical signals for a wide range of physiological parameters, even with low-cost standard communication media. The system developed is independent of the types and models of the signal-generating medical devices and is able to communicate worldwide over a broad range of communication medias. The results also show that there are differences in the transmission capacity among the communication media. These practical as well as theoretical differences are important for proper selection of communication devices. Anticipated activity in the field of communication technology (devices and protocols) towards higher data rates and lower costs is expected to further increase system performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>