gebhart/patrepeval huggingface dataset:
Rapid method for determining cholesteryl ester transitions of apoB-containing lipoproteins. (1982)

A wide variety of cholesteryl ester-rich apoB-containing lipoproteins undergo an order-disorder transition in the cholesteryl ester core at approximately normal body temperature. The transition occurs over several degrees C with the mid-point being as high as 57 degrees C in some cholesterol-fed animals. The transition mid-point of normal human low density lipoprotein (LDL) appears to vary from as low as 26 degrees C to about body temperature. However, to screen a large population of patients at risk for atheroscerlotic cardiovascular disease (ACD), a rapid method for determining the transition temperature of LDL is needed. Since apoB-containing lipoproteins (VLDL and LDL) are readily precipitated from plasma by dextran sulfate and magnesium sulfate, we have studied the thermal properties of this precipitate using differential scanning calorimetry (DSC). The VLDL-LDL precipitate undergoes a reversible thermal transition similar in transition temperature and enthalpy to the cholesteryl ester transition of isolated pure LDL. The transition is seen with the precipitate from VLDL-free plasma, but no transition is seen when VLDL and LDL have been removed. Cholesteryl ester-rich apoB containing lipoproteins were isolated from a variety of sources (man, cholesterol-fed monkeys, and rabbits) and their transition temperatures compared with the apoB-containing lipoprotein precipitates from the same source. The mid-point of individual transitions varied over a wide range (17-57 degrees C) and the correlation between the pure lipoprotein and the plasma precipitate was strong (r = 0.98, P < 0.001. Thus, DSC of the plasma apoB precipitate may be used as a rapid method of determining the cholesteryl ester transition of LDL and other apoB-containing lipoproteins.-Waugh, D. A., and D. M. Small. Rapid method for determining cholesteryl ester transitions of apoB-containing lipoproteins.
Trafficking of Antigen-Specific CD8+ T Lymphocytes to Mucosal Surfaces following Intramuscular Vaccination (2008)

A critical goal of vaccine development for a wide variety of pathogens is the induction of potent and durable mucosal immunity. However, it has been assumed that this goal would be difficult to achieve by systemic vaccination due to the anatomic and functional distinctness of the systemic and mucosal immune systems and the resultant compartmentalization of immune responses. In this study, we show that Ag-specific CD8(+) T lymphocytes traffic efficiently to mucosal surfaces following systemic vaccination. Intramuscular immunization with recombinant adenovirus (rAd) vector-based vaccines expressing SIV Gag resulted in potent, durable, and functional CD8(+) T lymphocyte responses at multiple mucosal effector sites in both mice and rhesus monkeys. In adoptive transfer studies in mice, vaccine-elicited systemic CD8(+) T lymphocytes exhibited phenotypic plasticity, up-regulated mucosal homing integrins and chemokine receptors, and trafficked rapidly to mucosal surfaces. Moreover, the migration of systemic CD8(+) T lymphocytes to mucosal compartments accounted for the vast majority of Ag-specific mucosal CD8(+) T lymphocytes induced by systemic vaccination. Thus, i.m. vaccination can overcome immune compartmentalization and generate robust mucosal CD8(+) T lymphocyte memory. These data demonstrate that the systemic and mucosal immune systems are highly coordinated following vaccination.
Plasma pharmacokinetic profile of fluralaner (Bravecto™) and ivermectin following concurrent administration to dogs (2015)

Concurrent administration of fluralaner and ivermectin does not alter the pharmacokinetics of either compound. Based on the plasma pharmacokinetic profile and the clinical observations, there is no evident interaction between fluralaner and ivermectin, and co-administration does not increase the risk of ivermectin associated neurotoxicity.
MerTK is required for apoptotic cell–induced T cell tolerance (2008)

Self-antigens expressed by apoptotic cells (ACs) may become targets for autoimmunity. Tolerance to these antigens is partly established by an ill-defined capacity of ACs to inhibit antigen-presenting cells such as dendritic cells (DCs). We present evidence that the receptor tyrosine kinase Mer (MerTK) has a key role in mediating AC-induced inhibition of DC activation/maturation. Pretreatment of DCs prepared from nonobese diabetic (NOD) mice with AC blocked secretion of proinflammatory cytokines, up-regulation of costimulatory molecule expression, and T cell activation. The effect of ACs on DCs was dependent on Gas6, which is a MerTK ligand. NOD DCs lacking MerTK expression (NOD.MerTK(KD/KD)) were resistant to AC-induced inhibition. Notably, autoimmune diabetes was exacerbated in NOD.MerTK(KD/KD) versus NOD mice expressing the transgenic BDC T cell receptor. In addition, beta cell-specific CD4(+) T cells adoptively transferred into NOD.MerTK(KD/KD) mice in which beta cell apoptosis was induced with streptozotocin exhibited increased expansion and differentiation into type 1 T cell effectors. In both models, the lack of MerTK expression was associated with an increased frequency of activated pancreatic CD11c(+)CD8alpha(+) DCs, which exhibited an enhanced T cell stimulatory capacity. These findings demonstrate that MerTK plays a critical role in regulating self-tolerance mediated between ACs, DCs, and T cells.
Measles Virus Haemagglutinin Gene: Cloning, Complete Nucleotide Sequence Analysis and Expression in COS Cells (1986)

A measles virus (Hallé strain) cDNA library was prepared by cloning virus-induced mRNA directly into the expression vector PCD. Clones corresponding to the measles virus haemagglutinin (HA) gene were isolated and one, PCD-HA-15, which corresponded to the complete mRNA sequence, was further characterized. After transfection into COS-7 cells, measles virus HA antigen was detected by immunofluorescence. The [35S]methionine-labelled HA protein from transfected cells was immunoprecipitated by both polyclonal and monoclonal measles virus antibodies. Analysis by SDS-polyacrylamide gel electrophoresis revealed that the PCD-HA-15 protein migrated in a manner identical to the virus-induced HA. Nucleotide sequence analysis established that the gene contained 1949 nucleotides [exclusive of poly(A)] and coded for a protein containing 617 amino acids. A single hydrophobic domain likely to represent the transmembrane region was identified at the N-terminus. A second overlapping reading frame coded for a protein containing 70 amino acids. This contained a short hydrophobic region (16 amino acids) and had two potential N-glycosylation sites. Comparison of the HA gene of the Hallé strain with the published sequence of the Edmonston strain showed that there was a high degree of conservation (99.3%).
Reuse of imputed data in microarray analysis increases imputation efficiency (2004)

Sequential reuse of imputed data in KNN-based imputation greatly increases the efficiency of imputation. The SKNN method should be practically useful to save the data of some microarray experiments which have high amounts of missing entries. The SKNN method generates reliable imputed values which can be used for further cluster-based analysis of microarray data.
Quickest spectrum sensing in cognitive radio (2008)

Quickest detection is applied to frequency spectrum sensing in cognitive radio systems. Distribution change in frequency domain is detected for vacating secondary radio networks from licensed frequency band. A successive refinement based quickest detection is proposed to tackle the problem of unknown parameters of primary radio signal. Cooperative quickest detection is used to enhance the performance of quickest spectrum sensing in secondary radio systems without data fusion centers. Performance is evaluated using theoretical analysis and numerical simulations.
Affinity and kinetic analysis of the bovine plasma C‐type lectin collectin‐43 (CL‐43) interacting with mannan (1996)

Collectins are C-type lectins which have been implied to play an important role in the innate immune defence against microorganisms. The critical discriminatory event in the opsonization of microorganisms by collectins is the interaction of the C-type lectin domain with microbial carbohydrates. Surface plasmon resonance measurements allow for quantitative real-time measurements of binding interaction between immobilized carbohydrate and unlabelled lectin in solution. Binding analysis were carried out with purified collectin-43 (CL-43) which structurally is the simplest collectin consisting of only three polypeptides each terminating in a C-type lectin domain. The target was immobilized yeast mannan. The molecular mass of native CL-43 was determinated by mass spectroscopy to 99.8 kDa. The dissociation rate (kdiss) of the C-type lectin-carbohydrate binding was fast (1.19-1.36 x 10(-2) second-1), and the association rate (kass) was 4.37-5.07 x 10(5) M-1 second-1. The equilibrium constant for dissociation (Kd) was 2.68-2.72 x 10(-8) M.
Appearance Modeling for Tracking in Multiple Non-Overlapping Cameras (2005)

When viewed from a system of multiple cameras with non-overlapping fields of view, the appearance of an object in one camera view is usually very different from its appearance in another camera view due to the differences in illumination, pose and camera parameters. In order to handle the change in observed colors of an object as it moves from one camera to another, we show that all brightness transfer functions from a given camera to another camera lie in a low dimensional subspace and demonstrate that this subspace can be used to compute appearance similarity. In the proposed approach, the system learns the subspace of inter-camera brightness transfer functions in a training phase during which object correspondences are assumed to be known. Once the training is complete, correspondences are assigned using the maximum a posteriori (MAP) estimation framework using both location and appearance cues. We evaluate the proposed method under several real world scenarios obtaining encouraging results.
Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene (1992)

Having previously determined the complete amino acid sequence of 2-keto-4-hydroxyglutarate aldolase from Escherichia coli (C. J. Vlahos and E. E. Dekker, J. Biol. Chem. 263:11683-11691, 1988), we amplified the gene that codes for this enzyme by the polymerase chain reaction using synthetic degenerate deoxyoligonucleotide primers. The amplified DNA was sequenced by subcloning the polymerase chain reaction products into bacteriophage M13; the nucleotide sequence of the gene was found to be in exact agreement with the amino acid sequence of the gene product. Overexpression of the gene was accomplished by cloning it into the pKK223.3 expression vector so that it was under control of the tac promoter and then using the resultant plasmid, pDP6, to transform E. coli DH5 alpha F'IQ. When this strain was grown in the presence of isopropyl beta-D-thiogalactopyranoside, aldolase specific activity in crude extracts was 80-fold higher than that in wild-type cells and the enzyme constituted approximately 30% of the total cellular protein. All properties of the purified, cloned gene product, including cross-reactivity with antibodies elicited against the wild-type enzyme, were identical with the aldolase previously isolated and characterized. A strain of E. coli in which this gene is inactivated was prepared for the first time by insertion of the kanamycin resistance gene cartridge into the aldolase chromosomal gene.
Review: Glutamate and dopamine dysregulation in schizophrenia — a synthesis and selective review (2007)

The dopamine hypothesis of schizophrenia is the principal explanatory model of antipsychotic drug action. Recent discoveries extend our understanding of the neurochemistry of schizophrenia, with increasing evidence of dysfunction in glutamate and GABA as well as dopamine systems. In this review, we study the evidence for dopaminergic dysfunction in schizophrenia, drawing data from neurochemical imaging studies. We also review the NMDA receptor hypofunction hypothesis of schizophrenia as a supplementary explanatory model for the illness. We examine predictions made by the NMDA receptor hypofunction hypothesis and consider how they fit with current neurochemical findings in patients and animal models. We consider the case for glutamatergic excitotoxicity as a key process in the development and progression of schizophrenia, and suggest ways in which glutamate and dopamine dysregulation may interact in the condition.
Semantic segmentation of bioimages using convolutional neural networks (2016)

Convolutional neural networks have shown great promise in both general image segmentation problems as well as bioimage segmentation. In this paper, the application of different convolutional network architectures is explored on the C. elegans live/dead assay dataset from the Broad Bioimage Benchmark Collection. These architectures include a standard convolutional network which produces single pixel outputs, as well as Fully Convolutional Networks (FCN) for patch prediction. It was shown that the custom image processing pipeline, which achieved a worm segmentation accuracy of 94%, was outperformed by all of the architectures considered, with the best being 97.3% achieved by a FCN with a single downsampling layer. These results demonstrate the promise of employing convolutional neural network architectures as an alternative to ad-hoc image processing pipelines on optical microscopy images of C. elegans.
Optimization of Excitation and Detection Geometry for Multiplexed Capillary Array Electrophoresis of DNA Fragments (1995)

A new on-column excitation and detection geometry for multiplexed array capillary electrophoresis is evaluated. The detection limit is improved 100-fold for the same laser power because of more efficient coupling of the laser beam. The illumination is also more uniform over the entire array. Stray light and cross-talk are effectively suppressed by immersing the capillaries in water to roughly match the refractive index. A charge-coupled-device (CCD) camera combined with cutoff filters provides adequate sensitivity and speed for high-speed DNA sequencing based on sieving in a polymer-matrix solution.
Affective Labeling in a Content-Based Recommender System for Images (2012)

Affective labeling of multimedia content has proved to be useful in recommender systems. In this paper we present a methodology for the implicit acquisition of affective labels for images. It is based on an emotion detection technique that takes as input the video sequences of the users' facial expressions. It extracts Gabor low level features from the video frames and employs a k nearest neighbors machine learning technique to generate affective labels in the valence-arousal-dominance space. We performed a comparative study of the performance of a content-based recommender (CBR) system for images that uses three types of metadata to model the users and the items: (i) generic metadata, (ii) explicitly acquired affective labels and (iii) implicitly acquired affective labels with the proposed methodology. The results show that the CBR performs best when explicit labels are used. However, implicitly acquired labels yield a significantly better performance of the CBR than generic metadata while being an unobtrusive feedback tool.
Isolation of Acholeplasma laidlawii from Commercial, Serum-Free Tissue Culture Medium and Studies on Its Survival and Detection (1974)

This report documents the first isolation of Acholeplasma laidlawii from a commercial lot of serum-free Dulbecco basal medium. Experimental studies demonstrated survival of the organism for at least 1 year depending on the concentration of the contaminating organism as well as pH and temperature of storage of the serum-free medium. A comparison of isolation methods showed that concentration by filtration through 220-nm membrane filters and testing the filters for mycoplasma recovery, especially when using phenol red-diphasic Hayflick medium, was both sensitive and practical for the average laboratory.
Multiwavelength lightwave networks for computer communication (1993)

The different approaches being considered to build high-capacity lightwave networks are described. Two kinds of lightwave network architectures are examined: broadcast-and-select networks and wavelength-routing networks. A comparison of the two shows that broadcast-and-select networks may be more suitable for local area networks (LANs) and metropolitan area networks (MANs), while wavelength-routing networks are suitable for wide area networks (WANs). The overall network may then be a combination of broadcast subnets interconnected by a point-to-point wavelength-routing network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hybrid molecules: insights into plasminogen activator function. (1991)

Hybrid molecules containing the catalytic domain of either tissue plasminogen activator (tPA) or single chain urokinase-type plasminogen activator (scuPA), and the fibrin binding domain of a murine antifibrin monoclonal antibody were constructed using either cDNA or genomic DNA encoding the plasminogen activator and genomic DNA encoding antifibrin monoclonal antibody 59D8. In order to optimize expression of these fusion proteins in hybridoma cells, we compared plasminogen activator 3' UT domains (which decrease mRNA stability) with immunoglobulin and beta globin 3' UT domains (which increase mRNA stability). The presence of the plasminogen activator 3' UT domain resulted in approximately tenfold lower steady-state mRNA levels, and 300 to 500-fold lower levels of expressed functional protein. The initial goal of these studies was to increase the fibrinolytic potency and selectivity of tPA or scuPA. Fusion proteins comprising an antifibrin antibody domain and the catalytic domain of either tPA or scuPA were expressed and shown to have very different properties. The fusion protein that comprised the Fab portion of an antifibrin antibody and the catalytic domain of tPA, while displaying antigen binding properties indistinguishable from those of the parent antibody and amidolytic activity similar to that of tPA, was not more efficient than tPA in an in vitro clot lysis assay. In contrast, it had been shown that tPA chemically coupled to the same antibody was four- to sixfold more efficient in fibrinolysis both in vitro and in vivo. A recombinant scuPA-antifibrin antibody hybrid, however, was sixfold more potent than scuPA in vitro and 20-fold more potent in a rabbit thrombolysis model. An explanation for this apparent discrepancy may relate to the requirement for stimulation by fibrin in order for tPA to achieve its maximal catalytic activity, a property that was demonstrated to have been lost in the antifibrin-tPA fusion protein. In contrast, the activity of urokinase is independent of the presence of fibrin. This may explain the greater success achieved in enhancing catalytic activity in the urokinase-antifibrin fusion protein. It is of additional interest that fibrin or soluble fibrin fragments stimulate the catalytic activity of both tPA and the isolated tPA B chain, demonstrating that at least part of the enhanced catalytic activity of tPA observed in the presence of fibrin is independent of fibrin binding either by the tPA kringles or finger domain (or any heavy chain domain). These data indicate that it is possible to construct recombinant hybrid molecules in which both plasminogen activator catalytic function and antibody binding are preserved.(ABSTRACT TRUNCATED AT 400 WORDS)
Tunable Resistance of a Carbon Nanotube-Graphite Interface (2000)

The transfer of electrons from one material to another is usually described in terms of energy conservation, with no attention being paid to momentum conservation. Here we present results on the junction resistance between a carbon nanotube and a graphite substrate and show that details of momentum conservation also can change the contact resistance. By changing the angular alignment of the atomic lattices, we found that contact resistance varied by more than an order of magnitude in a controlled and reproducible fashion, indicating that momentum conservation, in addition to energy conservation, can dictate the junction resistance in graphene systems such as carbon nanotube junctions and devices.
Surviving sepsis: going beyond the guidelines (2011)

The Surviving Sepsis Campaign is a global effort to improve the care of patients with severe sepsis and septic shock. The first Surviving Sepsis Campaign Guidelines were published in 2004 with an updated version published in 2008. These guidelines have been endorsed by many professional organizations throughout the world and come regarded as the standard of care for the management of patients with severe sepsis. Unfortunately, most of the recommendations of these guidelines are not evidence-based. Furthermore, the major components of the 6-hour bundle are based on a single-center study whose validity has been recently under increasing scrutiny. This paper reviews the validity of the Surviving Sepsis Campaign 6-hour bundle and provides a more evidence-based approach to the initial resuscitation of patients with severe sepsis.
Overexpression and mutagenesis of the cDNA for rat liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase. Role of cysteines and tyrosines in catalysis. (1994)

The overexpression and purification of recombinant rat liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase (3 alpha-HSD; EC 1.1.1.50) in Escherichia coli are described. The properties of the homogeneous recombinant 3 alpha-HSD (r3 alpha-HSD) confirm that a single polypeptide can function as a HSD, as a dihydrodiol dehydrogenase, and as an aromatic aldehyde, ketone, and quinone reductase. Cys-170, Cys-242, and Cys-217, implicated by bromoacetoxysteroid affinity-labeling agents as points of contact for the C-3, C-11, and C-17 positions of steroid ligands, were mutated to alanines. Unexpectedly, the homogeneous C170A and C242A mutants were kinetically similar to wild-type r3 alpha-HSD. By contrast, the C217A mutant gave Km values that were 4-fold higher for androstanedione and 2-fold higher for NADH. Inspection of the recently solved crystal structure of rat liver 3 alpha-HSD (Hoog, S. S., Pawlowski, J. E., Alzari, P. M., Penning, T. M., and Lewis, M. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 2517-2521) places Cys-170 and Cys-242 on the periphery of an alpha/beta-barrel so that they cannot be involved in catalysis of steroid recognition. This demonstrates that bromoacetoxysteroid affinity-labeling agents may provide misleading information regarding the topography of steroid hormone binding sites. When NADPH was modeled into the crystal structure of 3 alpha-HSD, Tyr-55 was implicated as the general acid, since it is in close proximity to the C-4 position of the nicotinamide ring and could polarize the substrate carbonyl. In support of this model, the purified Y55F mutant was found to be catalytically inactive, but still formed an E-NADPH complex (measured by fluorescence titration) and an E-NADH-testosterone complex (measured by equilibrium dialysis). The ability of the Y55F mutant to form binary and ternary complexes, but not aid in hydride transfer, is consistent with Tyr-55 acting as the general acid. 3 alpha-HSD is a member of the aldo-keto reductase superfamily, and Tyr-55 is invariant in members of this family where it may perform a similar function. Tyr-205 is present in a pentapeptide sequence that is conserved in HSDs that belong to the short-chain alcohol dehydrogenase family and has been implicated as the general acid within these enzymes. The Y205F mutant was found to be kinetically similar to wild-type r3 alpha-HSD.(ABSTRACT TRUNCATED AT 400 WORDS)