gebhart/patrepeval huggingface dataset:
Enhanced visualization of cerebral blood vessels for X-ray angiograms (2013)

Neurologists frequently use X-ray angiographic techniques in order to establish the optimal treatment or intervention procedure. Neurosurgeries performed at blood vessels level are difficult procedures because of the low accessibility in the human brain. Therefore, the establishment of a correct diagnosis based on angiographies is of paramount importance. Enhanced visualization of blood vessels by separating veins and arteries from background can help, in many cases, in giving a more accurate diagnosis. In this article, three methods for arteries and veins classification and enhanced visualization are presented. From our study, it results that, using coefficients of wavelet transform as parameters for the classification, a better visual representation of small vessels is achieved.
Evaluating Nanoparticle Sensor Design for Intracellular pH Measurements (2011)

Particle-based nanosensors have over the past decade been designed for optical fluorescent-based ratiometric measurements of pH in living cells. However, quantitative and time-resolved intracellular measurements of pH in endosomes and lysosomes using particle nanosensors are challenging, and there is a need to improve measurement methodology. In the present paper, we have successfully carried out time-resolved pH measurements in endosomes and lyosomes in living cells using nanoparticle sensors and show the importance of sensor choice for successful quantification. We have studied two nanoparticle-based sensor systems that are internalized by endocytosis and elucidated important factors in nanosensor design that should be considered in future development of new sensors. From our experiments it is clear that it is highly important to use sensors that have a broad measurement range, as erroneous quantification of pH is an unfortunate result when measuring pH too close to the limit of the sensitive range of the sensors. Triple-labeled nanosensors with a pH measurement range of 3.2-7.0, which was synthesized by adding two pH-sensitive fluorophores with different pK(a) to each sensor, seem to be a solution to some of the earlier problems found when measuring pH in the endosome-lysosome pathway.
Symmetric Diblock Copolymer Thin Films on Rough Substrates. Kinetics and Structure Formation in Pure Block Copolymer Thin Films (2005)

The effect of substrate roughness on the orientation of lamellar microdomains of symmetric poly(styrene)-block-poly(methyl methacrylate) [PS-b-PMMA] was investigated. Thin films of three molecular weights of PS-b-PMMA were prepared on organic polyimide and inorganic indium tin oxide substrates whose surfaces were characterized for roughness and surface energy. It was shown, through cross-section transmission electron microscopy (TEM) and dynamic secondary ion mass spectroscopy (dSIMS), that above a critical substrate roughness all three molecular weights of PS-b-PMMA produced a perpendicular lamellar orientation. Using atomic force microscopy (AFM) and PS-b-PMMA thin films on an array of polyimide substrates of varied substrate roughness, a critical substrate roughness was identified, below which a parallel orientation was observed. This behavior was modeled simply and showed that the critical roughness determined by AFM represents an underestimate of the true critical roughness of the substrate. Finally, a series of TEM cross sections of thin films on rough and smooth substrates, annealed to different stages of reaching equilibrium, are shown and discussed in terms of the dynamics of ordering in block copolymer thin films.
Electrochemical Reduction of Carbon Dioxide in Water: Analysis of Reaction Mechanism on Ruthenium‐Titanium‐Oxide (1992)

Mixed ruthenium/titanium oxide electrodes were prepared by thermal decomposition of the halides on titanium sheets. The electrocatalytic activity of the metallic conductive electrodes towards hydrogen evolution and carbon dioxide reduction was investigated in aqueous solutions with rotating‐disk electrodes. Current‐voltage curves at show a current‐limiting behavior at small overpotentials for hydrogen evolution. In the presence of carbon dioxide, the current efficiency for reduction reaches a maximum under current‐limiting conditions for hydrogen ion reduction, before a steep onset of hydrogen evolution takes place due to the reduction of water. An analysis of the electrode kinetics for the formation of reaction intermediates is given which suggests that the surface recombination of adsorbed hydrogen with is the rate‐limiting step in the electrochemical reduction of .
Pump intensity noise and ASE spectrum of Raman amplification in non-zero dispersion-shifted fibers (2001)

We observe growth of narrow spectral features in the ASE spectrum of a Raman amplifier under certain dispersion conditions. Relative intensity noise of the counterpropagating pump is found to cause this when it exceeds −125 dB/Hz.
REVIEWS From the Perspective of the Self: Montaigne's Self-Portrait. By BRUSHCRAIG B.. New York, Fordham University Press, 1994. 321 pp. Hb $32.50. (1996)

Journal Article REVIEWS Get access From the Perspective of the Self: Montaigne's Self-Portrait. By CRAIG B. BRUSH. New York, Fordham University Press, 1994. 321 pp. Hb $32.50. IAN MACLEAN IAN MACLEAN THE QUEEN'S COLLEGEOXFORD Search for other works by this author on: Oxford Academic Google Scholar French Studies, Volume L, Issue 2, April 1996, Page 189, https://doi.org/10.1093/fs/L.2.189 Published: 01 April 1996
Site‐specific carbohydrate profiling of human transferrin by nano‐flow liquid chromatography/electrospray ionization mass spectrometry (2004)

Glycopeptides derived from a lysylendopeptidase digest of commercially available human transferrin were analyzed by nano-flow liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS), which permitted the carbohydrate profiles at Asn432 and Asn630 to be determined. Both are located in a well-known motif for N-glycosylation, Asn-Xaa-Ser/Thr. The contents of the carbohydrates at each site were significantly different from each other, and consisted of a variety of minor types of oligosaccharides in addition to the major one, a biantennary complex-type oligosaccharide. Nano-flow ESI tandem mass spectrometry (MS/MS) of the glycopeptides (Cys421-Lys433 and Ile619-Lys646) containing these two sites yielded predominantly ions originating from the non-reducing termini (oxonium ions) and reducing terminus, resulting from cleavage of the glycosidic bonds of the carbohydrate moieties; this permitted the structural read-out of a small minority of the carbohydrate moieties. In particular, the observation of oxonium ions at m/z 512.2 and 803.2 is useful for probing outer non-reducing terminal fucosylation, which represented carbohydrate structures consisting of Hex, dHex, and HexNAc, and NeuNAc, Hex, dHex, and HexNAc, respectively, from which the Lewis X structure (Galbeta1-4(Fucalpha1-3)GlcNAc) was readily deduced. Moreover, fucosylation at the reducing-terminal GlcNAc (Fucalpha1-6GlcNAc) specifically occurred at Asn630, as demonstrated by treatment of the glycopeptides with alpha1-3/4-L-fucosidase.
Nanofiltration, a New Specific Virus Elimination Method Applied to High-Purity Factor IX and Factor XI Concentrates (1994)

We have validated the use of two new regenerated multilayered structured cellulose membranes (BMM), Planova 15 N and Planova 35 N, with respective mean pore sizes of 15 and 35 nm, as a new filtration system to eliminate viruses in highly purified factor IX and factor XI concentrates. Virus spiking experiments indicated that single dead-end filtration on the membranes could remove more than 5.7-7.8 log10 of human immunodeficiency virus, bovine viral diarrhoea virus, porcine pseudorabies virus, reovirus type 3, and simian virus 40, as well as the small non-enveloped viruses, poliovirus Sabin type 1 and bovine parvovirus. In vitro control tests and animal studies (Wessler stasis model, rat hypotension model) of the two concentrates did not reveal any significant differences with the non-nanofiltered material. Viral filtration of plasma derivatives on porous polymeric membranes might be an essential step in the improvement of their viral safety.
Novel therapeutic agents for B-cell lymphoma: developing rational combinations (2010)

Several novel targeted therapies have recently emerged as active in the treatment of non-Hodgkin lymphoma, including small molecules that inhibit critical signaling pathways, promote apoptotic mechanisms, or modulate the tumor microenvironment. Other new agents target novel cell surface receptors or promote DNA damage. Although most of these drugs have single-agent activity, none have sufficient activity to be used alone. This article reviews the utility and potential role of these new agents in the treatment of non-Hodgkin lymphoma with a specific focus on data that highlight how these agents may be incorporated into current standard treatment approaches.
Meningococcal Outer Membrane Vesicle Vaccines Derived from Mutant Strains Engineered To Express Factor H Binding Proteins from Antigenic Variant Groups 1 and 2 (2008)

Meningococcal outer membrane vesicle (OMV) vaccines, which are treated with detergents to decrease endotoxin activity, are safe and effective in humans. However, the vaccines elicit serum bactericidal antibody responses largely directed against PorA, which is antigenically variable. We previously prepared a native (non-detergent-treated) OMV vaccine from a mutant of group B strain H44/76 in which the lpxL1 gene was inactivated, which resulted in penta-acylated lipid A with attenuated endotoxin activity. To enhance protection, we overexpressed factor H binding protein (fHbp) from the antigenic variant 1 group. The vaccine elicited broad serum bactericidal antibody responses in mice against strains with fHbp variant 1 (approximately 70% of group B isolates) but not against strains with variant 2 or 3. In the present study, we constructed a mutant of group B strain NZ98/254 with attenuated endotoxin that expressed both endogenous variant 1 and heterologous fHbp variant 2. A mixture of the two native OMV vaccines from the H44/76 and NZ98/254 mutants stimulated proinflammatory cytokine responses by human peripheral blood mononuclear cells similar to those stimulated by control, detergent-treated OMV vaccines from the wild-type strains. In mice, the mixture of the two native OMV vaccines elicited broad serum bactericidal antibody responses against strains with heterologous PorA and fHbp in the variant 1, 2, or 3 group. By adsorption studies, the principal bactericidal antibody target was determined to be fHbp. Thus, native OMV vaccines from mutants expressing fHbp variants have the potential to be safe for humans and to confer broad protection against meningococcal disease from strains expressing fHbp from each of the antigenic variant groups.
Fruit, vegetables, and cancer prevention: A review of the epidemiological evidence (1992)

Approximately 200 studies that examined the relationship between fruit and vegetable intake and cancers of the lung, colon, breast, cervix, esophagus, oral cavity, stomach, bladder, pancreas, and ovary are reviewed. A statistically significant protective effect of fruit and vegetable consumption was found in 128 of 156 dietary studies in which results were expressed in terms of relative risk. For most cancer sites, persons with low fruit and vegetable intake (at least the lower one-fourth of the population) experience about twice the risk of cancer compared with those with high intake, even after control for potentially confounding factors. For lung cancer, significant protection was found in 24 of 25 studies after control for smoking in most instances. Fruits, in particular, were significantly protective in cancers of the esophagus, oral cavity, and larynx, for which 28 of 29 studies were significant. Strong evidence of a protective effect of fruit and vegetable consumption was seen in cancers of the pancreas and stomach (26 of 30 studies), as well as in colorectal and bladder cancers (23 of 38 studies). For cancers of the cervix, ovary, and endometrium, a significant protective effect was shown in 11 of 13 studies, and for breast cancer a protective effect was found to be strong and consistent in a meta analysis. It would appear that major public health benefits could be achieved by substantially increasing consumption of these foods.
Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph (2010)

Supplementary data are available at Bioinformatics online.
Eosinophils generate brominating oxidants in allergen-induced asthma (2000)

Eosinophils promote tissue injury and contribute to the pathogenesis of allergen-triggered diseases like asthma, but the chemical basis of damage to eosinophil targets is unknown. We now demonstrate that eosinophil activation in vivo results in oxidative damage of proteins through bromination of tyrosine residues, a heretofore unrecognized pathway for covalent modification of biologic targets in human tissues. Mass spectrometric studies demonstrated that 3-bromotyrosine serves as a specific "molecular fingerprint" for proteins modified through the eosinophil peroxidase-H(2)O(2) system in the presence of plasma levels of halides. We applied a localized allergen challenge to model the effects of eosinophils and brominating oxidants in human lung injury. Endobronchial biopsy specimens from allergen-challenged lung segments of asthmatic, but not healthy control, subjects demonstrated significant enrichments in eosinophils and eosinophil peroxidase. Baseline levels of 3-bromotyrosine in bronchoalveolar lavage (BAL) proteins from mildly allergic asthmatic individuals were modestly but not statistically significantly elevated over those in control subjects. After exposure to segmental allergen challenge, lung segments of asthmatics, but not healthy control subjects, exhibited a >10-fold increase in BAL 3-bromotyrosine content, but only two- to threefold increases in 3-chlorotyrosine, a specific oxidation product formed by neutrophil- and monocyte-derived myeloperoxidase. These results identify reactive brominating species produced by eosinophils as a distinct class of oxidants formed in vivo. They also reveal eosinophil peroxidase as a potential therapeutic target for allergen-triggered inflammatory tissue injury in humans.
Defective Biliary Secretion during Total Parenteral Nutrition (1995)

Cholestasis associated with TPN is now diminishing in frequency. One factor is likely to be the early initiation of oral feeding. One of the effects of oral intake is to restore the enterohepatic circulation of bile acids. This in turn promotes lipid absorption, which leads to improved nutrition and a decreased in mucosal atrophy. The role of the enterohepatic cycling of bile acids has been explored in this review. In infants or children on TPN who have bile acid malabsorption, UDCA can be used to correct decreased secretion of endogenous bile acids. However, controlled studies showing that UDCA actually decreases moribidity and mortality in infants on prolonged TPN have not yet been performed and they are sorely needed. UDCA is nontoxic and acts as a natural bile acid after conjugation. An improved formulation of UDCA with rapid and efficient intestinal absorption has been developed, but the optimal formulation of UDCA is still not available. Cholylsarcosine, a new conjugated bile acid analogue that has been developed as a bile acid replacement agent, improves lipid absorption in animals with steatorrhea caused by bile acid malabsorption and intestinal resection. However, this compound has not been tested clinically.
Alzheimer's disease cybrids replicate beta-amyloid abnormalities through cell death pathways. (2000)

Alzheimer's disease (AD) is characterized by the deposition in brain of beta-amyloid (Abeta) peptides, elevated brain caspase-3, and systemic deficiency of cytochrome c oxidase. Although increased Abeta deposition can result from mutations in amyloid precursor protein or presenilin genes, the cause of increased Abeta deposition in sporadic AD is unknown. Cytoplasmic hybrid ("cybrid") cells made from mitochondrial DNA of nonfamilial AD subjects show antioxidant-reversible lowering of mitochondrial membrane potential (delta(gYm), secrete twice as much Abeta(1-40) and Abeta(1-42), have increased intracellular Abeta(1-40) (1.7-fold), and develop Congo red-positive Abeta deposits. Also elevated are cytoplasmic cytochrome c (threefold) and caspase-3 activity (twofold). Increased AD cybrid Abeta(1-40) secretion was normalized by inhibition of caspase-3 or secretase and reduced by treatment with the antioxidant S(-)pramipexole. Expression of AD mitochondrial genes in cybrid cells depresses cytochrome c oxidase activity and increases oxidative stress, which, in turn, lowers delta(psi)m. Under stress, cells with AD mitochondrial genes are more likely to activate cell death pathways, which drive caspase 3-mediated Abeta peptide secretion and may account for increased Abeta deposition in the AD brain. Therapeutic strategies for reducing neurodegeneration in sporadic AD can address restoration of delta(psi)m and reduction of elevated Abeta secretion.
Effect of the two different leukotriene receptor antagonists, montelukast and zafirlukast, on quality of life: a 12-week randomized study. (2005)

Many studies analyze the effects of many drugs on quality of life (QOL). The aim of this study is to compare the effectiveness of the leukotriene receptor antagonists on QOL. Forty mild asthmatic patients were randomized for 12 treatment-weeks and divided into two groups: the first group was treated with montelukast (MON; 10 mg daily) and the second one was treated with zafirlukast (ZAF; 40 mg daily). All patients underwent clinical examination, spirometry, and completed the Asthma Quality of Life Questionnaire. For each domain, a value of 1 (maximal impairment) and 7 (no impairment) was used. The MON group had in all items a basal median value of 4.7 compared with 5.5 after the treatment (p < 0.05). For physical activities, the mean value was 5.1 compared with 5.9 (p < 0.05). The median scores of 12 symptoms and 5 emotion items were 5.0 and 4.7, significantly lower than 5.7 and 5.3 (p < 0.05). For the environmental stimuli domain, the mean value was 4.6 compared with 5.3 (p < 0.05). The ZAF group had in all items a basal median value of 4.8 compared with 5.7 after the treatment (p < 0.05). For physical activities, the value was 5.0 compared with 5.7 (p < 0.05). Median scores of 12 symptoms and 5 emotions were 4.9 and 4.8, significantly lower than 5.6 and 5.8 (p < 0.05). For the environmental stimuli domain, the median score was 4.7, significantly lower than 5.6 (p < 0.05). The results did not show many differences between the two treatments, showing significant improvement for both MON and ZAF on QOL.
Interaction of a novel cysteine and histidine‐rich cytoplasmic protein with galectin‐3 in a carbohydrate‐independent manner (2000)

We have used the yeast two-hybrid system to search for cytoplasmic proteins that might assist in the intracellular trafficking of the soluble beta-galactoside-binding protein, galectin-3. We utilised as bait murine full-length galectin-3 to screen a murine 3T3 cDNA library. Several interacting clones were found to encode a partial open reading frame and a full-length clone was obtained by rapid amplification of cDNA ends methodology. In various assays in vitro the novel protein was shown to bind galectin-3 in a carbohydrate-independent manner. The novel protein contains an unusually high content of cysteine and histidine residues and shows significant sequence homologies with several metal ion-binding motifs present in known proteins. Confocal immunofluorescence microscopy of permeabilised 3T3 cells shows a prominent perinuclear, as well as cytoplasmic, localisation of the novel protein.
Vascular Endothelial Growth Factor (VEGF) as a Target of Bevacizumab in Cancer: From the Biology to the Clinic (2006)

Angiogenesis is important in the growth and progression of solid tumours. The main pro-angiogenic factor, namely vascular endothelial growth factor (VEGF), also known as vascular permeability factor, is a potent angiogenic cytokine that induces mitosis and also regulates the permeability of endothelial cells. The soluble isoform of VEGF is a dimeric glycoprotein of 36-46 kDa, induced by hypoxia and oncogenic mutation and it binds to two specific tyrosine-kinase receptors: VEGF-1 (flt-1) and VEGF-2 (KDR/flk1). An increase in VEGF expression in tumour tissue or some blood compartments (i.e. serum or plasma) has been found in solid and haematological malignancies of various origins and is associated with metastasis formation and poor prognosis. Bevacizumab, a recombinant humanised monoclonal antibody developed against VEGF, binds to soluble VEGF, preventing receptor binding and inhibiting endothelial cell proliferation and vessel formation. Pre-clinical and clinical studies have shown that bevacizumab alone or in combination with a cytotoxic agent decreases tumour growth and increases median survival time and time to tumour progression. Bevacizumab is the first anti-angiogenetic treatment approved by the American Food and Drug Administration in the first-line treatment of metastatic colorectal cancer. It has shown preliminary evidence of efficacy for breast, non-small-cell lung, pancreatic, prostate, head and neck and renal cancer as well as haematological malignancies. Common toxicities associated with bevacizumab include hypertension, proteinuria, bleeding episodes and thrombotic events. This review summarises the critical role of VEGF and discusses the data available on bevacizumab, from the humanisation of its parent murine monoclonal antibody (mAb) A.4.6.1 to its use in cancer clinical trials.
Editorials: Recombinant Human Erythropoietin: Has Treatment Reached its Full Potential? (2006)

For more than 15 years recombinant human erythropoietin (r-HuEPO) has been used for the treatment of renal anemia benefiting patients with improved quality of life and reduced need for blood transfusions. It is still early in the history of r-HuEPO treatment; therapy has changed little and there have been few investigations into whether current treatment strategies are optimal. Of note, current therapy makes little attempt to mimic normal erythropoietin biology. Large doses of drug are administered episodically resulting in great fluxes in serum erythropoietin levels. It is unlikely that this approach is very efficient from the erythropoietic standpoint. Furthermore the effects of these nonbiologic kinetics on extraerythroid organs that express erythropoietin receptors are unknown. In this review the current state of r-HuEPO treatment is compared to the normal biology of erythropoietin and potential pitfalls caused by divergences are explored.