gebhart/patrepeval huggingface dataset:
Creation and expression of myristylated forms of Rous sarcoma virus gag protein in mammalian cells (1989)

Rous sarcoma virus (RSV), a member of the avian sarcoma and leukosis family of retroviruses, has long been known to be capable of infecting and transforming mammalian cells; however, such transformed cells do not release virus particles. The RSV gag product (Pr76gag) produced in these cells is not released into the culture medium or proteolytically processed to release mature products. Thus, the behavior of Pr76gag in mammalian cells is much like that of mammalian retroviral Gag proteins which have been altered so as to block the addition of myristic acid at residue 2 (Gly). Because the RSV gag product does not possess a myristic acid addition site, we hypothesized that the creation of one by oligonucleotide-directed mutagenesis might permit particles to be released from mammalian cells. Two myristylated forms of Pr76 were created. In Pr76myr1, the first 10 amino acids have been exchanged for those of p60v-src, which are known to be sufficient for myristylation. In Pr76myr2, the Glu at the second residue has been substituted with Gly. The alleles encoding the modified and wild-type forms of Pr76 have been expressed at high levels in mammalian (CV-1) cells by using an SV40-based vector. Surprisingly, we have found that expression of high levels of the unmodified (wild-type) product, Pr76myr0, results in low levels of particle formation and precursor processing. This indicates that myristic acid is not the sole determinant for targeting. However, the addition of myristic acid to Pr76myr1 or Pr76myr2 resulted in a fivefold enhancement in Gag function. In all aspects examined, the behavior of myristylated Pr76 was identical to that of the authentic product produced in avian cells. We also show that processing is mediated by the gag-encoded protease and that removal of the amino terminus to create Pr76gagX results in an inability to form particles or be processed. This suggests that proper targeting is prerequisite for activation of the RSV protease in mammalian cells.
Tobacco mosaic virus and the virescence of biotechnology (1999)

There is a growing realization that a modern combination of molecular biology and agriculture will provide a photosynthetic basis for the biosynthesis of an increasing variety of complex and valuable molecules. This 'greening' of biotechnology may impact on the global environment in many beneficial ways, but will perhaps have its most significant impact on human health. In the past decade, the capacity to use plants as an expanded source of therapeutics has grown through the accelerated development of effective viral transfection vectors for gene transfer to cultivated crops. Recombinant vectors based on tobacco mosaic virus (TMV) and other members of the Tobamovirus genus are now used to transfect commercially meaningful quantities of plant biomass cultivated in enclosed greenhouses and multiacre fields. Viral RNA promoters are effectively manipulated for the synthesis of recombinant messenger RNAs in whole plants. Chimeric plant virus and virus-like particles are designed for peptide production and display from recombinant structural protein-gene fusions. Gene functions are assessed and modified by either virus-mediated expression or cytosolic inhibition of expression at the RNA level. Recombinant virus populations, propagated by inoculating plants with infectious RNA transcripts or recombinant virions, have proved to be genetically stable over product-manufacturing cycles. Large volumes of highly purified protein products isolated from transfected foliage conform reproducibly to the specifications required for well-characterized biologics. In some cases, they exceed the specific activities of molecules purified from alternative recombinant and native sources. The resulting products are then formulated according to the developing national regulatory guidelines appropriate for agriculture-based manufacturing. Each of these innovations was first realized by researchers using clones of tobamovirus genes and recombinant genomes. This progress is founded on the heritage of a century of fundamental TMV research.
Design and Synthesis of E-Selectin Antagonists (2001)

Selectin-mediated recruitment of leukocytes plays a crucial role in a number of diseases and pathological situations, for example in inflammation, reperfusion injury, rheumatoid arthritis and respiratory diseases. Substantial research efforts are directed toward development of carbohydrate-derived drugs that interfere with the inflammatory response by blocking the selectin binding site. This article describes two approaches for the improvement of the inhibitory potency of the lead structure sialyl Lewisx (sLex). One approach is based on the preorganization of mimics in their bioactive conformation to reduce entropic costs. For the conformational analysis of mimics, molecular modeling based tools were developed. They allow the rational design of selectin antagonists with simplified structures, but increased inhibitory potency. Alternatively, additional carbohydrate/lectin contacts can be identified for the improvement of enthalpic contributions. Following this approach, an additional hydrophobic interaction of the antagonists with E-selectin leads to a 60-fold improvement of E-selectin affinity. Antagonists have been synthesized using chemical or chemoenzymatic methods. Finally, a flow chart for the biological evaluation of the antagonists is presented.
Tumor Necrosis Factor-α Upregulates the Prostaglandin E 2 EP1 Receptor Subtype and the Cyclooxygenase-2 Isoform in Cultured Amnion WISH Cells (1998)

Recent studies have demonstrated a strong correlation between infection and preterm labor. Preterm delivery is also associated with high levels of cytokines and prostaglandins in amniotic fluid. The purpose of this study was to investigate the effect of tumor necrosis factor-alpha (TNF-alpha) on the levels of cyclooxygenase, prostaglandin E2 production (PGE2), and expression of the PGE2 receptor subtype EP1 in amnion WISH cell culture. Amnion WISH cell cultures were incubated in increasing concentrations of TNF-alpha (0-50 ng/ml). Changes in cyclooxygenase and EP1 receptor proteins were evaluated by Western blot analysis. Changes in EP1 mRNA were evaluated by Northern blot, and culture fluid concentrations of PGE2 were estimated by enzyme immunoassay (EIA). EP1 protein (p<0.01), EP1 mRNA (p<0.05), cyclooxygenase-2 (COX-2) protein (p<0.001), and PGE2 concentrations (p<0.01) all increased with increasing concentrations of TNF-alpha. Changes in COX-1 protein were not observed following TNF-alpha-incubation. The results suggest that TNF-alpha may play a role in infection-induced preterm labor by its pleiotropic ability to simultaneously stimulate COX-2 activity, PGE2 concentrations, and PGE2 EP1 receptor levels in human amnion.
Comitogenic effect of solid-phase immobilized anti-1F7 on human CD4 T cell activation via CD3 and CD2 pathways. (1990)

We have recently developed a mAb, anti-1F7, which defines a family of structures found to include the molecule recognized by anti-Ta1 (CD26). In this paper, we demonstrated that binding of 1F7 by solid-phase immobilized anti-1F7 mAb but not anti-Ta1 mAb has a comitogenic effect by inducing proliferation of human CD4+ T lymphocytes in conjunction with submitogenic doses of anti-CD3 or anti-CD2. The proliferative response induced via the CD3-1F7 or CD2-1F7 pathways is associated with the IL-2 autocrine pathway, including IL-2 production. IL-2R expression and anti-IL-2R (Tac) inhibition. Furthermore, solid-phase immobilization of anti-1F7 but not anti-Ta1 acts in conjunction with submitogenic doses of PMA to mediate a comitogenic effect in the absence of anti-CD3 or anti-CD2, leading to CD4+ T cell proliferation. PMA treatment, in the meantime, leads to enhanced expression of 1F7 on the T cell surface. Despite its functional association with both pathways of activation, however, the 1F7 structure is not comodulated with the CD3/TCR complex nor the CD2 molecule. These findings thus suggest that the CD26 Ag is involved in CD3 and CD2-induced human CD4+ T cell activation.
An imaging agent to detect androgen receptor and its active splice variants in prostate cancer (2016)

Constitutively active splice variants of androgen receptor (AR-Vs) lacking ligand-binding domain (LBD) are a mechanism of resistance to androgen receptor LBD-targeted (AR LBD-targeted) therapies for metastatic castration-resistant prostate cancer (CRPC). There is a strong unmet clinical need to identify prostate cancer patients with AR-V-positive lesions to determine whether they will benefit from further AR LBD-targeting therapies or should receive taxanes or investigational drugs like EPI-506 or galeterone. Both EPI-506 (NCT02606123) and galeterone (NCT02438007) are in clinical trials and are proposed to have efficacy against lesions that are positive for AR-Vs. AR activation function-1 (AF-1) is common to the N-terminal domains of full-length AR and AR-Vs. Here, we provide proof of concept for developing imaging compounds that directly bind AR AF-1 to detect both AR-Vs and full-length AR. <sup>123</sup>I-EPI-002 had specific binding to AR AF-1, which enabled direct visualization of CRPC xenografts that express full-length AR and AR-Vs. Our findings highlight the potential of <sup>123</sup>I-EPI-002 as an imaging agent for the detection of full-length AR and AR-Vs in CRPC.
Tethering of Epidermal Growth Factor (EGF) to Beta Tricalcium Phosphate (βTCP) via Fusion to a High Affinity, Multimeric βTCP-Binding Peptide: Effects on Human Multipotent Stromal Cells/Connective Tissue Progenitors (2015)

Transplantation of freshly-aspirated autologous bone marrow, together with a scaffold, is a promising clinical alternative to harvest and transplantation of autologous bone for treatment of large defects. However, survival proliferation, and osteogenic differentiation of the marrow-resident stem and progenitor cells with osteogenic potential can be limited in large defects by the inflammatory microenvironment. Previous studies using EGF tethered to synthetic polymer substrates have demonstrated that surface-tethered EGF can protect human bone marrow-derived osteogenic stem and progenitor cells from pro-death inflammatory cues and enhance their proliferation without detriment to subsequent osteogenic differentiation. The objective of this study was to identify a facile means of tethering EGF to clinically-relevant βTCP scaffolds and to demonstrate the bioactivity of EGF tethered to βTCP using stimulation of the proliferative response of human bone-marrow derived mesenchymal stem cells (hBMSC) as a phenotypic metric. We used a phage display library and panned against βTCP and composites of βTCP with a degradable polyester biomaterial, together with orthogonal blocking schemes, to identify a 12-amino acid consensus binding peptide sequence, LLADTTHHRPWT, with high affinity for βTCP. When a single copy of this βTCP-binding peptide sequence was fused to EGF via a flexible peptide tether domain and expressed recombinantly in E. coli together with a maltose-binding domain to aid purification, the resulting fusion protein exhibited modest affinity for βTCP. However, a fusion protein containing a linear concatamer containing 10 repeats of the binding motif the resulting fusion protein showed high affinity stable binding to βTCP, with only 25% of the protein released after 7 days at 37oC. The fusion protein was bioactive, as assessed by its abilities to activate kinase signaling pathways downstream of the EGF receptor when presented in soluble form, and to enhance the proliferation of hBMSC when presented in tethered form on commercial βTCP bone regeneration scaffolds.
Cell kinetics of rat 9L brain tumors determined by double labeling with iodo- and bromodeoxyuridine (1990)

Rats with 9L brain tumors received intraperitoneal injections of iododeoxyuridine (IUdR) and bromodeoxyuridine (BUdR) to estimate the duration of the deoxyribonucleic acid (DNA) synthesis phase (Ts) and the potential doubling time (Tp) of individual tumors. Different sequences and intervals (2 or 3 hours) of IUdR and BUdR administration were evaluated. After denaturation, tumor sections were reacted with Br-3, a monoclonal antibody that identifies only BUdR, and then were stained immunohistochemically by the avidinbiotin complex method. An antibody that recognizes both IUdR and BUdR, IU-4, was applied to the sections and identified by the alkaline phosphatase-antialkaline phosphatase method. Nuclei labeled only with IUdR stained blue, while those labeled with BUdR or with BUdR and IUdR stained brown. The fraction of cells that either left or entered the S-phase during the time between administration of IUdR and BUdR was measured to calculate Ts and Tp, assuming that the labeled cohort completed the DNA synthesis at a constant rate. The Ts was 8.8 hours (coefficient of variation (cv) = 0.05) and the Tp was 64.2 hours (cv = 0.08). The sequence and interval of administration of IUdR and BUdR had a minimal effect on Ts and Tp. In studies of 9L cells in monolayer culture, the Ts was 9.6 hours (cv = 0.08) and the TP was 30.6 hours (cv = 0.06). Double labeling with BUdR and IUdR allows the duration of the S-phase and potential doubling time of individual brain tumors to be estimated in situ from a single biopsy specimen.
Syntactic Stylometry for Deception Detection (2012)

Most previous studies in computerized deception detection have relied only on shallow lexico-syntactic patterns. This paper investigates syntactic stylometry for deception detection, adding a somewhat unconventional angle to prior literature. Over four different datasets spanning from the product review to the essay domain, we demonstrate that features driven from Context Free Grammar (CFG) parse trees consistently improve the detection performance over several baselines that are based only on shallow lexico-syntactic features. Our results improve the best published result on the hotel review data (Ott et al., 2011) reaching 91.2 % accuracy with 14% error reduction. 1
L‐Tyrosine production by recombinant Escherichia coli: Fermentation optimization and recovery (2007)

L-tyrosine (L-tyr) overproducing Escherichia coli strain derived from an L-phenylalanine (L-phe) overproducing strain is characterized in 10 L and 200 L scale fermentations. Deletion of the chromosomal region encoding for the pheA gene, chorismate mutase/prephenate dehydratase, its leader peptide (pheL) and its associated promoter resulted in significant increase in L-tyr production (Olson et al., 2007. Appl Microbiol Biotechnol 74(5):1031-1040). Further increase in titer was achieved by overexpressing tyrA, encoding chorismate mutase/prephenate dehydrogenase, from a strong non-native trc promoter (Olson et al., 2007. Appl Microbiol Biotechnol 74(5):1031-1040). Fermentation optimization studies include media component selection; glucose feed optimization, antifoam agent selection, and understanding fermentation parameters affecting foaming. Generational stability of the strain was evaluated along with rate, titer, and yield of tyrosine formation from glucose. L-tyr titer of 55 g/L in 48 h was demonstrated in 200 L batches, is the highest titer published till date. We have also evaluated two primary separations schemes to isolate and purify L-tyr from the fermentation broth. Physical separation of L-tyr crystals from biomass using a decanter type centrifuge, based on the density difference between the solids, is compared and contrasted with a strategy where L-tyr is first dissolved at pH 11.5 and then acid precipitated from clarified supernatants following removal of biomass using membrane filtration. L-tyr product purity of 98% with yields ranging from 90% to 95% is demonstrated.
Complete Remission of Metastatic Cervical Cancer with the Angiogenesis Inhibitor TNP-470 (1998)

To the Editor: Hunter et al. (Oct. 30 issue) 1 report that there is no significant correlation between breast cancer and plasma levels of 1,1 -dichloro-2,2-bis( p -chlorophenyl)ethylene (p,p -DDE) and polychlorinated biphenyls (PCBs) two to three years before diagnosis, but estrogenic chemicals in pesticides, plastics, and other products that could contribute significantly to the burden of environmental estrogens in the body were not examined. Hunter et al. state, "The blood levels of DDE and PCBs we measured reflect exposure that occurred over a period of many years." Although parent 2,2-bis( p -chlorophenyl)-1,1,1-trichloroethane (DDT) and PCB mixtures show estrogenic activity, persistent residues in plasma measured years after exposure to parent mixtures do not show a similar net estrogenic activity. Although p,p -DDE is the highly persistent in vivo metabolite of DDT, it acts primarily as an antiandrogen. 2 The most active estrogenic contaminant in commercial DDT is o,p -DDT, but neither o,p -DDT nor its in vivo metabolite is detected years after exposure. Only a small proportion of the 209 PCB congeners have been tested. Many of the estrogenic PCBs (and their more active in vivo metabolites) are not persistent and would also not be present in plasma years after exposure. Some persistent PCB metabolites typically found in plasma actually antagonize estrogenic actions. 3,4 The interaction of these chemicals with components of the endocrine system was thus not accurately described. Persistent PCB residues and p,p -DDE are often measured, because the analysis is relatively inexpensive, and they are always detected in human plasma. The analogy is looking under the nearest lamppost for lost keys because that is where there is light.
Chemoimmunotherapy With a Modified Hyper-CVAD and Rituximab Regimen Improves Outcome in De Novo Philadelphia Chromosome–Negative Precursor B-Lineage Acute Lymphoblastic Leukemia (2010)

The incorporation of rituximab into the hyper-CVAD regimen appears to improve outcome for younger patients with CD20-positive Ph-negative precursor B-lineage ALL.
Unmyelinated trigeminal pathways as assessed by laser stimuli in humans (2003)

Laser pulses excite superficial free nerve endings innervated by small-myelinated (Adelta) and unmyelinated (C) fibres. Whereas laser-evoked scalp potentials (LEPs) are now reliably used to assess function of the Adelta-fibre nociceptive pathways in patients with peripheral or central lesions, the selective activation of C-fibre receptors and recording of the related brain potentials remain difficult. To investigate trigeminal C-fibre function, we directed laser pulses to the facial skin and studied sensory perception and scalp evoked potentials related to Adelta- or C-fibre activation in healthy humans and patients--one having a bilateral facial palsy, two a trigeminal neuropathy, and two a Wallenberg syndrome. We also measured afferent conduction velocity and, with source analysis, studied the brain generators. Whereas laser pulses of low intensity and small irradiated area elicited pinprick sensations and standard Adelta-LEPs, laser pulses of very-low intensity and large irradiated area elicited warmth sensations and scalp potentials with a latency compatible with C-fibre conduction (negative wave 280 ms, positive wave 380 ms); the estimated conduction velocity was 1.2 m/s. The main waves of the scalp potentials originated from the anterior cingulate gyrus; they were preceded by activity in the opercular region and followed by activity in the insular region. The patient with bilateral facial palsy, who had absent trigeminal-facial reflexes, had normal Adelta- and C-related scalp potentials; the patients with trigeminal neuropathy, characterized by loss of myelinated and sparing of unmyelinated fibres, had absent Adelta- but normal C-related potentials; and the patients with Wallenberg syndrome had absent Adelta- and C-related potentials. We conclude that laser pulses with appropriate characteristics evoke brain potentials related to the selective activation of trigeminal nociceptive Adelta or thermal C fibres. The trigeminal territory yields rewarding LEP findings owing to the high density of thermal receptors and, because the short conduction distance, minimizes the problem of signal dispersion along slow-conducting unmyelinated afferents. The opercular-insular region and the cingulate gyrus are involved in the processing of C-fibre trigeminal inputs. The method we describe may prove useful in patients with lesions affecting the trigeminal thermal pain pathways.
SEMAPLAN: Combining Planning with Semantic Matching to Achieve Web Service Composition (2006)

In this paper, we present a novel algorithm to compose Web services in the presence of semantic ambiguity by combining semantic matching and AI planning algorithms. Specifically, we use cues from domain-independent and domain-specific ontologies to compute an overall semantic similarity score between ambiguous terms. This semantic similarity score is used by AI planning algorithms to guide the searching process when composing services. Experimental results indicate that planning with semantic matching produces better results than planning or semantic matching alone. The solution is suitable for semi-automated composition tools or directory browsers
Clinical efficacy of polyherbal formulation Eezpain spray for muscular pain relief. (2015)

The topical herbal formulation Eezpain spray consisting of natural ingredients that have been clinically proved for its analgesic and anti-inflammatory activity. The designed formulation on application knee and wrist joints, back of neck and shoulder, forearms and lower back exhibited significant efficacy. A total of 20 subjects both male and female applied Eezpain spray consisting of Gaultheria oil, Eucalyptus oil, Turpentine oil, Clove Oil, Menthol and Camphor. All the active materials are cited that these have analgesic activity in myalgia and neuralgia. The study design was prospective and opens as pilot study followed the inclusion and exclusion criteria. All the sign and symptoms were noted at baseline and at the end of 14 days treatment performance was evaluated. The statistical analysis was done by using Microsoft Excel2007 and SPSS version 18.0. It is concluded that Eezpain spray has shown efficacy in mild to moderate cases on applying locally to the affected parts to relieve pain from different ailments.
Disulphide reduction in lysosomes. The role of cysteine (1986)

Published evidence indicates that cystine-containing proteins have their disulphide bonds reduced during proteolysis in lysosomes. However, the intralysosomal accumulation of cystine in the cells of patients with cystinosis has been seen as evidence that protein cystine residues are not reduced. The data are reconcilable and fully in harmony if it is postulated that cysteine from the cytoplasm is the physiological reducing agent.