gebhart/patrepeval huggingface dataset:
Functionalized silk-based biomaterials for bone formation (2000)

Silks are being reassessed as biomaterial scaffolds due to their unique mechanical properties, opportunities for genetic tailoring of structure and thus function, and recent studies clarifying biocompatibility. We report on the covalent decoration of silk films with integrin recognition sequences (RGD) as well as parathyroid hormone (PTH, 1-34 amino acids) and a modified PTH 1-34 (mPTH) involved in the induction of bone formation. Osteoblast-like cell (Saos-2) responses to the decorated silk films indicate that the proteins serve as suitable bone-inducing matrices. Osteoblast-like cell adhesion was significantly increased on RGD and PTH compared to plastic, mPTH, and the control peptide RAD. At 2 weeks of culture, message levels of alkaline phosphatase were similar on all substrates, but by 4 weeks, alkaline phosphatase mRNA was greatest on RGD. At 2 weeks of culture, alpha 1(I) procollagen mRNA was elevated on silk, RGD, RAD, and PTH, and hardly detectable on mPTH and plastic. However, by 4 weeks RGD demonstrated the highest level compared to the other substrates. Osteocalcin message levels detected by RT-PCR were greatest on RGD at both time points. Calcification was also significantly elevated on RGD compared to the other substrates with an increase in number and size of the mineralized nodules in culture. Thus, RGD covalently decorated silk appears to stimulate osteoblast-based mineralization in vitro.
Novel Tyrosine Kinase Identified by Phosphotyrosine Antibody Screening of cDNA Libraries (1988)

In an attempt to clone protein tyrosine kinases, antiphosphotyrosine antibodies were used to screen lambda gt11 cDNA expression libraries. By this method, a 2.5-kilobase cDNA encoding a novel tyrosine kinase was isolated from a mouse liver cDNA library. This new gene is most closely related to the receptor tyrosine kinases ret, fms, and kit.
Rosacea-like demodicidosis associated with acquired immunodeficiency syndrome (2001)

We present a 35-year-old patient with acquired immunodeficiency syndrome who had demodicidosis on his face, characterized by multiple papules and papulopustules, associated pruritus, numerous mites on skin-surface biopsy and in biopsy specimens, and rapid response to topical treatment with permethrin. It seems likely that Demodex infestation does not manifest unless local or systemic immune function is altered, leading to the proliferation of the organism and subsequent disease.
Correspondence principle between anisotropic poroviscoelasticity and poroelasticity using micromechanics and application to compression of orthotropic rectangular strips (2012)

In this paper, the correspondence principle between poroviscoelasticity and poroelasticity in both time domain and Laplace transform domain is established for the general case of matrix anisotropy as well as solid constituent anisotropy using micromechanics considerations. Using this correspondence principle, any constitutive relation or formula for material coefficient of linear anisotropic poroviscoelasticity can be obtained from the corresponding expression in poroelasticity. Numerical examples of the complex behavior of the poroviscoelastic Biot’s effective stress coefficient for geomaterials and biomaterials are included as illustration. Moreover, analytical solutions for initial and boundary value problems in the Laplace transform domain in poroelasticity can now be readily transferred to poroviscoelasticity and vice versa. To illustrate this technique, analytical solutions for orthotropic poroelastic rectangular strips under either unconfined compression (Mandel’s problem) or confined compression (1D consolidation problem) subjected to either time-dependent force or time-dependent displacement loading have been derived and then transferred to poroviscoelasticity herein. Finally, a biomechanics analysis of laboratory testing on orthotropic articular cartilage illustrates the usefulness of the newly derived solutions.
Directed Evolution of Enantioselective Enzymes: Iterative Cycles of CASTing for Probing Protein‐Sequence Space (2006)

ReCASTing for success: The recently introduced method of combinatorial active-site saturation test (CAST) has been applied in iterative cycles in the directed evolution of enantioselective wild-type epoxide hydrolases (WT-EH).
Monokine-induced Neutrophil Chemotactic Factor Gene Expression in Human Fibroblasts (1989)

Although fibroblasts are important in providing a structural framework for most tissues, they also appear to be active participants in the inflammatory process via the production of specific mediators. The production of inflammatory mediators by fibroblasts is especially important in relation to their strategic location within connective tissue as they may act as a cellular communication bridge between the interstitium and vasculature. In this paper, we demonstrate that fibroblasts may participate in these inflammatory reactions by the production of a neutrophil chemotactic factor (NCF) with characteristics similar to a recently isolated and cloned monocyte-derived NCF. Either tumor necrosis factor-alpha-, interleukin-1 alpha-, or interleukin-1 beta-stimulated fibroblasts showed both a time- and dose-dependent increase in steady-state levels of NCF mRNA and secretion of chemotactic activity. In contrast, lipopolysaccharide and interleukin-6 failed to induce fibroblast-derived NCF. The expression of fibroblast-derived NCF mRNA was first detectable by 30 min poststimulation, whereas chemotactic activity was significantly observed 3-4 h postchallenge. Heat-inactivated monokine (100 degrees C) failed to induce NCF mRNA expression, suggesting that only the active proteins are capable of inducing NCF. Gel filtration analysis using high pressure liquid chromatography indicated peak chemotactic activity with an approximate molecular mass of 8000 daltons. This peak of NCF activity was found to be relatively stable to both heat and trypsin inactivation. Specificity of the fibroblast-derived neutrophil chemotactic activity was demonstrated with inhibition of chemotaxis by the addition of neutralizing antibody directed against recombinant human neutrophil chemotactic factor. These data provide evidence that monokine-treated fibroblasts can synthesize a potent chemotactic agent with molecular and physicochemical characteristics similar to monocyte-derived NCF and that this factor may contribute to neutrophil-mediated disease processes.
A chimeric Lym-1/interleukin 2 fusion protein for increasing tumor vascular permeability and enhancing antibody uptake. (1996)

A murine antihuman B-cell monoclonal antibody, Lym-1, has shown considerable promise for the treatment of human malignant lymphomas. To enhance its clinical potential, a genetically engineered fusion protein consisting of a chimeric Lym-1 (chLym-1) and interleukin 2 (IL-2) was tested for mediating cytotoxicity, increasing vasopermeability, and enhancing antibody uptake in human malignant lymphomas. The chLym-1/IL-2 fusion protein, which was expressed initially in a baculovirus system and more recently in the glutamine synthetase gene amplification system, was shown to be processed and assembled into a normal immunoglobulin monomer with two IL-2 molecules per antibody. It was found to be equivalent to the chLym-1 antibody in antigen-binding specificity and relative affinity. In addition, it maintains IL-2 cytokine activity as demonstrated by support of T-cell proliferation. Moreover, in antibody-dependent cellular cytotoxicity assays against Raji target cells, chLym-1/IL-2 had approximately 2-fold and 4-fold higher cytotoxicity than chLym-1 and murine Lym-1, respectively. Used as a pretreatment, chLym-1/IL-2 enhances the uptake of chLym-1 at the tumor site by altering the permeability of tumor vessels producing tumor:normal organ ratios of 420:1 for blood and 1708:1 for muscle at 3 days. The in vitro and in vivo activities of chLym-1/IL-2, therefore, suggest that this genetically engineered antibody fusion protein may represent a new immunotherapeutic reagent for the treatment of human malignant lymphomas.
Randomised trial of octreotide for long term management of cirrhosis after variceal haemorrhage (1997)

Long term octreotide may be a valuable adjuvant to endoscopic sclerotherapy for acute variceal haemorrhage in cirrhotic portal hypertension.
Protein synthesis in a device with nanoporous membranes and microchannels (2010)

Cell-free protein synthesis (CFPS) is an alternative approach to cell-based recombinant protein production. It involves in vitro transcription and translation in a cell-free medium. In this work, we implemented CFPS in a plastic array device. Each unit in the array consisted of an inner well and an outer well. Two synthesis steps, gene transcription and protein translation, took place in the inner well, in which a cell-free medium was used to provide ribosomes and additional components necessary for protein synthesis. The outer well was concentric to the inner well and it functioned as a nutrient reservoir. A nanoporous membrane was sandwiched between the inner and outer wells for retaining the synthesized proteins and removing the reaction byproducts. A microfluidic channel was employed to connect these two wells for supplying fresh nutrients for longer reaction time and higher expression yield. Synthesis of luciferase was shown to last 8 times longer and yield 10 times more proteins than in a conventional container. The device also enables more than 2 orders of magnitude reduction in reagent consumption compared to a bench-top instrument. The effects of the membrane pore size and microfluidic channel on the protein production yield were also studied. The array device has potential to become a platform for parallel protein expression for proteomics applications, matching high-throughput gene discovery.
Partitioning of Serpin-Proteinase Reactions between Stable Inhibition and Substrate Cleavage Is Regulated by the Rate of Serpin Reactive Center Loop Insertion into β-Sheet A (2000)

The serpin family of serine proteinase inhibitors is a mechanistically unique class of naturally occurring proteinase inhibitors that trap target enzymes as stable covalent acyl-enzyme complexes. This mechanism appears to require both cleavage of the serpin reactive center loop (RCL) by the proteinase and a significant conformational change in the serpin structure involving rapid insertion of the RCL into the center of an existing beta-sheet, serpin beta-sheet A. The present study demonstrates that partitioning between inhibitor and substrate modes of reaction can be altered by varying either the rates of RCL insertion or deacylation using a library of serpin RCL mutants substituted in the critical P(14) hinge residue and three different proteinases. We further correlate the changes in partitioning with the actual rates of RCL insertion for several of the variants upon reaction with the different proteinases as determined by fluorescence spectroscopy of specific RCL-labeled inhibitor mutants. These data demonstrate that the serpin mechanism follows a branched pathway, and that the formation of a stable inhibited complex is dependent upon both the rate of the RCL conformational change and the rate of enzyme deacylation.
LUZ-Y, a Novel Platform for the Mammalian Cell Production of Full-length IgG-bispecific Antibodies (2012)

The ability of bispecific antibodies to simultaneously bind two unique antigens has great clinical potential. However, most approaches utilized to generate bispecific antibodies yield antibody-like structures that diverge significantly from the structure of archetype human IgG, and those that do approach structural similarity to native antibodies are often challenging to engineer and manufacture. Here, we present a novel platform for the mammalian cell production of bispecific antibodies that differ from their parental mAbs by only a single point mutation per heavy chain. Central to this platform is the addition of a leucine zipper to the C terminus of the C(H)3 domain of the antibody that is sufficient to drive the heterodimeric assembly of antibody heavy chains and can be readily removed post-purification. Using this approach, we developed various antibody constructs including one-armed Abs, bispecific antibodies that utilize a common light chain, and bispecific antibodies that pair light chains to their cognate heavy chains via peptide tethers. We have applied this technology to various antibody pairings and will demonstrate the engineering, purification, and biological activity of these antibodies herein.
Apical and basal membrane ion transport mechanisms in bovine retinal pigment epithelium. (1991)

1. Intracellular voltage recordings using conventional and double-barrelled chloride-selective microelectrodes have been used to identify several transport mechanisms at the apical and basolateral membranes of the isolated bovine retinal pigment epithelium (RPE)-choroid preparation. Intracellular recordings were obtained from two cell populations, melanotic (pigmented) and amelanotic (non-pigmented). The electrical properties of these two populations are practically identical. For melanotic cells the average apical resting membrane potential (VA) is -61 +/- 2 mV (mean +/- S.E.M., n = 49 cells, thirty-three eyes). For these cells the ratio of apical to basolateral membrane resistance (a) was 0.22 +/- 0.02. The mean transepithelial voltage and resistance were 6 +/- 1 mV and 138 +/- 7 omega cm2, respectively. 2. The apical membrane, which faces the distal retina, contains a Ba(2+)-inhibitable K+ conductance and a ouabain-inhibitable, electrogenic Na(+)-K+ pump. In addition it contains a bumetanide-sensitive mechanism, the putative Na(+)-K(+)-Cl- cotransporter. The basolateral membrane contains a DIDS (4,4'-diisothiocyanostilbene-2,2'-disulphonic acid)-inhibitable chloride channel. The relative conductances of the apical and basolateral membranes to K+ and Cl- are TK approximately 0.9 and TCl approximately 0.7, respectively. 3. The ouabain-induced fast phase of apical membrane depolarization (0-30 s) was used to calculate the equivalent resistances of the apical (RA) and basolateral (RB) cell membranes, as well as the paracellular or shunt resistance (RS). They are: 3190 +/- 400, 17920 +/- 2730 and 2550 +/- 200 omega (mean +/- S.E.M., n = 9 tissues), respectively. From these data the equivalent electromotive forces (EMF) at the apical (EA) and basolateral (EB) membranes were also calculated. They are: -69 +/- 5.0 and -24 +/- 5.0 mV, respectively. 4. Intracellular Cl- activity (aiCl) was measured using double-barreled ion-selective microelectrodes. In the steady state aiCl = 61 +/- 4.0 mM and the Nernst potential ECl = -13.5 +/- 1.5 mV (mean +/- S.E.M., n = 4). 5. In the intact eye or in retina, RPE-choroid preparations it has been shown that the transition between light and dark alters the K+ concentration in the extracellular (or subretinal) space between the photoreceptors and the apical membrane of the RPE. These light-induced changes in subretinal [K+]o were qualitatively simulated in vitro by altering apical K+ between 5 and 2 mM. This produced a sequence of voltage changes at the apical and basolateral membranes that had three operationally distinct phases. Phase 1 is generated by the combination of an apical membrane K+ diffusion potential and inhibition of the electrogenic Na(+)-K+ pump.(ABSTRACT TRUNCATED AT 400 WORDS)
Constitutive expression of high affinity interleukin 2 receptors on human CD16-natural killer cells in vivo. (1990)

The majority of human NK cells express low affinity IgG Fc receptors (CD16+), whereas a minor subset of NK cells lack Fc receptor expression (CD16-). In contrast to CD16+ NK cells that express only p75 IL-2 receptors, CD16- NK cells constitutively co-express both p75 and p55 IL-2 receptors in vivo and preferentially respond to low concentrations of IL-2 with increased cytolytic activation and proliferation. Scatchard analysis demonstrated the presence of approximately 1,200 high affinity (approximately 25 pM kD) and approximately 9,600 intermediate affinity (approximately 2 nM kD) IL-2 receptors on CD16- NK cells. CD16+ NK cells expressed only a single intermediate affinity IL-2 receptor of approximately 1.9 nM kD (approximately 9,000 sites per cell). The IL-2 binding data thus substantiated the phenotypic and functional studies and definitively show that the differential responsiveness of CD16- and CD16+ NK cells to IL-2 is manifested through different affinity IL-2 receptors.
Simultaneous measurement of temperature and strain based on arc-induced long-period fibre gratings (2005)

A study on arc-induced long-period fibre gratings (LPFGs) revealed that their strain sensitivity depends on the electric current of the arc discharge. Based on that property, a sensor scheme comprising two concatenated LPFGs was implemented for discrimination of temperature and strain effects. This sensor presented resolutions of ±0.1°C/√Hz and ±35 µɛ/√Hz, respectively.
Laser ablation of aluminum from normal evaporation to phase explosion (2009)

A study of laser ablation of Aluminum sample by nanosecond laser pulses considering two simultaneous mechanisms of normal evaporation and phase explosion is theoretically carried out. The temperature distribution in the sample is calculated by a one dimensional heat conduction equation. Ablation depth due to the evaporation and explosion is calculated as a function of laser pulse energies. Variation in some effective sample parameters during the laser ablation and their effects on laser ablation mechanisms are taken into account. At low irradiance, ablation is mainly due to the evaporation, while after a threshold intensity, the phase explosion becomes the dominant mechanism. Theoretical results of transition from the normal evaporation to the phase explosion are in good agreement with the experimental results.
Combining Calcium Imaging with Other Optical Techniques (2013)

Ca 2+ imaging is a commonly used approach for measuring Ca 2+ signals at high spatial resolution. The method is often combined with electrode recordings to correlate electrical and chemical signals or to investigate Ca 2+ signals following an electrical stimulation. To obtain information on electrical activity at the same spatial resolution, Ca 2+ imaging must be combined with membrane potential imaging. Similarly, stimulation of subcellular compartments requires photostimulation. Thus, combining Ca 2+ imaging with an additional optical technique facilitates the study of a number of physiological questions. The aim of this article is to introduce some basic principles regarding the combination of Ca 2+ imaging with other optical techniques. We discuss the design of the optics, the design of experimental protocols, the optical characteristics of Ca 2+ indicators used in combination with an optical probe, and the affinity of the Ca 2+ indicator in relation to the type of measurement. This information will enable the reader to devise an optimal strategy for combined optical experiments.
Correlation between cathepsin D expression and p53 protein nuclear accumulation in oesophageal squamous cell carcinoma (2002)

The expression of cathepsin D by cancer cells may play an important role in the invasive growth of oesophageal SCC. Overexpression of both p53 and cathepsin D was seen frequently in tumours; p53 gene abnormalities may correlate with cathepsin D overexpression in oesophageal SCC.
Selective drop-out in longitudinal studies and non-biased prediction of behaviour disorders (2009)

Cohort studies are prone to selective drop-out and are likely to underestimate the prevalence of psychiatric disorder. This empirical study and the simulations confirm that the validity of regression models is only marginally affected despite range restrictions after selective drop-out.
Expression of an exogenous interleukin 6 gene in human Epstein Barr virus B cells confers growth advantage and in vivo tumorigenicity. (1990)

The biological role of interleukin 6 (IL-6) molecules in human B cell tumorigenesis was studied by using an episomal expression vector, pHEBoSV-IL6, to introduce stably the human IL-6 gene into human Epstein Barr virus (EBV)-transformed B lymphoblasts. The gene was present in the IL-6-transfected cells in a high copy number and was efficiently expressed, resulting in the secretion of consistent levels of IL-6 molecules. The constitutive expression of the IL-6 gene led to an altered pattern of growth and to a malignant phenotype, as shown by clonogenicity in to an altered pattern of growth and to a malignant phenotype, as shown by clonogenicity in soft agar cultures and tumorigenicity in nude mice. These data suggest that the combined action of EBV, which exerts an immortalizing function, and of the growth-promoting activity of IL-6 molecules, can give rise to fully transformed B cell tumors in immunodeficient subjects.
Antiplatelet action of R‐99224, an active metabolite of a novel thienopyridine‐type Gi‐linked P2T antagonist, CS‐747 (2001)

1. CS-747 is a novel thienopyridine-type platelet ADP inhibitor which lacks in vitro activity. This study examined pharmacological profiles of R-99224, a hepatic metabolite of CS-747. 2. R-99224 produced a concentration-dependent inhibition of in vitro platelet aggregation in washed human platelets (0.03 - 1 microg ml(-1)), which was relatively specific to ADP compared to collagen and thrombin. 3. R-99224 (0.1 - 3 microg ml(-1)) also elicited a similar inhibition of ADP-induced aggregation in rat platelets. The inhibition by R-99224 (10 microg ml(-1)) persisted even after platelets were washed three times. Intravenous injection of R-99224 (0.1 - 3 mg kg(-1)) to rats resulted in a dose-dependent inhibition of ex vivo ADP-induced platelet aggregation. 4. R-99224 (0.1 - 100 microM) decreased binding of [(3)H]-2-methylthio-ADP ([(3)H]-2-MeS-ADP), a stable ligand for platelet ADP receptors, to washed human platelets. The inhibition by R-99224 reached a plateau at a concentration of 3 microM (1.4 microg ml(-1)), but complete inhibition was not achieved even at the highest concentration used (100 microM). 5. R-99224 (10 microM) in combination with ARL-66096 (0.3 microM), an ATP analogue-type G(i)-linked P2T receptor antagonist, produced no additional inhibition of [(3)H]-2-MeS-ADP binding. In contrast, [(3)H]-2-MeS-ADP binding was completely abolished by R-99224 (10 microM) in combination with A3P5PS (300 microM), a selective P2Y(1) antagonist, suggesting that R-99224 selectively binds to the G(i)-linked P2T receptor. 6. R-99224 (0.01 - 3 microg ml(-1)) inhibited ADP-induced [(125)I]-fibrinogen binding to human platelets in a concentration-dependent manner. R-99224 (0.1 - 1 microg ml(-1)) also inhibited the ADP-induced decrease in cyclic AMP levels in PGE(1)-stimulated platelets, whereas the agent did not affect ADP (10 microM)-induced Ca(2+) mobilization. 7. These findings suggest that R-99224 is a selective and irreversible antagonist of G(i)-linked P2T receptors and that R-99224 is a responsible molecule for in vivo actions of CS-747.
Inhibition of Inflammatory and Neuropathic Pain by Targeting a Mu Opioid Receptor/Chemokine Receptor5 Heteromer (MOR-CCR5) (2015)

Chemokine release promotes cross-talk between opioid and chemokine receptors that in part leads to reduced efficacy of morphine in the treatment of chronic pain. On the basis of the possibility that a MOR-CCR5 heteromer is involved in such cross-talk, we have synthesized bivalent ligands (MCC series) that contain mu opioid agonist and CCR5 antagonist pharmacophores linked through homologous spacers (14-24 atoms). When tested on lipopolysaccharide-inflamed mice, a member of the series (MCC22; 3e) with a 22-atom spacer exhibited profound antinociception (i.t. ED50 = 0.0146 pmol/mouse) that was 2000× greater than morphine. Moreover, MCC22 was ~3500× more potent than a mixture of mu agonist and CCR5 antagonist monovalent ligands. These data strongly suggest that MCC22 acts by bridging the protomers of a MOR-CCR5 heteromer having a TM5,6 interface. Molecular simulation studies are consistent with such bridging. This study supports the MOR-CCR5 heteromer as a novel target for the treatment of chronic pain.