gebhart/patrepeval huggingface dataset:
The gene encoding the large subunit of human RNA polymerase II. (1985)

As a first step to approach the structural and functional analysis of DNA-dependent RNA polymerase II (EC 2.7.7.8), we have isolated genomic sequences for the large subunit of the human enzyme. The sequences homologous to Drosophila RNA polymerase II large subunit sequences are present in the genome as single copy genes, when assayed at high stringency. The polypeptide information is encoded in a mRNA of 7.35 kilobases, as determined by Northern blot analysis. In vitro translation reveals a polypeptide of 220 kDa, similar in electrophoretic mobility to the largest subunit of the enzyme. A fusion-polypeptide synthesized in bacteria contains a region that cross-reacts with anti-RNA polymerase II antiserum. Antiserum directed against the purified fusion protein reacts with the large subunit of RNA polymerase II, whether in the intact IIA (220 kDa) or in the degraded IIB (180 kDa) forms. Moreover, the antifusion protein antibody inhibits not only the purified calf thymus RNA polymerase II activity but also specific RNA polymerase II transcription in a HeLa cell extract. Thus, the DNA fragment isolated contains structural and functional domains of the human RNA polymerase II large subunit.
Control of muscle bioenergetic gene expression: implications for allometric scaling relationships of glycolytic and oxidative enzymes (2005)

Muscle metabolic properties vary with body size, with larger animals relying relatively less on oxidative metabolism as a result of lower specific activities of mitochondrial enzymes and greater specific activities of glycolytic enzymes. While many have argued reasons why such relationships might be grounded in physical relationships, an explanation for the regulatory basis of the differences in enzyme levels remains unexplored. Focusing on skeletal muscle, we review potential cellular and genetic explanations for the relationship between bioenergetic enzymes and body mass. Differences in myonuclear domain (the ratio of fiber volume to nuclei number) in conjunction with constitutive expression may explain part of the variation in mitochondrial content among fiber types and species. Superimposed on such constitutive determinants are (1) extrinsic signalling pathways that control the muscle contractile and metabolic phenotype and (2) intrinsic signalling pathways that translate changes in cellular milieu (ions, metabolites, oxygen, redox) arising through the contractile phenotype into changes in enzyme synthesis. These signalling pathways work through transcriptional regulation, as well as post-transcriptional, translational and post-translational regulation, acting via synthesis and degradation.
The effect of aspartate hydroxylation on calcium binding to epidermal growth factor-like modules in coagulation factors IX and X. (1993)

Hydroxylation of aspartic acid to erythro-beta-aspartic acid (Hya) occurs in epidermal growth factor (EGF)-like modules in numerous extracellular proteins with diverse functions. Several EGF-like modules with the consensus sequence for hydroxylation bind Ca2+, and it has therefore been suggested that the hydroxyl group is essential for Ca2+ binding. To determine directly the influence of beta-hydroxylation on calcium binding in the EGF-like modules from coagulation factors IX and X, we have now measured calcium binding to both the fully beta-hydroxylated and the non-beta-hydroxylated modules of the two proteins. At low ionic strength, the Hya-containing module of factor X has a slightly higher Ca2+ affinity, but at physiological salt concentrations this difference is no longer significant for either factor IX or X. Analysis of the 1H NMR chemical shift differences between the hydroxylated and nonhydroxylated factor X modules show that hydroxylation has no effect on the domain fold. Furthermore, measurements on factor IX show that hydroxylation has no effect on the Ca2+/Mg2+ specificity of the ion binding site. We conclude that the hydroxyl group is not a direct ligand for the calcium ion in these EGF-like modules, nor is it essential for high-affinity Ca2+ binding.
The National Problem in World War II under the Shadow of the Axis (2007)

In fact the national problem was another potential cause for World War II.The Axis,consisting of Nazi Germany,Fascistic Italy and Japan,not only had implemented the measures of genocide in some invaded countries before the war and in wartime,but also repeatedly took advantage of national problems inside the related countries to instigate antagonisms among nations.It was a historical evidence of distorting and abusing the principle of national self-determination,which served their strategic targets.The matter is worth keeping in mind for ever.
Prostate Cancer in Relation to Diet, Physical Activity, and Body Size in Blacks, Whites, and Asians in the United States and Canada (1995)

These data support a causal role in prostate cancer for saturated fat intake but suggest that other factors are largely responsible for interethnic differences in risk.
Flow cytometric analysis of the expression of PCNA during the cell cycle in hela cells and effects of the inhibition of DNA synthesis on it (1993)

Flow cytometric bivariate DNA/PCNA analysis was performed to investigate the expression of PCNA during the cell cycle and the implication in DNA replication in HeLa cells, using a monoclonal antibody (PC10) to PCNA. The expression of PCNA was evident in almost all cells growing exponentially, when cells were fixed in methanol. The total amount of PCNA altered a little during the cell cycle. However, the treatment with Triton X-100 extracted 80-89% of total PCNA from the cells, resulting in the dramatic change of bivariate DNA/PCNA distribution pattern. PCNA was completely removed from nuclei in both G1 and G2 phases by the detergent treatment, whereas a certain amount of PCNA remained in S phase nuclei. After the treatment of cells with Triton X-100, PCNA was detected exclusively in S phase cells. The bivariate DNA/PCNA distribution pattern in cells treated with Triton X-100 was strikingly so similar to the DNA/BrdUrd distribution pattern that it was unable to differentiate one from the other. It is concluded that the detergent treatment of cells allows the rapid analysis of the cell cycle. The inhibition of DNA synthesis with 10 mM hydroxyurea elevated cellular PCNA content mainly due to the increase in the fraction of the detergent extractable PCNA. It was apparent, however, that in cells incubated with Triton X-100, the pattern of the bivariate DNA/PCNA distribution was not basically different from that in cells without HU treatment. The level of PCNA bound to nuclear structures (PCNA not extracted with detergent) increased in cells arrested at the G1/S boundary with the time of hydroxyurea treatment.(ABSTRACT TRUNCATED AT 250 WORDS)
Novel Synthesis of Photochromic Polymers via ROMP (2000)

[reaction: see text] Ring-opening metathesis polymerization (ROMP) of a photochromic 1, 2-bis(3-thienyl)cyclopentene monomer generated a series of novel polymers. All polymers exhibit reversible light-activated interconversion between their colorless-open and their colored-closed forms.
Treatment of orthopaedic infections with electrically generated silver ions. A preliminary report. (1978)

Electrically generated silver ions have been shown previously to be a potent antibacterial agent with an exceptionally broad spectrum as indicated by in vitro testing. The present study reports on clinical experience using electrically generated silver ions as adjunctive treatment in the management of chronic osteomyelitis. Fourteen patients had fifteen treatment attempts: thirteen for chronic osteomyelitis of the tibia, one for acute and chronic pyarthrosis and osteomyelitis of the knee, and one for a chronically draining sinus after total hip replacement. Wound débridement, silver ion iontophoresis, and subsequent wound care (usually provided by the patient) resulted in control of the infection in twelve of the fifteen treatment attempts and in healing of the non-union after follow-up ranging from three to thirty-six months. The other three attempts led to two partial and one complete failure.
An effervescent reaction micropump for portable microfluidic systems (2006)

A water-activated, effervescent reaction was used to transport fluid in a controllable manner on a portable microfluidic device. The reaction between sodium bicarbonate and an organic acid, tartaric acid and/or benzoic acid, was modeled to analyze methods of controlling the generation of carbon-dioxide gas for the purposes of pumping fluids. Integration and testing of the effervescent reaction pump in a microfluidic device was made possible by using elastomeric polymers as both photopolymerizable septa and removable lids. These materials combined to enable facile access to otherwise gas-tight devices. Based on theoretical predictions for 0.33 mg of sodium bicarbonate and a stoichiometric amount of organic acid, the pumping flow rate could be varied from 0.01 microL s(-1) to 70 microL s(-1). The flow rate is controlled by adjusting any or all of the particle size of the least soluble reactant, the amount of reactants used, and the type of organic acid selected. The tartaric acid systems rapidly produce carbon dioxide; however, the gas generation rates dramatically decrease over the course of the reaction. In contrast, carbon dioxide production rate in the benzoic acid systems is lower and nearly constant for several minutes. Water activation and direct placement on a microfluidic device are key features of this micropump, which is therefore useful for portable microfluidic applications.
Endogenous Human Papillomavirus E6 and E7 Proteins Differentially Regulate Proliferation, Senescence, and Apoptosis in HeLa Cervical Carcinoma Cells (2002)

Cervical cancer cells express high-risk human papillomavirus (HPV) E6 and E7 proteins, and repression of HPV gene expression causes the cells to cease proliferation and undergo senescence. However, it is not known whether both HPV proteins are required to maintain the proliferative state of cervical cancer cells, or whether mutations that accumulate during carcinogenesis eliminate the need for one or the other of them. To address these questions, we used the bovine papillomavirus E2 protein to repress the expression of either the E6 protein or the E7 protein encoded by integrated HPV18 DNA in HeLa cervical carcinoma cells. Repression of the E7 protein activated the Rb pathway but not the p53 pathway and triggered senescence, whereas repression of the E6 protein activated the p53 pathway but not the Rb pathway and triggered both senescence and apoptosis. Telomerase activity, cyclin-dependent kinase activity, and expression of c-myc were markedly inhibited by repression of either E6 or E7. These results demonstrate that continuous expression of both the E6 and the E7 protein is required for optimal proliferation of cervical carcinoma cells and that the two viral proteins exert distinct effects on cell survival and proliferation. Therefore, strategies that inhibit the expression or activity of either viral protein are likely to inhibit the growth of HPV-associated cancers.
In vivo effects of macrophage colony‐stimulating factor on human monocyte function (1991)

Macrophage colony-stimulating factor (M-CSF) is reported to enhance a variety of functions of mature monocyte/macrophages in vitro. We have examined the effects of a 2 h intravenous infusion of M-CSF obtained from human urine (hM-CSF) on haematological parameters and selected monocyte functions. There was a rapid, small, but consistent reduction in Hb concentration (mean 6.5 +/- 2.3%, P less than 0.0005 by paired t test) by the completion of the hM-CSF infusion and small, transient falls in platelet, monocyte and neutrophil counts were noted in the 2 h following the end of the infusion. No effect on monocyte or neutrophil CD11b cellular adhesion molecule expression was detected. Exposure to hM-CSF in vivo did not directly stimulate the monocyte respiratory burst, but increased the percentage of monocytes responding to f-met-leu-phe from 9.8 +/- 2.5 to 16.6 +/- 4.2 (P less than 0.01). The number of candida ingested and degraded per 100 monocytes increased from 101 +/- 14 pre-infusion to 160 +/- 22 post-infusion (P less than 0.01). There was a rapid increase in the numbers of monocytes entering a skin window membrane from a mean of 226 +/- 71 pre-infusion to 1064 +/- 404 at the end of the infusion, with no effect on neutrophil migration. These data show that the administration of hM-CSF enhances several of the functions of peripheral blood monocytes in vivo, and this may be of benefit in the treatment of selected infections.
Detection of intestinal dysplasia using angle-resolved low coherence interferometry (2011)

Angle-resolved low coherence interferometry (a/LCI) is an optical biopsy technique that allows for depth-resolved, label-free measurement of the average size and optical density of cell nuclei in epithelial tissue to assess the tissue health. a/LCI has previously been used clinically to identify the presence of dysplasia in Barrett's Esophagus patients undergoing routine surveillance. We present the results of a pilot, ex vivo study of tissues from 27 patients undergoing partial colonic resection surgery, conducted to evaluate the ability of a/LCI to identify dysplasia. Performance was determined by comparing the nuclear morphology measurements with pathological assessment of co-located physical biopsies. A statistically significant correlation between increased average nuclear size, reduced nuclear density, and the presence of dysplasia was noted at the basal layer of the epithelium, at a depth of 200 to 300 μm beneath the tissue surface. Using a decision line determined from a receiver operating characteristic, a/LCI was able to separate dysplastic from healthy tissues with a sensitivity of 92.9% (13/14), a specificity of 83.6% (56/67), and an overall accuracy of 85.2% (69/81). The study illustrates the extension of the a/LCI technique to the detection of intestinal dysplasia, and demonstrates the need for future in vivo studies.
Response to rituximab in patients with rheumatoid arthritis in different compartments of the immune system (2011)

In the last decade, with the implementation of new targeted drugs, the efficacy of the treatment of rheumatoid arthritis (RA) has increased enormously. However, a subset of patients still does not respond to any of the available treatments. At this moment, the chimerical anti-CD20 monoclonal antibody rituximab is one of the therapeutic options in RA patients who failed anti-TNFα therapy (1). After infusion it leads to a fast and almost complete depletion of CD20 positive B cells in the peripheral blood. In contrast to the peripheral blood compartment that has been studied quite extensively, only limited data exist on the effect of rituximab on other compartments of the immune system, like lymph nodes, bone marrow and synovial tissue. By studying the mode of action in the different inflammatory compartments, we may gain a more detailed understanding of the pathogenesis of RA and the mechanism of action of rituximab (2). In light of personalized medicine, this knowledge could lead to the identification of patients with a potentially improved clinical response, compared to for example patients who might need intensified dosing regimens or may better be treated with other drugs. © 2011 American College of Rheumatology
Biodegradation of aromatic carboxylic acids byPseudomonas mira (1993)

Biodegradation of aromatic acids (ferulic, vanillic and sipapinic acids) by the soil bacterium Pseudomonas mira was studied by high-pressure liquid chromatography. The presence of glucose in the culture medium slowed down the degradation process but did not affect its mechanism. In addition to vanillic acid and hydroquinone, the products of degradation were found to include acetophenone derivatives. Probably, a mechanism capable of shortening the side chain by spontaneous decarboxylation of unstable 3-keto-3-phenylpropionic acid was present, in addition to the elimination of acetic acid via degradation of the cinnamic acid-type compounds.
Pilot Studies of Transdermal Continuous Glucose Measurement in Outpatient Diabetic Patients and in Patients during and after Cardiac Surgery (2008)

Continuous transdermal glucose monitoring was demonstrated successfully in diverse clinical settings. The performance of abrasion was equivalent to ultrasound skin permeation methodology for transdermal glucose monitoring.
Heme oxygenase-1-derived bilirubin ameliorates postischemic myocardial dysfunction (2000)

Bilirubin is a potent antioxidant generated intracellularly during the degradation of heme by the enzyme heme oxygenase. The purpose of this study was to determine the role of increased cardiac bilirubin in protection against postischemic myocardial dysfunction. Rat hearts were isolated and perfused according to the Langendorff technique to evaluate the recovery of myocardial function after 30 min of global ischemia and 60 min of reperfusion. We found that upregulation of the inducible isoform of heme oxygenase (HO-1) by treatment of animals with hemin 24 h before ischemia ameliorated myocardial function and reduced infarct size (tetrazolium staining) on reperfusion of isolated hearts. Tin protoporphyrin IX, an inhibitor of heme oxygenase activity, completely abolished the improved postischemic myocardial performance observed after hemin-mediated HO-1 induction. Likewise, cardiac tissue injury was exacerbated by treatment with tin protoporphyrin IX. Increased cardiac HO-1 expression and heme oxygenase activity were associated with enhanced tissue bilirubin content and an increased rate of bilirubin release into the perfusion buffer. Furthermore, exogenously administered bilirubin at concentrations as low as 100 nanomolar significantly restored myocardial function and minimized both infarct size and mitochondrial damage on reperfusion. Our data provide strong evidence for a primary role of HO-1-derived bilirubin in cardioprotection against reperfusion injury.
Cold atmospheric argon plasma significantly decreases bacterial load of chronic wounds in patients (2010)

Summary form only given. We are treating chronic wounds using a low-temperature argon plasma. The results of the clinical phase II of this study show a significant increase in the rate of germ reduction in plasma-treated wounds in comparison with wounds that received only standard wound care. This effect is found in all kinds of germs, regardless the resistance level.The observed bactericidal effect of plasma therapy relies on the synergy of UVR, charged particles, electric fields, ROS and RNS. The combination of these biologically active components makes plasma a promising tool for fighting multiresistant germs. The advantage of this indirect plasma device is that it can be designed and optimized for different purposes, such as germ specific biofilms or varying wound fluid compositions. Furthermore there is evidence that plasma can enhance wound healing itself.
Biological and experimental consequences of the zonal composition of solid tumors. (1981)

The K-1735 melanoma is a transplantable murine tumor which, when growing s.c., is composed of melanotic and amelanotic areas. Results from trocar transplantation studies of tumor fragments show that expression of this phenotypic diversity can be terminated within very few passages. In parallel experiments, passage of cell suspensions derived from the whole tumor maintains this heterogeneity of melanin production. The implications of these findings are discussed.
Tetravalent single-chain avidin: from subunits to protein domains via circularly permuted avidins (2005)

scAvd (single-chain avidin, where two dcAvd are joined in a single polypeptide chain), having four biotin-binding domains, was constructed by fusion of topologically modified avidin units. scAvd showed similar biotin binding and thermal stability properties as chicken avidin. The DNA construct encoding scAvd contains four circularly permuted avidin domains, plus short linkers connecting the four domains into a single polypeptide chain. In contrast with wild-type avidin, which contains four identical avidin monomers, scAvd enables each one of the four avidin domains to be independently modified by protein engineering. Therefore the scAvd scaffold can be used to construct spatially and stoichiometrically defined pseudotetrameric avidin molecules showing different domain characteristics. In addition, unmodified scAvd could be used as a fusion partner, since it provides a unique non-oligomeric structure, which is fully functional with four high-affinity biotin-binding sites. Furthermore, the subunit-to-domain strategy described in the present study could be applied to other proteins and protein complexes, facilitating the development of sophisticated protein tools for applications in nanotechnology and life sciences.
A study on biological effects of low-intensity millimeter waves (2002)

Resonance-like biological effects of millimeter-wave radiation at frequencies of approximately 42 GHz on the growth rate of E. coli and on DNA have been reported in several scientific publications. In order to explore these nonthermal effects, we have measured the growth rate and the absorption spectrum of E. coli, irradiated by millimeter waves in the frequency range from 41 to 43 GHz. In addition, the effect of this radiation on DNA was studied by measuring plasmid transformation efficiency. Both the growth rate variations with varying frequency and the variations in the result of the plasmid transformation efficiency experiments were found to be statistically insignificant. Resonance-like absorption features observed in the absorption spectrum of E. coli were identified as modes generated in the millimeter-wave system, when the sample was inserted. The experimental results indicate that resonance effects are unlikely in this particular frequency range.
Optical trapping of porous silicon nanoparticles (2011)

Silicon nanoparticles obtained by ball-milling of a 50% porosity silicon layer have been optically trapped when dispersed in a water-surfactant environment. We measured the optical force constants using linearly and radially polarized trapping beams finding a reshaping of the optical potential and an enhanced axial spring constant for the latter. These measurements open perspectives for the control and handling of silicon nanoparticles as labeling agents in biological analysis and fluorescence imaging techniques.
Synthesis of Spiro Heterocyclic Compounds (2009)

Reaction of isatin with acetophenone derivatives gave 3‐hydroxy‐3‐phenacyl oxindole derivatives (II) , dehydration of (II) gave 3‐phenacylidene‐2‐indolinone derivatives (III) . Condensation of (III) with hydrazine hydrate, phenylhydrazine and phenylthiourea afforded new spiropyrazolines (IV &amp; V) and spiropyrimidinethione (VI) respectively. The structures of the final products were established by physical and spectral means.