gebhart/patrepeval huggingface dataset:
High-sensitivity, disposable lab-on-a-chip with thin-film organic electronics for fluorescence detection (2008)

We report a high-sensitivity, disposable lab-on-a-chip with a thin-film organic light-emitting diode (OLED) excitation source and an organic photodiode (OPD) detector for on-chip fluorescence analysis. A NPB/Alq3 thin-film green OLED with an active area of 0.1 cm(2) was used as the excitation source, while a CuPC/C(60) thin-film OPD with 0.6 cm(2) active area was used as a photodetector. A novel cost-effective, cross-polarization scheme was used to filter out excitation light from a fluorescent dye emission spectrum. The excitation light from the OLED was linearly polarized and used to illuminate a microfluidic device containing a 1 microL volume of dye dissolved in ethanol. The detector was shielded by a second polarizer, oriented orthogonally to the excitation light, thus reducing the photocurrent due to excitation light leakage on the detector by approximately 25 dB. The fluorescence emission light, which is randomly polarized, is only attenuated by approximately 3 dB. Fluorescence signals from Rhodamine 6G (peak emission wavelength of 570 nm) and fluorescein (peak emission wavelength of 494 nm) dyes were measured in a dilution series in the microfluidic device with emission signals detected by the OPD. A limit-of-detection of 100 nM was demonstrated for Rhodamine 6G, and 10 microM for fluorescein. This suggests that an integrated microfluidic device, with an organic photodiode and LED excitation source and integrated polarizers, can be fabricated to realize a compact and economical lab-on-a-chip for point-of-care fluorescence assays.
Phosphate Sorption-Desorption Characteristics of some Ustifluvents of Punjab (2004)

A laboratory study conducted on 19 soils collected from flood plain areas of Punjab showed that the amount of phosphate sorption and desorption increased with increase in amount of P added and it varied with various soil properties viz. clay, CaCO3, Fe and Al oxides etc. Most of these soils were adsorbing more than 150 mg P kg−1 soil. Sorption parameters such as sorption maxima, buffering capacity and bonding energy constant related mainly to CaCO3, free Fe oxides, silt, clay and exchangeable Mg. The values of mobility constant (Kd) correlated significantly with clay (r = 0.467*), exchangeable Ca (r = 0.503*) and exchangeable Mg (r =0.648**). Organic carbon (r = 0.870**) and exchangeable Fe (r = 0.680**) showed highly significant relationship with maximum phosphate desorption (Dm). Supply parameter, maximum buffering capacity and bonding energy constant are important sorption parameters which control P availability to berseem in these soils.
Replacement of Threonine 558, a Critical Site of Phosphorylation of Moesin in Vivo, with Aspartate Activates F-actin Binding of Moesin (1999)

Point and deletion mutants of moesin were examined for F-actin binding by blot overlay and co-sedimentation, and for intra- and intermolecular interactions with N- and C-terminal domains with yeast two-hybrid and in vitro binding assays. Wild-type moesin molecules interact poorly with F-actin and each other, and bind neither C- nor N-terminal fragments. Interaction with F-actin is strongly enhanced by replacement of Thr558 with aspartate (T558D), by deletion of 11 N-terminal residues (DelN11), by deletion of the entire N-terminal membrane-binding domain of both wild type and T558D mutant molecules, and by exposure to phosphatidylinositol 4, 5-diphosphate. Activation of F-actin binding is accompanied by changes in inter- and intramolecular domain interactions. The T558D mutation renders moesin capable of binding wild type but not mutated (T558D) C-terminal or wild type N-terminal fragments. The interaction between the latter two is prevented. DelN11 truncation enables binding of wild type N and C domain fragments. These changes suggest that the T558D mutation, mimicking phosphorylation of Thr558, promotes F-actin binding by disruption of interdomain interactions between N and C domains and exposure of the high affinity F-actin binding site in the C-terminal domain. Oscillation between activated and resting state could thus provide the structural basis for transient interactions between moesin and the actin cytoskeleton in protruding and retracting microextensions.
Etanercept and efalizumab for the treatment of psoriasis: a systematic review (2006)

Clinical trial data indicate that both etanercept and efalizumab are efficacious in patients who are eligible for systemic therapy, but the economic evaluation demonstrates that these biological therapies are likely to be cost-effective only in patients with poor baseline QoL and who are at risk of hospitalisation. Efficacy trials conducted in the specific population for which etanercept and efalizumab are licensed are required, as are long-term comparisons of etanercept and efalizumab with other treatments for moderate to severe psoriasis. Long-term efficacy trials and safety/tolerability data for patients treated with etanercept or efalizumab are required, as are trials on the response of specific subtypes of psoriasis to different drugs. Research on the rate of inpatient hospitalisation in patients with moderate to severe psoriasis is warranted, and the effect of treatment on this rate.
STITCH: interaction networks of chemicals and proteins (2007)

The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH ('search tool for interactions of chemicals') integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/.
Apoptosis in podocytes induced by TGF-β and Smad7 (2001)

Primary and secondary forms of focal segmental glomerulosclerosis (FSGS) are characterized by depletion of podocytes and constitute a central manifestation of chronic progressive glomerular diseases. Here we report that podocytes undergo apoptosis at early stages in the course of progressive glomerulosclerosis in TGF-beta1 transgenic mice. Apoptosis is associated with progressive depletion of podocytes and precedes mesangial expansion. Smad7 protein expression is strongly induced specifically in damaged podocytes of transgenic mice and in cultured murine podocytes treated with TGF-beta. TGF-beta1 and Smad7 each induce apoptosis in podocytes, and their coexpression has an additive effect. Activation of p38 MAP kinase and caspase-3 is required for TGF-beta-mediated apoptosis, but not for apoptosis induced by Smad7. Unlike TGF-beta, Smad7 inhibits nuclear translocation and transcriptional activity of the cell survival factor NF-kappaB. Our results suggest a novel functional role for Smad7 as amplifier of TGF-beta-induced apoptosis in podocytes and a new pathomechanism for podocyte depletion in progressive glomerulosclerosis.
Use of modified diatomaceous earth for removal and recovery of viruses in water (1991)

Diatomaceous earth was modified by in situ precipitation of metallic hydroxides. Modification decreased the negative charge on the diatomaceous earth and increased its ability to adsorb viruses in water. Electrostatic interactions were more important than hydrophobic interactions in virus adsorption to modified diatomaceous earth. Filters containing diatomaceous earth modified by in situ precipitation of a combination of ferric chloride and aluminum chloride adsorbed greater than 80% of enteroviruses (poliovirus 1, echovirus 5, and coxsackievirus B5) and coliphage MS2 present in tap water at ambient pH (7.8 to 8.3), even after filtration of 100 liters of tap water. Viruses adsorbed to the filters could be recovered by mixing the modified diatomaceous earth with 3% beef extract plus 1 M NaCl (pH 9).
Expression of β2-Adrenergic Receptor in Oral Squamous Cell Carcinoma. (2008)

Objective: To investigate the expression and possible roles of β2-adrenergic receptor(β2-AR) in tumor development and metastasis in oral squamous cell carcinoma(OSCC).Methods: By using immunohistochemistry,Western blot and RT-PCR,expression of β2-AR was examined in 65 cases of OSCC,10 cases of normal oral mucosa,and Tca8113 cell line.The differences were statistically evaluated between β2-AR expression and various clinicopathological factors.Results: It revealed a significant different positive β2-AR expression between OSCC and normal controls(P=0.004).In OSCC,positive β2-AR expression was 85.3% in metastasis group vs.48.3% in non-metastasis group(P=0.001).RT-PCR and Western blot also confirmed positive β2-AR expression in OSCC and Tca8113 cell line,and negative β2-AR expression in normal oral mucosa.Conclusion: Increased expression of β2-AR may play an important role in the formation and metastasis of oral squamous cell carcinoma.
THE ROLE OF URINARY POTASSIUM IN THE PATHOGENESIS AND DIAGNOSIS OF INTERSTITIAL CYSTITIS (1998)

Chronic diffusion of urinary potassium into the bladder interstitium may induce sensory symptoms, damage tissue and be a major toxic factor in the pathogenesis of interstitial cystitis. Intravesical potassium sensitivity is a reliable method for detecting abnormal epithelial permeability. It discriminates between patients with interstitial cystitis and normal subjects with intact epithelial function, and it is a useful diagnostic test for interstitial cystitis. Potassium sensitivity correlates with increased potassium absorption in normal subjects, and potassium is far more provocative than sodium. Potassium sensitivity is also present in acute urinary tract infection and occasionally detrusor instability but not in BPH or chronic urinary tract infections.
Virions of primary human immunodeficiency virus type 1 isolates resistant to soluble CD4 (sCD4) neutralization differ in sCD4 binding and glycoprotein gp120 retention from sCD4-sensitive isolates (1992)

Primary isolates of human immunodeficiency virus type 1 (HIV-1) are much less sensitive to neutralization by soluble CD4 (sCD4) and sCD4-immunoglobulin (Ig) chimeras (CD4-IgG) than are HIV-1 strains adapted to growth in cell culture. We demonstrated that there are significant reductions (10- to 30-fold) in the binding of sCD4 and CD4-IgG to intact virions of five primary isolates compared with sCD4-sensitive, cell culture-adapted isolates RF and IIIB. However, soluble envelope glycoproteins (gp120) derived from the primary isolate virions, directly by detergent solubilization or indirectly by recombinant DNA technology, differed in affinity from RF and IIIB gp120 by only one- to threefold. The reduced binding of sCD4 to these primary isolate virions must therefore be a consequence of the tertiary or quaternary structure of the envelope glycoproteins in their native, oligomeric form on the viral surface. In addition, the rate and extent of sCD4-induced gp120 shedding from these primary isolates was lower than that from RF. We suggest that reduced sCD4 binding and increased gp120 retention together account for the relative resistance of these primary isolates to neutralization by sCD4 and CD4-IgG and that virions of different HIV-1 isolates vary both in the mechanism of sCD4 binding and in subsequent conformational changes in their envelope glycoproteins.
Coupling of Endoplasmic Reticulum Stress to CDDO-Me–Induced Up-regulation of Death Receptor 5 via a CHOP–Dependent Mechanism Involving JNK Activation (2008)

The synthetic triterpenoid methyl-2-cyano-3,12-dioxoolean-1,9-dien-28-oate (CDDO-Me) is in phase I clinical trials as a novel cancer therapeutic agent. We previously showed that CDDO-Me induces c-Jun NH(2)-terminal kinase (JNK)-dependent death receptor 5 (DR5) expression and augments death receptor-induced apoptosis. The current study focused on addressing how CDDO-Me induces JNK-dependent DR5 expression. Analysis of DR5 promoter regions defines that the CCAAT/enhancer binding protein homologous protein (CHOP) binding site is responsible for CDDO-Me-induced transactivation of the DR5 gene. Consistently, CDDO-Me induced DR5 expression and parallel CHOP up-regulation. Blockade of CHOP up-regulation also abrogated CDDO-Me-induced DR5 expression. These results indicate that CDDO-Me induces CHOP-dependent DR5 up-regulation. Moreover, the JNK inhibitor SP600125 abrogated CHOP induction by CDDO-Me, suggesting a JNK-dependent CHOP up-regulation by CDDO-Me as well. Importantly, knockdown of CHOP attenuated CDDO-Me-induced apoptosis, showing that CHOP induction is involved in CDDO-Me-induced apoptosis. Additionally, CDDO-Me increased the levels of Bip, phosphorylated eukaryotic translation initiation factor 2alpha, inositol requiring kinase 1alpha, and activating transcription factor 4, all of which are featured changes during endoplasmic reticulum (ER) stress. Furthermore, salubrinal, an inhibitor of ER stress-induced apoptosis, inhibited JNK activation and up-regulation of CHOP and DR5 by CDDO-Me and protected cells from CDDO-Me-induced apoptosis. Thus, ER stress seems to be important for CDDO-Me-induced JNK activation, CHOP and DR5 up-regulation, and apoptosis. Collectively, we conclude that CDDO-Me triggers ER stress, leading to JNK-dependent, CHOP-mediated DR5 up-regulation and apoptosis.
Nitrogen Assimilation by Plants (2001)

This publication contains the most important information acquired over the last twenty years in the area of nitrogen metabolism and envisages new strategies to improve plant species of agronomic value by devising new techniques for growing them.
The role of ethylenediamine tetraacetic acid (EDTA) as in vitro anticoagulant for diagnostic purposes (2007)

Anticoagulants are used to prevent clot formation both in vitro and in vivo. In the specific field of in vitro diagnostics, anticoagulants are commonly added to collection tubes either to maintain blood in the fluid state for hematological testing or to obtain suitable plasma for coagulation and clinical chemistry analyses. Unfortunately, no universal anticoagulant that could be used for evaluation of several laboratory parameters in a sample from a single test tube is available so far. Ethylenediamine tetraacetic acid (EDTA) is a polyprotic acid containing four carboxylic acid groups and two amine groups with lone-pair electrons that chelate calcium and several other metal ions. Calcium is necessary for a wide range of enzyme reactions of the coagulation cascade and its removal irreversibly prevents blood clotting within the collection tube. Historically, EDTA has been recommended as the anticoagulant of choice for hematological testing because it allows the best preservation of cellular components and morphology of blood cells. The remarkable expansion in laboratory test volume and complexity over recent decades has amplified the potential spectrum of applications for this anticoagulant, which can be used to stabilize blood for a variety of traditional and innovative tests. Specific data on the behavior of EDTA as an anticoagulant in hematology, including possible pitfalls, are presented. The use of EDTA for measuring cytokines, protein and peptides, and cardiac markers is described, with an outline of the protection of labile molecules provided by this anticoagulant. The use of EDTA in proteomics and in general clinical chemistry is also described in comparison with other anticoagulants and with serum samples. Finally, the possible uses of alternative anticoagulants instead of EDTA and the potential use of a universal anticoagulant are illustrated.
Identification of receptor ligands with phage display peptide libraries. (1999)

With the development and maturation of the technology of displaying peptides on bacteriophage, it has become possible to isolate peptide ligands to various targets. In the phage display strategy, up to 10(9) peptides of different permutations are expressed on the surface of filamentous phage. Thus, peptides capable of binding target molecules in vitro and even target tissues in vivo can be identified. In recent years, a series of libraries that display degenerate peptides of different lengths have been constructed, and specific ligands to cell surface receptors, such as integrins, have been isolated. In the in vivo biopanning, peptides targeting distinct organs or tumors have been rescued after intravenous administration of phage libraries into mice. In one application, the isolated peptide ligands have been used to direct a cytotoxic drug to tumor vasculature in mice. Further applications in radioimaging and radiotherapy are being investigated.
Characteristics of two types of meningococcal group C polysaccharide conjugates using tetanus toxoid as carrier protein. (1986)

Effective meningococcal vaccines have to induce protection against groups A, B, C, W-135 and Y meningocci. Polysaccharides are the most effective vaccine candidates against groups A, C, W-135 and Y meningococci. The vaccine potential of polysaccharides is enhanced by conjugating the polysaccharides to carrier proteins. This paper describes the preparation and immunological characterization of two types of group C polysaccharide - tetanus toxoid conjugate. Both types of conjugate were produced by different procedures. Procedure i. depends on cross-linking of both components with N-ethyl-N'-(3-dimethylaminopropyl) carbodimide. Procedure ii. is a more monofunctional way of conjugating partially depolymerized polysaccharide with tetanus toxoid by reductive amination. The antigenic activity of the tetanus toxoid component of the conjugates containing this carrier protein was studied in ELISA and showed differences between the conjugate preparations. The immunogenic activity of all conjugate preparations was tested in mice. All conjugates produced IgG antibodies to the polysaccharide component, although the booster effects of procedure ii. conjugates were less pronounced than those of procedure i. conjugates. The immunogenic activity of the tetanus toxoid component of the various conjugate preparations correlated rather well with their antigenic activities as measured in ELISA.
Phosphorylation of p53 in normal and simian virus 40-transformed NIH 3T3 cells. (1988)

We observed six major tryptic phosphopeptides in p53 from simian virus 40-transformed and normal NIH 3T3 cells. Analyses of the phosphopeptides indicated that serines 37, 310 and/or 312, 389 and one or more of serines 7, 9, 12, 18, and 23 were phosphorylated. Phosphorylation of serines 310 and/or 312 was twofold higher in the simian virus 40-transformed cells as compared with that in normal NIH 3T3 cells.
Is blood pressure inversely related to birth weight? The strength of evidence from a systematic review of the literature (1996)

Blood pressure is inversely related to birth weight in children and in adults. The positive results in neonates and the inconsistency in adolescence may be related to the unusual growth dynamics during these phases of growth. Further studies should concentrate on the mechanisms which underlie the relationship.
Reactive oxygen species in cell signaling (2000)

Reactive oxygen species (ROS) are generated as by-products of cellular metabolism, primarily in the mitochondria. When cellular production of ROS overwhelms its antioxidant capacity, damage to cellular macromolecules such as lipids, protein, and DNA may ensue. Such a state of "oxidative stress" is thought to contribute to the pathogenesis of a number of human diseases including those of the lung. Recent studies have also implicated ROS that are generated by specialized plasma membrane oxidases in normal physiological signaling by growth factors and cytokines. In this review, we examine the evidence for ligand-induced generation of ROS, its cellular sources, and the signaling pathways that are activated. Emerging concepts on the mechanisms of signal transduction by ROS that involve alterations in cellular redox state and oxidative modifications of proteins are also discussed.
Substitution of a Glycogen Synthase Kinase-3β Phosphorylation Site in Presenilin 1 Separates Presenilin Function from β-Catenin Signaling (2001)

The majority of cases with early onset familial Alzheimer's disease have been attributed to mutations in the presenilin 1 (PS1) gene. PS1 protein is a component of a high molecular weight membrane-bound complex that also contains beta-catenin. The physiological relevance of the association between PS1 and beta-catenin remains controversial. In this study, we report the identification and functional characterization of a highly conserved glycogen synthase kinase-3beta consensus phosphorylation site within the hydrophilic loop domain of PS1. Site-directed mutagenesis, together with in vitro and in vivo phosphorylation assays, indicates that PS1 residues Ser(353) and Ser(357) are glycogen synthase kinase-3beta targets. Substitution of one or both of these residues greatly reduces the ability of PS1 to associate with beta-catenin. By disrupting this interaction, we demonstrate that the association between PS1 and beta-catenin has no effect on Abeta peptide production, beta-catenin stability, or cellular susceptibility to apoptosis. Significantly, in the absence of PS1/beta-catenin association, we found no alteration in beta-catenin signaling using induction of this pathway by exogenous expression of Wnt-1 or beta-catenin and a Tcf/Lef transcriptional assay. These results argue against a pathologically relevant role for the association between PS1 and beta-catenin in familial Alzheimer's disease.
<i>cis</i>-Urocanic Acid Induces Mast Cell Degranulation and Release of Preformed TNF--α: A Possible Mechanism Linking UVB and <i>cis</i>-Urocanic Acid to Immunosuppression of Contact Hypersensitivity (1999)

The search for effective inhibitors of transdermal drug-induced contact sensitization was directed to dermal mast-cell-degranulating agents (MCDA). Human skin organ cultures were employed to test whether cis-urocanic acid (C-UA) and other potential MCDAs cause mast cell degranulation. These were then tested for their ability to inhibit the induction phase of the contact hypersensitivity reaction (CHR). C-UA at 1 microg/ml significantly depleted mast cell chymase, whereas trans-urocanic acid (T-UA) was relatively ineffective. C-UA, but not T-UA, induced local effects of liberated mast cell TNF-alpha, as detected by E-selectin expression on the microvascular dermal endothelium. C-UA significantly reduced (>70%) the ear swelling response in Balb/c mice, when applied 24 h prior to application of a sensitizing amount of dinitrochlorobenzene (DNCB), and induced a prolonged (>3 weeks) state of immune tolerance (>40%). Similar effects on local immunosuppression of CHR were observed with topical chloroquine and capsaicin, while cromolyn, a mast cell membrane stabilizer, was unable to inhibit DNCB-induced CHR. It is suggested that MCDAs may interfere with downstream events associated with accessory cell function.