gebhart/patrepeval huggingface dataset:
Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion (1995)

A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force-field reproduces excellently the geometry of quantum chemically optimized zinc complexes as well as the crystallographic geometry of the active site of alcohol dehydrogenase and small organic structures. The parameterization is used in molecular dynamics simulations and molecular mechanical energy minimizations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. The active-site zinc ion seems to prefer four-coordination over five-coordination by at least 36 kJ/mol. The only stable binding site of a fifth ligand at the active-site zinc ion is opposite to the normal substrate site, in a narrow cavity behind the zinc ion. Only molecules of the size of water or smaller may occupy this site. There are large fluctuations in the geometry of the zinc coordination sphere. A four-coordinate water molecule alternates frequently (every 7 ps) between the substrate site and the fifth binding site and even two five-coordinate water molecules may interchange ligation sites without prior dissociation. Ligand exchange at the zinc ion probably proceeds by a dissociative mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)
Cognitive Map Dimensions of the Human Value System Extracted from Natural Language (2007)

The notion of a human value system can be quantified as a cognitive map, the dimensions of which capture the semantics of concepts and the associated values. This can be done, if one knows (i) how to define the dimensions of the map, and (ii) how to allocate concepts in those dimensions. Regarding the first question, experimental studies with linguistic material using psychometrics have revealed that valence, arousal and dominance are primary dimensions characterizing human values. The same or similar dimensions are used in popular models of emotions and affects. In these studies, the choice of principal dimensions, as well as scoring concepts, was based on subjective reports or psycho-physiological measurements. Can a cognitive map of human values be constructed without testing human subjects? Here we show that the answer is positive, using generally available dictionaries of synonyms and antonyms. By applying a simple statistical-mechanic model to English and French dictionaries, we constructed multidimensional cognitive maps that capture the semantics of words. We calculated the principal dimensions of the resultant maps and found their semantics consistent across two languages as well as with previously known main cognitive dimensions. These results suggest that the linguistically derived cognitive map of the human value system is language-invariant and, being closely related to psychometrically derived maps, is likely to reflect fundamental aspects of the human mind.
Generalizations of the sampling theorem: Seven decades after Nyquist (2001)

The sampling theorem is one of the most basic and fascinating topics in engineering sciences. The most well-known form is Shannon's uniform-sampling theorem for bandlimited signals. Extensions of this to bandpass signals and multiband signals, and to nonuniform sampling are also well-known. The connection between such extensions and the theory of filter banks in DSP has been well established. This paper presents some of the less known aspects of sampling, with special emphasis on non bandlimited signals, pointwise stability of reconstruction, and reconstruction from nonuniform samples. Applications in multiresolution computation and in digital spline interpolation are also reviewed.
Selective inhibition by a synthetic hirudin peptide of fibrin-dependent thrombosis in baboons. (1991)

To determine the importance of the thrombin substrate recognition exosite for fibrinogen binding in the formation of both arterial and venous thrombi, we evaluated the antithrombotic effects of the tyrosine-sulfated dodecapeptide from residues 53-64 of hirudin (H peptide) in a nonhuman primate model. This peptide was studied because it inhibits thrombin cleavages of fibrinogen by simple competition without blocking enzyme catalytic-site function. When an exteriorized arteriovenous access shunt model was used in baboons (Papio anubis), thrombus formation was induced by placing a thrombogenic device made of (i) a segment of tubing coated covalently with type I collagen, which generated platelet-rich thrombi under arterial flow conditions, and (ii) two subsequent annular regions of flow expansion that produced fibrin-rich thrombi typically associated with venous valves and veins. Thrombus formation was quantified by measurements of 111In-labeled platelet and 125I-labeled fibrinogen deposition in both arterial-flow and venous-flow portions of the device. Continuous infusion of H peptide (0.5, 15, and 75 mg/kg) proximal to the device for 40 min interrupted, in a dose-response fashion, formation of fibrin-rich thrombus in the regions of disturbed flow and generation of fibrinopeptide A. In contrast, H peptide did not inhibit the capacity of platelets to deposit on the collagen surface (P greater than 0.2 at all doses) or to form hemostatic plugs (as assessed by measurements of bleeding time; P greater than 0.1 at all doses). These findings suggest that, by competitive inhibition of fibrinogen binding to thrombin, fibrin-rich venous-type thrombus formation may be selectively prevented. This strategy may be therapeutically attractive for preserving normal platelet function when conventional anticoagulant therapy is contraindicated.
Correlation between Soluble α-Klotho and Renal Function in Patients with Chronic Kidney Disease: A Review and Meta-Analysis (2018)

There exists a significant positive correlation between soluble <i>α</i>-Klotho and eGFR in patients with CKD. Also, a significant negative correlation between <i>α</i>-Klotho and FGF23 levels is proven. This raises hope to employ <i>α</i>Klotho and FGF23 as early biomarkers of CKD. However, further large prospective follow-up researches are needed to validate this hypothesis and to explore whether maintaining or elevating the Klotho level could improve renal function and complications in CKD patients.
Fast Ray Tracing for Modern General Purpose CPU (2002)

We present a study of the system implications of various aspects of the classic Ray Tracing algorithm. We show how these algorithms can be modified to yield the highest performance on any given system, and present some of the results that we obtained. 1.
The Fibroblast Growth Factor–Inducible 14 Receptor Is Highly Expressed in HER2-Positive Breast Tumors and Regulates Breast Cancer Cell Invasive Capacity (2008)

Genomic characterization is beginning to define a molecular taxonomy for breast cancer; however, the molecular basis of invasion and metastasis remains poorly understood. We report a pivotal role for the fibroblast growth factor-inducible 14 (Fn14) receptor in this process. We examined whether Fn14 and its ligand tumor necrosis factor-like weak inducer of apoptosis (TWEAK) were expressed in breast tumors and whether deregulation of Fn14 levels affected malignant behavior of breast cancer cell lines. Analysis of TWEAK and Fn14 in publicly available gene expression data indicated that high Fn14 expression levels significantly correlated with several poor prognostic indicators (P < 0.05). Fn14 expression was highest in the HER2-positive/estrogen receptor-negative (HER2(+)/ER(-)) intrinsic subtype (P = 0.0008). An association between Fn14 and HER2 expression in breast tumors was confirmed by immunohistochemistry. Fn14 levels were elevated in invasive, ER(-) breast cancer cell lines. Overexpression of Fn14 in weakly invasive MCF7 and T47D cells resulted in a marked induction of invasion and activation of nuclear factor-kappaB (NF-kappaB) signaling. Ectopic expression of Fn14tCT, a Fn14 deletion mutant that cannot activate NF-kappaB signaling, was not able to induce invasion. Moreover, ectopic expression of Fn14tCT in highly invasive MDA-MB-231 cells reduced their invasive capability. RNA interference-mediated inhibition of Fn14 expression in both MDA-MB-231 and MDA-MB-436 cells reduced invasion. Expression profiling of the Fn14-depleted cells revealed deregulation of NF-kappaB activity. Our findings support a role for Fn14-mediated NF-kappaB pathway activation in breast tumor invasion and metastasis.
Hypochlorous Acid, a Macrophage Product, Induces Endothelial Apoptosis and Tissue Factor Expression (2004)

HOCl can provoke EC death and desquamation by either apoptotic or oncotic cell-death pathways, and sublethal concentrations of HOCl can increase endothelial tissue factor. These results show that MPO-positive macrophage-derived HOCl in the subendothelium of atheromata may participate in ACS by promoting superficial erosion and increasing thrombogenicity.
Highly Electrically Insulating Tethered Lipid Bilayers for Probing the Function of Ion Channel Proteins (2003)

A method is presented to form gold-electrode-tethered lipid bilayers with exceptionally high electrical resistances. Electrical impedance spectroscopy is used to monitor the bilayer incorporation of a ligand-gated ion channel protein and the modulation of its channel activity by the selective binding of an antibody. Due to the low defect density of the tethered membrane, the effect of a few channels can be resolved thus opening the way to single-channel experiments on this highly stable and versatile platform. In turn, a minute quantity of analyte, here antibodies, can be measured, which is of great interest for bioanalytics.
Inertial sensors for smartphones navigation (2015)

The advent of smartphones and tablets, means that we can constantly get information on our current geographical location. These devices include not only GPS/GNSS chipsets but also mass-market inertial platforms that can be used to plan activities, share locations on social networks, and also to perform positioning in indoor and outdoor scenarios. This paper shows the performance of smartphones and their inertial sensors in terms of gaining information about the user's current geographical locatio n considering an indoor navigation scenario. Tests were carried out to determine the accuracy and precision obtainable with internal and external sensors. In terms of the attitude and drift estimation with an updating interval equal to 1 s, 2D accuracies of about 15 cm were obtained with the images. Residual benefits were also obtained, however, for large intervals, e.g. 2 and 5 s, where the accuracies decreased to 50 cm and 2.2 m, respectively.
Performance of an electronic nose for quality estimation of ground meat (1993)

An electronic nose is described, which consists of a gas sensor array combined with a pattern recognition routine. The sensor array used consists of ten metal-oxide-semiconductor field effect transistors with gates of catalytically active metals. It also contains four commercially available chemical sensors based on tin dioxide, so-called Taguchi sensors. In some studies, a carbon dioxide monitor based on infrared absorption is also used. Samples of ground beef and pork, stored in a refrigerator, have been studied. Gas samples from the meat were then led to the sensor array, and the resulting patterns of sensor signals were treated with pattern recognition software based on an artificial neural network as well as with an algorithm based on an abductory induction mechanism. When using all sensors for learning, the two nets could predict both type of meat and storage time quite well. Omitting the carbon dioxide monitor, both nets could predict type of meat, but storage time not so well. Finally, it is also shown how a net based on unsupervised training could be used to predict storage time for ground beef.
Learning the meaning of music (2005)

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2005.
MLST of housekeeping genes captures geographic population structure and suggests a European origin ofBorrelia burgdorferi (2008)

Lyme borreliosis, caused by the tick-borne bacterium Borrelia burgdorferi, has become the most common vector-borne disease in North America over the last three decades. To understand the dynamics of the epizootic spread and to predict the evolutionary trajectories of B. burgdorferi, accurate information on the population structure and the evolutionary relationships of the pathogen is crucial. We, therefore, developed a multilocus sequence typing (MLST) scheme for B. burgdorferi based on eight chromosomal housekeeping genes. We validated the MLST scheme on B. burgdorferi specimens from North America and Europe, comprising both cultured isolates and infected ticks. These data were compared with sequences for the commonly used genetic markers rrs-rrlA intergenic spacer (IGS) and the gene encoding the outer surface protein C (ospC). The study demonstrates that the concatenated sequences of the housekeeping genes of B. burgdorferi provide highly resolved phylogenetic signals and that the housekeeping genes evolve differently compared with the IGS locus and ospC. Using sequence data, the study reveals that North American and European populations of B. burgdorferi correspond to genetically distinct populations. Importantly, the MLST data suggest that B. burgdorferi originated in Europe rather than in North America as proposed previously.
Subband/Transform coding using filter bank designs based on time domain aliasing cancellation (2005)

A new, oddly stacked, critically sampled, single side-band (SSB) [7] analysis/synthesis system based on Time Domain Aliasing Cancellation (TDAC) [1],[2] is described in this paper. The specifications for the analysis and synthesis filter responses are developed and a number of designs which satisfy the reconstruction requirements are described. The application of TDAC systems to Subband/Transform coding is also discussed and the objective performance of a 32 band coder using several different window designs is presented and compared with a coder based on Frequency Domain Aliasing Cancellation (FDAC) filter banks [3]-[5].
Global Regulation of Expression of Antifungal Factors by aPseudomonas fluorescensBiological Control Strain (1994)

The root-colonizing bacterium Pseudomonas fluorescens BL915 protects a variety of seedlings from damping-off disease caused by the fungal pathogen Rhizoctonia solani. Spontaneous pleiotropic mutants of P. fluorescens strain BL915 which fail to synthesize antifungal factors such as chitinase, cyanide, and pyrrolnitrin and exhibit altered colony morphology were isolated. Such mutants fail to inhibit the growth of R. solani in vitro, and their biological control capability is sharply reduced. We characterized a genomic DNA fragment from strain BL915 which, when introduced into these pleiotropic mutants, restored the lost functions, the wild-type colony morphology, and bio-control activity. DNA sequence analysis of the genomic fragment revealed the presence of genes homologous to those of numerous bacterial global regulatory systems and identified a cluster of genes identical in organization to the Escherichia coli gene cluster consisting of uvrY, uvrC, pgsA, and glyW. Coordinate biosynthesis of multiple antifungal products in some heterologous Pseudomonas strains in response to the introduction of the strain BL915 genomic fragment confirmed the regulatory nature of sequences contained on this fragment. Further genetic analysis indicated a gene homologous to response regulators of bacterial two-component systems was sufficient to complement the pleiotropic mutants and to activate antifungal genes in heterologous strains. Marker exchange of a truncated version of this gene into the P. fluorescens BL915 chromosome generated pleiotropic mutants indistinguishable from the original spontaneous mutants. Cloning and sequencing of the response regulator gene from several spontaneous mutants allowed identification of various nucleotide changes associated with the gene in such mutants.
Full-Color Light-Emitting Diodes Based on Colloidal Quantum Dots (2010)

Abstract not Available.
The majority of the in vitro erythroid expansion potential resides in CD34- cells, outweighing the contribution of CD34+ cells and significantly increasing the erythroblast yield from peripheral blood samples (2010)

The study of human erythropoiesis in health and disease requires a robust culture system that consistently and reliably generates large numbers of immature erythroblasts that can be induced to differentiate synchronously. We describe a culture method modified from Leberbauer et al. (2005) and obtain a homogenous population of erythroblasts from peripheral blood mononuclear cells (PBMC) without prior purification of CD34(+) cells. This pure population of immature erythroblasts can be expanded to obtain 4x10(8) erythroblasts from 1x10(8) PBMC after 13-14 days in culture. Upon synchronized differentiation, high levels of enucleation (80-90%) and low levels of cell death (<10%) are achieved. We compared the yield of erythroblasts obtained from PBMC, CD34(+) cells or PBMC depleted of CD34(+) cells and show that CD34(-) cells represent the most significant early erythroid progenitor population. This culture system may be particularly useful for investigating the pathophysiology of anemic patients where only small blood volumes are available.
The essential Escherichia coli msbA gene, a multicopy suppressor of null mutations in the htrB gene, is related to the universally conserved family of ATP‐dependent translocators (1993)

We report the characterization of the msbA gene, isolated as a multicopy suppressor of the HtrB temperature-sensitive phenotype. The msbA gene maps to 20.5 min on the Escherichia coli genetic map and encodes a protein with an estimated molecular mass of 64,460 Da, with the properties of an integral membrane protein. The amino acid sequence of MsbA is very similar to those of the family of ATP-dependent translocators, which includes the haemolysin B protein of E. coli and the mammalian multidrug resistance (MDR) proteins. Mutational analysis of msbA indicates that it may form an operon with a downstream gene, orfE, and that both of these genes are essential for bacterial viability under all growth conditions tested.
Transfer of foreign gene to giant freshwater prawn (Macrobrachium rosenbergii) by spermatophore-microinjection (2000)

We developed a spermatophore-microinjection (SMI) technique that allows exogenous DNA fragments to be transferred easily into the giant freshwater prawn (Macrobrachium rosenbergii), an important aquacultural shellfish and aquatic invertebrate model. From 28 to 1, 000 ng of the circular plasmid pGL, in a total volume of 1 microl, were directly microinjected into spermatophores. Fertilization and hatching of prawns created with SMI were completed in vivo. Fertilization and hatching rates in the SMI treatments did not differ from those of the untreated control group. The genomes of free swimming, SMI-created larvae (21 days after fertilization) were analyzed using PCR and Southern blot analyses. A product with a molecular mass of 680 bp was amplified. It corresponded to amplifications of pGL, and Southern blot analysis revealed that the amplified band was positive. The gene transfer rate was primarily dependent on the concentration of DNA during SMI. The higher the concentration of pGL, the higher the rate of gene transfer. PCR and Southern blot analyses detected the existence of foreign DNA in 16 of 23 samples (70%) of genomic DNA isolated from hatched larvae in the 750 ng pGL SMI treatment. SMI, described here for the first time, is the simplest and most efficient method for mass producing transgenic giant freshwater prawns.
A Highly Active Catalyst for the Room-Temperature Amination and Suzuki Coupling of Aryl Chlorides (1999)

A unique combination of steric and electronic properties appears to determine the effectiveness of phosphanyl-substituted biphenyls as ligands in palladium-catalyzed aminations and Suzuki coupling of aryl chlorides at room temperature [Eq. (1)]. The oxidative addition step is greatly accelerated, and transmetalation (or Pd-N bond formation) and reductive elimination processes are facilitated. Use of these ligands allows for Suzuki coupling at very low catalyst loadings (as little as 10(-6) mol % Pd). R"=cyclohexyl, tert-butyl.
XQuery 1.0 : An XML Query Language (2007)

XML is a versatile markup language, capable of labeling the information content of diverse data sources including structured and semi-structured documents, relational databases, and object repositories. A query language that uses the
Recombinant pulmonary surfactant protein D. Post-translational modification and molecular assembly. (1994)

Pulmonary surfactant protein D (SP-D) is a member of a family of collagenous C-type lectins that includes the serum mannose binding proteins and surfactant protein A. Recent studies have shown that rat SP-D (rSP-D) molecules are assembled as tetramers of trimeric subunits (12 mers) and that dodecamers can participate in higher orders of molecular assembly involving interactions of the amino-terminal peptide domains. In order to further study the assembly of SP-D in vitro, Chinese hamster ovary K1 cells were transfected with a full-length rat SP-D cDNA, and stable transfectants with high levels of SP-D production (approximately 6 x 10(6) dodecamers/cell/24 h) were obtained using a glutamine synthetase selection system. The secreted molecules (RrSP-D), which were purified by affinity chromatography on maltosyl-agarose, comigrated with rSP-D on SDS-polyacrylamide gel electrophoresis in the presence and absence of reduction, and coeluted with rSP-D dodecamers from 4% agarose. The major bacterial collagenase-resistant peptide showed a decreased mobility on reduction consistent with the formation of intrachain disulfide bonds. A 17-kDa pepsin-resistant fragment was isolated following overnight digestion with pepsin at 27 degrees C, confirming the formation of a triple helical domain comparable in size and thermal stability to that of natural SP-D. The expressed protein contained sialylated endoglycosidase F-sensitive carbohydrate; amino acid analysis of acid and alkaline hydrolysates demonstrated essentially normal levels of hydroxyproline, hydroxylysine, and hydroxylysine-glycosides. Electron microscopic studies showed a molecular structure indistinguishable from lung SP-D, with a similar small subpopulation of molecules showing higher orders of multimerization. Solid-phase neoglycoprotein binding assays gave the same saccharide inhibition profile as natural rat SP-D, and both proteins showed efficient saccharide-dependent agglutination of Escherichia coli. These studies demonstrate that a single genetically distinct chain type can account for the various and complex molecular assemblies of SP-D, and further verify the potential physiologic significance of the disulfide-bonded multimers and higher aggregates isolated from rat, bovine, and human lung lavage.
Mechanisms in Protein O-Glycan Biosynthesis and Clinical and Molecular Aspects of Protein O-Glycan Biosynthesis Defects: A Review (2006)

We first discuss the biosynthesis of protein O-glycans from their building blocks to their secretion from the Golgi. Subsequently, we review 24 different genetic disorders in O-glycosylation and 10 different genetic disorders that affect both N- and O-glycosylation. The key clinical, metabolic, chemical, diagnostic, and genetic features are described. Additionally, we describe methods that can be used in clinical laboratory screening for protein O-glycosylation biosynthesis defects and their pitfalls. Finally, we introduce existing methods that might be useful for unraveling O-glycosylation defects in the future.