gebhart/patrepeval huggingface dataset:
Continuous bioprocessing: The real thing this time? (2014)

The Annual bioProcessUK Conference has acted as the key networking event for bioprocess scientists and engineers in the UK for the past 10 years. The following article is a report from the sessions that focused on continuous bioprocessing during the 10(th) Annual bioProcessUK Conference (London, December 2013). These sessions were organized by the 'EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies' hosted at University College London. A plenary lecture and workshop provided a forum for participants to debate topical issues in roundtable discussions with industry and academic experts from institutions such as Genzyme, Janssen, Novo Nordisk, Pfizer, Merck, GE Healthcare and University College London. The aim of these particular sessions was to understand better the challenges and opportunities for continuous bioprocessing in the bioprocessing sector.
Expression and function of 4-1BB and 4-1BB ligand on murine dendritic cells (2002)

4-1BB (CDw137) and its ligand (4-1BBL) have been implicated in cellular immune responses. To further characterize the expression and function of 4-1BBL, we newly generated an anti-mouse 4-1BBL mAb (TKS-1), which can inhibit the interaction of 4-1BBL with 4-1BB. Flow cytometric analyses using TKS-1 and an anti-mouse 4-1BB mAb indicated that 4-1BB was inducible on both CD4(+) and CD8(+) splenic T cells by stimulation with immobilized anti-CD3 mAb, but 4-1BBL was not expressed on resting or activated T cells. 4-1BBL expression was inducible on splenic B cells by stimulation with anti-IgM antibody plus anti-CD40 mAb, on peritoneal macrophages by stimulation with lipopolysaccharide (LPS) and on splenic dendritic cells (DC) by stimulation with anti-CD40 mAb or LPS. Interestingly, splenic DC expressed 4-1BB constitutively, which was down-regulated by anti-CD40 stimulation. Co-culture of splenic DC with 4-1BBL-transfected cells or 4-1BBL-expressing tumor cell lines led to cytokine (IL-6 and IL-12) production and co-stimulatory molecule up-regulation by splenic DC, indicating that 4-1BBL can directly activate DC. Moreover, IL-12 production by anti-CD40-stimulated DC was partially inhibited by TKS-1. These results suggest that 4-1BB expressed on DC may be involved in DC activation through DC--tumor interaction and DC--DC interaction.
Iodination of Phenols by Use of Benzyltrimethylammonium Dichloroiodate(1–) (1987)

Abstract The reaction of phenols with benzyltrimethylammonium dichloroiodate(1–) in dichloromethane-methanol in the presence of CaCO3 or NaHCO3 for several hours at room temperature gave iodophenols in good yields.
Fluorous‐Based Small‐Molecule Microarrays for the Discovery of Histone Deacetylase Inhibitors (2007)

Noncovalent immobilization is an attractive method for identifying inhibitors of histone deacetylases (HDACs). Fluorous-based small-molecule microarrays were validated as an effective method. Three enzymes and three assays (microarray, biochemical activity, and surface plasmon resonance) were used to identify inhibitors of HDACs and to compare them.
A new fusible-type programmable element composed of Aluminum and polysilicon (1986)

This paper describes the structure and programming characteristics of newly developed fusible-type programmable element called an Al-Si fuse. The Al-Si fuse, formed by an aluminum pattern formation process using the substitution reaction of aluminum for polysilicon (APSP) is made up of a polysilicon component and an aluminum component. The programming characteristics of the Al-Si fuse indicate bias polarity dependence. In the programming mode in which the substituted aluminum component is positively biased, programming characteristics are determined by the current and not by the power. Furthermore, the programming current is reduced to one-half of that for conventional polysilicon fuse. The programming current and voltage for a sample having a 3-µm width and 160-nm thickness are reduced to 5.5 mA and 3.2 v.
Anti-inflammatory effects of granulocyte colony-stimulating factor (1998)

The innate, unspecific immune response to bacterial and fungal infection is mediated primarily by neutrophilic granulocytes. Granulocyte colony-stimulating factor (G-CSF), an endogenous hematopoietic growth factor for neutrophils produced at the site of infection, is an integral part of this natural host defense. However, neutrophilic granulocytes also play a major role in the inflammatory response, resulting in tissue damage. Therefore, the indications for colony-stimulating factors in combating infectious diseases seemed to be limited for fear of their proinflammatory activity. In contrast to these concerns, G-CSF has proven itself to be an anti-inflammatory immunomodulator. Animal, volunteer, and patient studies have all shown that G-CSF reduces inflammatory activity by inhibiting the production or activity of the main inflammatory mediators interleukin-1, tumor necrosis factor-α, and inter-feron gamma. In conclusion, the body's G-CSF-regulated emergency recruitment of neutrophils is combined with a simultaneous limitation of the harmful inflammatory reaction. This unique pharmacologic combination of improving anti-infectious defense and inhibiting inflammation, opens up a range of new indications for G-CSF in the area of nonneu-tropenic infections.
Hypermedia topologies and user navigation (1989)

One of the major problems confronting users of large hypermedia systems is that of navigation: knowing where one is, where one wants to go, and how to get there from here. This paper contributes to this problem in three steps. First, it articulates a number of navigational strategies that people use in physical (geographical) navigation. Second, it correlates these with various graph topologies, showing how and why appropriately restricting the connectivity of a hyperbase can improve the ability of users to navigate. Third, it analyzes some common hypermedia navigational mechanisms in terms of navigational strategies and graph topology.
Overview of Protein Microarrays (2013)

Abstract Protein microarray technology is an emerging field that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high‐throughput manner. Protein microarrays are composed of two major classes: analytical and functional. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse‐phase protein microarray. Applications of protein microarrays, especially functional protein microarrays, have flourished over the past decade as the fabrication technology has matured. In this unit, advances in protein microarray technologies are reviewed, and then a series of examples are presented to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. Relevant areas of research include the detection of various binding properties of proteins, the study of protein post‐translational modifications, the analysis of host‐microbe interactions, profiling antibody specificity, and the identification of biomarkers in autoimmune diseases. Curr. Protoc. Protein Sci . 72:27.1.1‐27.1.16. © 2013 by John Wiley &amp; Sons, Inc.
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations (2007)

Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pK(a) values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al., Nucleic Acids Research, 32, W665-W667, 2004). Here we report the significantly expanded PDB2PQR that includes the following features: robust standalone command line support, improved pK(a) estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization.
Manipulating Programmed Cell Death for Better Living! Review and commentary on Apoptosis in Health and Disease ,  edited by Robert R. Ruffolo, Jr. and Frank Walsh,   Harwood Academic Publishers, Amsterdam, Netherlands, 2000, 249 pp. $80.00, ISBN: 90-5823-086-4 (2001)

Manolagas provides a succinct review of the book Apoptosis in Health and Disease. He praises the book for the clarity with which it covers the topics, but he also points out two missing health issues for which regulating apoptosis may prove clinically important: One is the health and regulation of the female reproductive system and the other is the treatment of osteoporosis.
Oral Glycoprotein IIb/IIIa Inhibition With Orbofiban in Patients With Unstable Coronary Syndromes (OPUS-TIMI 16) Trial (2000)

-Fixed-dose orbofiban failed to reduce major cardiovascular events and was associated with increased mortality in this broad population of patients with acute coronary syndromes; however, a benefit was observed among patients who underwent percutaneous coronary intervention.
Galectin-7 overexpression is associated with the apoptotic process in UVB-induced sunburn keratinocytes (1999)

Galectin-7 is a beta-galactoside binding protein specifically expressed in stratified epithelia and notably in epidermis, but barely detectable in epidermal tumors and absent from squamous carcinoma cell lines. Galectin-7 gene is an early transcriptional target of the tumor suppressor protein P53 [Polyak, K., Xia, Y., Zweier, J., Kinzler, K. & Vogelstein, B. (1997) Nature (London) 389, 300-305]. Because p53 transcriptional activity is increased by genotoxic stresses we have examined the possible effects of ultraviolet radiations (UVB) on galectin-7 expression in epidermal keratinocytes. The amounts of galectin-7 mRNA and protein are increased rapidly after UVB irradiation of epidermal keratinocytes. The increase of galectin-7 is parallel to P53 stabilization. UVB irradiation of skin reconstructed in vitro and of human skin ex vivo demonstrates that galectin-7 overexpression is associated with sunburn/apoptotic keratinocytes. Transfection of a galectin-7 expression vector results in a significant increase in terminal deoxynucleotidyltransferase-mediated UTP end labeling-positive keratinocytes. The present findings demonstrate a keratinocyte-specific protein involved in the UV-induced apoptosis, an essential process in the maintenance of epidermal homeostasis.
Excimer Laser Ablation of the Lens (1986)

Ablation of the bovine crystalline lens was studied using radiation from an excimer laser at four ultraviolet wave lengths as follows: 193 nm (argon fluoride), 248 nm (krypton fluoride), 308 nm (xenon chloride), and 351 nm (xenon fluoride). The ablation process was quantitated by measuring mass ablated with an electronic balance, and characterized by examining ablation craters with scanning electron microscopy. The highest ablation rate was observed at 248 nm with lower rates at 193 and 308 nm. No ablation was observed at 351 nm. Scanning electron microscopy revealed the smoothest craters at 193 nm while at 248 nm there was vacuolization in the crater walls and greater disruption of surrounding tissue. The craters made at 308 nm did not have as smooth a contour as the 193-nm lesions. The spectral absorbance of the bovine lens was calculated at the wavelengths used for ablation and correlated with ablation rates and thresholds. High peak-power, pulsed ultraviolet laser radiation may have a role in surgical removal of the lens.
PP.21.30 (2015)

Objective: To observe the reverse effect of different combined regimens on blood pressure and microalbuminuria(MAU) in hypertensive patients. Design and method: Ninety-four hypertensive patients with blood pressure > 140/90 mmHg (1 mmHg = 0.133 kPa) and positive MAU after treatment with inhibitors of angiotensin invertase and antagonists of angiotensin receptor were included in this study. The patients were randomly divided into L-amlodipine group (n = 52) and diuretics (HCTZ) group (n = 42). After the patients were treated with L-amlodipine(2.5–5 mg/d) and HCTZ(12.5–25 mg/d) respectively for 12 weeks, the reverse effect of different regimens on blood pressure and MAU was observed. Results: The normal blood pressure was achieved in 35(67.3%)and 27 patients(64.3%) respectively(P > 0.05), the negative MAU rate was 53.8% and 19.0% respectively (P < 0.01), the blood pressure was < 140/90 mmHg and the MAU was no less than30% in 80.8% and 64.3% of the patients in the two groups 12 weeks after treatment(P < 0.05). Conclusions: The effect of renin and angiotensin blocking agents in combination with calcium antagonists or HCTZ is similar to that of other regimens on blood pressure and other parameters, and is better than that of renin and angiotensin blocking agents in combination with HCTZ on MAU.
Antioxidants selectively suppress activation of NF-kappa B by human T-cell leukemia virus type I Tax protein (1992)

Oxygen radical scavengers, such as dithiocarbamates and cysteine derivatives, inhibit activation of the ubiquitous transcription factor nuclear factor kappa B (NF-kappa B) after treatment of cells with tumor necrosis factor, phorbol ester, and interleukin-1. An involvement of oxygen radicals was more directly evident from the induction of NF-kappa B by low concentrations of H2O2 and the demonstration that cells stimulated with various NF-kappa B inducers release H2O2 and superoxide. In this study, we used the antioxidant pyrrolidine dithiocarbamate (PDTC) to investigate whether the activation of NF-kappa B by the viral transactivator Tax from human T-cell leukemia virus type I also depends on the production of reactive oxygen intermediates. The Tax-induced activation of the DNA-binding activity of NF-kappa B in Jurkat T cells was potently suppressed by micromolar concentrations of PDTC. Within the same concentration range, PDTC and two other dithiocarbamates also strongly interfered with transactivation of the long terminal repeat (LTR) of human immunodeficiency virus type 1 by Tax but had no effect on transactivation of the same LTR by Tat. Transactivation of the human T-cell leukemia virus type I LTR by Tax was also barely influenced. Tax seems to activate NF-kappa B by a mechanism shared with all other inducers of NF-kappa B tested so far. It appears that one of the pleiotropic activities of Tax leads to an enhanced production of oxygen radicals that are required for activation of NF-kappa B.
Photopolymerized Cross-Linked Polyacrylamide Gels for On-Chip Protein Sizing (2004)

A new method for on-chip sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of proteins is reported. Miniaturization of SDS-PAGE has attracted significant attention because it offers rapid analysis times, excellent resolution, high throughput, and the potential for integration and automation, as compared to conventional counterparts. The presented on-chip SDS-PAGE technique employed photolithographically patterned, cross-linked gels fabricated in situ in <20 min. The effects of sieving gel composition on the migration properties of fluorescently labeled protein standards (ranging in molecular weight from 14.2 to 66 kDa) were quantified, as was the ability of the gels to function as a sieving matrix for biologically relevant species. Ferguson analysis was employed to calculate retardation coefficients and free solution mobilities. In conjunction with fluorescence imaging, the on-chip SDS-PAGE separation mechanism was evaluated in terms of separation performance indexes, as well as limiting behaviors (i.e., free solution mobility, exclusion characteristics). The photolithographically fabricated gels employed for on-chip SDS-PAGE allowed rapid (<30 s) separations of proteins in short separation lengths (4 mm) with efficiencies as high as 4.41 x 10(5) plates/m. The on-chip SDS-PAGE separations were approximately 100 times faster than conventional slab gel SDS-PAGE (60 min) and occurred in a fraction of the separation length required by slab gels. The migration behavior of protein standards correlated well with molecular weight and allowed molecular weight determination for interleukin-2, fibroblast growth factor, insulin-like growth factor, and tetanus toxin C-fragment.
Fetal DNA in maternal plasma: emerging clinical applications (2001)

The recent discovery of high concentrations of fetal DNA in maternal plasma represents a promising noninvasive approach to prenatal diagnosis. Compared with the analysis of the cellular fraction of maternal blood, the analysis of fetal DNA extracted from maternal plasma has the advantage of being rapid, robust, and easy to perform. The fetal DNA detected is limited to the current pregnancy. However, universal fetal gene sequences must be identified that allow analysis of genetic material from both male and female fetuses. Study of fetal DNA in maternal plasma can improve our understanding of fetomaternal biology and physiology. The long-term effects of maternal exposure to relatively high amounts of foreign DNA are unknown but represent an exciting area for future inquiry.
Clinical utility of five genetic variants for predicting prostate cancer risk and mortality (2008)

Genotypes for five SNPs plus family history are associated with a significant elevation in risk for prostate cancer and may explain up to 45% of prostate cancer in our population. However, they do not improve prediction models for assessing who is at risk of getting or dying from the disease, once known risk or prognostic factors are taken into account. Thus, this SNP panel may have limited clinical utility.
Aldolase-catalyzed C-C bond formation for stereoselective synthesis of nitrogen-containing carbohydrates (1990)

Rabbit muscle aldolase was found to catalyze stereoselective aldol addition of dihydroxyacetone phosphate (1) to 3-azido-2-hydroxypropana(2 ). The ketose 1-phosphates were isolated as barium salts, 4a/4b, and hydrolyzed with acid phosphatase. The mixture of 6-azido-6-deoxy-D-fructose(5) and 6-azido-6-deoxy-L-sorbose thus obtained was separated by anion-exchange chromatography. Reductive amination of 5 and 6 yielded, respectively, 1-deoxymannojirimycin (7) and 1-deoxynojirimycin (8), with high diastereoselectivity (&gt;98:2). Analogous aldol addition of 1 to 3-azido-2-hydroxybutanal( 9)( E:Z = 92:8) afforded a mixture of the 6-azido-6,7-dideoxyheptuloses 12 and 13, which contained 88% of 6-azido-6,7-dideoxy-D-altro-heptulose(13 ). After anion-exchange chromatography, 13 was isolated as a 18:82 mixture of the β/α anomers. Reductive amination of pure 13 gave a mixture of 2,6,7-trideoxy-2,6-imino-D-glycero-D-manno and D-gluco-heptitol (14 and 15) (3:2 molar ratio), which likewise was separated by anion-exchange chromatography. If a mixture of 12 and 13 was hydrogenated under identical conditions, 2,6,7-trideoxy-2,6-imino-L-glycero-L-gulo-heptitol(16) could be isolated besides 14 and 15.
The safety and efficacy of anterior cervical discectomy and fusion with polyetheretherketone spacer and recombinant human bone morphogenetic protein–2: a review of 200 patients (2008)

An ACDF performed using a PEEK spacer filled with rhBMP-2 leads to good to excellent clinical outcomes and solid fusion, even in multilevel cases and in patients who are smokers. The incidence of symptomatic dysphagia may be decreased with a lower dose of rhBMP-2 that is placed only within the PEEK spacer.
Passive Vibration Suppression of Beams Using Magnetomechanical Coating (1998)

Abstract This paper investigates the possibility of using magnetomechanical coating for enhancing high damping capacity on the high frequency structural response of beams. An analytical procedure is developed for modeling the dynamic behavior of beams coated with a plasma sprayed iron-chromium based coating. The effect of hysteresis nonlinear damping properties in terms of various stress or strain levels is investigated in the study. For the practical applications, in accordance with the proposed analytical procedure, a vibration formulation is presented. An extension to a continuous system is also discussed in this research.
Heparin‐binding Epidermal Growth Factor‐like Growth Factor: p91 Activation, Induction of Plasminogen Activator/Plasminogen Activator Inhibitor, and Tubular Morphogenesis in Human Microvascular Endothelial Cells (1996)

Epidermal growth factor (EGF) or transforming growth factor-alpha (TGF-alpha) stimulates cell migration, proliferation and the formation of tube-like structures of human microvascular endothelial cells in culture. Heparin-binding EGF-like growth factor(HB-EGF), which shows 35% homology with EGF/TGF-alpha, is a member of the EGF family, and it is ubiquitous in many tissues and organs. We examined whether or not HB-EGF induced angiogenic responses in human microvascular endothelial cells. HB-EGF inhibited the binding of (125) I-EGF to the EGF receptor and induced autophosphorylation of the receptor on endothelial cells. Exogenous HB-EGF induced the loss of more than 70% of the EGF receptor from the cell surface within 30 min, with similar kinetics to that of EGF. The level of c-fos mRNA markedly increased at 30 min in response to HB-EGF as well as EGF. A gel shift assay demonstrated the activation of the transcription factor p91 by HB-EGF and EGF. This factor directly interacts with EGF receptor and mediates the activation of c-fos gene promoter. HB-EGF enhanced the mRNA expression of tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor-1 (PAI-1) mRNA. However, the enhancement of t-PA and PAI-1 by HB-EGF was less than that by EGF. Heparitinase/chlorate, which digests the heparan sulfate proteoglycan of the endothelial cell surface, restored both t-PA and PAI-1 mRNA levels in response to HB-EGF in a manner similar to that by EGF. HB-EGF at 10 ng/ml developed tube-like structures in type I collagen gel at similar levels to that of EGF at 10 ng/ml, suggesting that HB-EGF is also a potent angiogenic factor in the model system for angiogenesis. The tubulogenesis activity of HB-EGF is discussed in relation to the expression of the t-PA and PAI-1 genes.
Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli (1991)

Anaerobic growth of Pseudomonas aeruginosa on nitrate or arginine requires the anr gene, which codes for a positive control element (ANR) capable of functionally complementing an fnr mutation in Escherichia coli. The anr gene was sequenced; it showed 51% identity with the fnr gene at the amino acid sequence level. Four cysteine residues known to be essential in the FNR protein are conserved in ANR. The anr gene product (deduced Mr 27,129) was visualized by the maxicell method and migrated like a 32 kDa protein in gel electrophoresis under denaturing conditions. An anr mutant of P. aeruginosa constructed by gene replacement was defective in nitrate respiration, arginine deiminase activity, and hydrogen cyanide biosynthesis, underscoring the diverse metabolic functions of ANR during oxygen limitation. Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas syringae, and Pseudomonas mendocina all had a functional analogue of ANR, indicating that similar anaerobic control mechanisms exist in these bacteria.