gebhart/patrepeval huggingface dataset:
Synthetic peptides as substrates and inhibitors of human immune deficiency virus-1 protease. (1988)

Retroviruses code for a virus-specific protease which is essential for polyprotein processing and viral infectivity. The human immune deficiency virus-1 protease is an aspartic protease of 9 kDa which was synthesized by recombinant DNA technology and arises by autocatalytic processing from a polyprotein precursor which has recently been demonstrated by use of a protease-specific monoclonal antibody. The protease was shown to form dimers. Here we demonstrate that synthetic peptides can be used as both model substrates as well as inhibitors for investigation of the protease. 14 synthetic peptides, 7-18 amino acids in length, containing putative protease cleavage sites of the viral polyprotein gag and pol precursors, have been analyzed with the partially purified protease by the use of high performance liquid chromatography. In seven cases, where cleavage was observed, the length of the peptides did not significantly influence the cleavage efficiencies, heptapeptides being large enough as model substrates. No cleavage was observed with a protein preparation purified in parallel from control bacteria not expressing the human immune deficiency virus-1 protease. The protease was not only able to cut next to a proline but also between other peptides indicating that the proline is not a prerequisite. Three peptides with either reduced bonds at the cleavage site or a substitution by statin were inhibitory while another uncleaved substrate was not. The usefulness of small model substrates for characterization of the protease is further demonstrated by determination of a kinetic optimum pH (3.5-5.5) and incubation temperature (37 degrees C).
Discrete Cleavage Motifs of Constitutive and Immunoproteasomes Revealed by Quantitative Analysis of Cleavage Products (2001)

Proteasomes are the main proteases responsible for cytosolic protein degradation and the production of major histocompatibility complex class I ligands. Incorporation of the interferon gamma--inducible subunits low molecular weight protein (LMP)-2, LMP-7, and multicatalytic endopeptidase complex--like (MECL)-1 leads to the formation of immunoproteasomes which have been associated with more efficient class I antigen processing. Although differences in cleavage specificities of constitutive and immunoproteasomes have been observed frequently, cleavage motifs have not been described previously. We now report that cells expressing immunoproteasomes display a different peptide repertoire changing the overall cytotoxic T cell--specificity as indicated by the observation that LMP-7(-/-) mice react against cells of LMP-7 wild-type mice. Moreover, using the 436 amino acid protein enolase-1 as an unmodified model substrate in combination with a quantitative approach, we analyzed a large collection of peptides generated by either set of proteasomes. Inspection of the amino acids flanking proteasomal cleavage sites allowed the description of two different cleavage motifs. These motifs finally explain recent findings describing differential processing of epitopes by constitutive and immunoproteasomes and are important to the understanding of peripheral T cell tolerization/activation as well as for effective vaccine development.
Targeting Hsp90 for the treatment of cancer. (2006)

Heat shock protein (Hsp)90 is a molecular chaperone that is responsible for the correct folding of a large number of proteins, which allows these proteins to achieve their functional conformation. Client proteins of Hsp90 include many overexpressed or mutated oncogenes that are known to be critical for the transformed phenotype observed in tumors. The compounds 17-AAG (Kosan Biosciences Inc/National Cancer Institute) and 17-DMAG (Kosan Biosciences Inc/National Cancer Institute) are Hsp90 inhibitors that are derived from the prototypical ansamycin natural product Hsp90 inhibitor geldanamycin. These compounds have demonstrated preclinical efficacy in mouse xenograft models, and are now undergoing phase II and I clinical trials, respectively. Preclinical efficacy studies of these compounds are collated and discussed in this review. More recent disclosures of small-molecule Hsp90 inhibitors include purine and resorcinol analogs, and the first small-molecule Hsp90 compounds showing oral efficacy have been described. Inhibition of Hsp90 not only results in the degradation of client proteins, but also results in the induction of another chaperone, Hsp70. Hsp70 is known to be anti-apoptotic, and therefore the induction of Hsp70 may ultimately limit the efficacy of Hsp90 inhibitors under certain circumstances. Histone deacetylase inhibitors have recently been demonstrated to exert some of their effect through modulation of Hsp90 chaperoning activity, and some mechanistic aspects of this control are also discussed herein.
A polynomial time generator for minimal perfect hash functions (1985)

A perfect hash function PHF is an injection F from a set W of M objects into the set consisting of the first N nonnegative integers where N ⩾ M. If N = M, then F is a minimal perfect hash function, MPHF. PHFs are useful for the compact storage and fast retrieval of frequently used objects such as reserved words in a programming language or commonly employed words in a natural language. The mincycle algorithm for finding PHFs executes with an expected time complexity that is polynomial in M and has been used successfully on sets of cardinality up to 512. Given three pseudorandom functions h 0 , h 1 , and h 2 , the mincycle algorithm searches for a function g such that F(w) = (h 0 (w) + g ° h 1 (w) + g ° h 2 (w)) mod N is a PHF.
Microstructure and Mechanical Properties of Electroless Copper Deposits (1991)

This article reviews published data on the mechanical properties of additively manufactured metallic materials. The additive manufacturing techniques utilized to generate samples covered in this review include powder bed fusion (e.g., EBM, SLM, DMLS) and ...Read More
The phagocyte 47-kilodalton cytosolic oxidase protein is an early reactant in activation of the respiratory burst. (1990)

Activation of the phagocyte NADPH oxidase requires participation of membrane-bound cytochrome b558 and cytosol proteins of 47 kDa (p47) and 67 kDa (p67). We examined the sequence of participation of p47 and p67 in activation of the oxidase using an arachidonate-activated cell-free superoxidase (O2-) generating assay requiring phagocyte membrane and cytosol. Neutrophil cytosol from patients with certain forms of autosomal recessive chronic granulomatous disease (CGD) lack either p47 or p67. Initial incubation of membrane and arachidonate with CGD cytosol deficient in either p47 or p67 fails to generate superoxide in the cell-free assay until addition of complementary cytosol. CGD cytosol was incubated with arachidonate and membrane for 5-15 min and the lag time of O2- generation was measured after addition of complementary CGD cytosol. The lag time is shortened when p47, but not p67, is present in the initial incubation. We have previously shown that the peptide, RGVHFIF, corresponding to a cytoplasmic carboxyl-terminal domain of the large subunit of cytochrome b558, inhibits activation of NADPH oxidase in the cell-free assay, but does not affect the enzyme activity of fully assembled oxidase. Experiments with sequential addition of complementary CGD cytosols were performed as above, except that RGVHFIF was added after the initial incubation. The peptide failed to inhibit when added after initial incubation if p47 was present during that incubation. In contrast, the peptide markedly inhibited oxidase activity if p47 was absent during the initial incubation. These results suggest that p47, but not p67, is a participant with membrane and/or other cytosol components in early arachidonate-dependent reactions. In the absence of p67, these reactions culminate in the irreversible formation of a metastable activation intermediate that is insensitive to inhibition by RGVHFIF. After addition of p67, this activation intermediate subsequently reacts to form the active NADPH oxidase.
Generation of T-Cell Immunity to the HER-2/neu Protein After Active Immunization With HER-2/neu Peptide–Based Vaccines (2002)

The majority of patients with HER-2/neu-overexpressing cancers can develop immunity to both HER-2/neu peptides and protein. In addition, the generation of protein-specific immunity, after peptide immunization, was associated with epitope spreading, reflecting the initiation of an endogenous immune response. Finally, immunity can persist after active immunizations have ended.
Monitoring Intracranial Pressure in Traumatic Brain Injury (2008)

Increased intracranial pressure (ICP) is an important cause of secondary brain injury, and ICP monitoring has become an established component of brain monitoring after traumatic brain injury. ICP cannot be reliably estimated from any specific clinical feature or computed tomography finding and must actually be measured. Different methods of monitoring ICP have been described but intraventricular catheters and microtransducer systems are most widely used in clinical practice. ICP is a complex variable that links ICP and cerebral perfusion pressure and provides additional information from identification and analysis of pathologic ICP wave forms. ICP monitoring can also be augmented by measurement of indices describing cerebrovascular pressure reactivity and pressure-volume compensatory reserve. There is considerable variability in the use of ICP monitoring and treatment modalities among head injury centers. However, there is a large body of clinical evidence supporting the use of ICP monitoring to detect intracranial mass lesions early, guide therapeutic interventions, and assess prognosis, and it is recommended by consensus guidelines for head injury management. There remains a need for a prospective, randomized, controlled trial to identify the value of ICP monitoring and management after head injury.
The Java Language Specification (1996)

From the Publisher:
Written by the inventors of the technology, The Java(tm) Language Specification, Second Edition is the definitive technical reference for the Java(tm) programming language. If you want to know the precise meaning of the language's constructs, this is the source for you. 
The book provides complete, accurate, and detailed coverage of the syntax and semantics of the Java programming language. It describes all aspects of the language, including the semantics of all types, statements, and expressions, as well as threads and binary compatibility.
Characterization of circulating and cutaneous IgA immune complexes in patients with dermatitis herpetiformis. (1985)

Dermatitis herpetiformis (DH) is a chronic, blistering skin disease characterized in part by deposits of IgA at the dermal-epidermal junction. Eighty-five percent of DH patients have granular IgA deposits and have an associated gluten-sensitive enteropathy (GSE). In contrast, 15% of DH patients have a linear pattern of IgA deposits and no associated intestinal abnormality. Although circulating IgA antibodies against skin are not present in these patients, 40% of DH patients do have IgA-containing circulating immune complexes (IgA-CIC). The role and origin of the cutaneous IgA and the IgA-CIC in patients with DH are unknown; however, the association of GSE with the granular IgA deposits suggests that a mucosal immune response may be important in the pathogenesis of DH. We have characterized the IgA subclass composition of the cutaneous IgA deposits in patients with DH, and have isolated and characterized the IgA-CIC from these patients. Twenty-nine of 29 patients with DH and granular IgA deposits were found to have only IgA1 deposits. Ten of 11 patients with linear IgA deposits also had only IgA1 deposits; one of 11 had IgA2 deposits. Isolated IgA-CIC from the sera of eight patients with DH and granular IgA deposits were found to contain both IgA1 (58% +/- 5, mean percent of total IgA +/- SEM) and IgA2 (42% +/- 5), as were IgA-CIC from two patients with ordinary GSE without cutaneous IgA deposits. The IgA subclass composition of the isolated immune complexes was significantly different from the serum IgA1 and IgA2 composition (serum IgA1 = 76% +/- 6; IgA2 = 24% +/- 5, p less than 0.025, Student's t-test), and suggests that the IgA-CIC may arise from gut-associated lymphoid tissue (GALT). Sequential anti-IgA1 absorption of serum which contained IgA-CIC did not remove all the IgA-CIC, suggesting that the complexes circulate as separate IgA1 and IgA2 complexes. The finding of IgA1 alone in the skin of patients with DH suggests that the cutaneous IgA may not arise from GALT, or that IgA1, possibly arising in GALT, is preferentially bound to DH skin. Because IgA-containing CIC which contain both IgA1 and IgA2 were found in the serum of patients with DH and with ordinary GSE, it seems unlikely that IgA-containing CIC are responsible for the cutaneous IgA deposits seen in DH.
Alert Detection in System Logs (2008)

We present Nodeinfo, an unsupervised algorithm for anomaly detection in system logs. We demonstrate Nodeinfo's effectiveness on data from four of the world's most powerful supercomputers: using logs representing over 746 million processor-hours, in which anomalous events called alerts were manually tagged for scoring, we aim to automatically identify the regions of the log containing those alerts. We formalize the alert detection task in these terms, describe how Nodeinfo uses the information entropy of message terms to identify alerts, and present an online version of this algorithm, which is now in production use. This is the first work to investigate alert detection on (several) publicly-available supercomputer system logs, thereby providing a reproducible performance baseline.
NH2-terminally truncated HER-2/neu protein: relationship with shedding of the extracellular domain and with prognostic factors in breast cancer. (1998)

We identified an NH2-terminally truncated HER-2/neu product of M(r) 95,000 with in vitro kinase activity by Western blotting and immunoprecipitations using domain-specific antibodies. p95 levels correlated with the extracellular domain (ECD) shed from different cells under varied conditions. Both ECD and p95 were at approximately 20-fold lower levels in SKOV3 ovarian carcinoma cells, as compared to BT474 breast carcinoma cells. Both were stimulated by treatment of cells with the phorbol ester tumor promoter phorbol 12-myristate 13-acetate and the lysosomotrophic agent chloroquine. The hydroxamate inhibitor of metalloproteases, TAPI, suppressed both p95 and ECD in a dose-dependent fashion, with maximal inhibition at < or = 10 microM in BT474 cells. Cancer tissues were analyzed by Western blotting and scored for p95HER-2/neu and for p185HER-2/neu expression. Breast and ovarian cancer tissues were both found to express p95HER-2/neu in addition to p185HER-2/neu. Of 161 breast cancer tissues, 22.4% expressed p95, 21.7% overexpressed p185, and 14.3% were p95 positive and overexpressed p185. A higher proportion of node-positive patients (23 of 78) than node-negative patients (9 of 63) expressed p95 in all tumors combined (P = 0.032). In the group that overexpressed p185, those that contained p95 were associated with node-positive patients (15 of 21), whereas those that were p95 negative were associated with node-negative patients (8 of 11; P = 0.017). Neither p95- nor p185-rich patients significantly correlated with tumor size or with hormone receptor status in this study. Our findings show that breast cancers, which express the HER-2/neu oncogene, are heterogeneous with respect to HER-2/neu protein products. p95HER-2/neu appears to distinguish tumors that have metastasized to the lymph nodes from those in node-negative patients.
Regulatory role of IgE-binding factors from rat T lymphocytes. II. Glycoprotein nature and source of IgE-potentiating factor. (1980)

Previous experiments have shown that Fc epsilon receptor-bearing (Fc epsilon R(+)) T lymphocytes in mesenteric lymph nodes (MLN) of rats infected with Nippostrongylus brasiliensis (Nb) release a soluble factor that selectively potentiates the IgE response. The IgE-potentiating factor has affinity for IgE, and can be detected by the ability to inhibit rosette formation of Fc epsilon R(+) cells with IgE-coated erythrocytes. The factor was bound to IgE-coated Sepharose and was eluted from the beads at acid pH. It was also found that the IgE-potentiating factor binds to lentil lectin-Sepharose, indicating that the factor is a glycoprotein. The affinity of the factor for IgE was lost after treatment with trypsin but was maintained after treatment with neuraminidase. However, the ability of the factor to potentiate the IgE response was lost after neuraminidase treatment. The results suggested that the factor's binding site for IgE is associated with a protein (peptide) moiety but that its carbohydrate moiety is essential for its biologic activity. When MLN cells were incubated at 37 degrees C, a substantial amount of the IgE-potentiating factor was released into culture medium within 4 hr even in the presence of cycloheximide. Pretreatment of the cells with trypsin, which removed Fc epsilon R, markedly diminished the release of IgE-potentiating factor, suggesting that the factor is derived from Fc epsilon R on the cell surface.
A ligand‐pseudoreceptor system based on de novo designed peptides for the generation of adenoviral vectors with altered tropism (2008)

We have established a new system to produce AdVs ablated of natural tropism. This system should permit the retargeting of AdVs by inserting new ligands within the fiber or through the interaction with bispecific adaptors.
Intranasal Insulin as a Treatment for Alzheimer’s Disease: A Review of Basic Research and Clinical Evidence (2013)

Research in animals and humans has associated Alzheimer's disease (AD) with decreased cerebrospinal fluid levels of insulin in combination with decreased insulin sensitivity (insulin resistance) in the brain. This phenomenon is accompanied by attenuated receptor expression of insulin and insulin-like growth factor, enhanced serine phosphorylation of insulin receptor substrate-1, and impaired transport of insulin across the blood-brain barrier. Moreover, clinical trials have demonstrated that intranasal insulin improves both memory performance and metabolic integrity of the brain in patients suffering from AD or its prodrome, mild cognitive impairment. These results, in conjunction with the finding that insulin mitigates hippocampal synapse vulnerability to beta amyloid, a peptide thought to be causative in the development of AD, provide a strong rationale for hypothesizing that pharmacological strategies bolstering brain insulin signaling, such as intranasal administration of insulin, could have significant potential in the treatment and prevention of AD. With this view in mind, the review at hand will present molecular mechanisms potentially underlying the memory-enhancing and neuroprotective effects of intranasal insulin. Then, we will discuss the results of intranasal insulin studies that have demonstrated that enhancing brain insulin signaling improves memory and learning processes in both cognitively healthy and impaired humans. Finally, we will provide an overview of neuroimaging studies indicating that disturbances in insulin metabolism--such as insulin resistance in obesity, type 2 diabetes and AD--and altered brain responses to insulin are linked to decreased cerebral volume and especially to hippocampal atrophy.
Distamycin Analogues with Enhanced Lipophilicity:  Synthesis and Antimicrobial Activity (2004)

Forty-eight heterocyclic amino acid trimers, analogues of distamycin, with a number of features that enhance lipophilicity are described. They contain alkyl or cycloalkyl groups larger than methyl; some are N-terminated by acetamide or methoxybenzamide and are C-terminated by dimethylaminopropyl or aliphatic heterocylic aminopropyl substituents. The ability of these compounds to bind principally to AT tracts of DNA has been evaluated using capillary zone electrophoresis. Significant antimicrobial activity against key organisms such as MRSA and Candida albicans is shown by several compounds, especially those containing a thiazole. Moreover, these compounds have low toxicity with respect to several mammalian cell lines.
Improved Performance of Transgenic Fructan-Accumulating Tobacco under Drought Stress (1995)

Fructans are polyfructose molecules produced by approximately 15% of the flowering plant species. It is possible that, in addition to being a storage carbohydrate, fructans have other physiological roles. Owing to their solubility they may help plants survive periods of osmotic stress induced by drought or cold. To investigate the possible functional significance of fructans, use was made of transgenic tobacco (Nicotiana tabacum) plants that accumulate bacterial fructans and hence possess an extra sink for carbohydrate. Biomass production was analyzed during drought stress with the use of lines differing only in the presence of fructans. Fructan-producing tobacco plants performed significantly better under polyethylene-glycol-mediated drought stress than wild-type tobacco. The growth rate of the transgenic plants was significantly higher (+55%), as were fresh weight (+33%) and dry weight (+59%) yields. The difference in weight was observed in all organs and was particularly pronounced in roots. Under unstressed control conditions the presence of fructans had no significant effect on growth rate and yield. Under all conditions the total nonstructural carbohydrate content was higher in the transgenic plants. We conclude that the introduction of fructans in this non-fructan-producing species mediates enhanced resistance to drought stress.
[Prognostic diagnosis of facial palsy with electroneuronography]. (1995)

We examined the accuracy of electroneuronography (ENoG) as a prognostic indicator in 58 patients with facial palsy: 47 patients with Bell's palsy and 11 patients with Ramsay-Hunt syndrome over a period of one year. For surface recording, the active electrodes were placed over the orbicularis oculi, orbicularis oris, quadratus labii, nasal alae or nasolabial fold, and the indifferent electrode over the same muscle in the opposite side. ENoG over nasal alae showed the most reliable value and the next was orbicularis oris. All other muscles were less reliable. We found that in 87.2% of cases, recovery was satisfactory in Bell's palsy and 63.6% cases in Ramsay-Hunt syndrome. Of the 47 Bell's palsy patients, 38 patients (80.9%) had a response to ENoG over nasal alae of 10% or greater, while 5 patients (45.5%) of the 11 patients with Ramsay-Hunt syndrome. All these patients recovered satisfactorily within four months. Nine of 47 patients (19.1%) with Bell's palsy and 6 of 11 patients (54.5%) with Ramsay-Hunt syndrome had a response of 10% or less. Satisfactory recovery rate among these patients was 33.3%. In conclusion, ENoG over nasal alae and orbicularis oris shows reliable values among other muscles. Patients with responses to ENoG over nasal alae of 10% or greater showed satisfactory recovery.