gebhart/patrepeval huggingface dataset:
A new human Duffy blood group specificity defined by a murine monoclonal antibody. Immunogenetics and association with susceptibility to Plasmodium vivax. (1987)

A new Duffy specificity, Fy6, defined by a murine monoclonal antibody of the IgG1 kappa class, is related to susceptibility to malarial invasion. In humans, Fy6 is present on the red cells of all persons except those of the Fy(a-b-) type, a distribution resembling that of Fy3. However proteolytic enzyme treatment of red cells enhances the reactivity of Fy3, whereas Fy6, like Fya and Fyb, is susceptible to degradation by this process. The number of Fy6 sites on human red cells was found to be 12,200 per cell, in close agreement with earlier estimates of the number of Fya sites. Anti-Fy6 reacted in western blots with a membrane glycoprotein of approximately 46,000 Mr, not significantly different from that of a molecule known to bear the Fya determinant. The Fy6 epitope is shown to be present on the red cells of some but not all nonhuman primate species, where it has a distribution not only distinctly different from Fya, Fyb, and Fy3, but in close accordance with susceptibility to penetration by Plasmodium vivax. Thus, the red cells of two species of macaques (Macaca mulatta and M. fascicularis), which are invaded by Plasmodium knowlesi but not by P. vivax are shown to have other Duffy antigens but to be devoid of Fy6. It appears, therefore, that the red cell epitopes used by these closely related species are distinct, and that susceptibility to P. vivax merozoite penetration is dependent on the presence of Fy6.
Catalytic Hydrogenation of the Sweet Principles of Stevia rebaudiana, Rebaudioside B, Rebaudioside C, and Rebaudioside D and Sensory Evaluation of Their Reduced Derivatives (2012)

Catalytic hydrogenation of rebaudioside B, rebaudioside C, and rebaudioside D; the three ent-kaurane diterpene glycosides isolated from Stevia rebaudiana was carried out using Pd(OH)(2). Reduction of steviol glycosides was performed using straightforward synthetic chemistry with the catalyst Pd(OH)(2) and structures of the corresponding dihydro derivatives were characterized on the basis of 1D and 2D nuclear magnetic resonance (NMR) spectral data indicating that all are novel compounds being reported for the first time. Also, the taste properties of all reduced compounds were evaluated against their corresponding original steviol glycosides and sucrose.
Input Versus Output Queueing on a Space-Division Packet Switch (1987)

Two simple models of queueing on an <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N \times N</tex> space-division packet switch are examined. The switch operates synchronously with fixed-length packets; during each time slot, packets may arrive on any inputs addressed to any outputs. Because packet arrivals to the switch are unscheduled, more than one packet may arrive for the same output during the same time slot, making queueing unavoidable. Mean queue lengths are always greater for queueing on inputs than for queueing on outputs, and the output queues saturate only as the utilization approaches unity. Input queues, on the other hand, saturate at a utilization that depends on <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</tex> , but is approximately <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(2 -\sqrt{2}) = 0.586</tex> when <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</tex> is large. If output trunk utilization is the primary consideration, it is possible to slightly increase utilization of the output trunks-upto <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(1 - e^{-1}) = 0.632</tex> as <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N \rightarrow \infty</tex> -by dropping interfering packets at the end of each time slot, rather than storing them in the input queues. This improvement is possible, however, only when the utilization of the input trunks exceeds a second critical threshold-approximately <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ln (1 +\sqrt{2}) = 0.881</tex> for large <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</tex> .
Multi-Domain Clock Skew Scheduling (2003)

The application of general clock skew scheduling is practically limited due to the difficulties in implementing a wide spectrum of dedicated clock delays in a reliable manner. This results in a significant limitation of the optimization potential. As an alternative, the application of multiple clocking domains with dedicated phase shifts that are implemented by reliable, possibly expensive design structures can overcome these limitations and substantially increase the implementable optimization potential of clock adjustments. In this paper we present an algorithm for constrained clock skew scheduling which computes for a given number of clocking domains the optimal phase shifts for the domains and the assignment of the individual registers to the domains. For the within-domain latency values, the algorithm can assume a zero-skew clock delivery or apply a user-provided upper bound. Our experiments demonstrate that a constrained clock skew schedule using a few clocking domains combined with small within-domain latency can reliably implement the full sequential optimization potential to date only possible with an unconstrained clock schedule.
Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa (2014)

The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at the transcriptional and post-transcriptional level. Here, we use RNA sequencing data from the ABI SOLiD platform to identify lncRNA and NATs obtained from samples of the filamentous fungus Neurospora crassa grown under different light and temperature conditions. We identify 939 novel lncRNAs, of which 477 are antisense to annotated genes. Across the whole dataset, the extent of overlap between sense and antisense transcripts is large: 371 sense/antisense transcripts are complementary over 500 nts or more and 236 overlap by more than 1000 nts. Most prevalent are 3' end overlaps between convergently transcribed sense/antisense pairs, but examples of divergently transcribed pairs and nested transcripts are also present. We confirm the expression of a subset of sense/antisense transcript pairs by qPCR. We examine the size, types of overlap and expression levels under the different environmental stimuli of light and temperature, and identify 11 lncRNAs that are up-regulated in response to light. We also find differences in transcript length and the position of introns between protein-coding transcripts that have antisense expression and transcripts with no antisense expression. These results demonstrate the ability of N. crassa lncRNAs and NATs to be regulated by different environmental stimuli and provide the scope for further investigation into the function of NATs.
Functional analysis of variant lysosomal acid glycosidases of Anderson‐Fabry and Pompe disease in a human embryonic kidney epithelial cell line (HEK 293 T) (2011)

The functional significance of missense mutations in genes encoding acid glycosidases of lysosomal storage disorders (LSDs) is not always clear. Here we describe a method of investigating functional properties of variant enzymes in vitro using a human embryonic kidney epithelial cell line. Site-directed mutagenesis was performed on the parental plasmids containing cDNA encoding for alpha-galactosidase A (α-Gal A) and acid maltase (α-Glu) to prepare plasmids encoding relevant point mutations. Mutant plasmids were transfected into HEK 293 T cells, and transient over-expression of variant enzymes was measured after 3 days. We have illustrated the method by examining enzymatic activities of four unknown α-Gal A and one α-Glu variants identified in our patients with Anderson-Fabry disease and Pompe diseases respectively. Comparison with control variants known to be either pathogenic or non-pathogenic together with over-expression of wild-type enzyme allowed determination of the pathogenicity of the mutation. One leader sequence novel variant of α-Gal A (p.A15T) was shown not to significantly reduce enzyme activity, whereas three other novel α-Gal A variants (p.D93Y, p.L372P and p.T410I) were shown to be pathogenic as they resulted in significant reduction of enzyme activity. A novel α-Glu variant (p.L72R) was shown to be pathogenic as this significantly reduced enzyme activity. Certain acid glycosidase variants that have been described in association with late-onset LSDs and which are known to have variable residual plasma and leukocyte enzyme activity in patients appear to show intermediate to low enzyme activity (p.N215S and p.Q279E α-Gal A respectively) in the over-expression system.
Constant Composition Distribution Matching (2015)

Distribution matching transforms independent and Bernoulli(1/2) distributed input bits into a sequence of output symbols with a desired distribution. Fixed-to-fixed length, invertible, and low complexity encoders and decoders based on constant composition and arithmetic coding are presented. The encoder achieves the maximum rate, namely, the entropy of the desired distribution, asymptotically in the blocklength. Furthermore, the normalized divergence of the encoder output and the desired distribution goes to zero in the blocklength.
Design of antenna radome composed of metamaterials for high gain (2006)

The design of antenna radome utilizing the left-handed materials at a frequency close to 5 GHz for the first time for enhancing the antenna gain is presented. We make use of the multi-layered structure composed of two materials with left-handed materials and air. The two materials have an average index of refraction around zero. The simulation results show that the antenna gain and the radiation patterns are effectively enhanced. The beamwidth is reduced by 37.5% and the antenna gain is increased to about 6 dBi. The results can be used in applications such as point-to-point communications between the buildings.
Description of a computerized adverse drug event monitor using a hospital information system. (1992)

To improve the detection and characterization of adverse drug events (ADEs) in hospitalized patients, a computerized adverse drug event monitor was developed. Computer programs were written to allow for voluntary as well as automated detection of adverse drug events using the HELP hospital information system, a large integrated hospital database containing computerized patient medical records and a knowledge base allowing for automated medical decisions. Programs were created to allow simple computer entry of potential adverse drug events by physicians, pharmacists, and nurses. Automated detection of potential adverse drug events relied on signals such as sudden medication stop orders, "antidote" orders, and selected abnormal laboratory values. Each day a list of all potential adverse drug events from these sources was generated and a pharmacist reviewed the medical records and interviewed healthcare personnel associated with patients identified as having potential adverse drug events. This process allowed for characterization of the event, causality assessment, and follow-up of the resulting clinical course by the pharmacist. The permanent storage of these results in the computerized patient medical record permits their future retrieval to prevent adverse drug events during subsequent hospital care. The authors conclude that fully integrated hospital systems will permit the further development and evaluation of computer-assisted methods for the detection of adverse drug events in hospitalized patients.
A pH-Dependent Colon-Targeted Oral Drug Delivery System Using Methacrylic Acid Copolymers. II. Manipulation of Drug Release Using Eudragit® L100 and Eudragit S100 Combinations (2000)

Tablets containing mesalazine as a model drug were coated using various combinations of two methacrylic acid copolymers, (Eudragit L100 and Eudragit S100) by spraying from aqueous systems. The Eudragit L100-Eudragit S100 (w/w) combinations studied were 1:0, 4:1, 3:2, 1:1, 2:3, 1:4, 1:5, and 0:1. The coated tablets were tested in vitro for their suitability for pH-dependent colon-targeted oral drug delivery. The dissolution profiles of the drug obtained from the studied tablets demonstrate that the release of the drug could be manipulated by changing the Eudragit L100-Eudragit S100 ratios in the combinations within the pH range between 6.0 and 7.0 in which the individual polymers are soluble, and a coating formulation consisting of a combination of the two polymers can overcome the issue of high gastrointestinal (GI) pH variability among individuals. The results also demonstrate the feasibility of using aqueous dispersions of Eudragit L100-Eudragit S100 combinations for coating tablets for colon-targeted delivery of drugs, and that the formulation can be adjusted to deliver drug(s) at any other desirable site of the intestinal region of the GI tract in which pH of the fluid is within the range 6.0 to 7.0. For colon-targeted delivery of drugs, the proposed combination system is superior to tablets coated with either Eudragit L100 or Eudragit S100 alone.
Blood cell dynamics in P-selectin-deficient mice (1995)

Abstract P-selectin is expressed on the surfaces of activated platelets and endothelium where it mediates binding to leukocytes. P-selectin- deficient mice were shown to exhibit peripheral neutrophilia (Mayadas et al: Cell 74:541, 1993). We now show that this is not caused by changes in bone marrow precursors nor by a lack of neutrophil margination. Both P-selectin-positive and -negative animals displayed similar increases in peripheral blood neutrophil numbers after injection of epinephrine. However, clearance of 51Chromium-labeled neutrophils is delayed in mice deficient for P-selectin, indicating that the neutrophilia is at least in part the result of delayed removal. We detected no obvious alterations in lymphocyte differentiation, distribution, or adhesion to high endothelial venules in peripheral lymph nodes. Through intravital microscopy, we examined the impact of P-selectin deficiency on leukocyte/endothelial interaction beyond the initial stages of inflammation. Four hours after the administration of an inflammatory irritant, leukocyte rolling was observed even in the absence of P-selectin. There were significantly fewer rolling cells relative to wild-type mice, and their velocity was reduced. Moreover, in the peritonitis model, the number of peritoneal macrophages in wild-type mice increased threefold at 48 hours, whereas the macrophages in the mutant mice remained near baseline levels. Thus, whereas P-selectin is known to be involved in early stages of an inflammatory response, our results indicate that it is additionally responsible for leukocyte rolling and macrophage recruitment in more prolonged tissue injury.
POWER_SAGE: comparing statistical tests for SAGE experiments (2000)

michael.man@pfizer.com
Understanding the growth of Eu2O3nanocrystal films made via electrophoretic deposition (2010)

Eu(2)O(3) nanocrystals, surface-functionalized with oleic acid, were assembled into transparent thin films via electrophoretic deposition (EPD). Suspended in a non-polar solvent (hexane), the nanocrystals were cast into stable films on both the cathode and the anode. We characterized the nanocrystal films using optical microscopy, energy dispersive spectroscopy and photoluminescence spectroscopy. Scanning electron microscopy and atomic force microscopy provided information regarding the morphology, topology and surface coverage of the films. These homogeneous, densely packed films were composed predominantly of agglomerates (approximately 15 nm) of the Eu(2)O(3) nanocrystals rather than of individual nanocrystals. Nonetheless, the films possessed low root mean square (RMS) roughness (approximately 1.4 nm). High transparency of the film in the visible region was facilitated by the dense packing and the small diameter of the agglomerates, which reduced transmission losses due to scattering. The effect of EPD process parameters (applied voltage and nanocrystal concentration) on the growth uniformity and the thickness of the films was examined via surface contact profilometry. We discovered a correlation among the said EPD process parameters, the overall quality and thickness of these transparent films, which provided insight into the mechanisms of the nanocrystal deposition process.
Hormonal regulation of cell death in rabbit uterine epithelium. (1987)

It is known that estrogen (E) and progesterone (P) play important roles in the regulation of endometrial growth. In the rabbit endometrial epithelium, a balance is maintained between cell proliferation and cell death which seems to be under ovarian hormonal control. In this study the authors determined cell proliferation by quantitating the mitotic index (MI) and cell death by quantitating the death index (DI) in uterine histologic sections from whole animals that were hormone treated versus control rabbits. E caused proliferation of uterine epithelial cells and decreased the DI transiently, while P also increased proliferation but decreased the DI dramatically. In a time course study, after a single injection of human chorionic gonadotropin to induce pseudopregnancy, there was transient decrease in the DI and an increase in the MI between Days 2 and 5. In pseudopregnant animals, hormones had no effect in intact animals, but after ovariectomy there was about a 124-fold increase in the DI, which could be prevented by P administration. The predominant type of cell death observed in this system is apoptosis (97.5%), as opposed to necrosis (2.5%). Thus, it is proposed that cell death may be as important as cell proliferation in the regulation of normal uterine epithelial growth.
T Cell Responses to an HLA-B*07-Restricted Epitope on the Dengue NS3 Protein Correlate with Disease Severity (2002)

Dengue hemorrhagic fever (DHF), the severe manifestation of dengue virus (DV) infection characterized by plasma leakage, is more common in secondary DV infections in previously infected individuals and is associated with high levels of immune activation. To determine the Ag specificity of this immune response, we studied the response to an HLA-B*07-restricted T cell epitope, residues 221-232 of the DV NS3 protein, in 10 HLA-B*07(+) Thai children who were studied during and after acute DV infections. Peptide-specific T cells were detected in 9 of 10 subjects. The frequency of peptide-specific T cells was higher in subjects who had experienced DHF than in those who had experienced DF. We also detected peptide-specific T cells in PBMC obtained at the time of the acute DV infection in 2 of 5 subjects. These data suggest that the NS3 (221-232) epitope is an important target of CD8(+) T cells in secondary DV infection and that the activation and expansion of DV-specific T cells is greater in subjects with DHF than in those with dengue fever. These findings support the hypothesis that activation of DV-specific CD8(+) T cells plays an important role in the pathogenesis of DHF.
Recent Progress in Wacker Oxidations:  Moving toward Molecular Oxygen as the Sole Oxidant (2007)

Wacker oxidations, the conversion of terminal olefins to methyl ketones with Pd(II) catalysts, have seen widespread use in synthetic applications. Standard synthetic Wacker conditions use catalytic PdCl2 with stoichiometric CuCl under an aerobic atmosphere in a mixed-solvent system of N,N-dimethylformamide and H2O. Though much attention has been directed toward elucidating the rate-determining step and the mechanism of nucleopalladation, the assumption that Cu does not participate in this portion of the catalytic cycle has recently been called into question based on an isolated Pd/Cu bimetallic species and the influence of Cu on product selectivity. Fortunately, recent advancements have been made toward the elimination of Cu additives, thereby alleviating these issues. Success in this area has come from the application of information gained in studying other direct-O2-coupled Pd(II) oxidation systems, including ligand modulation, something which could not be achieved in the presence of Cu. The developments in peroxide-mediated and direct-O2-coupled Wacker oxidations are highlighted herein.
Ships Service Electric Power: Enhanced Survivability Via Early Detection of Incipient Cable Faults (1993)

ABSTRACT Researchers at Texas A&amp;M University have studied the effects of battle damage on ship power distribution cables, with particular interest in damaged cables which did not fail immediately. The electrical signatures of partially damaged cables are significant and are detectable with advanced protection methods used on terrestrial power systems. Findings show that the damaged cable signatures are similar to those of arcing faults on terrestrial power distribution systems, which can be reliably detected using an on‐line expert system [1,2,3]. The implications of these findings are significant. Since the ability of a damaged ship to fight through an encounter is entirely dependent on keeping operational its various systems which rely on electric power, the ability to automatically detect and re‐route power around damaged regions is imperative. By identifying the characteristics of failing power cables before catastrophic failure occurs, the protection process can be integrated into the ship automatic control system. The overall result is a more survivable ship.
Efficient component labeling of images of arbitrary dimension represented by linear bintrees (1988)

An algorithm is presented to perform connected-component labeling of images of arbitrary dimension that are represented by a linear bintree. The bintree is a generalization of the quadtree data structure that enables dealing with images of arbitrary dimension. The linear bintree is a pointerless representation. The algorithm uses an active border which is represented by linked lists instead of arrays. This results in a significant reduction in the space requirements, thereby making it feasible to process three- and higher-dimensional images. Analysis of the execution time of the algorithm shows almost linear behavior with respect to the number of leaf nodes in the image, and empirical tests are in agreement. The algorithm can be modified easily to compute a (d-1)-dimensional boundary measure (e.g. perimeter in two dimensions and surface area in three dimensions) with linear performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>