gebhart/patrepeval huggingface dataset:
Role of Poly(ADP-ribose) Polymerase (PARP) Cleavage in Apoptosis (1999)

An early transient burst of poly(ADP-ribosyl)ation of nuclear proteins was recently shown to be required for apoptosis to proceed in various cell lines (Simbulan-Rosenthal, C., Rosenthal, D., Iyer, S., Boulares, H., and Smulson, M. (1998) J. Biol. Chem. 273, 13703-13712) followed by cleavage of poly(ADP-ribose) polymerase (PARP), catalyzed by caspase-3. This inactivation of PARP has been proposed to prevent depletion of NAD (a PARP substrate) and ATP, which are thought to be required for later events in apoptosis. The role of PARP cleavage in apoptosis has now been investigated in human osteosarcoma cells and PARP -/- fibroblasts stably transfected with a vector encoding a caspase-3-resistant PARP mutant. Expression of this mutant PARP increased the rate of staurosporine and tumor necrosis factor-alpha-induced apoptosis, at least in part by reducing the time interval required for the onset of caspase-3 activation and internucleosomal DNA fragmentation, as well as the generation of 50-kilobase pair DNA breaks, thought to be associated with early chromatin unfolding. Overexpression of wild-type PARP in osteosarcoma cells also accelerated the apoptotic process, although not to the same extent as that apparent in cells expressing the mutant PARP. These effects of the mutant and wild-type enzymes might be due to the early and transient poly(ADP-ribose) synthesis in response to DNA breaks, and the accompanying depletion of NAD apparent in the transfected cells. The accelerated NAD depletion did not seem to interfere with the later stages of apoptosis. These results indicate that PARP activation and subsequent cleavage have active and complex roles in apoptosis.
Epidemiology and Ecology of Onychomycosis (1997)

The epidemiology and ecology of onychomycosis are complex and little understood. Most is known about tinea unguium, dermatophytic nail infection, and its causative agents. This is often categorised according to the precise locus on the nail of the infection. The principal infectious propagules are thought to be the arthroconidia or chlamydospores which form within the solid substratum of invaded nail tissue. The process of infecting new hosts appears to be facilitated by abrasion, moistening and scratching. The role of the non-dermatophyte yeast Candida as an agent of onychomycosis per se may have been overestimated. The range of interactions between dermatophytes and non-dermatophytes in nails is complex and poorly understood. There may be at least six distinct ecological categories of non-dermatophyte isolations from nails. It would be of clinical interest to know which species found in mixed infections were never able to advance beyond 'secondary colonisation', as they would not require specific treatment.
Statistical Characterization of Face Spectral Reflectances and Its Application to Human Portraiture Spectral Estimation (2002)

Spectral reflectances of various parts of human faces from various ethnic races were measured as part of experiments on spectral imaging for human portraits. Principal components analysis (PCA) was applied to the spectral reflectances from the various races, and a variety of face parts. The first three principal components explain about 99.8% of cumulative contribution of variance of spectral reflectances for each race and each face part, and for all races as well. Color differences of spectral reconstruction either for individual races and all races or for individual face parts based on different sets of principal components were estimated. The results indicate that, when using three basis functions and under D50 illumination, the basis functions based only on spectra of Pacific&#x2013;Asian subjects will provide the best overall color reproduction. However, from a spectral matching point of view, three basis functions based on all spectra will provide the best spectral reproduction with minimum overall mean value of metameric indices. More analyses were applied to spectral reflectances of human facial skin from different sources and their corresponding spectral reconstruction based on different sets of principal components. Those results provide practical suggestions for imaging, or spectral imaging, system design, especially imaging systems for human portraiture.
A simple cell based assay to measure Parkin activity (2010)

Parkin is an ubiquitin-protein ligase mutated in Autosomal Recessive - Juvenile Parkinsonism. Here, we describe a cell-based assay to measure Parkin's ubiquitin-protein ligase activity. It relies on the ability of Parkin to recognise depolarised mitochondria and exploits a cell line where Parkin expression is inducible. In these cells, Parkin expression promotes mitophagy and accelerates cell death in response to mitochondrial depolarisers. Time-lapse imaging confirmed cell death and revealed increased perinuclear mitochondrial clustering following induction of Parkin expression in cells exposed to carbonyl cyanide m-chlorophenylhydrazone. Similar effects were not observed with α-synuclein or DJ-1, other proteins associated with the development of Parkinson's disease, confirming the specificity of the assay. We have used this assay to demonstrate that ligase-defective Parkin mutants are inactive, and cellular proteasomal activity (using the proteasomal inhibitors MG132, clasto-lactacystin β-lactone and epoxomicin) is essential for the Parkin mediated effect. As the assay is suitable for high-throughput screening, it has the potential to identify novel proteostasis compounds that stimulate the activity of Parkin mutants for therapeutic purposes, to identify modulators of kinase activities that impact on Parkin function, and to act as a functional read-out in reverse genetics screens aimed at identifying modifiers of Parkin function during mitophagy.
Pancreas and islet cell transplantation: now and then. (1996)

Pancreas transplantation currently can be offered with the same probability of success as other solid organ transplants. In diabetic uremic recipients of kidney transplants, the addition of a pancreas is routine in many centers. For selected patients with labile diabetes and hypoglycemia unawareness, a successful pancreas transplant can dramatically improve quality of life. Islet transplantation is an alternative to pancreas transplantation that can reduce surgical morbidity, but is much less successful at the moment. The theoretical, immunological advantages of islet transplantation have not yet been realized. Part of the problem lies in the reduced beta cell mass that occurs with organ dispersal and islet purification. Diabetogenic immunosuppressants need to be eliminated in order to allow optimal function of what is engrafted. The immunosuppressants (eg, mycophenolate mofetil, rapamycin) give this possibility. Whether islet transplantation will replace pancreas transplantation remains problematic. Ultimately, and neither should be needed for Type I diabetes, since autoimmune diseases should be preventable by appropriate manipulation of the immune system in those identified at risk. Our personal goals as transplanters should be obsolescence.
Bioluminescence-Based Detection of MicroRNA, miR21 in Breast Cancer Cells (2008)

A hybridization assay for the detection of microRNA, miR21 in cancer cells using the bioluminescent enzyme Renilla luciferase (Rluc) as a label, has been developed. MicroRNAs are small RNAs found in plants, animals, and humans that perform key functions in gene silencing and affect early-stage cell development, cell differentiation, and cell death. miRNAs are considered useful early diagnostic and prognostic markers of cancer, candidates for therapeutic intervention, and targets for basic biomedical research. However, methods for highly sensitive and rapid detection of miRNA directly from samples such as cells that can serve as a suitable diagnostics platform are lacking. In that regard, the utilization of the bioluminescent label, Rluc, that offers the advantage of high signal-to-noise ratio, allows for the development of highly sensitive assays for the determination of miRNA in a variety of matrixes. In this paper, we have described the development of a competitive oligonucleotide hybridization assay for the detection of miR21 using the free miR21 and Rluc-labeled miR21 that competes to bind to an immobilized miR21 complementary probe. The miR21 microRNA chosen for this study is of biomedical significance because its levels are elevated in a variety of cancers. Using the optimized assay, a detection limit of 1 fmol was obtained. The assay was employed for the detection of miR21 in human breast adenocarcinoma MCF-7 cells and nontumorigenic epithelial MCF-10A cells. The comparison of miR21 expression level in two cell lines demonstrated higher expression of miR21 in breast cancer cell line MCF-7 compared to the nontumorigenic MCF-10A cells. Further, using the assay developed, the miR21 quantification could be performed directly in cell extracts. The hybridization assay was developed in a microplate format with a total assay time of 1.5 h and without the need for sample PCR amplification. The need for early molecular markers and their detection methods in cancer diagnosis is tremendous. The characteristics of the assay developed in this work show its suitability for early cancer diagnosis based on miRNA as a biomarker.
Ion Pairing and Hydration in Polyelectrolyte Multilayer Films Containing Polysaccharides (2009)

Thin films constituted of poly(L-lysine) (PLL) as polycation and of the anionic polysaccharides hyaluronan (HA), chondroitin sulfate (CSA), and heparin (HEP) as polyanions with increasing sulfate contents have been investigated for their internal structure, including water content and ion pairing. Film buildup in physiological solutions was followed in situ by quartz crystal balance with dissipation monitoring (QCM-D) and attenuated total internal reflectance (ATR-FTIR), infrared spectroscopy (ATR-FTIR), which allows an unambiguous quantification of the groups (sulfate, carboxylate, ammonium) present on the side groups of the polyelectrolytes. HA- and CSA-based films were the most hydrated ones. The monomer ratio (disaccharide/lysine) was very similar for all the films, whatever the polyanion, and tended toward a plateau value at approximately 0.5, indicating that there are two lysine molecules per disaccharide monomer. Thanks to the possibility to selectively cross-link carboxylate and ammonium ions via carbodiimide chemistry, the COO-/NH3+ and SO3-/NH3+ ion pairing was determined. We found that 46% of NH3+ groups are unpaired (i.e., extrinsically compensated by counterions) in HA-based films, 21% in CSA-based films and none in HEP ones, which is indeed in agreement with fluorescence recovery after photobleaching (FRAP) measurements of fluorescently labeled PLL diffusion in the films. In addition, the ratio of SO3- versus COO- pairing with NH3+ groups was close to the stoechiometry of these groups in the dissacharide monomeric unit, that is, 2:1 for HEP-based films and 1:1 for CSA based films. Thus, hydration, ion pairing, and PLL diffusion in the films are interconnected properties that arise from the specific structures of the biomacromolecules constituting the films.
BIOKDD 2002 (2002)

article BIOKDD 2002: recent advances in data mining for bioinformatics Share on Authors: Mohammed J. Zaki Rensselaer Polytechnic Institute, Troy, NY Rensselaer Polytechnic Institute, Troy, NYView Profile , Jason T. L. Wang New Jersey Institute of Technology, Newark, NJ New Jersey Institute of Technology, Newark, NJView Profile , Hannu T. T. Toivonen University of Helsinki, Finland University of Helsinki, FinlandView Profile Authors Info & Claims ACM SIGKDD Explorations NewsletterVolume 4Issue 2December 2002 pp 112–114https://doi.org/10.1145/772862.772884Online:01 December 2002Publication History 2citation253DownloadsMetricsTotal Citations2Total Downloads253Last 12 Months1Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Making surgical simulation real (1996)

article Free Access Share on Making surgical simulation real Author: Dwight Meglan HT Medical HT MedicalView Profile Authors Info & Claims ACM SIGGRAPH Computer GraphicsVolume 30Issue 4Nov. 1996 pp 37–39https://doi.org/10.1145/240806.240811Online:01 November 1996Publication History 13citation35DownloadsMetricsTotal Citations13Total Downloads35Last 12 Months10Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
A Divergent and Selective Synthesis of Isomeric Benzoxazoles from a Single N–Cl Imine (2011)

A divergent and regioselective synthesis of either 3-substituted benzisoxazoles or 2-substituted benzoxazoles from readily accessible ortho-hydroxyaryl N-H ketimines is described. The reaction proceeds in two distinct pathways through a common N-Cl imine intermediate: (a) N-O bond formation to form benzisoxazole under anhydrous conditions and (b) NaOCl mediated Beckmann-type rearrangement to form benzoxazole, respectively. The reaction path also depends on the electronic nature of the aromatic ring, with the electron-rich aromatic rings favoring the rearrangement and the electron-deficient rings favoring the N-O bond formation. A Beckmann-type rearrangement mechanism via net [1,2]-aryl migration for the formation of 2-substituted benzoxazole is proposed.
Hereditary Prostate Cancer (2001)

One of the triumphs of molecular genetics during the past two decades has been the elucidation of the molecular mechanisms responsible for the inherited predisposition for a number of common human cancers. Genes such as BRCA1, BRCA2, VHL, APC and hMSH2—in which changes as small as single nucleotide substitutions result in greatly increased organ-specific cancer risk—have been identified through studies of familial breast, renal, and colorectal cancers. Major efforts are now underway worldwide to identify and characterize hereditary prostate cancer (HPC) genes through the study of prostate cancer families. Four separate loci suspected to harbor such genes have been identified to date, and efforts to clone the specific genes are in progress. A primary goal of these efforts is the development of genetic tests to determine which individuals carry high-risk prostate cancer alleles. This chapter provides an overview of the evidence supporting a hereditary form of prostate cancer, and summarizes the efforts to identify and characterize the genes responsible for hereditary prostate cancer (HPC).
Mediators of Inflammation in Acute Kidney Injury (2009)

Acute kidney injury (AKI) remains to be an independent risk factor for mortality and morbidity. Inflammation is now believed to play a major role in the pathophysiology of AKI. It is hypothesized that in ischemia, sepsis and nephrotoxic models that the initial insult results in morphological and/or functional changes in vascular endothelial cells and/or in tubular epithelium. Then, leukocytes including neutrophils, macrophages, natural killer cells, and lymphocytes infiltrate into the injured kidneys. The injury induces the generation of inflammatory mediators like cytokines and chemokines by tubular and endothelial cells which contribute to the recruiting of leukocytes into the kidneys. Thus, inflammation has an important role in the initiation and extension phases of AKI. This review will focus on the mediators of inflammation contributing to the pathogenesis of AKI.
Cytolysis of nucleated cells by complement: cell death displays multi-hit characteristics. (1983)

Lysis of nucleated cells by complement was studied to determine whether the lytic process by C5b-9 conforms to a one-hit mechanism as in the case of erythrocytes. Two nucleated cell lines, Molt 4 and U937, derived from human T lymphocytes and histiocytes, respectively, were employed as targets. The antibody-sensitized cells were used to develop the titration curves, measuring cell death as a function of limiting quantities of human C6 or C5,6 complex in the presence of an excess of other complement components. The cytolysis curves generated in both experiments were sigmoidal, in sharp contrast to the monotonic curves observed in lysis of erythrocytes treated similarly. The sigmoidal curves of cytolysis indicate a cooperative action of several molecules of C6 or acid-activated C5,6 complex, C(56)a. In contrast to the multi-hit characteristics of cytolysis, dose-response measurements of the release of 86Rb indicated that only one effective molecule of C6 per cell is required for assembly of a 86Rb-releasing channel. This divergence indicates that lysis requires formation of several channels or, alternatively, assembly of large channels that are formed by several molecules of C6. Because prior studies with erythrocyte ghosts have shown that only a single effective molecule of C6 is required for assembly of a transmembrane channel, regardless of size, we prefer to interpret the multi-hit characteristics of nucleated cell lysis as an indication of a multi-channel requirement, rather than channel enlargement.
Interleukin-6 and interleukin-11: same same but different (2013)

The pleiotropic physiological functions of interleukin (IL-)6 type cytokines range from embryonic development and tissue homoeostasis to neuronal development and T cell differentiation. In contrast, imbalance of the well-controlled cytokine signaling network leads to chronic inflammatory diseases and cancer. IL-6 and IL-11 both signal through a homodimer of the ubiquitously expressed β-receptor glycoprotein 130 (gp130). Specificity is gained through an individual IL-6/IL-11 α-receptor, which does not directly participate in signal transduction, although the initial cytokine binding event to the α-receptor leads to the final complex formation with the β-receptors. Both cytokines activate the same downstream signaling pathways, which are predominantly the mitogen-activated protein kinase (MAPK)-cascade and the Janus kinase/signal transducer and activator of transcription (Jak/STAT) pathway. However, recent studies have highlighted divergent roles of the two related cytokines. Here, we will discuss how the biochemical similarities are translated into unique and non-redundant functions of IL-6 and IL-11 in vivo and illustrate strategies for cytokine-specific therapeutic intervention.
Decentralized Markets versus Central Control: A Comparative Study (1999)

Multi-Agent Systems (MAS) promise to offer solutions to problems where established, older paradigms fall short. In order to validate such claims that are repeatedly made in software agent publications, empirical in-depth studies of advantages and weaknesses of multi-agent solutions versus conventional ones in practical applications are needed. Climate control in large buildings is one application area where multi-agent systems, and market-oriented programming in particular, have been reported to be very successful, although central control solutions are still the standard practice. We have therefore constructed and implemented a variety of market designs for this problem, as well as different standard control engineering solutions. This article gives a detailed analysis and comparison, so as to learn about differences between standard versus agent approaches, and yielding new insights about benefits and limitations of computational markets. An important outcome is that ``local information plus market communication produces global control''.
Induction of Experimental Periodontitis in Mice With Porphyromonas gingivalis‐ Adhered Ligatures (2000)

The use of a P. gingivalis-adhered ligature supported a long-lasting infection of P. gingivalis in mice, resulting in P. gingivalis-induced alveolar bone breakdown.
Protein purification by affinity binding to unilamellar vesicles (1989)

A novel purification technique is proposed which employs affinity-ligand-modified liposomes to specifically purify bioactive macromolecules from solution. This process is demonstrated with avidin as the model biomolecule and biotin as the affinity ligand. Biotin is covalently bound to the surface of small unilamellar vesicles composed of dimyristoyl phosphatidylcholine (DMPC) and dimyristoyl phosphatidylethanolamine (DMPE). The number of accessible binding sites on the liposomes is determined by titration with avidin, and the kinetics of binding are evaluated by monitoring the concentration of free avidin in solution after the addition of biotinylated liposomes. The specificity of the process is determined by following the affinity binding of avidin to biotinylated liposomes in the presence of model impurities (i.e., lysozyme and cytochrome C). Liposome-bound avidin is separated from the impurities by ultrafiltration through a membrane which retains the liposomes.
Recent results and latest views on microcavity LEDs (2004)

We are progressively approaching the physical limits of microcavity LEDs (MC-LEDs) for high brightness, high efficiency LEDs. They are promising high efficiency devices and they offer the very attractive prospect of full planar fabrication process. However, to compete with other high efficiency LED schemes, they need to approach or surpass the 50 % efficiency mark. We first explore the limits of planar MC-LEDs in both the GaAlInAsP and GaInAlN materials systems, and show that the single-step extraction limit is in the 40 % range at best, depending on the materials system used, with the largest part of the non-extracted light being emitted into guided modes. The waveguided light can itself be extracted by photon recycling, when the internal quantum efficiency is high. Otherwise, another extraction scheme for that light is provided by various photonic-crystal-assisted extraction schemes. Simple photonic crystals (PCs) appear to lack the omnidirectional extraction properties required. However, more rotation-invariant PCs like Archimedean tilings allow to obtain such extraction with added efficiencies already in the 10% range. We discuss the further improvements to such structures.