gebhart/patrepeval huggingface dataset:
cDNA Cloning and Expression of a Novel Human UDP- -acetyl-α-D-galactosamine (1996)

The glycosylation of serine and threonine residues during mucin-type O-linked protein glycosylation is carried out by a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-transferase). Previously two members, GalNAc-T1 and -T2, have been isolated and the genes cloned and characterized. Here we report the cDNA cloning and expression of a novel GalNAc-transferase termed GalNAc-T3. The gene was isolated and cloned based on the identification of a GalNAc-transferase motif (61 amino acids) that is shared between GalNAc-T1 and -T2 as well as a homologous Caenorhabditis elegans gene. The cDNA sequence has a 633-amino acid coding region indicating a protein of 72.5 kDa with a type II domain structure. The overall amino acid sequence similarity with GalNAc-T1 and -T2 is approximately 45%; 12 cysteine residues that are shared between GalNAc-T1 and -T2 are also found in GalNAc-T3. GalNAc-T3 was expressed as a soluble protein without the hydrophobic transmembrane domain in insect cells using a Baculo-virus vector, and the expressed GalNAc-transferase activity showed substrate specificity different from that previously reported for GalNAc-T1 and -T2. Northern analysis of human organs revealed a very restricted expression pattern of GalNAc-T3.
Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight (2003)

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating potato disease in the world. Control of late blight in the United States and other developed countries relies extensively on fungicide application. We previously demonstrated that the wild diploid potato species Solanum bulbocastanum is highly resistant to all known races of P. infestans. Potato germplasm derived from S. bulbocastanum has shown durable and effective resistance in the field. Here we report the cloning of the major resistance gene RB in S. bulbocastanum by using a map-based approach in combination with a long-range (LR)-PCR strategy. A cluster of four resistance genes of the CC-NBS-LRR (coiled coil-nucleotide binding site-Leu-rich repeat) class was found within the genetically mapped RB region. Transgenic plants containing a LR-PCR product of one of these four genes displayed broad spectrum late blight resistance. The cloned RB gene provides a new resource for developing late blight-resistant potato varieties. Our results also demonstrate that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system.
Relationship between Mineral Distributions in Dentine Lesions and Subsequent Remineralization in vitro (2000)

Though the mineral distribution of the dentine carious lesion varies largely from tooth to tooth and from patient to patient, there are two main distribution profiles that characterize natural carious lesions in dentine. These profiles include softened and subsurface lesion types. The mineral distribution relationship between the starting profile and the profile after remineralization is not known. In order to study the relational aspects, we have produced demineralized dentine samples in vitro with mineral profiles similar to those of typical natural carious lesions, and subsequently remineralized the samples in a remineralizing solution with various fluoride concentrations (0, 2 and 10 ppm F). The mineral distributions were obtained by using an improved microradiographic technique. In addition, the nature of deposited mineral was analyzed by diamond-coupled total internal reflectance spectroscopy. Definite relationship was observed between the original lesion mineral distribution and the mineral distributions following remineralization. The amount of mineral present in approximately the first 50 microm of the lesion influenced the overall mineral profile after remineralization, possibly through influencing ion transport. If the amount was high (> approximately 10 vol%), the deposited mineral was confined to the surface (0-50 microm). The original mineral at those depths acted like a nucleus of mineral regrowth when the amount of residual mineral was intermediate, and like a transport barrier when the surface layer was well mineralized. If a surface barrier was not present, mineral was deposited at deeper depths in the lesion. Fluoride effect on dentine remineralization was dependent on the original mineral content and its distribution in the lesion. Although a high concentration of fluoride was very effective in low-mineral lesions, it produced hyperremineralization on well-mineralized subsurface lesions so that it prevented effective remineralization especially in deeper lesions.
An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood* (2015)

Isolation and molecular characterization of rare cells (e.g. circulating tumor and stem cells) within biological fluids and tissues has significant potential in clinical diagnostics and personalized medicine. The present work describes an integrated platform of sample procurement, preparation, and analysis for deep proteomic profiling of rare cells in blood. Microfluidic magnetophoretic isolation of target cells spiked into 1 ml of blood at the level of 1000-2000 cells/ml, followed by focused acoustics-assisted sample preparation has been coupled with one-dimensional PLOT-LC-MS methodology. The resulting zeptomole detection sensitivity enabled identification of ∼4000 proteins with injection of the equivalent of only 100-200 cells per analysis. The characterization of rare cells in limited volumes of physiological fluids is shown by the isolation and quantitative proteomic profiling of first MCF-7 cells spiked into whole blood as a model system and then two CD133+ endothelial progenitor and hematopoietic cells in whole blood from volunteers.
Adsorption/Desorption of Water and Ethanol on 3A Zeolite in Near-Adiabatic Fixed Bed (2009)

A pilot scale adsorber apparatus was designed and constructed to investigate water and ethanol adsorption/desorption kinetics on 3A zeolite for the design purposes of a fuel ethanol dehydration pressure swing adsorption (PSA) process. Equilibrium studies have shown that 3A zeolite adsorbed a significant amount of water while very weak ethanol adsorption was observed. The breakthrough curves were utilized to study the effects of column pressure, temperature, flow rate, pellet size, and adsorbate concentration on the overall mass transfer resistance. Based on experimentally observed trends, both macropore and micropore diffusion were identified as relevant mass transfer mechanisms. A mathematical model for a bench scale adsorption bed included the linear driving force (LDF) adsorption rate model and the variation of axial velocity. A detailed heat transfer model was a necessity since the bed dynamics was affected by heat transfer in the bed wall. The model was used to analyze the experimental data and extract values of pertaining diffusion coefficients.
Human Mesenchymal Stem Cells as a Gene Delivery System to Create Cardiac Pacemakers (2004)

We tested the ability of human mesenchymal stem cells (hMSCs) to deliver a biological pacemaker to the heart. hMSCs transfected with a cardiac pacemaker gene, mHCN2, by electroporation expressed high levels of Cs+-sensitive current (31.1+/-3.8 pA/pF at -150 mV) activating in the diastolic potential range with reversal potential of -37.5+/-1.0 mV, confirming the expressed current as I(f)-like. The expressed current responded to isoproterenol with an 11-mV positive shift in activation. Acetylcholine had no direct effect, but in the presence of isoproterenol, shifted activation 15 mV negative. Transfected hMSCs influenced beating rate in vitro when plated onto a localized region of a coverslip and overlaid with neonatal rat ventricular myocytes. The coculture beating rate was 93+/-16 bpm when hMSCs were transfected with control plasmid (expressing only EGFP) and 161+/-4 bpm when hMSCs were expressing both EGFP+mHCN2 (P<0.05). We next injected 10(6) hMSCs transfected with either control plasmid or mHCN2 gene construct subepicardially in the canine left ventricular wall in situ. During sinus arrest, all control (EGFP) hearts had spontaneous rhythms (45+/-1 bpm, 2 of right-sided origin and 2 of left). In the EGFP+mHCN2 group, 5 of 6 animals developed spontaneous rhythms of left-sided origin (rate=61+/-5 bpm; P<0.05). Moreover, immunostaining of the injected regions demonstrated the presence of hMSCs forming gap junctions with adjacent myocytes. These findings demonstrate that genetically modified hMSCs can express functional HCN2 channels in vitro and in vivo, mimicking overexpression of HCN2 genes in cardiac myocytes, and represent a novel delivery system for pacemaker genes into the heart or other electrical syncytia.
Solid or not solid: vision for radar target validation (2004)

In the context of combining radar and vision sensors for a fusion application in dense city traffic situations, one of the major challenges is to be able to validate radar targets. We take a high-level fusion approach assuming that both sensor modalities have the capacity to independently locate and identify targets of interest. In this context, radar targets can either correspond to a vision target- in which case the target is validated without further processing- or not. It is the latter case that drives the focus of this paper. A non-matched radar target can correspond to some solid object which is not part of the objects of interest of the vision sensor (such as a guard-rail) or can be caused by reflections in which case it is a ghost target which does not match any physical object in the real world. We describe a number of computational steps for the decision making of non-matched radar targets. The computations combine both direct motion parallax measurements and indirect motion analysis- which are not sufficient for computing parallax but are nevertheless quite effective- and pattern classification steps for covering situations which motion analysis are weak or ineffective. One of the major advantages of our high-level fusion approach is that it allows the use of simpler (low cost) radar technology to create a combined high performance system.
Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium (1994)

An optical whole-cell biosensor based on a genetically engineered bioluminescent catabolic reporter bacterium was developed for continuous on-line monitoring of naphthalene and salicylate bioavailability and microbial catabolic activity potential in waste streams. The bioluminescent reporter bacterium, Pseudomonas fluorescens HK44, carries a transcriptional nahG-luxCDABE fusion for naphthalene and salicylate catabolism. Exposure to either compound resulted in inducible bioluminescence. The reporter culture was immobilized onto the surface of an optical light guide by using strontium alginate. This biosensor probe was then inserted into a measurement cell which simultaneously received the waste stream solution and a maintenance medium. Exposure under defined conditions to both naphthalene and salicylate resulted in a rapid increase in bioluminescence. The magnitude of the response and the response time were concentration dependent. Good reproducibility of the response was observed during repetitive perturbations with either naphthalene or salicylate. Exposure to other compounds, such as glucose and complex nutrient medium or toluene, resulted in either minor bioluminescence increases after significantly longer response times compared with naphthalene or no response, respectively. The environmental utility of the biosensor was tested by using real pollutant mixtures. A specific bioluminescence response was obtained after exposure to either an aqueous solution saturated with JP-4 jet fuel or an aqueous leachate from a manufactured-gas plant soil, since naphthalene was present in both pollutant mixtures.
High Effi ciency 4-kW Fiber Laser Cutting Machine (2011)

We have developed a commercial 4-kW fi ber laser consisting of seven, 600-W modules whose outputs
The collagen network of the heart. (1979)

An extensive collagen skeleton in the myocardium is clearly demonstrable by scanning electron microscopy. This system mechanically connects myocytes to contiguous myocytes, connects myocytes to contiguous capillaries, and is responsible for orienting myocytes into anatomical units. The extent and location of the system involves it in a variety of physical parameters of the heart under both normal and abnormal conditions. The myocyte to myocyte collagen struts may provide for sarcomere alignment from cell to cell, ensure equal stretch of contiguous cells, and prevent slippage of adjacent cells. The numerous myocyte to web network connections would ensure that the entire group of cells function in a consistent fashion. The origin and course of the myocyte to capillary collagen struts could account for capillary patency during systole in the presence of high ventricular wall pressures. The complex web network surrounds groups of myocytes and is mechanically coupled to the contained myocytes. The loose collagen connections between groups easily permits slippage and rearrangement of groups of cells as expected in acute dilation. The web network itself could be the site of some of the viscoelastic properties of the heart.
Evaluation of the relative contribution of nitric oxide and peroxynitrite to the suppression of mitochondrial respiration in immunostimulated macrophages using a manganese mesoporphyrin superoxide dismutase mimetic and peroxynitrite scavenger (1996)

Here we report that the cell-permeable superoxide dismutase mimetic Mn(III)tetrakis (4-benzoic acid) porphyrin (MnTBAP) inhibits the oxidation of dihydrorhodamine-123 by peroxynitrite, but does not scavenge nitric oxide (NO). MnTBAP protects against the suppression of mitochondrial respiration in J774 cells exposed to peroxynitrite or to NO donors. MnTBAP and N(G)-methyl-L-arginine provide additive protective effect against the suppression of respiration in immunostimulated cells. Our data suggest separate contributions of NO and peroxynitrite to the suppression of mitochondrial respiration and support the role of oxidative stress in the expression of the inducible isoform of NO synthase.
Stabilizing quantum information (2000)

The dynamical-algebraic structure underlying all the schemes for quantum information stabilization is argued to be fully contained in the reducibility of the operator algebra describing the interaction with the environment of the coding quantum system. This property amounts to the existence of a nontrivial group of symmetries for the global dynamics. We provide a unified framework that allows us to build systematically additional classes of error correcting codes and noiseless subsystems. It is shown that by using symmetrization strategies one can artificially produce noiseless subsystems supporting universal quantum computation.
Adjunctive Intracardiac Echocardiography to Guide Slow Pathway Ablation in Human Atrioventricular Nodal Reentrant Tachycardia (1997)

Radiofrequency ablation at the tricuspid valve's insertion into the AV muscular septum as identified by ICE reliably terminates anterograde SP conduction, supporting the hypothesis that the SP consistently traverses this anatomic location.
Adaptive event detection with time-varying poisson processes (2006)

Time-series of count data are generated in many different contexts, such as web access logging, freeway traffic monitoring, and security logs associated with buildings. Since this data measures the aggregated behavior of individual human beings, it typically exhibits a periodicity in time on a number of scales (daily, weekly,etc.) that reflects the rhythms of the underlying human activity and makes the data appear non-homogeneous. At the same time, the data is often corrupted by a number of bursty periods of unusual behavior such as building events, traffic accidents, and so forth. The data mining problem of finding and extracting these anomalous events is made difficult by both of these elements. In this paper we describe a framework for unsupervised learning in this context, based on a time-varying Poisson process model that can also account for anomalous events. We show how the parameters of this model can be learned from count time series using statistical estimation techniques. We demonstrate the utility of this model on two datasets for which we have partial ground truth in the form of known events, one from freeway traffic data and another from building access data, and show that the model performs significantly better than a non-probabilistic, threshold-based technique. We also describe how the model can be used to investigate different degrees of periodicity in the data, including systematic day-of-week and time-of-day effects, and make inferences about the detected events (e.g., popularity or level of attendance). Our experimental results indicate that the proposed time-varying Poisson model provides a robust and accurate framework for adaptively and autonomously learning how to separate unusual bursty events from traces of normal human activity.
Nanopore DNA sensors based on dendrimer-modified nanopipettes (2009)

A dendrimer-modified nanopipette is used to detect hybridization of a specific DNA sequence through evaluation of the extent of rectification of ion currents observed in the measured current-voltage response.
Analysis of the use of expansion osteotomes for the creation of implant beds. Technical contributions and review of the literature. (2006)

Sometimes, the severe superior maxillary atrophy compromises and even impide oral implants treatment. The use of rotatory instruments (drills) produce heat and lost of bone, but the osteotomes in implantology avoid this and simplifies the surgical treatment allowing implant installation with an easier technique. We present an expansive maxillary technique review, describing the main indications, advantages and disadvantages of this surgical procedure.
Hydrogenation of 5-hydroxymethylfurfural in supercritical carbon dioxide–water: a tunable approach to dimethylfuran selectivity (2013)

The use of supercritical carbon dioxide–water on the hydrogenation of 5-hydroxymethylfurfural (HMF) was investigated over a Pd/C catalyst. It was possible to achieve a very high yield (100%) of DMF within the reaction time of 2 hours at 80 °C. A significant effect of CO2 pressure was observed on the product distribution. Simply by tuning the CO2 pressure it was possible to achieve various key compound, such as tetrahydro-5-methyl-2-furanmethanol (MTHFM) (<10 MPa), 2,5-dimethylfuran (DMF) (10 MPa) and 2,5-dimethyltetrahydrofuran (DMTHF) (>10 MPa) with very high selectivity. Optimization of other reaction parameters revealed that H2 pressure, temperature, as well as the CO2–water mole ratio, played an important role in the selectivity to the targeted DMF. It is interesting to note that a very high yield of DMF was achieved when a combination of CO2 and water was used. For instance, in the absence of water or CO2, the selectivity of DMF was low; similarly, an excess of water against the fixed pressure of CO2 reduced the selectivity to DMF. Hence, an optimized amount of water was mandatory in the presence of CO2 for the formation of DMF with high selectivity. This method was successfully extended to the hydrogenation of furfural, which could afford 100% selectivity to 2-methylfuran with complete conversion within a very short reaction time of 10 min. The studied catalyst could be recycled successfully without significant loss of catalytic activity.
Surface Characterization of Mixed Self-Assembled Monolayers Designed for Streptavidin Immobilization (2001)

The self-assembly of streptavidin onto biotinylated alkylthiolate monolayers on gold has served as an important model system for protein immobilization at surfaces. Here, we report a detailed study of the surface composition and structure of mixed self-assembled monolayers (SAMs) containing biotinylated and diluent alkylthiolates and their use to specifically immobilize streptavidin. X-ray photoelectron spectroscopy (XPS), angle-resolved XPS (ARXPS), near-edge X-ray absorption fine structure (NEXAFS), and surface plasmon resonance (SPR) have been used to characterize the films produced on gold from a range of binary mixtures of a biotinylated alkylthiol (BAT) and either a C16 methyl-terminated thiol (mercaptohexadecane, MHD) or a C11-oligo(ethylene glycol)-terminated (OEG) thiol in ethanol. The correlation between the solution mole fraction of BAT and its surface mole fraction (χBAT,sur) indicates that it adsorbs ∼4-fold faster than OEG but slightly slower than MHD. ARXPS analysis demonstrates that the biotin terminus of the BAT is exposed at the surface of mixed monolayers with χBAT,sur < 0.5 but is randomly distributed through BAT-rich films. Thus, the OEG diluent not only adds nonfouling properties but induces an improved concentration of biotin at the surface and reduces the exposure of the methylene segments of BAT. NEXAFS characterization demonstrates that pure OEG and mixed BAT/OEG SAMs do not show significant anisotropy in C−C bond orientation, in contrast to MHD and mixed BAT/MHD SAMs, whose aliphatic segments exhibit pseudo-crystalline packing. SPR measurements of streptavidin binding to and competitive dissociation from the different mixed SAMs indicate that streptavidin binds both specifically and nonspecifically to the BAT/MHD SAMs but purely specifically to BAT/OEG SAMs with χBAT,sur < 0.5. For BAT/OEG mixtures with χBAT,sur = 0.1−0.5, specifically bound streptavidin coverages of ∼80% of the C(2,2,2) two-dimensional streptavidin crystalline density (∼280 ng/cm2) can be reproducibly achieved. These composite results clarify the relationship between the specificity of streptavidin recognition and the surface architecture and properties of the mixed SAMs.
Systematic Drug Repositioning Based on Clinical Side-Effects (2011)

Drug repositioning helps fully explore indications for marketed drugs and clinical candidates. Here we show that the clinical side-effects (SEs) provide a human phenotypic profile for the drug, and this profile can suggest additional disease indications. We extracted 3,175 SE-disease relationships by combining the SE-drug relationships from drug labels and the drug-disease relationships from PharmGKB. Many relationships provide explicit repositioning hypotheses, such as drugs causing hypoglycemia are potential candidates for diabetes. We built Naïve Bayes models to predict indications for 145 diseases using the SEs as features. The AUC was above 0.8 in 92% of these models. The method was extended to predict indications for clinical compounds, 36% of the models achieved AUC above 0.7. This suggests that closer attention should be paid to the SEs observed in trials not just to evaluate the harmful effects, but also to rationally explore the repositioning potential based on this "clinical phenotypic assay".