gebhart/patrepeval huggingface dataset:
Computerized detection of noncalcified plaques in coronary CT angiography: Evaluation of topological soft gradient prescreening method and luminal analysis (2014)

The topological soft-gradient prescreening method in combination with the luminal analysis for FP reduction was effective for detection of NCPs in cCTA, including NCPs causing positive or negative vessel remodeling. The accuracy of vessel segmentation, tracking, and centerline identification has a strong impact on NCP detection. Studies are underway to further improve these techniques and reduce the FPs of the CADe system.
Identification and Characterization of Novel Genetic Markers Associated with Biological Control Activities in Bacillus subtilis (2006)

ABSTRACT Suppressive subtractive hybridization (SSH) was used to identify genetic markers associated with biological control of plant pathogens by Bacillus subtilis. The genomes of two commercialized strains, GB03 and QST713, were compared with that of strain 168, which has no defined biocontrol capacities, to obtain a pool of DNA fragments unique to the two biocontrol strains. The sequences of 149 subtracted fragments were determined and compared with those present in GenBank, but only 80 were found to correspond to known Bacillus genes. Of these, 65 were similar to genes with a wide range of metabolic functions, including the biosynthesis of cell wall components, sporulation, and antibiotic biosynthesis. Sixteen subtracted fragments shared a high degree of similarity to sequences found in multiple B. subtilis strains with proven biocontrol capacities. Oligonucleotide primers specific to nine of these genes were developed. The targeted genes included five genes involved in antibiotic synthesis (bmyB, fenD, ituC,srfAA, and srfAB) and four additional genes (yndJ, yngG, bioA, and a hypothetical open reading frame) not previously associated with biological control. All nine markers were amplified from the commercialized B. subtilis strains GB03, QST713, and MBI600, with the exception of ituC, which was not detected in GB03. The markers also were amplified from four other B. subtilis isolates, but they were not amplified from other related Bacillus strains, including the plant growth-promoting rhizobacteria IN937a and IN937b. Sequencing of the amplified markers revealed that all seven of the isolates that scored positive for multiple markers were genotypically distinct strains. Interestingly, strains scored positive for the amplifiable markers generally were more effective at inhibiting the growth of Rhizoctonia solani and Pythium ultimum than other Bacillus isolates that lacked the markers. The potential utility of the defined genetic markers to further define the diversity, ecology, and biocontrol activities of B. subtilis are discussed.
A Novel Method for the Detection, Quantitation, and Breakpoint Cluster Region Determination of t(15;17) Fusion Transcripts Using a One-Step Real-Time Multiplex RT-PCR (2003)

Individuals with acute promyelocytic leukemia (APL) usually express 1 of 3 primary hybrid transcripts associated with a t(15;17). The 3 fusion transcripts are the result of heterogeneous breakpoint cluster regions (bcr) within the promyelocytic leukemia (PML) gene and are denoted bcr1 (long), bcr2 (variant), and bcr3 (short) forms. Many researchers have shown that real-time quantitative reverse transcriptase–polymerase chain reaction (RT-PCR) of the involved transcript is a valuable tool for monitoring APL and its treatment. In addition, some research suggests that identification of a specific breakpoint region may be used to predict an individual's likelihood of relapse and possibly their response to all-trans retinoic acid treatment. We describe the first reported 1-step multiplex RT-PCR assay capable of t(15;17) fusion transcript real-time relative quantitation and simultaneous transcript form identification in 2 reactions. This assay uses a novel dual-probe technique to achieve what has required a laborious procedure of 2 or more reactions followed by postamplification analysis. We found a correlation of 100% in detection and breakpoint determination of the long, short, and variant forms with a breakpoint 5' to nucleotide 1709 compared with results from traditional methods.
Development of nonlinear filter bank system for real-time beautification of facial video using GPGPU (2010)

A nonlinear filter bank named as an ∈-filter bank is implemented for real-time processing of video in order to make the skin in human faces look beautified. General-purpose computing on graphics processing units (GPGPU) is utilized for this real-time implementation. GPGPU has quite high computational power, and the facial beautification system using the ∈-filter bank is efficiently implemented in real time, although the amount of the computation of this system is large. A new language is developed to design and edit the ∈-filter bank, which enables this system to be edited conveniently by trial and error, reflecting the user's request concerning the smoothness of skin. Skin detection is also applied to limit the area to be processed within the face area, so that the other areas than the face, such as hair and background, are not influenced by the system. Experimental results verify its high performance.
A review of the latest clinical compounds to inhibit VEGF in pathological angiogenesis (2006)

Angiogenesis plays an important role in the formation of new blood vessels and is crucial for tumour development and progression. Imbalance between pro- and antiangiogenesis factors regulates the biological process of angiogenesis. The best characterised of the proangiogenic factors and the most potent is vascular endothelial growth factor (VEGF). The binding of VEGF to one of its transmembrane tyrosine kinase receptors, which are predominantly found on endothelial cells, results in receptor dimerisation, activation and autophosphorylation of the tyrosine kinase domain. This triggers a cascade of complex downstream signalling pathways. Several strategies targeting the VEGF signalling pathway have been developed. These include neutralising antibodies to VEGF (bevacizumab) or VEGF receptors (VEGFRs) (DC101), soluble VEGFR/VEGFR hybrids (VEGF-Trap), and tyrosine kinase inhibitors of VEGFRs (BAY43-9006, SU11248, ZD6474, AZD2171, PTK/ZK and others). Several of these agents are now being investigated in clinical trials.
E-Selectin Polymorphism Associated With Myocardial Infarction Causes Enhanced Leukocyte-Endothelial Interactions Under Flow Conditions (2003)

Our results suggest that the E-selectin Ser128Arg polymorphism can functionally alter leukocyte-endothelial interactions as well as biochemical and biological consequences, which may account for the pathogenesis of myocardial infarction.
Clustered Magnetite Nanocrystals Cross-Linked with PEI for Efficient siRNA Delivery (2010)

Magnetofection has been utilized as a powerful tool to enhance gene transfection efficiency via magnetic field-enforced cellular transport processes. The accelerated accumulation of nucleic acid molecules by applying an external magnetic force enables the rapid and improved transduction efficiency. In this study, we developed magnetite nanocrystal clusters (PMNCs) cross-linked with polyethylenimine (PEI) to magnetically trigger intracellular delivery of small interfering RNA (siRNA). PMNCs were produced by cross-linked assembly of catechol-functionalized branched polyethylenimine (bPEI) around magnetite nanocrystals through an oil-in-water (O/W) emulsion and solvent evaporation method. The physical properties of PMNC were characterized by TEM, DLS, TSA, and FT-IR. Finely tuned formulation of clustered magnetite nanocrystals with controlled size and shape exhibited superior saturation of magnetization value. Magnetite nanocrystal clusters could form nanosized polyelectrolyte complexes with negatively charged siRNA molecules, enabling efficient delivery of siRNA into cells upon exposure to an external magnetic field within a short time. This study introduces a new class of magnetic nanomaterials that can be utilized for magnetically driven intracellular siRNA delivery.
Evolution of the alpha-crystallin/small heat-shock protein family. (1993)

The common characteristic of the alpha-crystallin/small heat-shock protein family is the presence of a conserved homologous sequence of 90-100 residues. Apart from the vertebrate lens proteins--alpha A- and alpha B-crystallin--and the ubiquitous group of 15-30-kDa heat-shock proteins, this family also includes two mycobacterial surface antigens and a major egg antigen of Schistosoma mansoni. Multiple small heat-shock proteins are especially present in higher plants, where they can be distinguished in at least two classes of cytoplasmic proteins and a chloroplast-located class. The alpha-crystallins have recently been found in many tissues outside the lens, and alpha B-crystallin, in particular, behaves in many respects like a small heat-shock protein. The homologous sequences constitute the C-terminal halves of the proteins and probably represent a structural domain with a more variable C-terminal extension. These domains must be responsible for the common structural and functional properties of this protein family. Analysis of the phylogenetic tree and comparison of the biological properties of the various proteins in this family suggest the following scenario for its evolution: The primordial role of the small heat-shock protein family must have been to cope with the destabilizing effects of stressful conditions on cellular integrity. The alpha-crystallin-like domain appears to be very stable, which makes it suitable both as a surface antigen in parasitic organisms and as a long-living lens protein in vertebrates. It has recently been demonstrated that, like the other heat-shock proteins, the alpha-crystallins and small heat-shock proteins function as molecular chaperones, preventing undesired protein-protein interactions and assisting in refolding of denatured proteins. Many of the small heat-shock proteins are differentially expressed during normal development, and there is good evidence that they are involved in cytomorphological reorganizations and in degenerative diseases. In conjunction with the stabilizing, thermoprotective role of alpha-crystallins and small heat-shock proteins, they may also be involved in signal transduction. The reversible phosphorylation of these proteins appears to be important in this respect.
Synthesis and biological evaluation of cytotoxic analogs of somatostatin containing doxorubicin or its intensely potent derivative, 2-pyrrolinodoxorubicin (1998)

To create cytotoxic hybrid analogs of somatostatin (SST), octapeptides RC-160 (D-Phe-Cys-Tyr-D-Trp- Lys-Val-Cys-Trp-NH2) and RC-121 (D-Phe-Cys-Tyr-D-Trp- Lys-Val-Cys-Thr-NH2) were linked to doxorubicin (DOX) or its superactive derivative, 2-pyrrolino-DOX (AN-201). The conjugation was performed by coupling N-9-fluorenylmethoxycarbonyl (N-Fmoc)-DOX-14-O-hemiglutarate or 2-pyrrolino-DOX-14-O-hemiglutarate to the amino terminus of [Lys(Fmoc)5]RC-160 yielding AN-163 and AN-258, respectively, after deprotection. The respective cytotoxic conjugates of RC-121 (AN-162 and AN-238) were prepared similarly. In vitro tests on human cancer cell lines-MKN-45 gastric cancer, MDA-MB-231 breast cancer, PC-3 prostate cancer, and MIA PaCa-2 pancreatic cancer-demonstrated that the antiproliferative activity of the cytotoxic radicals in these conjugates was virtually retained. In H-345 human small cell lung carcinoma cell line, conjugates of RC-121 preserved the cytotoxic activity of their radicals, but the hybrids with RC-160 showed approximately 10 times lower activity. The ability of the carriers and the hybrids to inhibit the binding of 125I-labeled RC-160 to receptors for SST on rat pituitary membrane preparation was also determined. The cytotoxic conjugates inhibited 50% of the specific binding of the radioligand in the nanomolar concentration range (IC50 < 80 nM). When SST-like activities of AN-238 and its carrier, RC-121, were compared in the rat pituitary superfusion system, both compounds were found to suppress a stimulated growth hormone release at nanomolar concentrations. Preliminary studies in animal models of breast and prostate cancers showed that AN-238 is less toxic than AN-201 and more potent in inhibiting tumor growth. These highly active cytotoxic analogs of SST have been designed as targeted antitumor agents for the treatment of various cancers expressing receptors for SST octapeptides.
Integrated 3D Visualization of fMRI and DTI tractography (2006)

Figure 1.This overview image displays the 3D streamlines representing the DTI tracks, several functional areas, the vasculature and the underlying anatomy clipped at an oblique angle.The focus of this poster is the addition of the track geometry to an existing fMRI visualization application.On the right we can see the cortical spinal track (cyan) projecting from the left hand motor region (green).
Proteins of the Outer Membrane of Gram-Negative Bacteria (1980)

PORIN PROTEINS . Genetics and Regulation of Porin Proteins . . . . . . . . ......... . �. coli matrix proteins : ... ;; : • 'New membrane protems of E colt . Porins of Salmonella typhimurium ' .
Resveratrol: One molecule, many targets (2008)

Resveratrol is one of the numerous polyphenolic compounds found in several vegetal sources. In recent years, the interest in this molecule has increased exponentially following the major findings that resveratrol (i) is shown to be chemopreventive in some cancer models, (ii) is cardioprotective, and (iii) has positive effects on several aspects of metabolism, leading to increased lifespan in all the metazoan models tested thus far, including small mammals. Such remarkable properties have elicited a vast interest towards the identification of target proteins of resveratrol and have led to the identification of enzymes inhibited by resveratrol and others whose activation is enhanced. In the vast majority of cases, resveratrol displays inhibitory/activatory effects in the micromolar range, which is potentially attainable pharmacologically, although targets with affinities in the nanomolar range have also been reported. Here, we provide an overview of the various classes of enzymes known to be inhibited (or activated) by resveratrol. It appears that resveratrol, as a pharmacological agent, has a wide spectrum of targets. The biological activities of resveratrol may thus be dependent on its simultaneous activity on multiple molecular targets.
Microbial Production of 3‐Hydroxypropionic Acid from Renewable Sources: A Green Approach as an Alternative to Conventional Chemistry (2014)

3-Hydroxypropionic acid (3-HP) is a valuable platform chemical that can be produced from glucose or glycerol by biological processes. This chapter provides an overview and the current status of microbial 3-HP production. It also describes various constraints of microbial 3-HP production and possible solutions. Finally, economic outlook and future prospects of biological 3-HP production are discussed.
Preproabrin: genomic cloning, characterisation and the expression of the A‐chain in Escherichia coli (1991)

Synthetic oligonucleotides representing all possible sequences of an N-terminal and an internal region of the A-chain of abrin C were used to generate a probe specific for abrin-related sequences using the polymerase chain reaction on Abrus precatorius genomic DNA. A lambda phage library constructed from genomic DNA isolated from leaf tissue of A. precatorius was screened and positive hybridising clones were characterised by restriction enzyme analysis. The coding regions of unique clones were characterised by DNA sequencing. One clone encodes a preproprotein closely related to abrin C with 83% similarity between the A-chain sequences. Based on similarity with the ricin toxins and Ricinus communis agglutinin, the preproabrin consists of an A-chain of 251 amino acids preceded by 34 amino acids containing an N-terminal signal peptide, followed by a 14-amino-acid linker and a B-chain of 263 amino acids. The mature A-chain of the preproabrin has been expressed cytoplasmically in Escherichia coli and the soluble recombinant protein was produced at levels exceeding 6% of total cell protein. The recombinant A-chain has been purified to homogeneity and its ability to depurinate 28S rRNA in rat liver ribosomes has been demonstrated in vitro.
Antineoplastic Agents, 122. Constituents of Combretum caffrum (1987)

An investigation of the South African tree Combretum caffrum (Combretaceae) for antineoplastic constituents was conducted by employing the astrocytoma bioassay (9ASK). By this approach and a combination of solvent partition, steric exclusion, and adsorption chromatographic procedures, a substance designated combretastatin [1a] was isolated and found to display significant (71-90% astrocyte reversal at 1-100 micrograms/ml dose levels) astrocyte reversal and murine P-388 lymphocytic leukemia (PS) cell growth inhibition (ED50 0.011 micrograms/ml). The structure of (-)-combretastatin was elucidated by X-ray crystal structure analysis and confirmed by total synthesis. The absolute configuration at C-10 was assigned the R-configuration on the basis of Horeau esterification techniques. Other prominent, albeit PS-inactive, constituents were found to be 3,3',4'-tri-O-methylellagic acid [2] and acacetin [3].
Advances in Endoscopic Surgery (2011)

Surgeons from various domains have become fascinated by endoscopy with its very low complications rates, high diagnostic yields and the possibility to perform a large variety of therapeutic procedures. Therefore during the last 30 years, the number and diversity of surgical endoscopic procedures has advanced with many new methods for both diagnoses and treatment, and these achievements are presented in this book. Contributing to the development of endoscopic surgery from all over the world, this is a modern, educational, and engrossing publication precisely presenting the most recent development in the field. New technologies are described in detail and all aspects of both standard and advanced endoscopic maneuvers applied in gastroenterology, urogynecology, otorhinolaryngology, pediatrics and neurology are presented. The intended audience for this book includes surgeons from various specialities, radiologists, internists, and subspecialists.
Differential up‐regulation by tRNAs of ribosome‐inactivating proteins (1995)

Some plant ribosome-inactivating proteins (RIPs) with RNA-N-glycosidase activity on 28S RNA require, for the inactivation of ribosomes, the presence of macromolecular cofactors present in post-ribosomal supernatants. In the case of gelonin one of the cofactors is tRNATrp lacking one or two nucleotides at the 3'-CCA end [Brigotti, M., Carnicelli, D., Alvergna, P., Pallanca, A., Lorenzetti, R., Denaro, M., Sperti, S. and Montanaro, L. (1995) Biochem. J. 310, 249-253]. In the present study it is shown that tRNAs are involved in the up-regulation of all the cofactor-requiring RIPs up to now identified (agrostin, barley RIP, PAP and tritin, besides gelonin). Polyacrylamide gel electrophoresis shows that tRNA fractions with different mobilities stimulate different RIPs. With the identification of agrostin, the cofactor-requiring RIPs (italics) add to five out of a total of thirteen investigated: barley RIP, bryodin-R, gelonin, lychnin, momordin, momorcochin-S, PAP, saporin-6, tritin [Carnicelli, D., Brigotti, M., Montanaro, L. and Sperti, S. (1992) Biochem. Biophys. Res. Commun. 182, 579-582], agrostin, luffin, trichokirin and trichosanthin (present study).
Formation of Three-Dimensional Hydrogel Multilayers Using Enzyme-Mediated Redox Chain Initiation (2010)

Enzyme-mediated redox chain initiation involving glucose oxidase (GOX) was employed in an iterative solution dip-coating technique to polymerize multiple, three-dimensional hydrogel layers using mild aqueous conditions at ambient temperature and oxygen levels. To the best of our knowledge, sequential enzyme-mediated dip-coating resulting in an interfacial radical chain polymerization and subsequent formation of three-dimensional hydrogel layers has not been previously explored. Conformal, micrometer-scale, uniform poly(ethylene glycol) (PEG)-based hydrogel layers were polymerized within seconds and remained securely associated after incubation in water for 16 weeks. Incorporation of either small molecules (i.e., rhodamine-B acrylate, fluorescein acrylate) or fluorescent nanoparticles into crosslinked hydrogel layers during the polymerization reaction was also achieved. The encapsulation of 0.2 microm-diameter nanoparticles into hydrogels during polymerization of a 2-hydroxyethyl acrylate (HEA)/PEG(575) diacrylate monomer formulation, using the GOX-mediated initiation, resulted in minimal effects on polymerization kinetics, with final acrylate conversions of 95% (+/- 1%) achieved within minutes. The temporal control and spatial localization afforded by this interfacial redox approach resulted in the polymerization of uniform secondary layers ranging between 150 (+/- 10) microm and 650 (+/- 10) microm for 15 and 120 s immersion times, respectively. Moreover, increasing the PEG(575)-fraction within the initial hydrogel substrate from 10 to 50% decreased the subsequent layer thicknesses from 690 (+/- 30) microm to 490 (+/- 10) microm because of lowered glucose concentration at the hydrogel interface. The ability to sequentially combine differing initiation mechanisms with this coating approach was achieved by using GOX-mediated interfacial polymerization on hydrogel substrates initially photopolymerized in the presence of glucose. The strict control of layer thicknesses combined with the rapid, water-soluble, and mild polymerization will readily benefit applications requiring formation of stratified, complex, and three-dimensional polymer structures.
Extracellular Discontinuities in Cardiac Muscle (1998)

It has become of fundamental importance to understand variations in the shape of the upstroke of the action potential in order to identify structural loading effects. One component of this goal is a detailed experimental analysis of the time course of the foot of the cardiac action potential (Vm foot) during propagation in different directions in anisotropic cardiac muscle. To this end, we performed phase-plane analysis of transmembrane action potentials during anisotropic propagation in adult working myocardium. The results showed that during longitudinal propagation there was initial slowing of Vm foot that resulted in deviations from a simple exponential; corollary changes occurred at numerous sites during transverse propagation. We hypothesized that the effect on Vm foot observed in the experimental data was created by the microscopic structure, especially the capillaries. This hypothesis predicts that the phase-plane trajectory of Vm foot will deviate from linearity in the presence of a high density of capillaries, and that a linear trajectory will occur in the absence of capillaries. Comparison of the results of Fast and Kléber (Circ Res. 1993;73:914-925) in a monolayer of neonatal cardiac myocytes, which is devoid of capillaries, and our results in newborn ventricular muscle, which is rich in capillaries, showed drastic differences in Vm foot as predicted. Because this comparison provided experimental support for the capillary hypothesis, we explored the underlying biophysical mechanisms due to interstitial electrical field effects, using a "2-domain" model of myocytes and capillaries separated by interstitial space. The model results show that a propagating interstitial electrical field induces an inward capacitive current in the inactive capillaries that causes a feedback effect on the active membrane (source) that slows the initial rise of its action potential. The results show unexpected mechanisms related to extracellular structural loading that may play a role in selected conduction disturbances, such as in a reperfused ischemic region surrounded by normal myocardium.