gebhart/patrepeval huggingface dataset:
Polyprenol formation in the yeast Saccharomyces cerevisiae: effect of farnesyl diphosphate synthase overexpression (1997)

Biosynthesis of polyprenols was followed in the erg mutants of Saccharomyces cerevisiae impaired in various steps of the mevalonate pathway. The end products of the enzymatic reaction carried out in vitro, in the wild type yeast and all mutants tested, were identified as dehydrodolichols (alpha-unsaturated polyprenols) whereas in vivo, yeast synthesize dolichols (alpha-saturated polyprenols) (Biochimie, 1996.78:111-112.) The strain defective in the farnesyl diphosphate (FPP) synthase, (coded by the erg20-2 gene) required the presence of exogenous FPP for synthesis of dehydrodolichols to occur in vitro. Overexpression of the ERG20 gene restored synthesis of polyprenols in vitro indicating that FPP is the allylic "starter" for cis-prenyltransferase in yeast. Overexpression of the ERG20 gene in the erg 9 mutant, defective in squalene synthase activity, not only restored synthesis of dehydrodolichols in vitro, but also increased the synthesis of dolichols in vivo, almost 10-fold in comparison with wild type yeast. On the other hand overexpression of the mutated FPP synthase, coded by the gene erg20-2 in the same genetic background, resulted in a 100-fold increase of the amount of dehydrodolichols. Interestingly, in addition to the family of typical for yeast C60-C80 compounds, dehydrodolichols of chain length up to C135 were synthesized both in vitro and in vivo.
Rendering of Eyes for Eye-Shape Registration and Gaze Estimation (2015)

Images of the eye are key in several computer vision problems, such as shape registration and gaze estimation. Recent large-scale supervised methods for these problems require time-consuming data collection and manual annotation, which can be unreliable. We propose synthesizing perfectly labelled photo-realistic training data in a fraction of the time. We used computer graphics techniques to build a collection of dynamic eye-region models from head scan geometry. These were randomly posed to synthesize close-up eye images for a wide range of head poses, gaze directions, and illumination conditions. We used our model's controllability to verify the importance of realistic illumination and shape variations in eye-region training data. Finally, we demonstrate the benefits of our synthesized training data (SynthesEyes) by out-performing state-of-the-art methods for eye-shape registration as well as cross-dataset appearance-based gaze estimation in the wild.
Membrane topology of the L6 antigen and identification of the protein epitope recognized by the L6 monoclonal antibody. (1994)

The murine monoclonal antibody (mAb) L6 recognizes an integral membrane glycoprotein that is highly expressed on lung, breast, colon, and ovarian carcinomas and is referred to as the L6 antigen. This antigen is an attractive target for therapeutic intervention due to its high level expression on malignant cells. We have previously reported the isolation of a cDNA encoding the human L6 antigen (H-L6). Here, we report the isolation of a cDNA clone encoding the murine L6 antigen (M-L6). This cDNA contains one long open reading frame, which encodes a 220-amino acid polypeptide that is 78% homologous to H-L6. This protein contains short NH2- and COOH-terminal hydrophilic domains and four hydrophobic regions, each long enough to span the plasma membrane. Each of these hydrophobic domains is separated by a hydrophilic domain, the longest of which contains one possible N-linked glycosylation site and is located between the third and fourth hydrophobic domains. We have previously demonstrated that the murine L6 mAb recognizes a protein epitope expressed on human tumor-derived cell lines. Now, using chimeric cDNA constructs encoding human-murine L6 antigen hybrids in conjunction with monoclonal antibody binding experiments, we show that the 42-residue hydrophilic domain of the L6 antigen, located between the third and fourth hydrophobic domains, is outside the cell and that residues in the NH2-terminal region of this domain are critical for the binding of the murine L6 mAb to H-L6.
Scintillation and spectroscopy of the pure and Ce3 -doped elpasolites: Cs2LiYX6(X Cl, Br) (2002)

The optical and scintillation properties of pure and Ce3+-doped Cs2LiYX6 (X = Cl, Br) are presented. X-ray-excited optical luminescence spectra, optical excitation and emission spectra, time-resolved excitation and emission spectra, scintillation pulse height spectra and scintillation decay time spectra of Ce3+-doped Cs2LiYX6 (X = Cl, Br) crystals measured from 10 to 300 K are presented. Factors influencing the scintillation mechanism and the presence of core–valence luminescence are discussed.
Fibrinogen γ Overexpression in Pancreatic Cancer Identified by Large-scale Proteomic Analysis of Serum Samples (2006)

Detection of serum markers for pancreatic cancer has been elusive. Although CA 19-9 is most commonly used, its sensitivity and specificity are modest. We used large-scale proteomics to identify potential serum markers for pancreatic cancer. Samples were analyzed using high-resolution two-dimensional gel electrophoresis to identify differentially expressed proteins in 32 normal and 30 pancreatic cancer patients. Up to 1,744 protein spots were resolved for each serum sample. Candidate proteins were identified using mass spectrometry. ANOVA was used to identify proteins that could discriminate cancer from normal sera. Serum fibrinogen level was also measured using enzymatic assay. Immunohistochemistry was used to detect fibrinogen in resected pancreatic cancers. One hundred fifty-four proteins were commonly overexpressed in all pancreatic cancers. Nine protein spots (four with identifications by mass spectrometry) could effectively separate cancer from normal controls using cross-validation. These proteins successfully discriminated all pancreatic cancer samples (30 of 30) and 94% of normal (30 of 32) samples. Prominent among these candidates was fibrinogen gamma, which was subsequently confirmed to be overexpressed in pancreatic cancer sera by enzymatic analysis (54.1 +/- 64.1 versus 0.0 +/- 0.0 mg/dL, P < 0.05) and tissue by immunohistochemistry (67% versus 29%, P < 0.05) relative to normal pancreas. Proteomic analysis combining two-dimensional gel electrophoresis and mass spectrometry successfully identified 154 potential serum markers for pancreatic cancer. Of these, fibrinogen gamma, a protein associated with the hypercoagulable state of pancreatic cancer, discriminated cancer from normal sera. Fibrinogen is a potential tumor marker in pancreatic cancer.
Nanoparticles enhance brain delivery of blood–brain barrier-impermeable probes for in vivo optical and magnetic resonance imaging (2011)

Several imaging modalities are suitable for in vivo molecular neuroimaging, but the blood-brain barrier (BBB) limits their utility by preventing brain delivery of most targeted molecular probes. We prepared biodegradable nanocarrier systems made up of poly(n-butyl cyanoacrylate) dextran polymers coated with polysorbate 80 (PBCA nanoparticles) to deliver BBB-impermeable molecular imaging probes into the brain for targeted molecular neuroimaging. We demonstrate that PBCA nanoparticles allow in vivo targeting of BBB-impermeable contrast agents and staining reagents for electron microscopy, optical imaging (multiphoton), and whole brain magnetic resonance imaging (MRI), facilitating molecular studies ranging from individual synapses to the entire brain. PBCA nanoparticles can deliver BBB-impermeable targeted fluorophores of a wide range of sizes: from 500-Da targeted polar molecules to 150,000-Da tagged immunoglobulins into the brain of living mice. The utility of this approach is demonstrated by (i) development of a "Nissl stain" contrast agent for cellular imaging, (ii) visualization of amyloid plaques in vivo in a mouse model of Alzheimer's disease using (traditionally) non-BBB-permeable reagents that detect plaques, and (iii) delivery of gadolinium-based contrast agents into the brain of mice for in vivo whole brain MRI. Four-dimensional real-time two-photon and MR imaging reveal that brain penetration of PBCA nanoparticles occurs rapidly with a time constant of ∼18 min. PBCA nanoparticles do not induce nonspecific BBB disruption, but collaborate with plasma apolipoprotein E to facilitate BBB crossing. Collectively, these findings highlight the potential of using biodegradable nanocarrier systems to deliver BBB-impermeable targeted molecular probes into the brain for diagnostic neuroimaging.
Structure and dynamics of colloidal depletion gels: Coincidence of transitions and heterogeneity (2006)

Transitions in structural heterogeneity of colloidal depletion gels formed through short-range attractive interactions are correlated with their dynamical arrest. The system is a density and refractive index matched suspension of 0.20 volume fraction poly(methyl methacyrlate) colloids with the nonadsorbing depletant polystyrene added at a size ratio of depletant to colloid of 0.043. As the strength of the short-range attractive interaction is increased, clusters become increasingly structurally heterogeneous, as characterized by number-density fluctuations, and dynamically immobilized, as characterized by the single-particle mean-squared displacement. The number of free colloids in the suspension also progressively declines. As an immobile cluster to gel transition is traversed, structural heterogeneity abruptly decreases. Simultaneously, the mean single-particle dynamics saturates at a localization length on the order of the short-range attractive potential range. Both immobile cluster and gel regimes show dynamical heterogeneity. Non-Gaussian distributions of single particle displacements reveal enhanced populations of dynamical trajectories localized on two different length scales. Similar dependencies of number density fluctuations, free particle number, and dynamical length scales on the order of the range of short-range attraction suggests a collective structural origin of dynamic heterogeneity in colloidal gels.
Convolutional Neural Network-Based Block Up-Sampling for Intra Frame Coding (2017)

Inspired by the recent advances of image super-resolution using convolutional neural network (CNN), we propose a CNN-based block up-sampling scheme for intra frame coding. A block can be down-sampled before being compressed by normal intra coding, and then up-sampled to its original resolution. Different from previous studies on down/up-sampling-based coding, the up-sampling methods in our scheme have been designed by training CNN instead of hand-crafted. We explore a new CNN structure for up-sampling, which features deconvolution of feature maps, multi-scale fusion, and residue learning, making the network both compact and efficient. We also design different networks for the up-sampling of luma and chroma components, respectively, where the chroma up-sampling CNN utilizes the luma information to boost its performance. In addition, we design a two-stage up-sampling process, the first stage being within the block-by-block coding loop, and the second stage being performed on the entire frame, so as to refine block boundaries. We also empirically study how to set the coding parameters of down-sampled blocks for pursuing the frame-level rate-distortion optimization. Our proposed scheme is implemented into the high-efficiency video coding (HEVC) reference software, and a comprehensive set of experiments have been performed to evaluate our methods. Experimental results show that our scheme achieves significant bits saving compared with the HEVC anchor, especially at low bit rates, leading to on average 5.5% BD-rate reduction on common test sequences and on average 9.0% BD-rate reduction on ultrahigh definition test sequences.
Sketch2Cartoon (2011)

In this paper, we introduce the Sketch2Cartoon system, which is an automatic cartoon making system by leveraging a novel sketch-based clipart image search engine. Different from existing work, most of which either limited users to the pre-prepared characters or only used keyword queries to search materials, Sketch2Cartoon enables users to sketch major curves of characters and props in their mind, and real-time search results from millions of clipart images could be selected to compose the cartoon images. The selected components are vectorized and thus could be further edited. By enabling sketch-based input, the cartoon image making process becomes more natural, and even a child who is too young to read or write can draw whatever he/she imagines and get interesting cartoon images.
Bulk storage applications in the illiac IV system (1971)

In the next year several fourth generation machines with performance in the 100 million instructions per second range will become available. The Illiac IV is one of these machines. With the advent of these machines it will become practical to include an extra dimension, or to greatly increase the resolution of many mesh calculations. Problems which are currently constrained to two spatial dimensions can be expanded to three dimensions, and problems which are currently limited to one spatial dimension can be expanded to include two. This expansion in dimensionality and refinement in resolution implies an increase of approximately two orders of magnitude in the size of the problem's data base. The Unicon 690 mass-memory system will have two distinct uses in the Illiac IV system. The primary use of the Unicon 690 will be to act as a replacement for the conventional restart-output tapes which are generated in the course of large mesh calculations. The Unicon 690 will also act as a storage resource for the Advanced Research Projects Agency (ARPA) network. The ARPA net is a collection of some twenty computers, interconnected by a 50 000 bit/s network of telephone lines and interface message processors. To facilitate the use as a resource on the ARPA net, a conventional computer will be interfaced to the 690 to act as a file manager. Performance parameters of the Unicon 690 are certainly not optimal for this requirement. As is generally the case, higher transfer and lower access time are desirable.
Functional and biochemical analysis of CD16 antigen on natural killer cells and granulocytes. (1988)

CD16 Ag is associated with the low affinity FcR for IgG expressed on human NK cells and granulocytes. In this study, we demonstrate that NK cells specifically lyse murine anti-CD16 hybridoma cell lines, but do not lyse hybridomas against other cell surface differentiation Ag expressed on NK cells. Moreover, the CD18 structure is involved in the CD16-specific xenogeneic interaction between human effector cells and murine hybridoma target cells. Although interaction with anti-CD16 hybridomas or antibodies triggers the cytolytic mechanism of NK cells, this interaction does not induce cellular proliferation. In contrast to NK cells, CD16+ granulocytes do not lyse anti-CD16 hybridoma cell targets and do not mediate ADCC against antibody-coated human tumor cell targets. These findings indicate a fundamental difference in the antibody-dependent cellular cytotoxicity mechanisms of NK cells and granulocytes. Comparative biochemical analysis of CD16 on NK cells and granulocytes revealed significant differences in the size of the polypeptides obtained after removal of N-linked carbohydrate residues with endo-F and N-glycanase digestion.
Status and perspectives of CO2 conversion into fuels and chemicals by catalytic, photocatalytic and electrocatalytic processes (2013)

This review highlights recent developments and future perspectives in carbon dioxide usage for the sustainable production of energy and chemicals and to reduce global warming. We discuss the heterogeneously catalysed hydrogenation, as well as the photocatalytic and electrocatalytic conversion of CO2 to hydrocarbons or oxygenates. Various sources of hydrogen are also reviewed in terms of their CO2 neutrality. Technologies have been developed for large-scale CO2 hydrogenation to methanol or methane. Their industrial application is, however, limited by the high price of renewable hydrogen and the availability of large-volume sources of pure CO2. With regard to the direct electrocatalytic reduction of CO2 to value-added chemicals, substantial advances in electrodes, electrolyte, and reactor design are still required to permit the development of commercial processes. Therefore, in this review particular attention is paid to (i) the design of metal electrodes to improve their performance and (ii) recent developments of alternative approaches such as the application of ionic liquids as electrolytes and of microorganisms as co-catalysts. The most significant improvements both in catalyst and reactor design are needed for the photocatalytic functionalisation of CO2 to become a viable technology that can help in the usage of CO2 as a feedstock for the production of energy and chemicals. Apart from technological aspects and catalytic performance, we also discuss fundamental strategies for the rational design of materials for effective transformations of CO2 to value-added chemicals with the help of H2, electricity and/or light.
Mononucleoside Phosphotriester Derivatives with S-Acyl-2-thioethyl Bioreversible Phosphate-Protecting Groups: Intracellular Delivery of 3'-Azido-2',3'-dideoxythymidine 5'-Monophosphate (1995)

The synthesis, in vitro anti-HIV-1 activity, and decomposition pathways of several mononucleoside phosphotriester derivatives of 3'-azido-2',3'-dideoxythymidine (AZT) incorporating a new kind of carboxylate esterase-labile transient phosphate-protecting group, namely, S-acyl-2-thioethyl, are reported. All the described compounds showed marked antiviral activity in thymidine kinase-deficient CEM cells in which AZT was virtually inactive. The results strongly support the hypothesis that such pronucleotides exert their biological effects via intracellular delivery of the 5'-mononucleotide of AZT. This point was corroborated by decomposition studies in cell extracts and culture medium.
C-Nap1, a Novel Centrosomal Coiled-Coil Protein and Candidate Substrate of the Cell Cycle–regulated Protein Kinase Nek2 (1998)

Nek2 (for NIMA-related kinase 2) is a mammalian cell cycle-regulated kinase structurally related to the mitotic regulator NIMA of Aspergillus nidulans. In human cells, Nek2 associates with centrosomes, and overexpression of active Nek2 has drastic consequences for centrosome structure. Here, we describe the molecular characterization of a novel human centrosomal protein, C-Nap1 (for centrosomal Nek2-associated protein 1), first identified as a Nek2-interacting protein in a yeast two-hybrid screen. Antibodies raised against recombinant C-Nap1 produced strong labeling of centrosomes by immunofluorescence, and immunoelectron microscopy revealed that C-Nap1 is associated specifically with the proximal ends of both mother and daughter centrioles. On Western blots, anti-C-Nap1 antibodies recognized a large protein (>250 kD) that was highly enriched in centrosome preparations. Sequencing of overlapping cDNAs showed that C-Nap1 has a calculated molecular mass of 281 kD and comprises extended domains of predicted coiled-coil structure. Whereas C-Nap1 was concentrated at centrosomes in all interphase cells, immunoreactivity at mitotic spindle poles was strongly diminished. Finally, the COOH-terminal domain of C-Nap1 could readily be phosphorylated by Nek2 in vitro, as well as after coexpression of the two proteins in vivo. Based on these findings, we propose a model implicating both Nek2 and C-Nap1 in the regulation of centriole-centriole cohesion during the cell cycle.
Transcatheter measurement of myocardium electrical impedance: 2 versus 3 electrode method (2004)

We are interested in the use of electrical impedance spectroscopy for on-line in-situ monitorization of the state of the myocardium tissue using a transcatheter method. In this study we evaluate a new 3 electrode measurement method (3EM) in comparison with the standard two electrode method (2EM). We analyze the effect of the tip distance to the myocardium wall and the catheter angle for both methods. We used the finite element model in order to compare both measurement methods. Experimental in-vitro measurements were performed to validate the mathematical model. Results show that the measured impedance depends of the contrast (conductivity of blood divided by conductivity of tissue) and the distance. This dependence is stronger for the 2EM than for the 3EM. The impedance spectrum with the 3EM is more appropriate than the 2EM for tissue characterization.
Association between inflammation and systolic blood pressure in RA compared to patients without RA (2018)

Across a broad range of CRP observed in RA and non-RA outpatients, we found an inverse U-shaped relationship between CRP and SBP, highlighting a relationship not previously observed when studying the general population.
Interstitial cells of Cajal mediate inhibitory neurotransmission in the stomach. (1996)

The structural relationships between interstitial cells of Cajal (ICC), varicose nerve fibers, and smooth muscle cells in the gastrointestinal tract have led to the suggestion that ICC may be involved in or mediate enteric neurotransmission. We characterized the distribution of ICC in the murine stomach and found two distinct classes on the basis of morphology and immunoreactivity to antibodies against c-Kit receptors. ICC with multiple processes formed a network in the myenteric plexus region from corpus to pylorus. Spindle-shaped ICC were found within the circular and longitudinal muscle layers (IC-IM) throughout the stomach. The density of these cells was greatest in the proximal stomach. IC-IM ran along nerve fibers and were closely associated with nerve terminals and adjacent smooth muscle cells. IC-IM failed to develop in mice with mutations in c-kit. Therefore, we used W/W(V) mutants to test whether IC-IM mediate neural inputs in muscles of the gastric fundus. The distribution of inhibitory nerves in the stomachs of c-kit mutants was normal, but NO-dependent inhibitory neuro-regulation was greatly reduced. Smooth muscle tissues of W/W(V) mutants relaxed in response to exogenous sodium nitroprusside, but the membrane potential effects of sodium nitroprusside were attenuated. These data suggest that IC-IM play a critical serial role in NO-dependent neurotransmission: the cellular mechanism(s) responsible for transducing NO into electrical responses may be expressed in IC-IM. Loss of these cells causes loss of electrical responsiveness and greatly reduces responses to nitrergic nerve stimulation.
Optical coherence micro-elastography: mechanical-contrast imaging of tissue microstructure (2014)

We present optical coherence micro-elastography, an improved form of compression optical coherence elastography. We demonstrate the capacity of this technique to produce en face images, closely corresponding with histology, that reveal micro-scale mechanical contrast in human breast and lymph node tissues. We use phase-sensitive, three-dimensional optical coherence tomography (OCT) to probe the nanometer-to-micrometer-scale axial displacements in tissues induced by compressive loading. Optical coherence micro-elastography incorporates common-path interferometry, weighted averaging of the complex OCT signal and weighted least-squares regression. Using three-dimensional phase unwrapping, we have increased the maximum detectable strain eleven-fold over no unwrapping and the minimum detectable strain is 2.6 με. We demonstrate the potential of mechanical over optical contrast for visualizing micro-scale tissue structures in human breast cancer pathology and lymph node morphology.