gebhart/patrepeval huggingface dataset:
The Positively Charged Surface of Herpes Simplex Virus UL42 Mediates DNA Binding (2008)

Herpes simplex virus DNA polymerase is a heterodimer composed of UL30, a catalytic subunit, and UL42, a processivity subunit. Mutations that decrease DNA binding by UL42 decrease long chain DNA synthesis by the polymerase. The crystal structure of UL42 bound to the C terminus of UL30 revealed an extensive positively charged surface ("back face"). We tested two hypotheses, 1) the C terminus of UL30 affects DNA binding and 2) the positively charged back face mediates DNA binding. Addressing the first hypothesis, we found that the presence of a peptide corresponding to the UL30 C terminus did not result in altered binding of UL42 to DNA. Addressing the second hypothesis, previous work showed that substitution of four conserved arginine residues on the basic face with alanines resulted in decreased DNA affinity. We tested the affinities for DNA and the stimulation of long chain DNA synthesis of mutants in which the four conserved arginine residues were substituted individually or together with lysines and also a mutant in which a conserved glutamine residue was substituted with an arginine to increase positive charge on the back face. We also engineered cysteines onto this surface to permit disulfide cross-linking studies. Last, we assayed the effects of ionic strength on DNA binding by UL42 to estimate the number of ions released upon binding. Our results taken together strongly suggest that the basic back face of UL42 contacts DNA and that positive charge on this surface is important for this interaction.
IMPORTANCE OF TYPE I AND TYPE II MECHANISMS IN THE PHOTODYNAMIC INACTIVATION OF VIRUSES IN BLOOD WITH ALUMINUM PHTHALOCYANINE DERIVATIVES (1992)

The relative importance of type I and type II mechanisms in the photodynamic treatment of red blood cell concentrations (RBCC) to inactivate viruses was studied using aluminum phthalocyanine tetrasulfonate (AlPcS4), visible light and quenching or enhancing agents of reactive forms of oxygen. Treatment of a human RBCC with 10-13 microM AlPcS4 and 25-26 mW/cm2 visible light resulted in the rapid and complete inactivation of added vesicular stomatitis virus (VSV). The addition of mannitol, glycerol, reduced glutathione (GSH), or superoxide dismutase (SOD), known quenching agents of type I mechanisms, had little to no effect on the rate of inactivation of VSV. Significant inhibition of VSV kill was observed on addition of tryptophan or sodium azide, known quenchers of type II mechanisms. Additionally, the rate of VSV kill was enhanced in the presence of D2O. Taken together, these results indicate a predominant role of singlet oxygen in the inactivation of VSV on photodynamic treatment of RBCC. The relative importance of type I and type II mechanisms on cellular toxicity was also evaluated. Little, if any hemoglobin release was observed on treatment of human or rabbit RBCC with 10 microM AlPcS4 and 44 J/cm2 of visible light in the presence or absence of the above mentioned quenchers. The effect of the addition of quenchers on the recovery and circulatory survival of treated, autologous rabbit RBCC, labeled with 51Cr, was also assessed.(ABSTRACT TRUNCATED AT 250 WORDS)
Multiple forms of ubiquitin-activating enzyme E1 from wheat. Identification of an essential cysteine by in vitro mutagenesis. (1992)

Ubiquitin-activating enzyme, E1, directs the ATP-dependent formation of a thiol ester linkage between itself and ubiquitin. The energy in this bond is ultimately used to attach ubiquitin to various intracellular proteins. We previously reported the isolation of multiple E1s from wheat and the characterization of a cDNA encoding this protein (UBA1). We now report the derived amino acid sequence of two additional members of this gene family (UBA2 and UBA3). Whereas the amino acid sequence of UBA2 is nearly identical to UBA1, the sequence of UBA3 is significantly different. Nevertheless, the protein encoded by UBA3 catalyzes the ATP-dependent activation of ubiquitin in vitro. Comparison of derived amino acid sequences of genes encoding E1 from plant, yeast, and animal tissues revealed 5 conserved cysteine residues, with one potentially involved in thiol ester bond formation. To identify this essential residue, codons corresponding to each of the 5 cysteines in UBA1 were individually altered using site-directed mutagenesis. The mutagenized enzymes were expressed in Escherichia coli and assayed for their ability to activate ubiquitin. Only substitution of the cysteine at position 626 abolishes E1 activity, suggesting that this residue forms the thiol ester linkage with ubiquitin.
A unified fuzzy feature indexing scheme for region based online image querying (2004)

We describe a novel indexing and retrieval methodology integrating color, texture and shape information for content-based image retrieval in online image databases. This methodology, called PicSearcher, applies unsupervised image segmentation to partition an image into a set of regions, then fuzzy color histogram as well as fuzzy texture and shape properties of each region is calculated to be part of their signatures. The fuzzification procedures resolve the recognition uncertainty stemming from color quantization and human perception of colors. At the same time, this unified fuzzy scheme incorporates the segmentation-related uncertainties into the retrieval algorithm. Then an adaptive and effective measure for the overall similarity between images is developed by integrating properties of all the regions in the image. An implemented prototype system of PicSearcher has demonstrated a promising retrieval performance for an online test database containing 10,000 general-purpose color images, as compared with its peer systems in the literature.
Switching of Electron- to Energy-Transfer by Selective Excitation of Different Chromophores in Arrays Based on Porphyrins and a Polypyridyl Iridium Complex (2002)

Excitation at 350−355 nm of the dyads PAu−Ir, PH2−Ir and of the triads PH2−Ir−PAu and PZn−Ir−PAu where Ir, iridium(III) bis-terpyridine, is covalently linked to gold (III), free-base and zinc(II) tetraaryl-porphyrins (PAu, PH2, PZn), produces to a predominant extent the ligand centered triplet excited state of the iridium complex unit, 3Ir. The processes occurring in the arrays upon UV excitation have been characterized by steady state and time-resolved spectroscopic methods. Energy transfer to the porphyrin triplets dominates the deactivation of 3Ir in PAu−Ir, PH2−Ir, and PH2−Ir−PAu, with rates of 2.9 × 1010 s-1 (3Ir → 3PAu) and ca. 1011 s-1 (3Ir → 3PH2), in contrast to what has been shown to occur upon selective excitation of the PH2 unit, which yields electron transfer leading to charge separation. The different outcome is discussed on the basis of the overlap of the HOMO and LUMO orbitals involved in the electron-transfer reaction for the Ir acceptor unit and the PH2 donor unit, with the aid of semiempirical calculations. Remarkably, the PZn based array PZn−Ir−PAu displays efficient electron transfer with the formation of a charge separated state with unitary yield, irrespective of the component which is excited. A very high driving force, ΔG° = −1.1 eV, could explain the prevalence of the electron-transfer reaction in the latter case.
Renal Inflammation: Targeted Iron Oxide Nanoparticles for Molecular MR Imaging in Mice (2010)

Injection of CR2-conjugated SPIO caused a significant reduction in T2-weighted MR imaging signal and T2 relaxation time in nephritic kidneys.
Thermostable alanine racemase from Bacillus stearothermophilus: DNA and protein sequence determination and secondary structure prediction (1988)

The nucleotide sequence of the alanine racemase (EC 5.1.1.1) gene from a thermophile, Bacillus stearothermophilus, was determined by the dideoxy chain termination method with universal and synthetic site-specific primers. The amino acid sequence of the enzyme predicted from the nucleotide sequence was confirmed by peptide sequence information derived from the N-terminal amino acid residues and several tryptic fragments. The alanine racemase gene consists of 1158 base pairs encoding a protein of 386 amino acid residues; the molecular weight of the apoenzyme is estimated as 43,341. The racemase gene of B. stearothermophilus has a closely similar size (1158 vs 1167 base pairs) to that of the gene of a mesophile, B. subtilis, but shows a higher preference for codons ending in G or C. A comparison of the amino acid sequence with those of Bacillus subtilis and Salmonella typhimurium dadB and alr enzymes revealed overall sequence homologies of 31-54%, including an identical octapeptide bearing the pyridoxal 5'-phosphate binding site. Although the residues common in the four racemases are not continuously arrayed, these constitute distinct domains and their hydropathy profiles are very similar. The secondary structure of B. stearothermophilus alanine racemase was predicted from the results obtained by theoretical analysis and circular dichroism measurement.
The Major Receptor for C-Reactive Protein on Leukocytes Is Fcγ Receptor II (1999)

C-reactive protein (CRP) is an acute phase serum protein that shares several functions with immunoglobulin (Ig)G including complement activation and binding to receptors on monocytes and neutrophils. The identity of the receptor for CRP has been the target of extensive research. We previously determined that CRP binds to the high affinity receptor for IgG, FcgammaRI (CD64). However, this interaction could not account for the majority of binding of CRP to neutrophils or monocytic cells. We now determine that CRP also interacts with FcgammaRIIa (CD32), the low affinity receptor for IgG on monocytes and neutrophils. COS-7 cells were transfected with a construct containing the human FcgammaRIIA cDNA. CRP binding and the presence of CD32 were detected by mAb and analyzed by two-color flow cytometry. Cells expressing CD32 bound CRP in a dose-dependent and saturable manner consistent with receptor binding. CRP bound to transfectants and K-562 cells with similar kinetics, and in both cases binding was completely inhibited by aggregated IgG. On monocytic cell lines, treatment with Bt(2)cAMP increased FcgammaRII expression and enhanced CRP binding. CRP also specifically precipitated FcgammaRI and FcgammaRII from the monocytic cell line, THP-1. It is suggested that the major receptor for CRP on phagocytic cells is FcgammaRII.
The Therapeutic Potential of 4-1BB (CD137) in Cancer (2005)

Techniques for modulating immune cells for cancer therapy have been widely studied. One key approach that is being clinically tested is developing tumor-destructive cell-mediated immune responses by regulating co-stimulatory molecules. 4-1BB (CD137), a member of the TNF receptor family, is expressed following activation of T and NK cells. Recently, it has been reported that DCs also express 4-1BB. Cross-linking of 4-1BB provides a potent co-stimulatory signal for lymphocytes via signal transduction pathways that modulate a number of cellular responses. One remarkable response is stimulation of anti-tumor activity in vivo and in vitro. We here review the potential role of 4-1BB in cancer immunotherapy focusing on the cellular and molecular mechanisms involved.
Neurodegeneration in Multiple Sclerosis: Relationship to Neurological Disability (1999)

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the CNS. Most MS patients follow a relapsing-remitting course (RR-MS) for 8 to 15 years that transforms into a secondary progressive disease course (SP-MS). In this review, we discuss current data that describe MS as a neurodegenerative disease in which axonal loss is the major cause of irreversible neurological disability in MS patients. Neurological deficits in MS patients have two pathogeneses: acute inflammatory demyelination and axonal degeneration. Disability caused by inflammatory demyelination clinically dominates the early stages of RR-MS and is reversible. Axonal transection occurs at sites of inflammation and begins at disease onset but is clinically silent in RR-MS because the CNS compensates for neuronal loss. Once a threshold of axon loss is ex ceeded, MS patients enter an irreversible secondary progressive stage. In SP-MS, axonal degeneration is caused by chronic demyelination and may be irreversibly progressive. This view of MS provides a concep tional framework that explains conversion of RR-MS to SP-MS and provides a rationale for early aggressive anti-inflammatory and neuroprotective therapies. NEUROSCIENTIST 5:48-57, 1999
Current status and future trends of SiGe BiCMOS technology (2001)

The silicon germanium (SiGe) heterojunction bipolar transistor (HBT) marketplace covers a wide range of products and product requirements, particularly when combined with CMOS in a BiCMOS technology. A new base integration approach is presented which decouples the structural and thermal features of the HBT from the CMOS. The trend is to use this approach for future SiGe technologies for easier migration to advanced CMOS technology generations. Lateral and vertical scaling are used to achieve smaller and faster SiGe HBT devices with greatly increased current densities. Improving both the f/sub T/ and f/sub MAX/ will be a significant challenge as the collector and base dopant concentrations are increased. The increasing current densities of the SiGe HBT will put more emphasis on interconnects as a key factor in limiting transistor layout. Capacitors and inductors are two very important passives that must improve with each generation. The trend toward increasing capacitance in polysilicon-insulator-silicon (MOSCAP), polysilicon-insulator-polysilicon (Poly-Poly), and metal-insulator-metal (MIM) capacitors is discussed. The trend in VLSI interconnections toward thinner interlevel dielectrics and metallization layers is counter to the requirements of high Q inductors, potentially requiring a custom last metallization layer.
Evaluation of linear polyethyleneimine/nitric oxide adduct on wound repair: therapy versus toxicity (1998)

A full‐thickness wound model was used to evaluate the effects of a topically applied polyethyleneimine‐based nitric oxide donor on wound repair in aged rats. Polymer applications were applied over a 10‐day period on days 0, 2, 4, 6, and 8 comparing treatment (linear polyethyleneimine‐nitric oxide) and control groups (linear polyethyleneimine). Urinary nitrate excretion was quantified as a measure of nitric oxide released. The nitric oxide released from the linear polyethyleneimine‐nitric oxide group was significant compared with controls ( p ≤0.001), with a maximal nitrate level of 40 µmol on day 1 and an average sustained delivery of 34 µmol/day for the remainder of the study. Wound closure was examined using a computer‐based video‐imaging analysis system. The wounds of both the linear polyethyleneimine‐nitric oxide treatment and linear polyethyleneimine control groups exhibited minimal wound closure; however, the wound closure of the treatment group was significant as compared with the control group ( p ≤0.05). A phosphate‐buffered saline solution‐wounded control was performed that showed cleaner and faster healing wounds, similar to normal healing, than either of the polymer application groups. The histological data showed very little wound healing, on a cellular level, implicating the linear polyethyleneimine‐nitric oxide as well as the carrier compound as contributing to the adverse tissue reactions that occurred in the wound bed. Thus, we report the toxic effects of a polyethyleneimine‐based compound, as well as the toxic effects of sustained delivery of excess levels of nitric oxide on the wound‐repair process. Our findings suggest that there exists indeterminate parameters between therapy and toxicity of nitric oxide delivery to wounds.
Tunable optical-wavelength conversion using a multielectrode distributed-feedback laser diode with a saturable absorber (1987)

Optical wavelength conversion with tunability greater than 2.2 Å is demonstrated for the first time using a multielectrode DFB LD with a saturable absorber. This device can operate with both TE- and TM-polarised optical input. The device also has optical gain and pulse-shaping functions.
In Vivo Three-Dimensional Evaluation of Leukocyte Behavior in Retinal Microcirculation of Mice (2004)

New methods have been demonstrated for the three-dimensional and quantitative evaluation of leukocyte behavior in mouse retina.
Up-regulation of WNT8B mRNA in human gastric cancer (2002)

WNT - beta-catenin - TCF signaling pathway is activated by Xenopus wnt-8 (Xwnt-8) during Xenopus early development, and dysregulated activation of beta-catenin - TCF signaling pathway in mammalian cells leads to carcinogenesis. We have previously cloned and characterized human WNT8A, one of human orthologues of Xwnt-8. Here, we cloned and characterized human WNT8B by using bioinformatics, cDNA-PCR, and RACE. WNT8B gene of about 23-kb in size consisted of six exons, and encoded a 351-amino-acid polypeptide with the N-terminal signal peptide and two N-linked glycosylation sites. C-terminal region of WNT8B, WNT8A, WNT2, and WNT2B were longer than that of other human WNTs. Thirty-five nucleotide changes between WNT8B isolated by us and WNT8B isolated by another group resulted in Gly230Ala and Arg284Leu amino-acid substitutions. Gly230 and Arg284 of WNT8B were conserved in WNT8A. Gly230-Arg284 WNT8B allele was also identified in human genome draft sequences AL133352.10, AL359759.18, and human EST BF732616. These results indicate that the Gly230-Arg284 WNT8B cDNA isolated in this study is derived from the more common WNT8B allele. WNT8B mRNAs of 4.4- and 3.5-kb in size were weakly detected in a colorectal cancer cell line SW480, but were undetectable in any normal human tissues by using Northern blot analyses. WNT8B was significantly up-regulated in gastric cancer cell lines KATO-III (signet-ring cell carcinoma) and MKN45 (poorly differentiated adenocarcinoma), and also in 5 out of 10 cases of primary gastric cancer. WNT8B might play key roles in gastric cancer through activation of the beta-catenin - TCF signaling pathway.
Growth factors and angiogenesis (1993)

The list of growth factors with angiogenic potential is growing. It is not clear why so many factors with angiogenic potential exist, although Folkman postulated that this apparent redundancy is indicative of the essential nature of the angiogenic response. Additionally, these factors or their close relatives have other biological activities, including developmental morphogenesis, tumourigenesis, regeneration of injured tissue, and immunosignalling. Recent advances in the understanding of these factors include primary peptide sequence for all but one peptide growth factor included in this review, identification of cell surface receptors for many, and extensive characterisation of biological potential. Despite the torrent of data on angiogenic growth factors in the last decade, the chasm between form and physiology remains formidable.
A Preliminary Study on Microwave Monitoring of Moisture Content in Wheat (1977)

Relations between attenuation and phase shift of microwave signals at 9.4 GHz and moisture content, density, and temperature of grain for different varieties of wheat are presented. Differences in bulk density appeared to be the main factor limiting the accuracy of moisture content measurement by the microwave method, thus a few means of minimizing or eliminating this effect are considered in the paper.
Binding of extracellular matrix proteins to the surface of anaerobic bacteria (1996)

The binding of fibronectin, vitronectin, collagen and sialoprotein to 65 anaerobic strains was investigated by means of latex agglutination tests. The binding of fibronectin, collagen and lactoferrin to the same strains was also tested by means of 125I-labelled proteins. The strains were isolated from abdominal infections (55%), from the faeces of healthy subjects (29%) or from the depths of tonsils removed at tonsillectomy (16%). The binding of fibronectin and collagen to Bacteroides fragilis strains, tested by the latex agglutination assay, was stronger than their binding to other species. The vitronectin binding of the strains was less common, but was always accompanied by fibronectin binding. Binding to fibronectin-coated beads was inhibited by pre-incubation of the bacterial cells with soluble fibronectin and by heat or protease treatment of the bacterial suspension. No inhibition of the binding was observed with carbohydrates. None of the 65 strains exhibited any binding to fetuin or asialofetuin; 8% of the strains had a binding site for mucin. The binding to mucin-coated beads was inhibited by pre-incubation of the cells with mucin. The radiolabelling method indicated a low binding to 125I-fibronectin. The binding of 125I-collagen-I and 125I-lactoferrin was higher for the anaerobic strains tested.
En bloc transfer of extracellular matrixin vitro (1996)

We conclude that ECM produced by various cell lines can be harvested and transferred by this technique. The transferred ECM promotes cell reattachment and inhibits RPE cell apoptosis. Harvesting and transfer of ECM at the time of RPE transplantation may inhibit apoptosis and promote survival of the transplant.
Principles of Competitive Binding Assays (Saturation Analyses). II. Sequential Saturation (1974)

Abstract The principles of sequential saturation as a form of competitive binding assays are discussed in detail and differentiated from those of equilibrium techniques. The rationale of its applicability in practice and its potential to increase sensitivity under certain assay conditions are demonstrated with three binding systems involving digoxin, insulin, and folates. The advantages and disadvantages of the sequential saturation technique are outlined.
Enfermedad de Alzheimer: Situación actual y estrategias terapéuticas (1999)

Se revisaron los conceptos más actuales en relación con la epidemiología y el impacto de la enfermedad de Alzheimer en el nivel mundial. Se describieron los marcadores biológicos potenciales, en particular la atrofia hipocampal, la presencia de la proteína Tau y el beta-amiloide en líquido cefalorraquídeo, así como el ser portador del genotipo de la apolipoproteína E4 y la alfa 2 macroglobulina. Se propuso una secuencia diagnóstica para el estudio de pacientes con trastornos cognitivos. Se hizo referencia a las estrategias terapéuticas actuales en el tratamiento de las manifestaciones cognitivas y conductuales de esta enfermedad.<br>The most updated concepts of Alzheimer disease epidemiology and impact worldwide were reviewed. Ptential biological markers were described particularly hippocampal formation atrophy, presence of Tau protein and amyloid beta in cerebrospinal fluid, apoliprotein E4 genotype carrier and Alpha 2 macroglobulin. A diagnostic sequence was suggested to study patients with cognitive disorders, and also reference was made to present therapeutical strategies in treating cognitive and behavioral manifestations of this disease.
Principles of Electricity (1991)

About 100 basic substances or chemical elements are known to man, each element consisting of a number of smaller parts known as atoms. Each atom comprises several much smaller particles, the principle ones being electrons, protons and neutrons.