gebhart/patrepeval huggingface dataset:
Structure‐Function Relationships for some Metalloalkaline Phosphatases of E. coli (1969)

The alkaline phosphatase of Escherichia coli is a zinc metalloprotein with a metal to enzyme ratio of 4. Inorganic phosphate protects the four zinc atoms against removal by EDTA. Cadmium and manganese can replace zinc on its four binding sites. Samples of phosphatase with different proportions of zinc and cadmium or of zinc and manganese have been prepared and tested for their enzymatic activity. These results together with others suggest a model which involves two functional and two structural zinc atoms. The zinc atoms necessary for the activity would have different apparent binding constants for the apoenzyme. This conclusion is in agreement with Cohen and Wilson's scheme postulated in 1966. Dissociation constants for Me 2+ ‐apophosphatase complexes were determined (Me 2+ = Zn 2+ , Ni 2+ , Cd 2+ , Co 2+ , Mn 2+ ). These constants follow the order Ni 2+ &gt; Co 2+ &gt; Zn 2+ &gt; Cd 2+ = Mn 2+ . The optical rotatory dispersion spectra of these different metallophosphatases are very similar between 25° and 55° suggesting little change in protein structure. However, only Co 2+ and Zn 2+ alkaline phosphatases are active enzymes.
Silent Polymorphisms Speak: How They Affect Pharmacogenomics and the Treatment of Cancer (2007)

Polymorphisms in the human genome contribute to wide variations in how individuals respond to medications, either by changing the pharmacokinetics of drugs or by altering the cellular response to therapeutic agents. The goal of the emerging discipline of pharmacogenomics is to personalize therapy based on an individual's genotype. Due to the relatively large frequency of single-nucleotide polymorphisms (SNP) in the human genome, synonymous SNPs are often disregarded in many pharmacogenomic studies based on the assumption that these are silent. We have shown recently that synonymous SNPs in ABCB1 (P-glycoprotein), which is implicated both in determining drug pharmacokinetics and multidrug resistance in human cancer cells, can affect protein conformation and function. We discuss the importance of polymorphisms in drug metabolizing enzymes and transporters in anticancer therapy and suggest that synonymous polymorphisms may play a more significant role than is currently assumed.
Measures of residue density in protein structures (1999)

A hierarchy of residue density assessments and packing properties in protein structures are contrasted, including a regular density, a variety of charge densities, a hydrophobic density, a polar density, and an aromatic density. These densities are investigated by alternative distance measures and also at the interface of multiunit structures. Amino acids are divided into nine structural categories according to three secondary structure states and three solvent accessibility levels. To take account of amino acid abundance differences across protein structures, we normalize the observed density by the expected density defining a density index. Solvent accessibility levels exert the predominant influence in determinations of the regular residue density. Explicitly, the regular density values vary approximately linearly with respect to solvent accessibility levels, the linearity parameters depending on the amino acid. The charge index reveals pronounced inequalities between lysine and arginine in their interactions with acidic residues. The aromatic density calculations in all structural categories parallel the regular density calculations, indicating that the aromatic residues are distributed as a random sample of all residues. Moreover, aromatic residues are found to be over-represented in the neighborhood of all amino acids. This result might be attributed to nucleation sites and protein stability being substantially associated with aromatic residues.
Epithelial to Mesenchymal Transition Is a Determinant of Sensitivity of Non–Small-Cell Lung Carcinoma Cell Lines and Xenografts to Epidermal Growth Factor Receptor Inhibition (2005)

Treatment of second- and third-line patients with non-small-cell lung carcinoma (NSCLC) with the epidermal growth factor receptor (EGFR) kinase inhibitor erlotinib significantly increased survival relative to placebo. Whereas patient tumors with EGFR mutations have shown responses to EGFR inhibitors, an exclusive role for mutations in patient survival benefit from EGFR inhibition is unclear. Here we show that wild-type EGFR-containing human NSCLC lines grown both in culture and as xenografts show a range of sensitivities to EGFR inhibition dependent on the degree to which they have undergone an epithelial to mesenchymal transition (EMT). NSCLC lines which express the epithelial cell junction protein E-cadherin showed greater sensitivity to EGFR inhibition in vitro and in xenografts. In contrast, NSCLC lines having undergone EMT, expressing vimentin and/or fibronectin, were insensitive to the growth inhibitory effects of EGFR kinase inhibition in vitro and in xenografts. The differential sensitivity of NSCLC cells with epithelial or mesenchymal phenotypes to EGFR inhibition did not correlate with cell cycle status in vitro or with xenograft growth rates in vivo, or with total EGFR protein levels. Cells sensitive to EGFR inhibition, with an epithelial cell phenotype, did exhibit increased phosphorylation of EGFR and ErbB3 and a marked increase in total ErbB3. The loss of E-cadherin and deregulation of beta-catenin associated with EMT have been shown to correlate with poor prognosis in multiple solid tumor types. These data suggest that EMT may be a general biological switch rendering non-small cell lung tumors sensitive or insensitive to EGFR inhibition.
The cellulose‐binding domain (CBDCex) of an exoglucanase from Cellulomonas fimi: Production in Escherichia coli and characterization of the polypeptide (1993)

The gene fragment encoding the cellulose-binding domain (CBD) of an exoglucanase (Cex) from Cellulomonas fimi was subcloned and expressed in Escherichia coli. Transcription from the lac promoter coupled with translation from a consensus prokaryotic ribosome binding site led to the production of large quantities of CBD(Cex) (up to 25% total soluble cell protein). The polypeptide leaked into the culture supernatant (up to 50 mg . L(-1)), facilitating one-step purification by affinity chromatography on cellulose. The 11-kDa polypeptide reacted with Cex antiserum. Absence of free thiols indicated that the two Cys residues of CBD(Cex) form a disulfide bridge. It had the same N-terminal amino acid sequence as CBD(Cex) prepared from Cex by proteolysis, plus two additional N-terminal amino acid residues (Ala and Ser) encoded by the Nhel site introduced during plasmid construction. CBD(Cex) bound to a variety of beta-1, 4-glycans with different affinities and saturation levels. Adsorption to bacterial microcrystalline cellulose was dependent on the temperature, but not on the pH.
Amphipathic polyethyleneglycols effectively prolong the circulation time of liposomes (1990)

Incorporation of dioleoyl N-(monomethoxy polyethyleneglycol succinyl)phosphatidylethanolamine (PEG-PE) into large unilamellar liposomes composed of egg phosphatidylcholine:cholesterol (1:1) does not significantly increase the content leakage when the liposomes are exposed to 90% human serum at 37 degrees C, yet the liposomes show a significant increase in the blood circulation half-life (t1/2 = 5 h) as compared to those without PEG-PE(t1/2 less than 30 min). The PEG-PE's activity to prolong the circulation time of liposomes is greater than that of the ganglioside GM1, a well-described glycolipid with this activity. Another amphipathic PEG derivative, PEG stearate, also prolongs the liposome circulation time, although its activity is less than that of GM1. Amphipathic PEGs may be useful for the sustained release and the targeted drug delivery by liposomes.
A clinical evaluation of the effcacy and safety of singlet oxygen in cleansing and disinfecting stagnating wounds (2011)

The centres were supplied with the study product by the sponsor. The authors have no financial interest in writing this article.
Hypolipidemic Activities of DietaryPleurotus ostreatusin Hypercholesterolemic Rats (2011)

This work was conducted to investigate dietary supplementation of oyster mushroom fruiting bodies on biochemical and histological changes in hyper and normocholesterolemic rats. Six-week old female Sprague-Dawley albino rats were divided into three groups of 10 rats each. Feeding a diet containing a 5% powder of Pleurotus ostreatus fruiting bodies to hypercholesterolemic rats reduced plasma total cholesterol, triglyceride, low-density lipoprotein (LDL), total lipid, phospholipids, and LDL/high-density lipoprotein ratio by 30.18, 52.75, 59.62, 34.15, 23.89, and 50%, respectively. Feeding oyster mushrooms also significantly reduced body weight in hypercholesterolemic rats. However, it had no adverse effects on plasma albumin, total bilirubin, direct bilirubin, creatinin, blood urea nitrogen, uric acid, glucose, total protein, calcium, sodium, potassium, chloride, inorganic phosphate, magnesium, or enzyme profiles. Feeding mushroom increased total lipid and cholesterol excretion in feces. The plasma lipoprotein fraction, separated by agarose gel electrophoresis, indicated that P. ostreatus significantly reduced plasma β and pre-β-lipoprotein but increased α-lipoprotein. A histological study of hepatic cells by conventional hematoxylin-eosin and oil red O staining revealed normal findings for mushroom-fed hypercholesterolemic rats. These results suggest that a 5% P. ostreatus diet supplement provided health benefits by acting on the atherogenic lipid profile in hypercholesterolemic rats.
Sputum Biomarkers and the Prediction of Clinical Outcomes in Patients with Cystic Fibrosis (2012)

Lung function, acute pulmonary exacerbations (APE), and weight are the best clinical predictors of survival in cystic fibrosis (CF); however, underlying mechanisms are incompletely understood. Biomarkers of current disease state predictive of future outcomes might identify mechanisms and provide treatment targets, trial endpoints and objective clinical monitoring tools. Such CF-specific biomarkers have previously been elusive. Using observational and validation cohorts comprising 97 non-transplanted consecutively-recruited adult CF patients at the Intermountain Adult CF Center, University of Utah, we identified biomarkers informative of current disease and predictive of future clinical outcomes. Patients represented the majority of sputum producers. They were recruited March 2004-April 2007 and followed through May 2011. Sputum biomarker concentrations were measured and clinical outcomes meticulously recorded for a median 5.9 (interquartile range 5.0 to 6.6) years to study associations between biomarkers and future APE and time-to-lung transplantation or death. After multivariate modeling, only high mobility group box-1 protein (HMGB-1, mean=5.84 [log ng/ml], standard deviation [SD] =1.75) predicted time-to-first APE (hazard ratio [HR] per log-unit HMGB-1=1.56, p-value=0.005), number of future APE within 5 years (0.338 APE per log-unit HMGB-1, p<0.001 by quasi-Poisson regression) and time-to-lung transplantation or death (HR=1.59, p=0.02). At APE onset, sputum granulocyte macrophage colony stimulating factor (GM-CSF, mean 4.8 [log pg/ml], SD=1.26) was significantly associated with APE-associated declines in lung function (-10.8 FEV(1)% points per log-unit GM-CSF, p<0.001 by linear regression). Evaluation of validation cohorts produced similar results that passed tests of mutual consistency. In CF sputum, high HMGB-1 predicts incidence and recurrence of APE and survival, plausibly because it mediates long-term airway inflammation. High APE-associated GM-CSF identifies patients with large acute declines in FEV(1)%, possibly providing a laboratory-based objective decision-support tool for determination of an APE diagnosis. These biomarkers are potential CF reporting tools and treatment targets for slowing long-term progression and reducing short-term severity.
Further analysis of Del (D‐elute) using polymerase chain reaction (PCR) with RHD gene‐specific primers (1997)

Del (D-elute) in the Rh blood group system is a variant with very weak D antigen and no agglutination is found by the indirect antiglobulin test. This variant is characterized by the presence of anti-D eluate obtained after an adsorption-elution test using anti-D antibodies. We studied here the molecular genetic status of Del by using polymerase chain reaction with sequence-specific primers (PCR-SSP). We screened 306 serologically apparent D-negative Japanese donors comprising 102 Del types for exons 7, 4 and 10 of the RHD gene. No PCR product was found in all 204 non-Del samples from the D-seronegative donors. However, PCR products were found in all 102 Del samples and all 70 D-seropositive samples tested by the three PCR methods for exons 7, 4 and 10 analysis. Del was found with CCee, CcEe and Ccee, but not with CCEe, CcEE, ccEE, ccEe or ccee phenotype. The incidences of Del in the samples with the serological phenotypes CCee, CcEe and Ccee were 80.0% (4/5), 68.2% (45/66) and 61.6% (53/86), respectively. The results provide evidence that Del samples have exons 4, 7 and 10 of an RHD gene present in some form. This is consistent with the evidence that D antigen is present on the cells although only detected by antibody adsorption and elution. The PCR-SSP method in the present study is useful to confirm Del among serologically apparent D-negative samples.
Field Evaluation of CDC and Mosquito Magnet® X Traps Baited With Dry Ice, Co2Sachet, and Octenol Against Mosquitoes (2008)

The Centers for Disease Control and Prevention (CDC) light traps and Mosquito Magnet X (MMX) traps baited with dry ice, octenol, and a new formulation (granular) of carbon dioxide (CO2) were evaluated against adult mosquitoes in the field. The results showed that the MMX traps (68.6%) baited with dry ice collected more mosquitoes compared to the CDC light traps (32.4%) only. The CDC traps baited with dry ice (64%) collected significantly more mosquitoes than traps baited with CO2 sachets (11%) or octenol (23%). The MMX traps baited with dry ice (85.5%) collected significantly more mosquitoes than traps baited with CO2 sachets (6.5%) or octenol (9%). The CDC traps baited with the formulations of normal and slow release CO2 sachets collected more mosquitoes than the formulation of fast release sachets. The CDC traps baited with fresh sachets and 24-h-exposed sachets collected significantly more mosquitoes than the traps baited with 48-h- and 72-h-exposed sachets.
Plasmonic phenomena in indium tin oxide and ITO-Au hybrid films (2009)

The observation of surface-plasmon resonances in indium tin oxide (ITO) thin films is complemented with the effects of hybrid ITO/Au conducting layers where charge densities can be tuned. Where carrier densities are similar (ITO and nanoparticle Au), the plasmonic behavior is that of a monolithic ITO thin film. Where the carrier density of one layer is much greater than that of the other (ITO and Au metal), boundary conditions lead to cancelation of the surface plasmon. In the latter case a capacitivelike plasmon resonance is observed for sufficiently thin films.
Characterization of Post-Transcriptionally Suppressed Transgene Expression That Confers Resistance to Tobacco Etch Virus Infection in Tobacco (1997)

Matthew M. Tanzer, William F. Thompson, Marc D. Law, Earl A. Wernsman, Scott Uknes, Characterization of Post-Transcriptionally Suppressed Transgene Expression That Confers Resistance to Tobacco Etch Virus Infection in Tobacco, The Plant Cell, Vol. 9, No. 8 (Aug., 1997), pp. 1411-1423
Platelet activation by simultaneous actions of diacylglycerol and unsaturated fatty acids. (1992)

Several cis-unsaturated fatty acids such as oleic, linoleic, linolenic, eicosapentaenoic, and docosahexaenoic acids added directly to intact human platelets greatly enhance protein kinase C activation as judged by the phosphorylation of its specific endogenous substrate, a 47-kDa protein. This enhancement absolutely requires the presence of a membrane-permeant diacylglycerol, 1,2-dioctanoylglycerol, or a tumor-promoting phorbol ester, phorbol 12-myristate 13-acetate. In the presence of ionomycin and either 1,2-dioctanoylglycerol or phorbol 12-myristate 13-acetate, the release of serotonin from the platelets is also remarkably increased by cis-unsaturated fatty acids. The effect of these fatty acids is observed at concentrations less than 50 microM. Saturated fatty acids and trans-unsaturated fatty acids are inactive. Titration of ionomycin to induce a release reaction and measurement of the intracellular Ca2+ level by the fura-2 procedure indicate that cis-unsaturated fatty acids increase an apparent sensitivity of the platelet response to Ca2+. The results suggest that cis-unsaturated fatty acids, which are presumably produced from phosphatidylcholine by signal-dependent activation of phospholipase A2, may take part directly in cell signaling through the protein kinase C pathway.
Anti-CD11b/CD18 antibodies reduce inflammation in acute colitis in rats (1995)

The influx of monocytes and neutrophils into the inflamed tissue could be an important aspect in the pathogenesis of inflammatory bowel disease (IBD). A membrane protein involved in the monocyte/neutrophil adherence to endothelium is CD11b/CD18 or alpha M beta 2 (complement receptor type 3 = CR3). In the present study the role of CD11b/CD18 in experimental IBD was studied by treatment with ED7 and OX42, two MoAbs against CD11b/CD18. Colitis was induced in rats by a single, rectal administration of 30 mg 2,4,6-trinitrobenzene sulfonic acid (TNBS) dissolved in ethanol 30%. Two hours before and 3 days after induction of colitis, the animals were given an i.v. dose of 0.5 mg of either ED7 or OX42 in 1 ml PBS. Controls received PBS or an irrelevant MoAb. Four days after the last treatment with the antibodies, the rats were killed, and macroscopic damage scores of the colon were determined. Macrophages and granulocytes were studied by immunohistochemistry and quantified by Interaktives Bild Analysen System (IBAS), and myeloperoxidase (MPO) activity in colonic tissue was measured. After treatment with ED7 and OX42 the mean damage score of the colon was reduced from 4.2 in IBD animals to 1.0 and 1.3, respectively. Smaller areas of ulcerations and a decrease in the number of ulcerations were observed compared with PBS-treated rats. Furthermore, the amount of infiltrating monocytes and leucocytes in the submucosa was enormously reduced, as well as MPO activity in the colonic tissue. These results show that treatment with MoAbs against CD11b/CD18 reduces clinical signs of experimental IBD in rats by a partial blockade of infiltrating macrophages and granulocytes.
SeamSeg: Video Object Segmentation Using Patch Seams (2014)

In this paper, we propose a technique for video object segmentation using patch seams across frames. Typically, seams, which are connected paths of low energy, are utilised for retargeting, where the primary aim is to reduce the image size while preserving the salient image contents. Here, we adapt the formulation of seams for temporal label propagation. The energy function associated with the proposed video seams provides temporal linking of patches across frames, to accurately segment the object. The proposed energy function takes into account the similarity of patches along the seam, temporal consistency of motion and spatial coherency of seams. Label propagation is achieved with high fidelity in the critical boundary regions, utilising the proposed patch seams. To achieve this without additional overheads, we curtail the error propagation by formulating boundary regions as rough-sets. The proposed approach out-perform state-of-the-art supervised and unsupervised algorithms, on benchmark datasets.
Stem Cell Therapy Restores Transparency to Defective Murine Corneas (2009)

Corneal scarring from trauma and inflammation disrupts vision for millions worldwide, but corneal transplantation, the primary therapy for corneal blindness, is unavailable to many affected individuals. In this study, stem cells isolated from adult human corneal stroma were examined for the ability to correct stromal opacity in a murine model by direct injection of cells into the corneal stroma. In wild-type mice, injected human stem cells remained viable for months without fusing with host cells or eliciting an immune T-cell response. Human corneal-specific extracellular matrix, including the proteoglycans lumican and keratocan, accumulated in the treated corneas. Lumican-null mice have corneal opacity similar to that of scar tissue as a result of disruption of stromal collagen organization. After injection with human stromal stem cells, stromal thickness and collagen fibril defects in these mice were restored to that of normal mice. Corneal transparency in the treated mice was indistinguishable from that of wild-type mice. These results support the immune privilege of adult stem cells and the ability of stem cell therapy to regenerate tissue in a manner analogous to organogenesis and clearly different from that of normal wound healing. The results suggest that cell-based therapy can be an effective approach to treatment of human corneal blindness.
Chemical Vapor Deposition (2006)

Graphical Abstract The history of creation and development of ALD, which has been known in the USSR-Russia as molecular layering technique (ML), is described. The “framework” hypothesis and its connection with principles of the method ML, provides information about the ML groups in Russia and their scientific results from the 1960s to the present time.
Medical Applications of Microwave Imaging (1986)

Abstract : The Microwave Theory and Techniques Society of the Institute of Electrical and Electronics Engineers (IEEE) sponsored a workshop on Microwave Dosimetric Imagery as part of the 1980 International Microwave Symposium in Washington, D.C. The purpose of this workshop was to bring together papers on a variety of techniques for microwave imagery with the goal of enhancing their application to medicine in the context of microwave dosimetry. These original papers have been supplemented by reports of related work (Guo et al., Slaney et al.) that has taken place between the time of the symposium and the publication of this volume. These methods of microwave imagery are pertinent to dosimetry because as a class they represent the best hope for noninvasive dosimetry analysis of biosystems exposed to microwave radiation.
Translational control of C/EBPalpha and C/EBPbeta isoform expression. (2000)

Transcription factors derived from CCAAT/enhancer binding protein (C/EBP)alpha and C/EBPbeta genes control differentiation and proliferation in a number of cell types. Various C/EBP isoforms arise from unique C/EBPbeta and C/EBPalpha mRNAs by differential initiation of translation. These isoforms retain different parts of the amino terminus and therefore display different functions in gene regulation and proliferation control. We show that PKR and mTOR signaling pathways control the ratio of C/EBP isoform expression through the eukaryotic translation initiation factors eIF-2alpha and eIF-4E, respectively. An evolutionary conserved upstream open reading frame in C/EBPalpha and C/EBPbeta mRNAs is a prerequisite for regulated initiation from the different translation initiation sites and integrates translation factor activity. Deregulated translational control leading to aberrant C/EBPalpha and C/EBPbeta isoform expression or ectopic expression of truncated isoforms disrupts terminal differentiation and induces a transformed phenotype in 3T3-L1 cells. Our results demonstrate that the translational controlled ratio of C/EBPalpha and C/EBPbeta isoform expression determines cell fate.