gebhart/patrepeval huggingface dataset:
A fuzzy approach to content-based image retrieval (2003)

In this paper we present a fuzzy approach to content-based retrieval of segmented images. Our proposed methodology uses fuzzy attributed relational graphs (FARGs) and an efficient fuzzy graph matching algorithm (FGM). The graph matching algorithm is of low computational complexity and hence is suitable for content-based retrieval. Experimental results on random (sub)graph matching and content-based retrieval applications are also provided. The results indicate that the FARG-FGM framework of representing and retrieving images is efficient and accurate.
Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging (2012)

Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own "personalities" regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching. Understanding photophysics is critical in the design and interpretation of single-molecule experiments.
Mechanism of asymmetric epoxidation. 2. Catalyst structure (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of asymmetric epoxidation. 2. Catalyst structureM. G. Finn and K. Barry SharplessCite this: J. Am. Chem. Soc. 1991, 113, 1, 113–126Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/ja00001a019https://doi.org/10.1021/ja00001a019research-articleACS PublicationsRequest reuse permissionsArticle Views6915Altmetric-Citations304LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity (2016)

Hematopoietic stem cell (HSC) transplantation is curative for malignant and genetic blood disorders, but is limited by donor availability and immune-mismatch. Deriving HSCs from patient-matched embryonic/induced-pluripotent stem cells (ESCs/iPSCs) could address these limitations. Prior efforts in murine models exploited ectopic HoxB4 expression to drive self-renewal and enable multi-lineage reconstitution, yet fell short in delivering robust lymphoid engraftment. Here, by titrating exposure of HoxB4-ESC-HSC to Notch ligands, we report derivation of engineered HSCs that self-renew, repopulate multi-lineage hematopoiesis in primary and secondary engrafted mice, and endow adaptive immunity in immune-deficient recipients. Single-cell analysis shows that following engraftment in the bone marrow niche, these engineered HSCs further specify to a hybrid cell type, in which distinct gene regulatory networks of hematopoietic stem/progenitors and differentiated hematopoietic lineages are co-expressed. Our work demonstrates engineering of fully functional HSCs via modulation of genetic programs that govern self-renewal and lineage priming.
Continuous Intravenous Heparin Compared with Intermittent Subcutaneous Heparin in the Initial Treatment of Proximal-Vein Thrombosis (1986)

We performed a randomized double-blind trial comparing continuous intravenous heparin with intermittent subcutaneous heparin in the initial treatment of 115 patients with acute proximal deep-vein thrombosis. Intermittent subcutaneous heparin as administered in this trial was inferior to continuous intravenous heparin in preventing recurrent venous thromboembolism. The subcutaneous heparin regimen induced an initial anticoagulant response below the target therapeutic range in the majority of patients and resulted in a high frequency of recurrent venous thromboembolism (11 of 57 patients, 19.3 percent), which was virtually confined to patients with a subtherapeutic anticoagulant response. In contrast, continuous intravenous heparin induced a therapeutic anticoagulant response in the majority of patients and a low frequency of recurrent events (3 of 58 patients, 5.2 percent; P = 0.024); the recurrences were limited to patients with an initial subtherapeutic anticoagulant response. The results of this trial establish the efficacy of intravenous heparin in the treatment of proximal venous thrombosis and suggest a relation between the effectiveness of heparin and the levels of anticoagulation achieved; such a relation could explain the observed failure of the subcutaneous regimen.
Regulation of cytochrome p450 by inflammatory mediators: why and how? (2001)

Expression and activities of cytochrome P450 enzymes are down-regulated in the liver during the host response to inflammation or infection, leading to alterations in drug clearance and toxin activation. This review focuses on recent studies on the mechanisms of this down-regulation, as well as the cytokines and cell types involved. Possible reasons for cytochrome P450 down-regulation are discussed.
Unusual strategies for using indium gallium nitride grown on silicon (111) for solid-state lighting (2011)

Properties that can now be achieved with advanced, blue indium gallium nitride light emitting diodes (LEDs) lead to their potential as replacements for existing infrastructure in general illumination, with important implications for efficient use of energy. Further advances in this technology will benefit from reexamination of the modes for incorporating this materials technology into lighting modules that manage light conversion, extraction, and distribution, in ways that minimize adverse thermal effects associated with operation, with packages that exploit the unique aspects of these light sources. We present here ideas in anisotropic etching, microscale device assembly/integration, and module configuration that address these challenges in unconventional ways. Various device demonstrations provide examples of the capabilities, including thin, flexible lighting "tapes" based on patterned phosphors and large collections of small light emitters on plastic substrates. Quantitative modeling and experimental evaluation of heat flow in such structures illustrates one particular, important aspect of their operation: small, distributed LEDs can be passively cooled simply by direct thermal transport through thin-film metallization used for electrical interconnect, providing an enhanced and scalable means to integrate these devices in modules for white light generation.
Expression of mRNA for interleukin-5 in mucosal bronchial biopsies from asthma. (1991)

We have attempted to identify mRNA for IL-5 in endobronchial mucosal biopsies from asthmatics and controls, using the technique of in situ hybridization. Bronchial biopsies were obtained from 10 asthmatics and 9 nonatopic normal controls. A radio-labeled cRNA probe was prepared from an IL-5 cDNA and hybridized to permeabilized sections. These were washed extensively before processing for autoradiography. An IL-5-producing T cell clone derived from a patient with the hyper-IgE syndrome was used as a positive control. As a negative control, sections were also treated with a "sense" IL-5 probe. Specific hybridization signals for IL-5 mRNA were demonstrated within the bronchial mucosa in 6 out of the 10 asthmatic subjects. Cells exhibiting hybridization signals were located beneath the epithelial basement membrane. In contrast, there was no hybridization in the control group. No hybridization was observed with the sense probe. The six IL-5 mRNA-positive asthmatics tended to have more severe disease than the negative asthmatics, as assessed by symptoms and lung function, and showed a significant increase in the degree of infiltration of the bronchial mucosa by secreting (EG2+) eosinophils and activated (CD25+) T lymphocytes. Within the subjects who showed positive IL-5 mRNA, there was a correlation between IL-5 mRNA expression and the number of CD25+ and EG2+ cells and total eosinophil count. This study provides evidence for the cellular localization of IL-5 mRNA in the bronchial mucosa of asthmatics and supports the concept that this cytokine regulates eosinophil function in bronchial asthma.
Carotenoid pigments: their possible role in protecting against photooxidation in eyes and photoreceptor cells (1982)

Abstract The effect of light on animal tissues is ambivalent. Light is necessary for many functions, e. g. for vision and, as in the flagellate halobacterium, to gain energy. But light is potentially dangerous: it is capable of destroying cells or their components by photooxidation, especially in the presence of sensitizing pigments such as haems and cytochromes, which are ubiquitous in aerobic cells. Several different examples are discussed to show how a compromise is achieved in animal tissues that for functional reasons receive high exposure to light. Carotenoid pigments, present in many eyes and photoreceptors, seem especially suited to protect against the deleterious effects of light because they absorb the dangerous short wavelength part of the light spectrum. In plant tissue, carotenoids are also well known to be capable of ‘quenching’ photoexcited states of sensitizing pigments and of oxygen, a function that they might have also in animal tissues. A consequence of the considerations is that whenever animal tissues are exposed to higher than usual light levels and/or oxygen pressures cellular damage might occur. Examples are discussed; strategies to circumvent the deleterious effects by photooxidation follow directly from the arguments.
Abstract A7: Differential glucose metabolites in prostate cancer aggressivity by ethnicity (2009)

The observation that chromosome 8q24 has multiple prostate cancer susceptibility loci that independently affect inherited risk for disease aggressivity suggested an underlying genetic basis for the observed disparities in prostate cancer risks between African Americans and Caucasians. We reasoned that genetic differences in glucose metabolism leading to subtle quantitative alterations in levels of glucose metabolites synergizes with genetic defects to selectively and adversely modulate disease onset, disease progression and disease outcome in African Americans compared to Caucasians. Consistent with this notion, we hypothesized that distinct and quantifiable differences in glucose metabolites underlie the prevalence of aggressive prostate cancer in African Americans relative to Caucasians. Towards this end, we have used 13 C tracer-based methodology and quantitative 1 H NMR and 1 H- 1 H TOCSY to perform comparative metabolomic analysis of age- and stage-matched representative cell lines derived from American American (PCa2b) and Caucasian (PC3). The data shows substantial differences in rates of glucose utilization and in rates of lactate secretion. Additional quantitative alterations were observed in key glucose metabolites. Differences in the genetic regulation of glucose metabolism and of its metabolites provide additional alternative explanation for the increased incidence and the poorer prognosis of prostate cancer in African-Americans compared to Caucasians.
Spheroids from equine amnion mesenchymal stem cells: an in vitro study (2015)

Background: Equine amnion mesenchymal stem cells (EAMSCs) from amnion isolated after the foal birth represented an alternative source of easy collection of mesenchymal cells used in equine regenerative medicine.&#13;\n&#13;\nMethods: These cells grown as 2D culture in α-MEM medium supplemented with EGF were differentiated in adipogenic, chondrogenic and osteogenic cells. Half a million cells as pellet were left in 15ml tubes with the same differentiation media for 20 days. After the pellets were collected, embedded in paraffin for morphological study.&#13;\n&#13;\nResults: 2D culture showed EAMSCs with an embryonic phenotype (C-kit+, CD105+, Oct-4+) and a differentiation potential in adipogenic, chondrogenic and osteogenic multipotent cells. By a reproducible method of 3D culture, at day 20 the Authors evidenced a formation of small aggregated spheroids gradually gathering. In cross sections the surface of spheroid evidenced flattened cells embedded in a red matrix by Alizarin staining and occasionally a core of calcium precipitation. A network of apoptotic or necrotic cells in a not mineralized matrix was present into the center of nodules. The 3D spheroids appeared larger (mean diameter of 605±53 µm for gathering spheroids and 1486±79 µm for spheroids already gathered) than those from standard monolayer cultures (mean diameter of 200 ± 73 µm).&#13;\n&#13;\nConclusions: EAMSCs cultured in 3D method preserve their in vitro multipotent differentiation than adherent 2D culture method. These EAMSCs included in extracellular matrix not mineralized at day 20 seem to be a good source of MSCs for tissue repair and regeneration in equine medicine.
LA ESCUELA NACIONAL DE MUSICA ALCANZO LA MAYORIA DE SUS METAS (1987)

LA EN DE LA UNAM ALCANZO LA MAYORIA DE SUS METAS MINIMAS PARA 1986, ANO DURANTE EL CUAL MUCHOS DE LOS OBJETIVOS LOGRADOS FUERON ADICIONALES. TODO ELLO, LEJOS DE ALENTAR EL CONFORMISMO, CONSTITUYE UN MOTIVO MAS PARA CONTINUAR EN LA BUSQUEDA DE MAYORES Y MEJORES REALIZACIONES.
Hydrocarbon constrained peptides – understanding preorganisation and binding affinity (2016)

The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID). Our biophysical and structural analyses illustrate that whilst the introduction of the constraint increases the population of the bioactive α-helical conformation of the peptide in solution, it does not enhance the inhibitory potency against pro-apoptotic Bcl-x<sub>L</sub> and Mcl-1 PPIs. SPR analyses indicate binding occurs <i>via</i> an induced fit mechanism whilst X-ray analyses illustrate none of the key interactions between the helix and protein are disturbed. The behaviour derives from enthalpy-entropy compensation which may be considered in terms of the ground state energies of the unbound constrained and unconstrained peptides; this has implications for the design of preorganised peptides to target protein-protein interactions.
Apolipoprotein E Protects Against Bacterial Lipopolysaccharide-induced Lethality (2001)

Septic shock is the most common cause of death in intensive care units and no effective treatment is available at present. Lipopolysaccharide (LPS) is the primary mediator of Gram-negative sepsis by inducing the production of macrophage-derived cytokines. Previously, we showed that apolipoprotein E (apoE), an established modulator of lipid metabolism, can bind LPS, thereby redirecting LPS from macrophages to hepatocytes in vivo. We now report that intravenously administered LPS strongly increases the serum levels of apoE. In addition, apoE can prevent the LPS-induced production of cytokines and subsequent death in rodents. Finally, apoE-deficient mice show a significantly higher sensitivity toward LPS than control wild-type mice. These findings indicate that apoE may have a physiological role in the protection against sepsis, and recombinant apoE may be used therapeutically to protect against LPS-induced endotoxemia.
Measurements of the Oxygen Tension in the Lumen of the Small Intestine of the Domestic Duck (1965)

ABSTRACT By use of an oxygen electrode measurements of oxygen tension have been made in the lumen of the small intestine of the domestic duck in the region occupied by the acanthocephalan parasite, Polymorphus minutus. The tension was found to vary from 25 mm. Hg close to the villi to less than 0·5 mm. Hg in the centre of the lumen.
Screening of Large Molecule Diversities by Phage Display (2011)

Molecules with tailored binding specificities are needed for many purposes such as the development of therapeutics, the detection and purification of biomolecules or in chemical biology for the study and manipulation of biological systems. With phage display technology, polypeptides with binding affinities to targets of interest can be isolated from billions of polypeptide variants with a modest amount of effort, time and cost. The technology was initially used for the generation and screening of peptide and antibody libraries and was later applied to many different protein scaffolds. More recently, chemically and structurally diverse molecule libraries were generated by chemically modifying phage-displayed polypeptides. In this article, the different classes of natural and non-natural structures that can be encoded and screened by phage display are reviewed with a special focus on bicyclic peptides that we routinely generate in our laboratory.
Vascular endothelial growth factor (VEGF)-C synergizes with basic fibroblast growth factor and VEGF in the induction of angiogenesis in vitro and alters endothelial cell extracellular proteolytic activity (1998)

Vascular endothelial growth factor-C (VEGF-C) is a recently characterized member of the VEGF family of angiogenic polypeptides. We demonstrate here that VEGF-C is angiogenic in vitro when added to bovine aortic or lymphatic endothelial (BAE and BLE) cells but has little or no effect on bovine microvascular endothelial (BME) cells. As reported previously for VEGF, VEGF-C and basic fibroblast growth factor (bFGF) induced a synergistic in vitro angiogenic response in all three cells lines. Unexpectedly, VEGF and VEGF-C also synergized in the in vitro angiogenic response when assessed on BAE cells. Characterization of VEGF receptor (VEGFR) expression revealed that BME, BAE, and BLE cell lines express VEGFR-1 and -2, whereas of the three cell lines assessed, only BAE cells express VEGFR-3. We also demonstrate that VEGF-C increases plasminogen activator (PA) activity in the three bovine endothelial cell lines and that this is accompanied by a concomitant increase in PA inhibitor-1. Addition of α2-antiplasmin to BME cells co-treated with bFGF and VEGF-C partially inhibited collagen gel invasion. These results demonstrate, first, that by acting in concert with bFGF or VEGF, VEGF-C has a potent synergistic effect on the induction of angiogenesis in vitro and, second, that like VEGF and bFGF, VEGF-C is capable of altering endothelial cell extracellular proteolytic activity. These observations also highlight the notion of context, i.e., that the activity of an angiogenesis-regulating cytokine depends on the presence and concentration of other cytokines in the pericellular environment of the responding endothelial cell. J. Cell. Physiol. 177:439–452, 1998. © 1998 Wiley-Liss, Inc.
Tuna fishmeal as a source of DHA for n−3 PUFA enrichment of pork, chicken, and eggs (2002)

Enriching foods with long-chain n-3 PUFA (LC n-3 PUFA) is an important approach to increasing the dietary intake of these beneficial nutrients. Enrichment of meat and eggs can be achieved by adding flaxseed, fish oil, or fishmeal to pig or poultry feeds. However, utilization of these sources, particularly fishmeal, has been limited by concerns about adverse effects on sensory qualities. In this study, we evaluated the use of PorcOmega (POM), a stabilized tuna fishmeal formulation, as a source of DHA for enrichment of pork and poultry products. Pigs, broilers, and laying hens were fed rations containing varying levels of POM for varying time periods, and its impact on the LC n-3 PUFA content and sensory qualities of cooked meat and eggs was examined. Pork and chicken products, including chops, sausages, and eggs, with substantially increased (up to sevenfold) levels of LC n-3 PUFA (predominantly DHA) were achieved by including up to 10% POM in rations. The increases were retained after cooking. Some sensory deficits were noted when using higher levels of POM (exceeding 15% in meat and 10% in eggs). However, at modest rates of feeding (5-10% POM), palatable meat and eggs were obtained with worthwhile levels of enrichment. The fishmeal feeding strategy used in this study offers a viable means of producing a range of alternative dietary sources of LC n-3 PUFA.
Energizing cell‐free protein synthesis with glucose metabolism (2005)

In traditional cell-free protein synthesis reactions, the energy source (typically phosphoenolpyruvate (PEP) or creatine phosphate) is the most expensive substrate. However, for most biotechnology applications glucose is the preferred commercial substrate. Previous attempts to use glucose in cell-free protein synthesis reactions have been unsuccessful. We have now developed a cell-free protein synthesis reaction where PEP is replaced by either glucose or glucose-6-phosphate (G6P) as the energy source, thus allowing these reactions to compete more effectively with in vivo protein production technologies. We demonstrate high protein yields in a simple batch-format reaction through pH control and alleviation of phosphate limitation. G6P reactions can produce high protein levels ( approximately 700 microg/mL of chloramphenical acetyl transferase (CAT)) when pH is stabilized through replacement of the HEPES buffer with Bis-Tris. Protein synthesis with glucose as an energy source is also possible, and CAT yields of approximately 550 mug/mL are seen when both 10 mM phosphate is added to alleviate phosphate limitations and the Bis-Tris buffer concentration is increased to stabilize pH. By following radioactivity from [U-(14)C]-glucose, we find that glucose is primarily metabolized to the anaerobic products, acetate and lactate. The ability to use glucose as an energy source in cell-free reactions is important not only for inexpensive ATP generation during protein synthesis, but also as an example of how complex biological systems can be understood and exploited through cell-free biology.