gebhart/patrepeval huggingface dataset:
Protein Organic Chemistry and Applications for Labeling and Engineering in Live‐Cell Systems (2013)

The modification of proteins with synthetic probes is a powerful means of elucidating and engineering the functions of proteins both in vitro and in live cells or in vivo. Herein we review recent progress in chemistry-based protein modification methods and their application in protein engineering, with particular emphasis on the following four strategies: 1) the bioconjugation reactions of amino acids on the surfaces of natural proteins, mainly applied in test-tube settings; 2) the bioorthogonal reactions of proteins with non-natural functional groups; 3) the coupling of recognition and reactive sites using an enzyme or short peptide tag-probe pair for labeling natural amino acids; and 4) ligand-directed labeling chemistries for the selective labeling of endogenous proteins in living systems. Overall, these techniques represent a useful set of tools for application in chemical biology, with the methods 2-4 in particular being applicable to crude (living) habitats. Although still in its infancy, the use of organic chemistry for the manipulation of endogenous proteins, with subsequent applications in living systems, represents a worthy challenge for many chemists.
The Position of the Polycystic Kidney Disease 1 (PKD1) Gene Mutation Correlates with the Severity of Renal Disease (2002)

The severity of renal cystic disease in the major form of autosomal dominant polycystic kidney disease (PKD1) is highly variable. Clinical data was analyzed from 324 mutation-characterized PKD1 patients (80 families) to document factors associated with the renal outcome. The mean age to end-stage renal disease (ESRD) was 54 yr, with no significant difference between men and women and no association with the angiotensin-converting enzyme polymorphism. Considerable intrafamilial variability was observed, reflecting the influences of genetic modifiers and environmental factors. However, significant differences in outcome were also found among families, with rare examples of unusually late-onset PKD1. Possible phenotype/genotype correlations were evaluated by estimating the effects of covariants on the time to ESRD using proportional hazards models. In the total population, the location of the mutation (in relation to the median position; nucleotide 7812), but not the type, was associated with the age at onset of ESRD. Patients with mutations in the 5' region had significantly more severe disease than the 3' group; median time to ESRD was 53 and 56 yr, respectively (P = 0.025), with less than half the chance of adequate renal function at 60 yr (18.9% and 39.7%, respectively). This study has shown that the position of the PKD1 mutation is significantly associated with earlier ESRD and questions whether PKD1 mutations simply inactivate all products of the gene.
Establishment of human endometrial cell cultures (1988)

Epithelial and stromal endometrial cells from 19 patients at different phases of the menstrual cycle were enzymatically separated, isolated by successive centrifugation and primary cultures established for in-vitro studies on implantation. The behaviour of cells in vitro was evaluated using Nomarski's inverted optics, May-Grunwald-Giemsa stained coverslips and scanning electron microscopy. Epithelial and stromal cells from all patients grew successfully in Chang's medium and formed a mixed confluent monolayer of epithelioid and fibroblastic cells in 3-7 days and such monolayers could be maintained alive up to 3-4 weeks. Epithelioid cells were polyhedral and grew as islands in a whorl-like wavy pattern around glandular fragments. Fibroblasts were spindle-shaped, more long-lived and grew rapidly to form parallel bundles of cells. Significant differences were observed in the number of multinucleated cells and cells with intracytoplasmic vacuoles between endometrium from proliferative, postovulatory and secretory phases (P less than 0.01). Scanning electron micrographs showed cells with cilia with varying densities of microvilli and apical protrusions. Endometrial cells in culture showed structural features remarkably similar to those described for cells in situ. The method described allows the propagation in vitro of separate endometrium cell types which can be used to study implantation mechanisms in unstimulated and stimulated cycles.
Immunodominant Domains Present on theBordetella pertussisVaccine Component Filamentous Hemagglutinin (1997)

To identify immunologically important domains on filamentous hemagglutinin (FHA), a Bordetella pertussis protein included in new acellular pertussis vaccines (ACPVs), a series of monoclonal antibodies, sera from infants vaccinated with ACPVs or whole cell pertussis vaccine (WCPV), and sera from patients with pertussis were analyzed by immunoblots containing FHA fragments and recombinant FHA proteins. Immunodominant domains located at the COOH-terminus of FHA (type I domain) and near the NH2-terminus (type II domain) were defined by the reactivity with monoclonal antibodies. The sera from patients with pertussis and sera from infants vaccinated with WCPV or with 6 different investigational ACPVs specifically recognized well-defined regions within the type I and type II domains. Identification of these prominent immunologic epitopes on FHA should be useful for the construction of more well-defined pertussis vaccines and for the interpretation of human serologic responses, which may correlate with efficacy of pertussis vaccines.
Functional analysis of 44 mutant androgen receptors from human prostate cancer. (2002)

Mutations of the androgen receptor gene are believed to contribute to the androgen-independent growth of prostate cancer cells. To date, 56 missense mutations of the androgen receptor have been identified in human prostate cancer. The functional status of most of these mutants has not yet been investigated. To address their functional properties, we generated 44 androgen receptor mutants that have been identified in human prostate cancer and used a colorimetric yeast reporter assay to analyze their transactivational activities in response to seven different ligands. We found that these mutant androgen receptors exhibited diverse transactivational activity: seven (16%) showed loss of function, three (7%) had wild-type function, 14 (32%) had partial function, and 20 (45%) had gains of function. Five of 20 gain-of-function mutants had promiscuous activity, being transactivated by non-androgens. We also found that the combination of estradiol and progesterone at physiological concentrations weakly or moderately activated an additional seven mutant androgen receptors. Our findings provide essential information for understanding the role of mutant androgen receptors in prostate cancer.
The DPP4 Inhibitor Linagliptin Protects from Experimental Diabetic Retinopathy (2016)

Our data suggest that linagliptin has a protective effect on the microvasculature of the diabetic retina, most likely due to a combination of neuroprotective and antioxidative effects of linagliptin on the neurovascular unit.
Nanoscale Imaging of Whole Cells Using a Liquid Enclosure and a Scanning Transmission Electron Microscope (2009)

Nanoscale imaging techniques are needed to investigate cellular function at the level of individual proteins and to study the interaction of nanomaterials with biological systems. We imaged whole fixed cells in liquid state with a scanning transmission electron microscope (STEM) using a micrometer-sized liquid enclosure with electron transparent windows providing a wet specimen environment. Wet-STEM images were obtained of fixed E. coli bacteria labeled with gold nanoparticles attached to surface membrane proteins. Mammalian cells (COS7) were incubated with gold-tagged epidermal growth factor and fixed. STEM imaging of these cells resulted in a resolution of 3 nm for the gold nanoparticles. The wet-STEM method has several advantages over conventional imaging techniques. Most important is the capability to image whole fixed cells in a wet environment with nanometer resolution, which can be used, e.g., to map individual protein distributions in/on whole cells. The sample preparation is compatible with that used for fluorescent microscopy on fixed cells for experiments involving nanoparticles. Thirdly, the system is rather simple and involves only minimal new equipment in an electron microscopy (EM) laboratory.
cis-Disubstituted Cyclopropanesvia Asymmetric Catalytic Cyclopropenation: Synthesis of Cyclopropyl-dehydroamino Acids and of Dictyopterene C′ (1998)

The cyclopropenation of diethoxypropyne (1) with methyl diazoacetate in the presence of [Rh2{(2S)-mepy}4] (mepy=methyl 5-oxopyrrolidine-2-carboxylate) proceeds with >95% ee. The resulting cyclopropenecarboxylate 2 underwent stereoselective hydrogenation to the cis-cyclopropane 3. Hydrolysis of the acetal function of 3 liberated the formyl cyclopropenecarboxylate 4, which was transformed by Wittig reaction with the phosphonate 5 to afford dehydroamino acid 6 as a mixture of (Z)- and (E)-isomers in various proportions. The (Z)-isomer 6a was hydrolyzed, and the structure and the absolute configuration of the (Z)-dicarboxylic acid 7a were established by X-ray crystallography. The cis-divinylcyclopropane 11 (ee>95%), in turn, was synthesized from 4 via Wittig reaction to afford 8, which was transformed to the aldehyde 10 and subjected to a second Wittig reaction. Thermolysis of 11 afforded (+)-dictyopterene C′ (12) in quantitative yield.
Angiogenesis research: from laboratory to clinic. (2000)

Accumulating experimental evidence demonstrates that tumour growth and lethality are dependent on angiogenesis. When angiogenesis is inhibited by administering molecules which specifically suppress the growth of vascular endothelial cells, tumours in animals can be limited to a dormant microscopic size where they are essentially harmless. The most recent evidence that vascular endothelial cells exert potent growth control over tumour cells comes from the following studies, i. administration of an angiogenesis inhibitor specific for proliferating vascular endothelium in the tumour bed; ii. optimisation of the dose and schedule of conventional cytotoxic chemotherapy for the vascular endothelium; iii. targeting of low dose cytotoxic chemotherapy only to the vascular endothelium in the tumour bed; or iv. sensitisation of vascular endothelium in the tumour bed to radiotherapy by co-administration of an angiogenesis inhibitor. In the future, anti-angiogenic therapy may be added to conventional chemotherapy, radiotherapy, immunotherapy or other novel modalities such as gene therapy. Also, angiogenesis inhibitors may be administered together for increased efficacy. The overall goal of anti-angiogenic therapy is to reduce toxicity, reduce the risk of drug resistance and to increase anti-cancer efficacy.
Comparison of the polyphenolic composition and antioxidant activity of European commercial fruit juices (2010)

Thirty six commercial European fruit juices were tested to ascertain their antioxidant capacity and polyphenolic composition. Six of the products were labelled 100% pomegranate juice, the others included 20 brands of diluted pomegranate juice or pomegranate blended with other fruit juices and 10 different non-pomegranate fruit juices. The antioxidant capacity of all the juices was determined while anthocyanin, ellagitannin and ellagic acid profiles of the 26 pomegranate juices and pomegranate juice blends were obtained using HPLC-PDA-MS(2). Additional analysis was conducted on seven of the juices using HPLC with an on-line antioxidant detection system. Three of the "pure" pomegranate juices had the highest ellagitannin content and the highest antioxidant capacity. Only one of these three juices was rich in anthocyanins. The other "pure juices" had differences in their HPLC "pomegranate" fingerprint and also had a lower antioxidant capacity, in some cases lower than that of some of the blended juices. Vitamin C rather than phenolic compounds was the major contributor to the antioxidant capacity for some of the juices. Statistical analysis of both the antioxidant assay and the HPLC on-line antioxidant data demonstrated that the ellagitannins were the major antioxidants in the pomegranate juices. The complexity of the polyphenolic profile of pomegranates necessitates the use of HPLC-PDA-MS(2) for a thorough evaluation of juice composition and authenticity.
A white paper describing produced water from production of crude oil, natural gas, and coal bed methane. (2004)

One of the key missions of the U.S. Department of Energy (DOE) is to ensure an abundant and affordable energy supply for the nation. As part of the process of producing oil and natural gas, operators also must manage large quantities of water that are found in the same underground formations. The quantity of this water, known as produced water, generated each year is so large that it represents a significant component in the cost of producing oil and gas. Produced water is water trapped in underground formations that is brought to the surface along with oil or gas. It is by far the largest volume byproduct or waste stream associated with oil and gas production. Management of produced water presents challenges and costs to operators. This white paper is intended to provide basic information on many aspects of produced water, including its constituents, how much of it is generated, how it is managed and regulated in different settings, and the cost of its management.
Circulatory Disturbances after Experimental Fracture (1975)

Early hemodynamic and angiographic effects after fracture with a minimum of soft tissue injury were investigated in anesthetized dogs. A close relation between hemodynamic and angiographic findings was observed. The fracture procedure did not change the regional blood flow in the soft tissues outside the bone in the injured extremity.
Cross-national epidemiology of DSM-IV major depressive episode (2011)

MDE is a significant public-health concern across all regions of the world and is strongly linked to social conditions. Future research is needed to investigate the combination of demographic risk factors that are most strongly associated with MDE in the specific countries included in the WMH.
A Novel Approach to Indoor RSSI Localization by Automatic Calibration of the Wireless Propagation Model (2009)

We propose a novel localization algorithm of mobile sensors based on wireless sensor networks providing RSSI measurements between the mobile and the fixed sensors (anchors) in the network. The algorithm selects and weights the RSSI measurements according to their strength, and it uses a propagation model to transform RSSI measurements into distances, in order to estimate the position of the mobile. The algorithm also uses a virtual calibration method of the propagation model that does not require human intervention. By an experimental setup we show that the localization algorithm increases the performance with respect to the commonly used least mean square algorithm showing also how to achieve a wished accuracy increasing the anchor density.
The Physicochemical Characteristics of Freeze-Dried Scutellarin-Cyclodextrin Tetracomponent Complexes (2005)

In an effort to improve the solubility of the insoluble drug scutellarin, a novel complexation of scutellarin with beta-cyclodextrin (beta-CD) was studied. Tetracomponent freeze-dried complex was prepared with scutellarin, beta-CD, Hydroxypropyl Methylcellulose (HPMC), and triethanolamine. To confirm complex formation, complex was characterized by Fourier transform infrared spectroscopy (FT-IR), powder X-ray diffraction, and differential scanning calorimetry (DSC). Phase-solubility analysis suggested the soluble complexes having 1:1 stoichiometry. The beta-CD solubilization of scutellarin could be improved significantly by combining water-soluble polymer and pH adjuster. Comparing the binary, ternary solid systems with tetrary systems, tetracomponent freeze-dried complex showed the best effect of solubilization. A maximal solubility of scutellarin (23.65 mg/ml) was achieved with tetracomponent freeze-dried complex, up to 148-fold increase over scutellarin solubility in water, and the solubility of scutellarin is 15.35 microg/ml (up to 6-fold) in simulated gastric fluid.
Pharmacological Inhibitors of the NLRP3 Inflammasome (2019)

Inflammasomes play a crucial role in innate immunity by serving as signaling platforms which deal with a plethora of pathogenic products and cellular products associated with stress and damage. By far, the best studied and most characterized inflammasome is NLRP3 inflammasome, which consists of NLRP3 (nucleotide-binding domain leucine-rich repeat (NLR) and pyrin domain containing receptor 3), ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain), and procaspase-1. Activation of NLRP3 inflammasome is mediated by highly diverse stimuli. Upon activation, NLRP3 protein recruits the adapter ASC protein, which recruits the procaspase-1 resulting in its cleavage and activation, inducing the maturation, and secretion of inflammatory cytokines and pyroptosis. However, aberrant activation of the NLRP3 inflammasome is implicated in various diseases including diabetes, atherosclerosis, metabolic syndrome, cardiovascular, and neurodegenerative diseases; raising a tremendous clinical interest in exploring the potential inhibitors of NLRP3 inflammasome. Recent investigations have disclosed various inhibitors of the NLRP3 inflammasome pathway which were validated through <i>in vitro</i> studies and <i>in vivo</i> experiments in animal models of NLRP3-associated disorders. Some of these inhibitors directly target the NLRP3 protein whereas some are aimed at other components and products of the inflammasome. Direct targeting of NLRP3 protein can be a better choice because it can prevent off target immunosuppressive effects, thus restrain tissue destruction. This paper will review the various pharmacological inhibitors of the NLRP3 inflammasome and will also discuss their mechanism of action.
Development of Phosphorylated Glucomannan-Coated Chitosan Nanoparticles as Nanocarriers for Protein Delivery (2006)

The aim of the present work was to develop a new nanoparticle carrier, adapted for the oral administration of proteins and their delivery to the immune system. Chitosan and phosphorylated glucomannan were chosen as major constituents of the nanoparticles. Chitosan nanoparticles were formed by ionic gelation and then coated with glucomannan. Two different protocols were adopted for the formation of the glucomannan coating: protocol I, in which chitosan nanoparticles were isolated before their coating; protocol II, in which chitosan nanoparticles were not isolated, but coated with glucomannan in the presence of free chitosan. The results showed that, under the selected formulation conditions, the sizes of the nanoparticles ranged between 170 and 300 nm and their zeta potential values were inverted from positive to negative by the glucomannan coating. The nanoparticles prepared by the two protocols could be freeze-dried, in the presence or absence of cryoprotective agents, preserving their original characteristics. The results of the stability study evidenced the positive role of the glucomannan coating in preventing the aggregation of the nanoparticles in buffered media. Finally, the association of the inmunomodulatory protein complex P1 to the chitosan-glucomannan nanoparticles was investigated. The results showed that the association was not dependent on the chitosan: sodium tripoliphosphate ratio, but it was significantly affected by the presence of sodium phosphate in the protein structure.
Protein resistant surfaces: Comparison of acrylate graft polymers bearing oligo-ethylene oxide and phosphorylcholine side chains (2006)

The objective of this work was to compare poly(ethylene glycol) (PEG) and phosphorylcholine (PC) moieties as surface modifiers with respect to their ability to inhibit protein adsorption. Surfaces were prepared by graft polymerization of the methacrylate monomers oligo(ethylene glycol) methyl ether methacrylate (OEGMA, MW 300, PEG side chains of length n=4.5) and 2-methacryloyloxyethyl phosphorylcholine (MPC, MW 295). The grafted polymers thus contained short PEG chains and PC, respectively, as side groups. Grafting on silicon was carried out using surface-initiated atom transfer radical polymerization (ATRP). Graft density was controlled via the surface density of the ATRP initiator, and chain length of the grafts was controlled via the ratio of monomer to sacrificial initiator. The grafted surfaces were characterized by water contact angle, x-ray photoelectron spectroscopy, and atomic force microscopy. The effect of graft density and chain length on fibrinogen adsorption from buffer was investigated using radio labeling methods. Adsorption to both MPC- and OEGMA-grafted surfaces was found to decrease with increasing graft density and chain length. Adsorption on the MPC and OEGMA surfaces for a given chain length and density was essentially the same. Very low adsorption levels of the order of 7 ngcm(2) were seen on the most resistant surfaces. The effect of protein size on resistance to adsorption was studied using binary solutions of lysozyme (MW 14 600) and fibrinogen (MW 340 000). Adsorption levels in these experiments were also greatly reduced on the grafted surfaces compared to the control surfaces. It was concluded that at the lowest graft density, both proteins had unrestricted access to the substrate, and the relative affinities of the proteins for the substrate (higher affinity of fibrinogen) determined the composition of the layer. At the highest graft density also, where the adsorption of both proteins was very low, no preference for one or the other protein was evident, suggesting that adsorption did not involve penetration of the grafts and was occurring at the outer surface of the graft layer. It thus seems likely that preference among different proteins based on ability to penetrate the graft layer would occur, if at all, at a grafting density intermediate between 0.1 and 0.39 cm(2). Again the MPC and OEGMA surfaces behaved similarly. It is suggested that the main determinant of the protein resistance of these surfaces is the "water barrier layer" resulting from their hydrophilic character. In turn the efficacy of the water barrier depends on the monomer density in the graft layer.
Characterization of hematopoietic progenitor cells that express the transcription factor SCL, using a lacZ “knock-in” strategy (1998)

Gene targeting experiments have demonstrated that the transcription factor SCL is essential for primitive and definitive hematopoiesis in the mouse. To study the functional properties of hematopoietic cells expressing SCL, we have generated mutant mice (SCLlacZ/w) in which the Escherichia coli lacZ reporter gene has been "knocked in" to the SCL locus, thereby linking beta-galactosidase expression to transcription from the SCL promoter. Bone marrow cells from heterozygous SCLlacZ/w mice were sorted into fractions expressing high, intermediate and low levels of beta-galactosidase (designated lacZhigh, lacZint, and lacZneg). Cells that were lacZhigh or lacZint were enriched for day 12 spleen colony-forming units and myeloid and erythroid colony-forming cells (CFCs). These fractions included >99% of the erythroid and >90% of the myeloid CFCs. Culture of sorted bone marrow populations on stromal cells secreting interleukin-7 or in fetal thymic organ cultures showed that B and T lymphoid progenitors were also present in the lacZhigh and lacZint fractions. These data provide a functional correlation between SCL expression and colony-forming ability in immature hematopoietic cells. Our data also suggested that expression of SCL was transient and confined to hematopoietic stem and/or progenitor cells, because the differentiated progeny of most lineages (except the erythroid) were beta-galactosidase-negative.