gebhart/patrepeval huggingface dataset:
Using Ambient Ion Beams to Write Nanostructured Patterns for Surface Enhanced Raman Spectroscopy (2014)

Electrolytic spray deposition was used to pattern surfaces with 2D metallic nanostructures. Spots that contain silver nanoparticles (AgNP) were created by landing solvated silver ions at desired locations using electrically floated masks to focus the metal ions to an area as little as 20 μm in diameter. The AgNPs formed are unprotected and their aggregates can be used for surface-enhanced Raman spectroscopy (SERS). The morphology and SERS activity of the NP structures were controlled by the surface coverage of landed silver ions. The NP structures created could be used as substrates onto which SERS samples were deposited or prepared directly on top of predeposited samples of interest. The evenly distributed hot spots in the micron-sized aggregates had an average SERS enhancement factor of 10(8) . The surfaces showed SERS activity when using lasers of different wavelengths (532, 633, and 785 nm) and were stable in air.
Power Densities Using Different Cathode Catalysts (Pt and CoTMPP) and Polymer Binders (Nafion and PTFE) in Single Chamber Microbial Fuel Cells (2005)

Cathode catalysts and binders were examined for their effect on power densities in single chamber, air-cathode, microbial fuel cells (MFCs). Chronopotentiometry tests indicated thatthe cathode potential was only slightly reduced (20-40 mV) when Pt loadings were decreased from 2 to 0.1 mg cm(-2), and that Nafion performed better as a Pt binder than poly(tetrafluoroethylene) (PTFE). Replacing the precious-metal Pt catalyst (0.5 mg cm(-2); Nafion binder) with a cobalt material (cobalt tetramethylphenylporphyrin, CoTMPP) produced slightly improved cathode performance above 0.6 mA cm(-2), but reduced performance (<40 mV) at lower current densities. MFC fed batch tests conducted for 35 cycles (31 days) using glucose showed that replacement of the Nafion binder used for the cathode catalyst (0.5 mg of Pt cm(-2)) with PTFE reduced the maximum power densities (from 400 +/- 10 to 480 +/- 20 mW m(-2) to 331 +/- 3 to 360 +/- 10 mW m(-2)). When the Pt loading on cathode was reduced to 0.1 mg cm(-2), the maximum power density of MFC was reduced on average by 19% (379 +/- 5 to 301 +/- 15 mW m(-2); Nafion binder). Power densities with CoTMPP were only 12% (369 +/- 8 mW m(-2)) lower over 25 cycles than those obtained with Pt (0.5 mg cm(-2); Nafion binder). Power densities obtained using with catalysts on the cathodes were approximately 4 times more than those obtained using a plain carbon electrode. These results demonstrate that cathodes used in MFCs can contain very little Pt, and that the Pt can even be replaced with a non-precious metal catalyst such as a CoTMPP with only slightly reduced performance.
Distinct Reactivity Differences of Metal Oxo and Its Corresponding Hydroxo Moieties in Oxidations: Implications from a Manganese(IV) Complex Having Dihydroxide Ligand (2011)

The Mn+OH moiety in a manganese(IV) complex has more powerful electron-transfer capability than its corresponding Mn+O moiety. An Mn+O moiety can abstract hydrogen from a substrate, then rebind the OH group from its reduced M(n−1)+OH form to the substrate radical. In contrast, the active center with an Mn+OH cannot perform similar rebound from its reduced M(n−1)+OH2 group (see scheme; HAT=hydrogen abstraction). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Nucleotide sequence stability of the genome of hepatitis delta virus (1995)

Cultured cells were cotransfected with a fully sequenced 1,679-base cDNA clone of human hepatitis delta virus (HDV) RNA genome and a cDNA for the genome of woodchuck hepatitis virus (WHV). The HDV particles released were able to infect a woodchuck that was chronically infected with WHV. The HDV so produced was passaged a total of six times in woodchucks in order to determine the stability of the HDV nucleotide sequence. During a final chronic infection with such virus, liver RNA was extracted, and the HDV nucleotide sequence for the 352-base region, positions 905 to 1256, was obtained. By means of PCR, we obtained double-stranded cDNA both for direct sequencing and also for molecular cloning followed by sequencing. By direct sequencing, we found that a consensus sequence existed and was identical to the original sequence. From the sequences of 31 clones, we found 32% (10 of 31) to be identical to the original single nucleotide sequence. For the remainder, there were neither insertions nor deletions but there was a small number of single-nucleotide changes. These changes were predominantly transitions rather than transversions. Furthermore, the transitions were largely of just two types, uridine to cytidine and adenosine to guanosine. Of the 40 changes detected on HDV, 35% (14 of 40) occurred within an eight-nucleotide region that included position 1012, previously shown to be a site of RNA editing. These findings may have significant implications regarding both the stability of the HDV RNA genome and the mechanism of RNA editing.
Hypertension, the endothelial cell, and the vascular complications of diabetes mellitus. (1992)

Hypertension is a major factor that contributes to the development of the vascular complications of diabetes mellitus, which primarily include atherosclerosis, nephropathy, and retinopathy. The mechanism of the pathophysiological effects of hypertension lies at the cellular level in the blood vessel wall, which intimately involves the function and interaction of the endothelial and vascular smooth muscle cells. Both hypertension and diabetes mellitus alter endothelial cell structure and function. In large and medium size vessels and in the kidney, endothelial dysfunction leads to enhanced growth and vasoconstriction of vascular smooth muscle cells and mesangial cells, respectively. These changes in the cells of smooth muscle lineage play a key role in the development of both atherosclerosis and glomerulosclerosis. In diabetic retinopathy, damage and altered growth of retinal capillary endothelial cells is the major pathophysiological insult leading to proliferative lesions of the retina. Thus, the endothelium emerges as a key target organ of damage in diabetes mellitus; this damage is enhanced in the presence of hypertension. An overall approach to the understanding and treatment of diabetes mellitus and its complications will be to elucidate the mechanisms of vascular disease and endothelial cell dysfunction that occur in the setting of hypertension and diabetes.
Evolution of Two-Component Signal Transduction (2000)

Two-component signal transduction (TCST) systems are the principal means for coordinating responses to environmental changes in bacteria as well as some plants, fungi, protozoa, and archaea. These systems typically consist of a receptor histidine kinase, which reacts to an extracellular signal by phosphorylating a cytoplasmic response regulator, causing a change in cellular behavior. Although several model systems, including sporulation and chemotaxis, have been extensively studied, the evolutionary relationships between specific TCST systems are not well understood, and the ancestry of the signal transduction components is unclear. Phylogenetic trees of TCST components from 14 complete and 6 partial genomes, containing 183 histidine kinases and 220 response regulators, were constructed using distance methods. The trees showed extensive congruence in the positions of 11 recognizable phylogenetic clusters. Eukaryotic sequences were found almost exclusively in one cluster, which also showed the greatest extent of domain variability in its component proteins, and archaeal sequences mainly formed species-specific clusters. Three clusters in different parts of the kinase tree contained proteins with serine-phosphorylating activity. All kinases were found to be monophyletic with respect to other members of their superfamily, such as type II topoisomerases and Hsp90. Structural analysis further revealed significant similarity to the ATP-binding domain of eukaryotic protein kinases. TCST systems are of bacterial origin and radiated into archaea and eukaryotes by lateral gene transfer. Their components show extensive coevolution, suggesting that recombination has not been a major factor in their differentiation. Although histidine kinase activity is prevalent, serine kinases have evolved multiple times independently within this family, accompanied by a loss of the cognate response regulator(s). The structural and functional similarity between TCST kinases and eukaryotic protein kinases raises the possibility of a distant evolutionary relationship.
Genetic investigation of cAMP-dependent protein kinase function in Drosophila development. (1993)

The cAMP-dependent protein kinase (PKA) has been shown to mediate the vast majority of cellular responses to the intracellular second messenger, cAMP, in eukaryotes. To study the role of cAMP signal transduction in Drosophila development, we have isolated and molecularly characterized mutations of varying severity in the Drosophila PKA gene, DC0. Biochemical measurements indicate that DC0 is either the sole or the major PKA catalytic subunit gene in Drosophila. Adult females heterozygous for a strong and a weak DC0 allele fail to lay eggs and show a striking and novel defect in oogenesis that includes the formation of egg chambers containing multinucleate nurse cells. Females heterozygous for two weak DC0 alleles are fertile but produce offspring showing a variety of defects in embryogenesis, including preblastoderm arrest and alterations in cuticular patterning. Animals zygotically null for DC0 die as morphologically normal first-instar larvae, implying that maternally encoded protein, which perdures for at least 12 hr, suffices for embryogenesis. Animals hemizygous for weak DC0 alleles survive for several days as larvae but grow slowly. Mitotic recombination experiments in the adult eye indicate that the DC0 gene is not required autonomously either for cell viability or normal growth rates. These results argue that cAMP-mediated signal transduction is essential at a variety of stages during the development of a metazoan.
In vivo competition between iron and manganese for occupancy of the active site region of the manganese-superoxide dismutase of Escherichia coli. (1991)

Three forms of the dimeric manganese superoxide dismutase (MnSOD) were isolated from aerobically grown Escherichia coli which contained 2 Mn, 1 Mn and 1 Fe, or 2 Fe, respectively. These are designated Mn2-MnSOD, Mn,Fe-MnSOD, and Fe2-MnSOD. Substitution of iron in place of manganese, eliminated catalytic activity, decreased the isoelectric point, and increased the native electrophoretic anodic mobility, although circular dichroism, high performance liquid chromatography gel exclusion chromatography, and sedimentation equilibrium revealed no gross changes in conformation. Moreover, replacement of iron by manganese restored enzymatic activity. Fe2-MnSOD and the iron-superoxide (FeSOD) of E. coli exhibit distinct optical absorption spectra. These data indicate that the active site environments of E. coli MnSOD and FeSOD must differ. They also indicate that competition between iron and manganese for nascent MnSOD polypeptide chains occurs in vivo, and copurification of these variably substituted MnSODs can explain the substoichiometric manganese contents and the variable specific activities which have been reported for this enzyme.
Design of model amphipathic peptides having potent antimicrobial activities (1992)

Induced amphipathic alpha-helical conformations play an important role in the biological activity of peptides. By using reversed-phase high-performance liquid chromatography (RP-HPLC) as a means to study the secondary structure of peptides at aqueous/lipid interfaces, a sequence (Ac-LKLLKKLLKKLKKLLKKL-NH2) was found to readily adopt an amphipathic alpha-helical conformation upon interacting with the lipid groups of the stationary phase during RP-HPLC. This peptide exhibited potent antimicrobial activities against both Gram-positive and Gram-negative bacteria. We have prepared a complete set of omission, as well as of leucine and lysine substitution, analogs of this sequence. These analogs were used to investigate the effects of such alterations on the parent sequence's antimicrobial and hemolytic activities relative to each analog's behavior during RP-HPLC. The potential for the formation of ion channels through cell membranes by this amphipathic model peptide was also evaluated through preparation of analogs which varied in length from 8 to 22 residues, while maintaining their amphipathicity.
Zinc as a Cofactor for Heparin Neutralization by Histidine-rich Glycoprotein (1997)

We have studied the ability of histidine-rich glycoprotein (HRG) to neutralize the anticoagulant activity of heparin in plasma and in a purified component clotting assay. Addition of HRG to plasma or to the purified component assay did not neutralize the anticoagulant activity of heparin unless micromolar concentrations of zinc were present. Higher zinc concentrations were required for citrated than for heparinized plasmas due to competition of citrate with HRG for zinc binding. Zinc concentrations as low as 1.25 microM revealed HRG to be a powerful competitor of antithrombin for heparin in the purified component assays. HRG binding of heparin also was shown by affinity chromatography of HRG from immobilized heparin in the presence and absence of zinc. In the absence of zinc, HRG was eluted by 0.1 M NaCl, but, in the presence of zinc, elution of HRG required 1.0 M NaCl. Investigation of other divalent cations (copper and magnesium) indicated that augmentation of heparin binding by HRG in the presence of antithrombin was restricted to zinc. The HRG.Zn complex effectively competes with antithrombin for heparin, which restricts the availability of heparin to bind antithrombin and allows thrombin-mediated fibrinogenesis to proceed unimpeded. This could be initiated by zinc released from activated platelets.
Human atherosclerosis. II. Immunocytochemical analysis of the cellular composition of human atherosclerotic lesions. (1986)

The authors have performed immunocytochemical investigations of the distribution of various cell types in human atherosclerotic plaques using monoclonal antibodies specific to smooth muscle cells (CGA7 [Gown et al, J Cell Biol 1985, 100:807-813] and HHF35 [Tsukada et al, Am J Pathol (In press)] ); lymphocytes (T200 antigen); endothelial cells (Factor VIII and the Ulex europeus agglutinin); and macrophages, the latter with a new macrophage-specific antibody HAM56. All studies were performed on methanol-Carnoy's-fixed, paraffin-embedded tissues. In areas of grossly normal aorta, significant numbers of macrophages were noted within areas of diffuse intimal thickening. The cellular composition of the following three types of raised lesions were analyzed: fibro-fatty lesions, which, despite their gross appearance, consistent with fibrous plaques, were composed almost exclusively of macrophages and lymphocytes and almost devoid of smooth muscle cells; fibrous plaques, which were predominantly composed of smooth muscle cells displaying considerable morphologic heterogeneity and an admixture of blood-borne cells; advanced plaques, which were characterized by complex layers of smooth muscle cells and macrophages with considerable variation from region to region. Also noted were foci of medial and even intimal vascularization subjacent to the more advanced plaques. These studies demonstrate the application of monoclonal antibody technology to the study of the cellular composition of human atherosclerotic lesions.
Fever: Basic Mechanisms and Management (1991)

History of clinical thermometry clinical thermoregulators thermoregulation the normal tempterature circadian rhythms pyrogenic cytokines and the febrile reponse hyperthermia fever - blessing or curse? fever therapy antipyresis fever patterns relationships between temperature and severity of illness fever in children fever in the elderly fever in HIV-infected patients fever in immunosuppressed patients fever of unknown origin.
Evaluación de la evidencia científica (1995)

El articulo describe las principales escalas de clasificacion de la evidencia cientifica disponibles.
Presenta el esquema de gradacion utilizado en la Agencia d’Avaluacio de Tecnologia Medica (AATM) y muestra el proceso de formulacion de recomendaciones a partir del analisis y de la sintesis de la evidencia cientifica.
Isolation and characterization of C-reactive protein and serum amyloid P component in the rat. (1982)

C-reactive protein (RP) and serum amyloid P component (SAP) have been identified for the first time in rat serum and isolated by calcium-dependent affinity chromatography. Rat CRP closely resembled human CRP in its amino acid composition, in having five subunits per molecule and in its electron microscopic appearance as a pentameric annular disc. It differed, however, from all other mammalian CRP's characterised hitherto in being a glycoprotein bearing a single complex oligosaccharide on each polypeptide subunit. Furthermore one pair of tis subunits per molecule was linked by a interchain disulphide bridges whereas in other animals the subunits of both CRP and SAP are all non-covalently associated. The serum concentration of CRP in normal healthy laboratory rats and in specific pathogen-free rats was 300-600 micrograms/ml which is much greater than has been described in any other species and exceeds even maximal acute phase levels of CRP in man. Following injections of casein or croton oil, serum CRP levels rose to a maximum of about 900 micrograms/ml. Rat CRP bound to pneumococcal C-polysaccharide (CPS( but, in marked contrast to the behaviour of CRP from man, rabbit and marine teleost fish, it did not precipitate with CPS solutions, agglutinate CPS-coated sheep erythrocytes or initiate complement activation. Rat SAP, like SAP of other species, was a glycoprotein but unlike them it was composed only of a single pentameric disc not two such discs interacting face-to-face. The normal level of SAP in rat serum was 20-50 micrograms/ml, very similar to the levels seen in man, and it did not behave as an acute phase reactant in response to casein or croton-oil injections. In this respect it resembled human SAP but differed from murine SAP which is a major acute phase reactant.
Simple and Quantitative Mechanochemical Preparation of a Porous Crystalline Material Based on a 1D Coordination Network for Uptake of Small Molecules (2005)

Kneading them in: A versatile porous material based on the 1D coordination network [CuCl2(dace)]∞ (dace=trans-1,4-diaminocyclohexane) can be inexpensively prepared by a mechanochemical reaction followed by mild thermal treatment. The system is able to reversibly absorb molecules from solution or by simple kneading, while guest desorption from the product invariably leads back to the unsolvated form.
Assignment of a novel bifurcated SET domain gene, SETDB1, to human chromosome band 1q21 by in situ hybridization and radiation hybrids (1999)

We have identified a human gene encoding an unusual bifurcated SET domain protein containing a large "insertion" between the most highly conserved parts of the SET domain. The existence of an evolutionarily related C. elegans gene encoding a similarly bifurcated SET domain suggests that SET domains may generally be composed of two functionally distinct subdomains. We mapped this gene, called SETDB1, to human chromosome 1q21. This region is targeted by a large number of recurrent translocations, suggesting that like the SET domain protein MLL, mutant forms of SETDB1 may be associated with human neoplasias.
A 90 nm logic technology featuring 50 nm strained silicon channel transistors, 7 layers of Cu interconnects, low k ILD, and 1 μm/sup 2/ SRAM cell (2003)

A leading edge 90 nm technology with 1.2 nm physical gate oxide, 50 nm gate length, strained silicon, NiSi, 7 layers of Cu interconnects, and low k carbon-doped oxide (CDO) for high performance dense logic is presented. Strained silicon is used to increase saturated NMOS and PMOS drive currents by 10-20% and mobility by >50%. Aggressive design rules and unlanded contacts offer a 1.0 /spl mu/m/sup 2/ 6-T SRAM cell using 193 nm lithography.
[6-mercaptopurine levels and study of blood lymphocyte subsets during azathioprine treatment of Crohn's disease]. (1998)

Monitoring of 6-mercaptopurine plasma concentration and blood lymphocyte subpopulations is of little value in Crohn's disease patients treated with azathioprine.
S100.alpha., CAPL, and CACY: molecular cloning and expression analysis of three calcium-binding proteins from human heart (1992)

Elevated levels of intracellular calcium are a major cause of myocardial dysfunction. To find possible mediators of the deregulated calcium we searched for EF-hand calcium-binding proteins of the S100 family. By PCR technology we identified three members of the S100 protein family (S100 alpha, CACY, and CAPL) in the human heart. We cloned the corresponding cDNAs and examined their expression levels in various human tissues by Northern blot analysis. All three proteins are expressed at high levels in the human heart. Whereas CACY and CAPL mRNAs are expressed ubiquitously, S100 alpha mRNA is restricted to heart, skeletal muscle, and brain. Interestingly, the expression pattern of S100 alpha, CACY, and CAPL in human tissues differs significantly from that in rodent tissues.
B-cell surface antigen B7 provides a costimulatory signal that induces T cells to proliferate and secrete interleukin 2. (1991)

Occupancy of the T-cell receptor complex does not appear to be a sufficient stimulus to induce a T-cell-mediated immune response. Increasing evidence suggests that cognate cell-cell interaction between an activated T cell and an antigen-presenting cell may provide such a stimulus. A candidate T-cell surface molecule for this costimulatory signal is the T-cell-restricted CD28 antigen. Following crosslinking with anti-CD28 mAb, suboptimally stimulated CD28+ T cells show increased proliferation and markedly increased secretion of a subset of lymphokines. Recently, the B-cell surface activation antigen B7 was shown to be a natural ligand for the CD28 molecule, and both B7 and CD28 are members of the immunoglobulin superfamily. Here we report that B7-transfected CHO cells can induce suboptimally activated CD28+ T cells to proliferate and secrete high levels of interleukin 2. The response is identical whether T cells are submitogenically stimulated with either phorbol myristate acetate or anti-CD3 to activate the T cells. This response is specific and can be totally abrogated with anti-B7 monoclonal antibody. As has previously been observed for anti-CD28 monoclonal antibody, B7 ligation induced secretion of interleukin 2 but not interleukin 4. We have previously demonstrated that B7 expression is restricted to activated B lymphocytes and interferon gamma-activated monocytes. Since these two cellular populations are involved in antigen presentation as well as cognate interaction with T lymphocytes, B7 is likely to represent a central constimulatory signal that is capable of amplifying an immune response.
The relationship of FcγRIIIa genotype to degree of B cell depletion by rituximab in the treatment of systemic lupus erythematosus (2003)

These results highlight the potential variability of B cell depletion by rituximab in the treatment of autoimmune disease and indicate that Fc receptors are an important determinant of that variability. The findings further suggest the importance of antibody-dependent cell-mediated cytotoxicity and/or apoptosis induction via FcgammaRIIIa-expressing effector cells in the mechanism of B cell depletion by this widely used monoclonal antibody.