gebhart/patrepeval huggingface dataset:
Antineoplastic Agents. 565. Synthesis of Combretastatin D-2 Phosphate and Dihydro-combretastatin D-2 (2009)

A modified synthetic route to combretastatin D-2 (5) was devised in order to further evaluate its biological activity, for its conversion to phosphate prodrugs (25-28), and as a route to obtaining dihydro-combretastatin D-2 (42). A parallel first total synthesis of dihydro-combretastatin D-2 was completed, proceeding from a saturated 3-phenylpropionic ester intermediate via the Ullmann biaryl ether reaction (39-41). In contrast to the cancer cell growth inhibitory activity exhibited by combretastatin D-2, relatively minor structural modifications (41, 42) caused elimination of those properties.
Overexpression of transforming growth factor β1 in arterial endothelium causes hyperplasia, apoptosis, and cartilaginous metaplasia (1998)

Uninjured rat arteries transduced with an adenoviral vector expressing an active form of transforming growth factor beta1 (TGF-beta1) developed a cellular and matrix-rich neointima, with cartilaginous metaplasia of the vascular media. Explant cultures of transduced arteries showed that secretion of active TGF-beta1 ceased by 4 weeks, the time of maximal intimal thickening. Between 4 and 8 weeks, the cartilaginous metaplasia resolved and the intimal lesions regressed almost completely, in large part because of massive apoptosis. Thus, locally expressed TGF-beta1 promotes intimal growth and appears to cause transdifferentiation of vascular smooth muscle cells into chondrocytes. Moreover, TGF-beta1 withdrawal is associated with regression of vascular lesions. These data suggest an unexpected plasticity of the adult vascular smooth muscle cell phenotype and provide an etiology for cartilaginous metaplasia of the arterial wall. Our observations may help to reconcile divergent views of the role of TGF-beta1 in vascular disease.
Vagal nerve monitoring: a comparison of techniques in a canine model. (1997)

Four techniques of intraoperative, EMG vagal nerve monitoring were compared in a canine model. The results suggest that EMG recordings can be obtained successfully through a variety of techniques and that the laryngeal surface electrode appears to be the most sensitive technique in the canine model.
Consumption of Human Milk Oligosaccharides by Gut-Related Microbes (2010)

Human milk contains large amounts of complex oligosaccharides that putatively modulate the intestinal microbiota of breast-fed infants by acting as decoy binding sites for pathogens and as prebiotics for enrichment of beneficial bacteria. Several bifidobacterial species have been shown to grow well on human milk oligosaccharides. However, few data exist on other bacterial species. This work examined 16 bacterial strains belonging to 10 different genera for growth on human milk oligosaccharides. For this propose, a chemically defined medium, ZMB1, was used, which allows vigorous growth of a number of gut-related microorganisms in a fashion similar to complex media. Interestingly, Bifidobacterium longum subsp. infantis, Bacteroides fragilis , and Bacteroides vulgatus strains were able to metabolize milk oligosaccharides with high efficiency, whereas Enterococcus , Streptococcus , Veillonella , Eubacterium , Clostridium , and Escherichia coli strains grew less well or not at all. Mass spectrometry-based glycoprofiling of the oligosaccharide consumption behavior revealed a specific preference for fucosylated oligosaccharides by Bi. longum subsp. infantis and Ba. vulgatus. This work expands the current knowledge of human milk oligosaccharide consumption by gut microbes, revealing bacteroides as avid consumers of this substrate. These results provide insight on how human milk oligosaccharides shape the infant intestinal microbiota.
Characterization of quartz-etched PSM masks for KrF lithography at the 100-nm node (2002)

The application of strong phase shift masks (PSM's) such as AAPSM and Chromeless using KrF 248-nm lithography is increasingly in demand for production of advanced devices at the 130 nm node and below. Implementation of dual exposure PSM technology is becoming widely accepted as a method to achieve sub-wavelength gate and contact layer resolution for microprocessors, DRAM and thin film heads. This requires a stable and repeatable phase-shift mask process that will perform for the wafer lithographer and is manufacturable using today's leading edge photomask fabrication methods. The focus of this study is the characterization of the photomask quartz etch process. The effect of the photomask's phase depth control and the quartz etch CD control will be examined. A comprehensive mask metrology study will be supplemented by lithography process latitude data, both simulation and experimentally based. The effect of fabricating the photomask quartz trenches using either resist or chrome defined etch masks will also be studied as well as the impact on lithography process latitude. A key goal of this study is the determination of a realistic specification for the quartz etch process required for leading- edge phase-shift photomasks.
Safety, Tolerability, and Effectiveness of High Doses of Adjunctive Daily Left Prefrontal Repetitive Transcranial Magnetic Stimulation for Treatment-Resistant Depression in a Clinical Setting (2010)

These uncontrolled data suggest that higher doses of daily left prefrontal rTMS may safely be used in outpatients with major depressive episode even as an adjunctive treatment.
EBNA1-Mediated Recruitment of a Histone H2B Deubiquitylating Complex to the Epstein-Barr Virus Latent Origin of DNA Replication (2009)

The EBNA1 protein of Epstein-Barr virus (EBV) plays essential roles in enabling the replication and persistence of EBV genomes in latently infected cells and activating EBV latent gene expression, in all cases by binding to specific recognition sites in the latent origin of replication, oriP. Here we show that EBNA1 binding to its recognition sites in vitro is greatly stimulated by binding to the cellular deubiquitylating enzyme, USP7, and that USP7 can form a ternary complex with DNA-bound EBNA1. Consistent with the in vitro effects, the assembly of EBNA1 on oriP elements in human cells was decreased by USP7 silencing, whereas assembly of an EBNA1 mutant defective in USP7 binding was unaffected. USP7 affinity column profiling identified a complex between USP7 and human GMP synthetase (GMPS), which was shown to stimulate the ability of USP7 to cleave monoubiquitin from histone H2B in vitro. Accordingly, silencing of USP7 in human cells resulted in a consistent increase in the level of monoubquitylated H2B. The USP7-GMPS complex formed a quaternary complex with DNA-bound EBNA1 in vitro and, in EBV infected cells, was preferentially detected at the oriP functional element, FR, along with EBNA1. Down-regulation of USP7 reduced the level of GMPS at the FR, increased the level of monoubiquitylated H2B in this region of the origin and decreased the ability of EBNA1, but not an EBNA1 USP7-binding mutant, to activate transcription from the FR. The results indicate that USP7 can stimulate EBNA1-DNA interactions and that EBNA1 can alter histone modification at oriP through recruitment of USP7.
Invasion of Human Oral Epithelial Cells by Prevotella intermedia (1998)

Invasion of oral epithelial cells by pathogenic oral bacteria may represent an important virulence factor in the progression of periodontal disease. Here we report that a clinical isolate of Prevotella intermedia, strain 17, was found to invade a human oral epithelial cell line (KB), whereas P. intermedia 27, another clinical isolate, and P. intermedia 25611, the type strain, were not found to invade the cell line. Invasion was quantified by the recovery of viable bacteria following a standard antibiotic protection assay and observed by electron microscopy. Cytochalasin D, cycloheximide, monodansylcadaverine, and low temperature (4 degreesC) inhibited the internalization of P. intermedia 17. Antibodies raised against P. intermedia type C fimbriae and against whole cells inhibited invasion, but the anti-type-C-fimbria antibody inhibited invasion to a greater extent than the anti-whole-cell antibody. This work provides evidence that at least one strain of P. intermedia can invade an oral epithelial cell line and that the type C fimbriae and a cytoskeletal rearrangement are required for this invasion.
Using green fluorescent protein to understand the mechanisms of G-protein-coupled receptor regulation (1998)

G protein-coupled receptor (GPCR) activation is followed rapidly by adaptive changes that serve to diminish the responsiveness of a cell to further stimulation. This process, termed desensitization, is the consequence of receptor phosphorylation, arrestin binding, sequestration and down-regulation. GPCR phosphorylation is initiated within seconds to minutes of receptor activation and is mediated by both second messenger-dependent protein kinases and receptor-specific G protein-coupled receptor kinases (GRKs). Desensitization in response to GRK-mediated phosphorylation involves the binding of arrestin proteins that serve to sterically uncouple the receptor from its G protein. GPCR sequestration, the endocytosis of receptors to endosomes, not only contributes to the temporal desensitization of GPCRs, but plays a critical role in GPCR resensitization. GPCR down-regulation, a loss of the total cellular complement of receptors, is the consequence of both increased lysosomal degradation and decreased mRNA synthesis of GPCRs. While each of these agonist-mediated desensitization processes are initiated within a temporally dissociable time frame, recent data suggest that they are intimately related to one another. The use of green fluorescent protein from the jellyfish Aqueora victoria as an epitope tag with intrinsic fluorescence has facilitated our understanding of the relative relationship between GRK phosphorylation, arrestin binding, receptor sequestration and down-regulation.
Types of Dietary Fat and Risk of Coronary Heart Disease: A Critical Review (2001)

During the past several decades, reduction in fat intake has been the main focus of national dietary recommendations to decrease risk of coronary heart disease (CHD). Several lines of evidence. however, have indicated that types of fat have a more important role in determining risk of CHD than total amount of fat in the diet. Metabolic studies have long established that the type of fat, but not total amount of fat, predicts serum cholesterol levels. In addition, results from epidemiologic studies and controlled clinical trials have indicated that replacing saturated fat with unsaturated fat is more effective in lowering risk of CHD than simply reducing total fat consumption. Moreover, prospective cohort studies and secondary prevention trials have provided strong evidence that an increasing intake of n-3 fatty acids from fish or plant sources substantially lowers risk of cardiovascular mortality. In this article, we review evidence from epidemiologic studies and dietary intervention trials addressing the relationship between dietary fat intake and risk of CHD, with a particular emphasis on different major types of fat, n-3 fatty acids and the optimal balance between n-3 and n-6 fatty acids. We also discuss the implications of the available evidence in the context of current dietary recommendations.
Comparison of Tacrine-Induced Cytotoxicity in Primary Cultures of Rat, Mouse, Monkey, Dog, Rabbit, and Human Hepatocytes (1996)

Tacrine is the first drug approved for the treatment of Alzheimer's disease. Approximately 50% of patients treated with tacrine develop elevated serum aminotransferase levels, an indication of potential hepatotoxicity. The mechanism of human hepatoxicity has been difficult to study, because of the absence of an animal model. Therefore, this study compared the cytotoxicity induced by tacrine in primary rat, mouse, monkey, dog, rabbit and human hepatocytes to determine differences in response to tacrine between species in vitro. Cytotoxicity was assessed by determination of extra- and intracellular lactate dehydrogenase. The ratio of intracellular enzyme to total enzyme (i.e. intracellular and extracellular) was used to represent the viabilities of the cultures. Concentration-dependent cytotoxicity occurred after four and 24-hour exposure over a tacrine concentration range of 0 to 380 micrograms/ml. Cytotoxic potency of tacrine in hepatocytes from human, dog, mouse and rat was not significantly different; monkey hepatocytes appeared slightly more sensitive, while rabbit hepatocytes appeared slightly less sensitive than human hepatocytes. Increased time of exposure to tacrine decreased the concentration necessary to induce a cytotoxic response. This in vitro model suggests only minimal differences in sensitivity to tacrine-induce cytotoxicity; therefore, cytotoxicity in primary cultures of hepatocytes from various species would appear to be related to common metabolite(s) and/or mechanism of cellular injury.
Differentiation of a human neuroblastoma into neuron‐like cells increases their susceptibility to transduction by herpesviral vectors (2006)

Gene transfer is a powerful tool for functional gene analysis in human cells. In this respect, there is a need to develop experimental models that involve homogeneous cultures of human neuron-like cells susceptible to gene transduction and that are easy to handle. Here we describe an optimized and reproducible procedure to differentiate human SH-SY5Y neuroblastoma cells into a homogeneous population of neuron-like cells. The fully differentiated cells are postmitotic and resemble primary cultured neurons in terms of their cytoskeletal polarity. Notably, differentiated SH-SY5Y cells are far more susceptible to transduction by herpes simplex virus (HSV-1)-based vectors than proliferating SH-SY5Y cells. This increase in transduction efficiency after neuronal differentiation may be due to the up-regulation of cell surface receptors for herpesvirus entry. In summary, we propose that fully differentiated human neuron-like cells obtained from the SH-SY5Y neuroblastoma may constitute an excellent and versatile experimental tool for gene transfer and functional genomic studies with HSV-1 vectors.
Atomic force microscopy of liquid-covered surfaces: Atomic resolution images (1987)

Images of graphite surfaces that are covered with oil reveal the hexagonal rings of carbon atoms. Images of a sodium chloride surface, protected from moisture by oil, exhibit a monoatomic step. Together, these images demonstrate the potential of atomic force microscopy (AFM) for studying both conducting and nonconducting surfaces, even surfaces covered with liquids. Our AFM uses a cross of double wires with an attached diamond stylus as a force sensor. The force constant is ≊40 N/m. The resonant frequency is ≊3 kHz. The lateral and vertical resolutions are 0.15 nm and 5 pm.
Porous, Hyper-cross-linked, Three-Dimensional Polymer as Stable, High Rate Capability Electrode for Lithium-Ion Battery (2016)

Organic materials containing active carbonyl groups have attracted considerable attention as electrodes in Li-ion batteries due to their reversible redox activity, ability to retain capacity, and, in addition, their ecofriendly nature. Introduction of porosity will help accommodate as well as store small ions and molecules reversibly. In the present work, we introduce a mesoporous triptycene-related, rigid network polymer with high specific surface area as an electrode material for rechargeable Li-ion battery. The designed polymer with a three-dimensional (3D), rigid porous network allows free movement of ions/electrolyte as well as helps in interacting with the active anhydride moieties (containing two carbonyl groups). Considerable intake of Li<sup>+</sup> ions giving rise to very high specific capacity of 1100 mA h g<sup>-1</sup> at a discharge current of 50 mA g<sup>-1</sup> and ∼120 mA h g<sup>-1</sup> at a high discharge current of 3 A g<sup>-1</sup> are observed with excellent cyclability up to 1000 cycles. This remarkable rate capability, which is one of the highest among the reported organic porous polymers to date, makes the triptycene-related rigid 3D network a very good choice for Li-ion batteries and opens up a new method to design polymer-based electrode materials for metal-ion battery technology.
Placement Algorithms for Arbitrarily Shaped Blocks (1979)

New placement algorithms have been developed which are suitable for the layout of Very Large Scale Integrated (VLSI) circuits. Hierarchical decomposition is used to reduce the circuit function to a size that can be comprehended by the designer and is computationally feasible to layout. At each hierarchical level the problem consists of the placement of interconnected rectangular blocks of arbitrary size and shape such that the area occupied by the blocks and their interconnections is minimal. Constructive initial placement and iterative improvement algorithms are presented.
Historias contadas por profesores de cursos a distancia:: Experiencias de aprendizaje mediadas por la tecnología ¿Centralidad del estudiante o disminución del rol de facilitación? (2006)

En la presente investigacion, se analizan 15 textos de experiencias de profesores al impartir cursos en linea, se adopto el metodo de narrativa. Se destacan en el estudio el rol del facilitador y la centralidad del estudiante. Desde las historias, se advierte una naciente disociacion entre lo que es asumido hacia tales temas por profesores y aprendices, toda vez que el rol fuerte de facilitacion auto percibido por los profesores es apenas reconocido por quienes aprenden, los profesores a su vez, solo reconocen una centralidad parcial de los estudiantes al tiempo que estos empiezan a hacer cuestionamientos abiertos al rol del facilitador.
Hexameric Assembly of the Bifunctional Methylerythritol 2,4-Cyclodiphosphate Synthase and Protein-Protein Associations in the Deoxy-xylulose-dependent Pathway of Isoprenoid Precursor Biosynthesis (2004)

The bifunctional methylerythritol 4-phosphate cytidylyltransferase methylerythritol 2,4-cyclodiphosphate synthase (IspDF) is unusual in that it catalyzes nonconsecutive reactions in the 1-deoxy-D-xylulose 5-phosphate (DOXP) pathway of isoprenoid precursor biosynthesis. The crystal structure of IspDF from the bacterial pathogen Campylobacter jejuni reveals an elongated hexamer with D3 symmetry compatible with the dimeric 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase and trimeric 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase monofunctional enzymes. Complex formation of IspDF with 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE), the intervening enzyme activity in the pathway, has been observed in solution for the enzymes from C. jejuni and Agrobacterium tumefaciens. The monofunctional enzymes (2C-methyl-D-erythritol-4-phosphate cytidylyltransferase, IspE, and 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase) involved in the DOXP biosynthetic pathway of Escherichia coli also show physical associations. We propose that complex formation of the three enzymes at the core of the DOXP pathway can produce an assembly localizing 18 catalytic centers for the early stages of isoprenoid biosynthesis.
Scatter segmentation in dynamic SPECT images using principal component analysis (2003)

Dynamic single photon emission computed tomography (dSPECT) provides time-varying spatial information about changes of tracer distribution in the body from data acquired using a standard (single slow rotation) protocol. Variations of tracer distribution observed in the images might be due to physiological processes in the body, but may also stem from reconstruction artefacts. These two possibilities are not easily separated because of the highly underdetermined nature of the dynamic reconstruction problem. Since it is expected that temporal changes in tracer distribution may carry important diagnostic information, the analysis of dynamic SPECT images should consider and use this additional information. In this paper we present a segmentation scheme for aggregating voxels with similar time activity curves (TACs). Voxel aggregates are created through region merging based on a similarity criterion on a reduced set of features, which is derived after transformation into eigenspace. Region merging was carried out on dSPECT images from simulated and patient myocardial perfusion studies using various stopping criteria and ranges of accumulated variances in eigenspace. Results indicate that segmentation clearly separates heart and liver tissues from the background. The segmentation quality did not change significantly if more than 99% of the variance was incorporated into the feature vector. The heart behaviour followed an expected exponential decay curve while some variation of time behaviour in liver was observed. Scatter artefacts from photons originating from liver could be identified in long as well as in short studies.
DNA Plasmon (1988)

As a consequence of the charged nature of a dissolved DNA polymer and its sheath of counterions we predict that there should exist normal modes of the system characterized by substantial longitudinal electric fields and relatively small motion of the atoms and ions. This longitudinal phonon is the one-dimensional counterpart of the plasmon excitation of three-dimensional conductors, and of the surface plasmon of two-dimensional charged systems. The frequency of the DNA plasmon, as a function of excitation wavelength, is linear in inverse wavelength at long wavelengths.
BACTERIOCIN EXPOSURE AND FOOD INGREDIENTS INFLUENCE ON GROWTH AND VIRULENCE OF LISTERIA MONOCYTOGENES IN A MODEL MEAT GRAVY SYSTEM (2003)

ABSTRACT The antilisterial activity of bacteriocin‐producing Lactobacillus sakei 1 bac + alone and combined with food ingredients (sodium chloride, D‐glucose, oregano, black pepper) was studied in a model meat gravy (1.8% proteose peptone, 1.2% meat extract, 0.6% yeast extract, 2.0% corn starch) kept under refrigeration for 10 days. Two strains of L. monocytogenes (serotypes 4b and 1/2a) were employed in coinoculation experiments and Lactobacillus sakei ATCC 15521 was used as a negative control for bacteriocin production. The LAB bac + strain was more effective in inhibiting both L. monocytogenes serotypes than the LAB bac − strain. The serotype 4b was more sensitive to bacteriocin than serotype 1/2a. The effect of the ingredients on inhibition of L. monocytogenes was serotype dependent. Bacteriocin exposure did not affect sensitivity to ampicilin and rifampicin. However, L. monocytogenes partially lost their hemolytic activity after exposure to bacteriocin‐producing Lb. sakei 1 and food ingredients.
Immune semaphorins: a new area of semaphorin research (2003)

The semaphorin family comprises soluble and membrane-bound proteins originally identified as axonal guidance cues that function during neuronal development. Emerging evidence suggests that a subset of semaphorins, called 'immune semaphorins', function in the immune system. The class IV semaphorins Sema4D/CD100 and Sema4A use CD72 and Tim-2, respectively, as receptors during immune responses; these receptors comprise a set distinct from those used by semaphorins in the nervous system. Sema4D/CD100, which is expressed constitutively by T cells, is involved in the activation of B cells and dendritic cells, whereas Sema4A is preferentially expressed on B cells and dendritic cells, and is involved in the activation of T cells. Additionally, increasing evidence suggests that some other semaphorins, including viral-encoded semaphorins, might also play important roles in the immune system.