gebhart/patrepeval huggingface dataset:
Direct Association of p300 with Unmodified H3 and H4 N Termini Modulates p300-dependent Acetylation and Transcription of Nucleosomal Templates (2003)

The nature of histone acetylation events in active chromatin is an important issue in transcriptional regulation. We have systematically analyzed the ability of p300, either alone or in response to an interacting activator, to acetylate specific recombinant histones in the context of free histones, histone octamers, or nucleosomal arrays. Our results indicate that p300 has an intrinsic ability to acetylate all core histones but that the level and specificity of histone acetylation is indeed context-dependent. Thus, H3 and H4 are preferentially acetylated in free octamers, whereas all histones are nearly equally acetylated, in an activator-dependent manner, in chromatin. Moreover, H3 and H4 show H2A and H2B tail-independent acetylation in chromatin, whereas maximal H2A and H2B acetylation in this context is dependent upon H3 and H4 tails (but not their acetylation). In further support of an apparent intrinsic preference of p300 for the H3 and H4 tails, as well as an important role for direct interactions of p300 with unacetylated H3 and H4 tails in both acetylation and transcription, we have shown that p300 selectively acetylates isolated H3 and H4 tails, that p300 strongly and selectively binds to free unacetylated H3 and H4 tails, and that p300-mediated acetylation of nucleosomal histones and transcriptional activation are selectively inhibited by isolated (unacetylated) H3 and H4 tails.
Effect of Tip Functionalization on Transport through Vertically Oriented Carbon Nanotube Membranes (2005)

Ionic flux through a composite membrane structure, containing vertically aligned carbon nanotubes crossing a polystyrene matrix film, was studied as a function of chemical end groups at the entrance to carbon nanotubes' (CNTs) cores. Plasma oxidation during the membrane fabrication process introduced carboxylic acid groups on the CNTs' tips that were modified using carbodiimide mediated coupling between the carboxylic acid and an accessible amine groups of the functional molecule. Functionalization molecules included straight chain alkanes, anionically charged dye molecules, and an aliphatic amine elongated by polypeptide spacers. Functionalization was confirmed by FTIR spectroscopy, and areal functional density was estimated by transmission electron microscopy studies of thiol terminated sites decorated by nanocrystalline gold. The transport through the membrane of two different sized but equally charged molecules (ruthenium bipyridine [Ru-(bipy)3(2+)] and methyl viologen [MV2+]) was quantified in a U-tube permeation cell by UV-vis spectroscopy. Relative selectivity of the permeates varied from 1.7 to 3.6 as a function of tip-functionalization chemistry. Anionic charged functional groups sharply increased the flux of the cationic permeates. This effect was reduced at higher solution ionic strength consistent with shorter Debye screening length. The observed selectivities were consistent with a hindered diffusion model with functionalization at the CNT tip and not along the length of the CNT core.
A Mutation within the Leucine-Rich Repeat Domain of the Arabidopsis Disease Resistance Gene RPS5 Partially Suppresses Multiple Bacterial and Downy Mildew Resistance Genes (1998)

Recognition of pathogens by plants is mediated by several distinct families of functionally variable but structurally related disease resistance (R) genes. The largest family is defined by the presence of a putative nucleotide binding domain and 12 to 21 leucine-rich repeats (LRRs). The function of these LRRs has not been defined, but they are speculated to bind pathogen-derived ligands. We have isolated a mutation in the Arabidopsis RPS5 gene that indicates that the LRR region may interact with other plant proteins. The rps5-1 mutation causes a glutamate-to-lysine substitution in the third LRR and partially compromises the function of several R genes that confer bacterial and downy mildew resistance. The third LRR is relatively well conserved, and we speculate that it may interact with a signal transduction component shared by multiple R gene pathways.
Three-dimensional structure of human RNase 1ΔN7 at 1.9 Å resolution (2001)

Human pancreatic ribonuclease 1 (RNase 1) is considered to be the human counterpart of bovine pancreatic RNase A. Truncation of seven amino-acid residues from the amino-terminal sequence resulted in RNase 1 Delta N7, which has a reduced ribonucleolytic activity and a lower affinity for the human placental RNase inhibitor (PRI). This RNase 1 variant has been cloned, heterologously overexpressed, purified and crystallized. Its crystal structure has been determined and refined using data to 1.9 A resolution. The molecule displays the alpha + beta folding topology typical of members of the RNase A superfamily. The main distinct features found in RNase 1 Delta N7 are basically located in three loops affecting the fitting of the enzyme to the active site of subtilisin and the shape of the B2 subsite. These changes, taken with the lack of the catalytically active residue Lys7, may explain the reduced affinity of RNase 1 Delta N7 for PRI and the low ribonucleolytic activity of the protein when compared with the native enzyme.
Accurate and efficient characterization of streak camera using etalon and fitting method with constraints (2011)

Streak camera is widely used in continuous time diagnostics in fast physical process. To produce accurate result, it requires delicate calibration and a reliable analysis method. High quality sweep-rate data with uncertainty smaller than 0.5% are obtained over the full record area by a constrained fitting method of peak position measurement, with a short pulse laser and an etalon as the fiducial source. The temporal response is linearized by this full-screen sweep-rate data, which eliminates errors in measurement due to nonlinearity and space-distortion inherent in streak camera.
Haemorrhagic Fever with Renal Syndrome: an analysis of the outbreaks in Belgium, France, Germany, the Netherlands and Luxembourg in 2005 (2007)

This article aims to describe the Haemorrhagic Fever with Renal Syndrome (HFRS) situation in 2005 in five neighbouring countries (Belgium, France, Germany, the Netherlands and Luxembourg) and define the most affected areas. The 2005 HFRS outbreaks in these countries were the most significant in the region since 1990, with a total of 1,114 confirmed cases. The main feature of the epidemic was the extension of the known endemic area in several of the affected countries, with the involvement of urban areas for the first time. A significant increase in the number of cases was noted for the first time in the province of Liège in Belgium and in the Jura department in France.
Trends in power semiconductor devices (1996)

This paper reviews recent trends in power semiconductor device technology that are leading to improvements in power losses for power electronic systems. In the case of low voltage (<100 V) power rectifiers, the silicon P-i-N rectifier has been displaced by the silicon Schottky rectifier, and it is projected that the silicon TMBS rectifier will be the preferred choice in the future. In the case of high voltage (>100 V) power rectifiers, the silicon P-i-N rectifier continues to dominate but significant improvements are expected by the introduction of the silicon MPS rectifier followed by the GaAs and SiC based Schottky rectifiers. Equally important developments are occurring in power switch technology. The silicon bipolar power transistor has been displaced by silicon power MOSFETs in low voltage (<100 V) systems and by the silicon IGBTs in high voltage (>100 V) systems. The process technology for these MOS-gated devices has shifted from V-MOS in the early 1970s to DMOS in the 1980s, with more recent introduction of the UMOS technology in the 1990s. For the very high power systems, the thyristor and GTO continue to dominate, but significant effort is underway to develop MOS-gated thyristors (MCTs, ESTs, DG-BRTs) to replace them before the turn of the century. Beyond that time frame, it is projected that silicon carbide based switches will begin to displace these silicon devices.
Breaking the diffraction limit by saturation in stimulated-Raman-scattering microscopy: A theoretical study (2014)

We present a theoretical investigation on the saturation of stimulated Raman scattering (SRS) and propose an application of it to break the diffraction limit in SRS microscopy. In our proposed scheme, a donut-shaped Stokes beam is used to saturate SRS at the rim of a focused Gaussian pump beam; thus the addition of another Gaussian Stokes beam can only induce additional stimulated Raman loss to the pump beam in a small area inside the donut-shaped beam. Resembling stimulated-emission-depletion microscopy, this method can significantly improve the lateral imaging resolution. Compared with the diffraction-limited resolution, theoretical simulations show that it may be possible to double the spatial resolution with a few ${\mathrm{TW/cm}}^{2}$ of laser intensity. Such super-resolution could greatly enhance the advantage of SRS microscopy for potential applications.
Biomaterial surfaces. (1987)

The nature of a biomaterial surface governs the processes involved in biological response. Surface properties such as surface chemistry, surface energy, and morphology may be measured in order to understand the surface region of a biomaterial. In this article, we describe the surface characteristics of a few common biomaterials, review the techniques used to measure surface properties, and discuss the application of surface information in developing novel and improved biomaterials.
Biannual Radiographic Assessments of Hands and Feet in a Three‐Year Prospective Followup of Patients with Early Rheumatoid Arthritis (1992)

In a prospective followup study of 147 patients with rheumatoid arthritis of recent onset, we assessed the progression of radiographic evidence of joint damage on films of the patients' hands and feet obtained biannually. Patients were receiving first-line and second-line treatment. Ninety patients were followed up for 3 years, and 57 were followed up for only 2 years. Radiographic damage was determined by a modification of the method described by Sharp, and to ensure comparability of findings, we determined the percentage of damage per joint group (actual score divided by the maximum possible score). After 3 years, radiographic damage was present in 70% of the patients, all of whom could be identified after 1 year of study. Overall, 18-20% of the joints of the hands and feet were affected after 3 years, with relatively little abnormality per joint (approximately 8% of maximum possible score). During the entire followup, more foot joints than hand joints were affected. The rate of progression in the first year was significantly higher than in the second and third years of study, indicating a flattening of the curve of radiographic progression of joint damage.
Omega‐3 fatty acid supplementation increases anti‐inflammatory cytokines and attenuates systemic disease sequelae in experimental pancreatitis (2002)

Altering eicosanoid mediator precursor availability by infusion of (omega-3 fatty acid increases anti-inflammatory cytokines in this model of AP. This together with improved renal and respiratory function suggests that the systemic response to pancreatic injury is attenuated.
Properties of Chromatographically Purified Bovine Pancreatic Deoxyribonuclease (1969)

Preparations of bovine pancreatic deoxyribonuclease obtained by the ammonium sulfate precipitation procedure of Kunitz can be further purified by chromatography on sulfoethyl-Sephadex at pH 4.70.The instability of earlier preparations of the enzyme has usually been attributed to the sensitivity of the protein
Amorolfine nail lacquer: a novel formulation (1995)

Abstract Onychomycosis is difficult to treat. Systemic therapy with the potent oral azoles may be restricted by their potential side-effects; an attractive alternative is topical application of an antifungal directly to the nail. Several such formulations have been developed, including creams and lotions which are largely ineffective due to poor drug penetration into and through the nail structure. Nail keratin is thick and compact; its permeability is low. Transungual drug diffusion depends on the characteristics of the nail (especially degree of hydration) and the properties of the chemical (molecular weight and size, and lipophilic/hydrophilic profile). A nail lacquer containing 5% amorolfine was recently introduced; the volatile vehicle evaporates, leaving an occlusive film on the surface of the nail. The film acts as a drug depot, while at the same time increasing the hydration of the nail and the thermodynamic activity of the drug, thereby enhancing diffusion, particularly of hydrophilic compounds. Amorolfine has been shown to penetrate human nail from the film at clinically effective concentrations. In addition, the effect is long lasting: a single application of lacquer provides protection for 1 week. Release and rate of diffusion can be optimized by selecting the components of the lacquer formulation (solvent, polymer, plasticizer). Transungual drug delivery via nail lacquer is a major addition in the dermatologist's therapeutic arsenal.
Structure of Intercalated Cs in Zeolite ITQ-4: An Array of Metal Ions and Correlated Electrons Confined in a Pseudo-1D Nanoporous Host (2002)

The presence of Cs+ ions in the pseudo-1D nanopores of zeolite ITQ-4, Si32O64, is confirmed by x-ray diffraction and atomic pair distribution function analysis. Inside the nanopores the Cs+ ions are found to assemble in zigzag chains and thus form an extended, positively charged sublattice providing charge balance for a low-density electron gas also confined to the nanopores.
Formation of robust mesoscopic ring structures by self-assembly of SiCl3-terminated dendrimers (2001)

Robust sub-micrometer ring structures are easily prepared using SiCl3-terminated dendrimers.
Physiology and molecular genetics of poly(β‐hydroxyalkanoic acid) synthesis in Alcaligenes eutrophus (1991)

The Alcaligenes eutrophus genes for beta-ketothiolase, NADPH-dependent acetoacetyl-CoA reductase and poly(beta-hydroxybutyric acid) synthase (PHB synthase) which comprise the three-step PHB-biosynthetic pathway, were cloned. Molecular studies revealed that these genes are organized in a single operon. The A. eutrophus PHB-biosynthetic genes are readily expressed in other bacteria, and DNA fragments harbouring the operon can be used as a cartridge to confer to other bacteria the ability to synthesize PHB from acetyl-CoA. The biochemical and physiological capabilities of A. eutrophus for the synthesis of a wide variety of polyhydroxyalkanoates are discussed.
Loss of imprinting and genetic alterations of the cyclin-dependent kinase inhibitor p57KIP2 gene in head and neck squamous cell carcinoma. (2000)

The p57KIP2 is a maternally expressed and paternally imprinted cyclin-dependent kinase inhibitor located on chromosome 11p15.5. Because of its location, biochemical functions, and imprinting status, p57KIP2 has been considered a candidate tumor suppressor gene. To determine, for the first time, the involvement of this gene in the development of head and neck squamous carcinoma (HNSC), we analyzed the imprinting and expression status and loss of heterozygosity (LOH) within the p57KIP2 gene flanking loci on the 11p15.5 region in 64 primary untreated tumors. Of the 30 (47%) informative cases for this gene, loss of imprinting and LOH were noted in 4 (13%) and 10 tumors (33%), respectively. Analysis of the microsatellite markers flanking the p57KIP2 gene on chromosome 11p showed infrequent alterations at these loci. p57KIP2 was expressed in all tumors with LOH within and around the gene. Quantitative reverse transcription-PCR analysis showed elevated p57 mRNA expression in tumor with loss of imprinting. Sequencing analysis of exons 1 and 2 of the p57KIP gene failed to detect any mutations. Our data indicate: (a) infrequent genomic abnormalities at the p57KIP2 gene in HNSC; (b) leaky or incomplete imprinting of the paternal allele is associated with increased expression of this gene in a subset of tumors; and (c) minimal evidence for suppressor function for this gene in HNSC.
Cloning of a Second Dendritic Cell-associated C-type Lectin (Dectin-2) and Its Alternatively Spliced Isoforms (2000)

Using a subtractive cDNA cloning strategy, we isolated previously five novel genes that were expressed abundantly by the murine dendritic cell (DC) line XS52, but not by the J774 macrophage line. One of these genes encoded a unique, DC-associated C-type lectin, termed "dectin-1." Here we report the characterization of a second novel gene that was also expressed in a DC-specific manner. Clone 1B12 encoded a type II membrane-integrated polypeptide of 209 amino acids containing a single carbohydrate recognition domain motif in the COOH terminus. The expression pattern of this molecule, termed "dectin-2," was almost indistinguishable from that for dectin-1; that is, both were expressed abundantly at mRNA and protein levels by the XS52 DC line, but not by non-DC lines, and both were detected in spleen and thymus, as well as in skin resident DC (i.e. Langerhans cells). Interestingly, reverse transcriptase-polymerase chain reaction and immunoblotting revealed multiple bands of dectin-2 transcripts and proteins suggesting molecular heterogeneity. In fact, we isolated additional cDNA clones encoding two distinct, truncated dectin-2 isoforms. Genomic analyses indicated that a full-length dectin-2 (alpha isoform) is encoded by 6 exons, whereas truncated isoforms (beta and gamma) are produced by alternative splicing. We propose that dectin-2 and its isoforms, together with dectin-1, represent a unique subfamily of DC-associated C-type lectins.
Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification (2001)

Rolling circle amplification (RCA) is a surface-anchored DNA replication reaction that can be exploited to visualize single molecular recognition events. Here we report the use of RCA to visualize target DNA sequences as small as 50 nts in peripheral blood lymphocytes or in stretched DNA fibers. Three unique target sequences within the cystic fibrosis transmembrane conductance regulator gene could be detected simultaneously in interphase nuclei, and could be ordered in a linear map in stretched DNA. Allele-discriminating oligonucleotide probes in conjunction with RCA also were used to discriminate wild-type and mutant alleles in the cystic fibrosis transmembrane conductance regulator, p53, BRCA-1, and Gorlin syndrome genes in the nuclei of cultured cells or in DNA fibers. These observations demonstrate that signal amplification by RCA can be coupled to nucleic acid hybridization and multicolor fluorescence imaging to detect single nucleotide changes in DNA within a cytological context or in single DNA molecules. This provides a means for direct physical haplotyping and the analysis of somatic mutations on a cell-by-cell basis.
On the distribution of elastic fibers in the filiform papillae of Suncus murinus. (1989)

The distribution of elastic fibers in the filiform papillae of 1, 2, 3, 4 and 5 week-old and 6 month-old Suncus (Suncus murinus; insectivora) was examined by both Weigert's resorcin-fuchsin method and ultrastructural means. In the adult Suncus (6 months old), elastic fibers in the connective tissue core of the papillae were aligned perpendicularly to the epithelial surface and formed a palisade-like structure which encircled the margin of each connective tissue core. This characteristic structure was restricted to the filiform papillae in the anterior half of the lingual dorsum. In the filiform papillae of the posterior half, elastic fibers were markedly reduced and the palisade-like structure was not present. This characteristic pattern of elastic fiber distribution was established by 3 weeks of age. These observations reveal a characteristic structure consisting of elastic fibers in the connective tissue core of the filiform papillae and the regional distribution of this structure in the tongue. This suggests that the function of the structure in the connective tissue core is to protect against mechanical stress in mastication. The regional distribution of this structure may reflect the difference of mechanical strength between the anterior and posterior of the tongue caused by tongue movement during mastication.
Restoration of surface IgM-mediated apoptosis in an anti-IgM-resistant variant of WEHI-231 lymphoma cells by HS1, a protein-tyrosine kinase substrate. (1995)

The HS1 protein is one of the major substrates of non-receptor-type protein-tyrosine kinases and is phosphorylated immediately after crosslinking of the surface IgM on B cells. The mouse B-lymphoma cell line WEHI-231 is known to undergo apoptosis upon crosslinking of surface IgM by anti-IgM antibodies. Variants of WEHI-231 that were resistant to anti-IgM-induced apoptosis expressed dramatically reduced levels of HS1 protein. Expression of the human HS1 protein from an expression vector introduced into one of the variant cell lines restored the sensitivity of the cells to apoptosis induced by surface IgM crosslinking. These results suggest that HS1 protein plays a crucial role in the B-cell antigen receptor-mediated signal transduction pathway that leads to apoptosis.
Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir (2021)

Remdesivir (RDV) is a direct-acting antiviral agent that is approved in several countries for the treatment of coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2. RDV exhibits broad-spectrum antiviral activity against positive-sense RNA viruses, for example, severe acute respiratory syndrome coronavirus and hepatitis C virus, and nonsegmented negative-sense RNA viruses, for example, Nipah virus, whereas segmented negative-sense RNA viruses such as influenza virus or Crimean-Congo hemorrhagic fever virus are not sensitive to the drug. The reasons for this apparent efficacy pattern are unknown. Here, we expressed and purified representative RNA-dependent RNA polymerases and studied three biochemical parameters that have been associated with the inhibitory effects of RDV-triphosphate (TP): (i) selective incorporation of the nucleotide substrate RDV-TP, (ii) the effect of the incorporated RDV-monophosphate (MP) on primer extension, and (iii) the effect of RDV-MP in the template during incorporation of the complementary UTP. We found a strong correlation between antiviral effects and efficient incorporation of RDV-TP. Inhibition in primer extension reactions was heterogeneous and usually inefficient at higher NTP concentrations. In contrast, template-dependent inhibition of UTP incorporation opposite the embedded RDV-MP was seen with all polymerases. Molecular modeling suggests a steric conflict between the 1'-cyano group of the inhibitor and residues of the structurally conserved RNA-dependent RNA polymerase motif F. We conclude that future efforts in the development of nucleotide analogs with a broader spectrum of antiviral activities should focus on improving rates of incorporation while capitalizing on the inhibitory effects of a bulky 1'-modification.