gebhart/patrepeval huggingface dataset:
Effects of high mobility group protein box 1 and toll like receptor 4 pathway on warts caused by human papillomavirus (2014)

Accumulative evidence has demonstrated that inflammation has an important role in human papillomavirus (HPV) oncogenicity. However, the effects of high mobility group protein box 1 (HMGB1)-toll like receptor 4 (TLR4) signaling pathway associated inflammation on epidermal warts caused by HPV remain unclear. The present study investigated the HMGB1, TLR4 and nuclear factor-κB p65 expression in condyloma acuminatum (CA) and verruca vulgaris (VV). Immunohistochemistry and western blot analysis revealed that p65 expression in epithelial nuclei in VV and CA was significantly higher than in normal skin (NS) (P<0.01), and p65 in CA was higher than in VV but this difference was not significant. The level of extracellular HMGB1 increased significantly and progressively from NS to VV to CA (P<0.05). The level of TLR4 on the surface of epithelial membranes in the CA samples was significantly higher than in NS (P<0.01), and TLR4 in VV samples was significantly lower than in NS (P<0.01). There was a positive correlation between p65 expression in the epithelial nuclei and HMGB1 in the epithelial intercellular spaces (r=0.5199, P<0.01). These findings indicate that inflammation is intensified in warts caused by HPV. HMGB1-TLR4 pathway-associated inflammation may therefore have a pivotal role in CA. HMGB1, rather than TLR4, may be a vital mediator of inflammation in VV. Therapies targeting HMGB1 may be a potential strategy for the treatment of HPV-associated warts.
Contamination of Zeolites Used in Oxygen Production by PSA: Effects of Water and Carbon Dioxide (2008)

Pressure swing adsorption (PSA) is one of the technologies used for producing oxygen from air. Besides the cycles employed, the adsorbent used plays an important role. Many adsorbents are nowadays available showing different adsorption properties. The adsorbent contamination that may occur in a working PSA unit has a great impact on the performance of the separation; it is then important to know the behavior of the selected adsorbent toward major contaminants such as water vapor and carbon dioxide. From the study conducted it was possible to conclude that some adsorbents are contaminated in a large extent even after being regenerated at 70 °C for 2 h. In this paper, the adsorption equilibrium data for several adsorbents used for oxygen production from air are presented. Oxysiv MDX and Oxysiv 7 from UOP as well as AgLiLSX from Air Products and Chemicals are shown to have very good selectivities for the separation of oxygen from air. The contamination study in a working laboratorial PSA unit packed with MS S 624 from Grace Davison is also presented. In the selected operating conditions, about 30% of the bed was contaminated.
The XbaI-BlnI-CeuI genomic cleavage map of Salmonella typhimurium LT2 determined by double digestion, end labelling, and pulsed-field gel electrophoresis (1993)

Endonuclease digestion of the 4,800-kb chromosome of Salmonella typhimurium LT2 yielded 24 XbaI fragments, 12 BlnI fragments, and 7 CeuI fragments, which were separated by pulsed-field gel electrophoresis. The 90-kb plasmid pSLT has one XbaI site and one BlnI site. The locations of the fragments around the circular chromosome and of the digestion sites of the different endonucleases with respect to each other were determined by excision of agarose blocks containing fragments from single digestion, redigestion with a second enzyme, end labelling with 32P by using T7 DNA polymerase, reelectrophoresis, and autoradiography. Forty-three cleavage sites were established on the chromosome, and the fragments and cleavage sites were designated in alphabetical order and numerical order, respectively, around the chromosome. One hundred nine independent Tn10 insertions previously mapped by genetic means were located by pulsed-field gel electrophoresis on the basis of the presence of XbaI and BlnI sites in Tn10. The genomic cleavage map was divided into 100 units called centisomes; the endonuclease cleavage sites and the genes defined by the positions of Tn10 insertions were located by centisome around the map. There is very good agreement between the genomic cleavage map, defined in centisomes, and the linkage map, defined in minutes. All seven rRNA genes were located on the map; all have the CeuI digestion site, all four with the tRNA gene for glutamate have the XbaI and the BlnI sites, but only four of the seven have the BlnI site in the 16S rRNA (rrs) gene. Their inferred orientation of transcription is the same as in Escherichia coli. A rearrangement of the rrnB and rrnD genes with respect to the arrangement in E. coli, observed earlier by others, has been confirmed. The sites for all three enzymes in the rrn genes are strongly conserved compared with those in E. coli, but the XbaI and BlnI sites outside the rrn genes show very little conservation.
CD40 ligand acts as a costimulatory signal for neonatal thymic gamma delta T cells. (1994)

The stimulatory requirements for T cells bearing gamma delta T cell receptors are distinct from those of alpha beta T cells. We have analyzed the ability of the CD40 ligand (CD40L) to activate neonatal thymic gamma delta T cells. CD40L is expressed on activated T cells and has been shown to induce B cell proliferation and Ig secretion as well as monocyte activation. We now demonstrate that, in the presence of an anti-TCR-gamma delta Ab, CD40L is able to induce the proliferation of neonatal thymic gamma delta cells. The presence of CD40L also leads to enhanced expression of a variety of activation-associated Ag including CD25, CD69, CD44, and Ly6C. In addition to proliferation, CD40L induces lectin-mediated cytolytic activity in thymic gamma delta T cells as well as the production of IFN-gamma and TNF-alpha. We were unable to detect IL-2 or IL-4 production in response to CD40L, and Ab-blocking studies indicate that the mechanism of activation appears to involve IL-1 but is independent of IL-2, IL-4, and IL-7. These results suggest that, in addition to its effects on B cells and monocytes, CD40L can costimulate the activation of thymic gamma delta T cells.
Phase I Study of Lentiviral-Transduced Chimeric Antigen Receptor-Modified T Cells Recognizing Mesothelin in Advanced Solid Cancers (2019)

This phase I study investigated the safety and activity of lentiviral-transduced chimeric antigen receptor (CAR)-modified autologous T cells redirected against mesothelin (CART-meso) in patients with malignant pleural mesothelioma, ovarian carcinoma, and pancreatic ductal adenocarcinoma. Fifteen patients with chemotherapy-refractory cancer (n = 5 per indication) were treated with a single CART-meso cell infusion. CART-meso cells were engineered by lentiviral transduction with a construct composed of the anti-mesothelin single-chain variable fragment derived from the mouse monoclonal antibody SS1 fused to intracellular signaling domains of 4-1BB and CD3zeta. Patients received 1-3 × 10<sup>7</sup> or 1-3 × 10<sup>8</sup> CART-meso cells/m<sup>2</sup> with or without 1.5 g/m<sup>2</sup> cyclophosphamide. Lentiviral-transduced CART-meso cells were well tolerated; one dose-limiting toxicity (grade 4, sepsis) occurred at 1-3 × 10<sup>7</sup>/m<sup>2</sup> CART-meso without cyclophosphamide. The best overall response was stable disease (11/15 patients). CART-meso cells expanded in the blood and reached peak levels by days 6-14 but persisted transiently. Cyclophosphamide pre-treatment enhanced CART-meso expansion but did not improve persistence beyond 28 days. CART-meso DNA was detected in 7/10 tumor biopsies. Human anti-chimeric antibodies (HACA) were detected in the blood of 8/14 patients. CART-meso cells were well tolerated and expanded in the blood of all patients but showed limited clinical activity. Studies evaluating a fully human anti-mesothelin CAR are ongoing.
ESOL:  Estimating Aqueous Solubility Directly from Molecular Structure (2004)

This paper describes a simple method for estimating the aqueous solubility (ESOL--Estimated SOLubility) of a compound directly from its structure. The model was derived from a set of 2874 measured solubilities using linear regression against nine molecular properties. The most significant parameter was calculated logP(octanol), followed by molecular weight, proportion of heavy atoms in aromatic systems, and number of rotatable bonds. The model performed consistently well across three validation sets, predicting solubilities within a factor of 5-8 of their measured values, and was competitive with the well-established "General Solubility Equation" for medicinal/agrochemical sized molecules.
Regulation of protein kinase CKII during the cell division cycle. (1994)

Protein kinase CKII is a prevalent serine/threonine protein kinase whose structure is highly conserved among eukaryotic organisms. Its involvement in the eukaryotic cell division cycle has been implicated by genetic experiments in yeast, antisense DNA, and inhibitory antibody experiments in mammalian cells, changes in activity during growth stimulation experiments, and protection of cells from radiation damage to replicating DNA. In addition, the cdc2 protein kinase, which is central to cell division cycle control, serves as a substrate for CKII specifically during the G1 phase of human cells. In this report, extracts of HeLa cells were prepared using neutral, aqueous buffers at low ionic strength. The cells were enriched for specific stages of the cell division cycle by treatment with drugs or by centrifugal elutriation. The results indicate that CKII activity in these extracts is highest during the G1 phase, and there appears to be a reduction in soluble CKII activity during the S phase. These data are consistent with the hypothesis that high CKII is necessary for a normal G1 phase but that progression through the S phase requires inhibition of CKII.
Neonatal rotavirus vaccination with RIT 4237 bovine rotavirus vaccine (1987)

We vaccinated 244 newborn infants orally with RIT 4237 bovine rotavirus vaccine or placebo and followed them serologically and clinically for 16 months. Initially 39 of the 119 (33%) vaccine recipients compared with 1 of the 120 placebo recipients seroconverted by enzyme-linked immunosorbent assay-immunoglobulin M. After the first winter rotavirus season, at 7 months of age 55% of the vaccinated infants and 37% of the unvaccinated infants were rotavirus-seropositive by enzyme-linked immunosorbent assay-immunoglobulin G (P less than 0.01, chi square test). At 12 months of age, after a low rotavirus prevalence season, 34% of the vaccinated children and 23% of the unvaccinated children remained seropositive. There were 14 confirmed episodes of rotavirus gastroenteritis in the vaccine group and 10 episodes in the placebo group during the first 16 months. However, only 1 of the episodes in the vaccine group was severe, 4 were moderately severe and 9 were mild, whereas 7 episodes in the placebo group were severe and 3 were moderately severe (P less than 0.001 between groups, Fisher's exact test). There was no clear correlation between vaccine-induced clinical protection and initial serologic response (enzyme-linked immunosorbent assay-immunoglobulin M) to vaccination, but during follow-up severe rotavirus gastroenteritis was more likely to occur in children with no serum rotavirus immunoglobulin G antibody at the time of infection. We conclude at the present stage that neonatal rotavirus vaccination with RIT 4237 vaccine gives no protection against rotavirus infection but appears to modify the severity of gastroenteritis.
A Smart Object Centric Indoor Location Model for Future Ubiquitous and Grid Services (2009)

One of the primary requirements for future ubiquitous environment is to exploit location information to provide contextual services. Typical indoor location systems are heavily infra-structured making it difficult to deploy practically in home settings. In this article we propose a lightweight location model utilizing existing physical objects in our environment. Our approach is to use sensor augmented daily life objects surrounding us for extracting location information. Some of these everyday objects are static in nature and have designated location, like a bed in the bedroom, a refrigerator in the kitchen, etc. Utilizing this characteristics, we present ”Spreha”, a light weight hierarchical location model where static physical objects are used as reference points for identifying mobile objects like a chair, a watch, a lamp, etc. The model is organized in a tree structure representing the containment relationship and is independent of underlying sensing infrastructure. A prototype implementation of the model has been constructed as a pluggable module of a generic middleware using Bluetooth technology. This paper discusses about the design, architecture and findings of the prototype implementation. The implication of such lightweight location model is very important in realizing future environments where ubiquitous services will merge with grid services.
Stimulation of 24R,25-dihydroxyvitamin D3 synthesis by metabolites of vitamin D3 (1983)

Previously we have shown that the isolated perfused kidney from vitamin D-deficient rats converts [3H]25(OH)D3 into [3H]1 alpha,25(OH)2D3. When certain vitamin D metabolites were added to perfusate the same kidney began to synthesize [3H]24R,25(OH)2D3. In this study we investigated the structural requirements of the vitamin D molecule necessary to stimulate synthesis of [3H]24R,25(OH)2D3 in a 1-hydroxylating kidney. Kidneys were perfused with tracer [3H]25(OH)D3 (450 pM) alone and in the presence of a variety of hydroxylated metabolites and fluorinated analogues of vitamin D3 at concentrations of 450 pM to 25 microM. Tracer [3H]25(OH)D3 alone resulted in synthesis of only [3H]1 alpha,25(OH)2D3 during the 6-h perfusion period. 25-Hydroxylated metabolites [25(OH)D3, 25 nM; 1 alpha,25(OH)2D3, 25 nM; 24R,25(OH)2D3, 25 nM; 24(F)2,25(OH)D3, 50 nM] stimulated [3H]24R,25(OH)2D3 production at 2 h of perfusion. On the other hand, analogues without the 25-hydroxyl group [D3; 1 alpha(OH)D3; 25(F)D3; 1 alpha(OH),25(F)D3; 1 alpha(F)D3; 1 beta(F)D3]; did not stimulate [3H]24R,25(OH)2D3 synthesis. We conclude that the 25-hydroxyl group is an essential determinant of 24-hydroxylation.
Critical thickness of GaN thin films on sapphire (0001) (1996)

Synchrotron x-ray diffraction was employed to measure the lattice constants a and c of GaN films grown with an AlN buffer layer on sapphire (0001) over a thickness range of 50 Å to 1 μm. We used multiple reflections and a least-squares fit method for high reliability. As the thickness increased, the lattice constant a increased from 3.133 Å to 3.196 Å and c decreased from 5.226 Å to 5.183 Å. The expected trend was fitted to an equilibrium theory, allowing the critical thickness of GaN on AlN to be estimated at 29 Å ± 4 Å in good agreement with a theoretical prediction.
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae (2002)

A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented. Interrelations of this algorithm with alternative methods proposed in the literature and the theory of small world networks are discussed. The applicability of our method is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae, which is an organism of considerable medical interest. The decomposition gives rise to 19 subnetworks. Three of these are here discussed in biochemical terms: arginine degradation, the tetrahydrofolate system, and nucleotide metabolism. The interrelations of pathway analysis of biochemical networks with Petri net theory are outlined.
Complement C3 Is a Risk Factor for the Development of Diabetes (2005)

Cross-sectional studies have reported strong correlations between plasma levels of complement C3, insulin, and glucose. This prospective study explored whether elevated levels of C3, C4, and other inflammation-sensitive plasma proteins (ISPs; fibrinogen, orosomucoid, alpha1-antitrypsin, haptoglobin, and ceruloplasmin) are associated with the development of diabetes. Plasma proteins were measured in 2,815 nondiabetic healthy men, age 38-50 years, who were reexamined after a mean follow-up of 6.1 years. Diabetes development (n = 123) was studied in relation to baseline levels of plasma proteins. After adjusting for age, screening year, and glucose at baseline, the odds ratio (95% CI) for developing diabetes was 1.00, 2.4 (1.1-5.3), 2.9 (1.4-6.0), and 5.6 (2.8-10.9), respectively, for men with C3 in the 1st, 2nd, 3rd, and 4th quartiles (trend: P < 0.00001). Fibrinogen, haptoglobin, C4, and the number of elevated ISPs were also related to future diabetes in this model. Only C3 was significantly associated with diabetes development after further adjustments for potential confounders, including BMI, insulin, and other inflammatory markers. We concluded that the risk of developing diabetes is related to levels of complement C3.
Role of Glutaredoxin-3 and Glutaredoxin-4 in the Iron Regulation of the Aft1 Transcriptional Activator in Saccharomyces cerevisiae (2006)

The transcription factors Aft1 and Aft2 from Saccharomyces cerevisiae regulate the expression of genes involved in iron homeostasis. These factors induce the expression of iron regulon genes in iron-deficient yeast but are inactivated in iron-replete cells. Iron inhibition of Aft1/Aft2 was previously shown to be dependent on mitochondrial components required for cytosolic iron sulfur protein biogenesis. We presently show that the nuclear monothiol glutaredoxins Grx3 and Grx4 are critical for iron inhibition of Aft1 in yeast cells. Cells lacking both glutaredoxins show constitutive expression of iron regulon genes. Overexpression of Grx4 attenuates wild type Aft1 activity. The thioredoxin-like domain in Grx3 and Grx4 is dispensable in mediating iron inhibition of Aft1 activity, whereas the conserved cysteine that is part of the conserved CGFS motif in monothiol glutaredoxins is essential for this function. Grx3 and Grx4 interact with Aft1 as shown by two-hybrid interactions and co-immunoprecipitation assays. The interaction between glutaredoxins and Aft1 is not modulated by the iron status of cells but is dependent on the conserved glutaredoxin domain Cys residue. Thus, Grx3 and Grx4 are novel components required for Aft1 iron regulation that most likely occurs in the nucleus.
Elucidation of the Primary and Three-Dimensional Structure of the Uterotonic Polypeptide Kalata B1 (1995)

The amino acid sequence and structure of a uterotonic polypeptide extracted from the African plant Oldenlandia affinis DC have been determined. The peptide, kalata B1, consists of 29 amino acid residues and is rich in cysteine (6), threonine (5), and glycine (5). Enzyme cleavage studies show that the polypeptide backbone is cyclic. The three-dimensional solution structure has been determined using two-dimensional nuclear magnetic resonance (NMR) spectroscopy and distance-restrained simulated annealing. Kalata B1 is composed mainly of beta-strands connected by tight turns, forming regions of beta-sheet, except in the case of one section which forms a longer, less structured loop. The tertiary fold, together with the disulfides that form a sulfur core, produces a striking and unusual surface in which the majority of the hydrophobic residues form a solvent-exposed patch. The hydrophobic side of kalata B1 is flanked by two diametrically opposed and opposite-charged residues. The structure calculations have been used to predict the previously unknown disulfide bond connectivities using two approaches. In the first, a family of structures was calculated on the basis of NOE constraints without the assumption of a specific disulfide connectivity. The resultant structures were examined to determine whether the calculated position of the sulfur atoms suggested that one set of disulfide connectivities was more likely than the other, theoretically possible, sets. In the second approach, a separate family of structures (50 per set) was calculated for each of the 15 possible disulfide-bonded molecules. The resultant families of structures were compared to see whether one was favored over the others. Both approaches led to the same global fold, and the most likely disulfide connectivity is predicted to be 5-22, 13-27, and 17-29. In the calculated structure the cyclic peptide backbone is folded back onto itself and braced with disulfide pairs across diagonally opposed beta-strands. This structure involves one of the disulfide bonds (5-22) threading through the eight amino acid loop formed by the other two disulfide bonds and the peptide fragments connecting them.
Prolonged in vivo anticoagulant activity of a hirudin–albumin fusion protein secreted from Pichia pastoris (2001)

Hirudin is a small, proteinaceous thrombin inhibitor that clears rapidly from the circulation. A hexahistidine-tagged hirudin-rabbit serum albumin (RSA) fusion protein, HLAH6, was characterized following secretion from Pichia pastoris. HLAH6 bound to immobilized nickel, anti-RSA, and anti-hexahistidine antibodies, and contained the expected (ITYTD) N-terminus. Its spectrometric mass was 74,490 (versus the theoretical mass of 74,410 and sodium dodecyl sulfate-polyacrylamide gel electrophoresis mobility of 84 kDa). The terminal catabolic half-life in rabbits of HLAH6, recombinant Pichia-derived His-tagged RSA, or plasma-derived RSA did not differ. Injection of 2 mg/kg HLAH6 into rabbits raised the activated partial thromboplastin time (aPTT) above initial values for 4-24 h, while the equimolar dose of unfused hirudin was without significant effect. A higher dose of HLAH6 (3 mg/kg functional HLAH6, equivalent to 37.6 thrombin-inhibitory units/g) raised the aPTT by 2.0- to 2.5-fold; the elevation persisted for > 48 h. Importantly, both HLAH6 and unfused hirudin inhibited clot-bound thrombin. Our results suggest that HLAH6 exhibits not only delayed clearance, but also prolonged biological activity in vivo compared with unfused hirudin.
Synthesis of cannabinoids carrying ω-carboxy substituents: the cannabidiols, cannabinol and Δ1- and Δ6-tetrahydrocannabinols of this series (1988)

A convenient synthesis of methyl 5-(3,5-dihydroxyphenyl)pentanoate adaptable for isotopic side-chain labelling is reported. Using acid-catalysed terpenylations involving (1S,4R)-(+)-trans-p-menthadienol, conditions for making (3R,4R)-o-and p-cannabidiols, (3R,4R)-Δ1-THC's, (3R,4R)-Δ6-THC's and cannabinol in ω-carboxylated or methoxycarbonylated formats are described. Multigram amounts of the thermodynamically labile (3R,4R)-Δ1-THC-ω-ester, readily convertible to the ω-acid, were made: the acid is a mammalian and microbial metabolite of Δ1-THC and is of interest for membrane studies as well as for spin-labelling and radioimmunoassay purposes. A convenient synthesis of (2E,4E)-5-(3,5-dihydroxyphenyl)penta-2,4-dienoate allows its conversion into the crystalline Δ6-THC analogue having a conjugated dienoic esterside chain. Chromatographic information is tabulated for esters of the ω-carboxy cannabinoid series along with data for esters of the naturally occurring Ar-carboxylated cannabinoid series made synthetically in earlier work.