gebhart/patrepeval huggingface dataset:
Compact red-green-blue beam illuminator and expander (2002)

A compact multicolor beam illuminator and a compact multicolor beam expander are presented. The illuminator performs the dual task of demultiplexing a narrow red-green-blue (RGB) input beam into three separate beams, each of a different color, and expanding them to yield three separate magnified plane waves. The beam expander expands a narrow RGB input beam into a single magnified RGB plane wave. The design and recording procedures, along with experimental results for a beam illuminator and a beam expander with a magnification of approximately 3, are presented.
Fast-learning VIEWNET architectures for recognizing three-dimensional objects from multiple two-dimensional views (1995)

The recognition of three-dimensional (3-D) objects from sequences of their two-dimensional (2-D) views is modeled by a family of self-organizing neural architectures, called VIEWNET, that use View Information Encoded With NETworks. VIEWNET incorporates a preprocessor that generates a compressed but 2-D invariant representation of an image, a supervised incremental learning system that classifies the preprocessed representations into 2-D view categories whose outputs are combined into 3-D invariant object categories, and a working memory that makes a 3-D object prediction by accumulating evidence from 3-D object category nodes as multiple 2-D views are experienced. The simplest VIEWNET achieves high recognition scores without the need to explicitly code the temporal order of 2-D views in working memory. Working memories are also discussed that save memory resources by implicitly coding temporal order in terms of the relative activity of 2-D view category nodes, rather than as explicit 2-D view transitions. Variants of the VIEWNET architecture may be used for scene understanding by using a preprocessor and classier that can determine both what objects are in a scene and where they are located. The present VIEWNET preprocessor includes the CORT-X 2 filter, which discounts the illuminant, regularizes and completes figural boundaries, and suppresses image noise. This boundary segmentation is rendered invariant under 2-D translation, rotation, and dilation by use of a log polar transform. The invariant spectra undergo Gaussian coarse coding to further reduce noise and 3-D foreshortening effects, and to increase generalization. These compressed codes are input into the classifier, a supervised learning system based on the fuzzy ARTMAP algorithm. Fuzzy ARTMAP learns 2-D view categories that are invariant under 2-D image translation, rotation, and dilation as well as 3-D image transformations that do not cause a predictive error. Evidence from sequences of 2-D view categories converges at 3-D object nodes that generate a response invariant under changes of 2-D view. These 3-D object nodes input to a working memory that accumulates evidence over time to improve object recognition. In the simplest working memory, each occurrence (nonoccurrence) of a 2-D view category increases (decreases) the corresponding node's activity in working memory. The maximally active node is used to predict the 3-D object. Recognition is studied with noisy and clean images using slow and fast learning. Slow learning at thefuzzy ARTMAP mapfield is adapted to learn the conditional probability of the 3-D object given the selected 2-D view category. VIEWNET is demonstrated on an MIT Lincoln Laboratory database of 128 × 128 2-D views of aircraft with and without additive noise. A recognition rate of up to 90% is achieved with one 2-D view and of up to 98.5% correct with three 2-D views. The properties of 2-D view and 3-D object category nodes are compared with those of cells in monkey inferotemporal cortex.
Confirmation of Primary Active Substances from High Throughput Screening of Chemical and Biological Populations:  A Statistical Approach and Practical Considerations (2000)

Many biologically important substances are discovered through screening of relevant chemical or biological libraries. The ability to find the active substances ("hits") from any random collection is largely determined by the quality of the assay and screening conditions. When a large population is screened for a specific characteristic, each member of that population is usually tested only once. Errors in the measurements require additional follow-up tests to confirm that each hit from the primary screen is truly active. In this report, we present a statistical model system that predicts the reliability of hits from a primary test as affected by the error in the assay and the choice of the hit threshold (hit limit). The hit confirmation rate, as well as false positive (representing substances that initially fall above the hit limit but whose true activity are below the hit limit) and false negative (representing substances that initially fall below the hit limit but whose true activity are in fact greater than the hit limit) rates have been analyzed with this model by computational simulation. This model can also be used in screen validation and post-screening data analysis. The statistical analysis presented here has broad implications and is applicable to screening of any large population for any specific characteristic. Obvious applications include drug discovery, gene chip analysis, population biology, directed molecular evolution, biological panning, and combinatorial material sciences.
HRTF magnitude synthesis via sparse representation of anthropometric features (2014)

We propose a method for the synthesis of the magnitudes of Head-related Transfer Functions (HRTFs) using a sparse representation of anthropometric features. Our approach treats the HRTF synthesis problem as finding a sparse representation of the subject's anthropometric features w.r.t. the anthropometric features in the training set. The fundamental assumption is that the magnitudes of a given HRTF set can be described by the same sparse combination as the anthropometric data. Thus, we learn a sparse vector that represents the subject's anthropometric features as a linear superposition of the anthropometric features of a small subset of subjects from the training data. Then, we apply the same sparse vector directly on the HRTF tensor data. For evaluation purpose we use a new dataset, containing both anthropometric features and HRTFs. We compare the proposed sparse representation based approach with ridge regression and with the data of a manikin (which was designed based on average anthropometric data), and we simulate the best and the worst possible classifiers to select one of the HRTFs from the dataset. For instrumental evaluation we use log-spectral distortion. Experiments show that our sparse representation outperforms all other evaluated techniques, and that the synthesized HRTFs are almost as good as the best possible HRTF classifier.
Site-directed Mutagenesis of Human Leukotriene C4Synthase (1997)

The functional characteristics of leukotriene C4 synthase (LTC4S), which specifically conjugates leukotriene A4 with GSH, were assessed by mutagenic analysis. Human LTC4S and the 5-lipoxygenase-activating protein share substantial amino acid identity and predicted secondary structure. The mutation of Arg-51 of LTC4S to Thr or Ile abolishes the enzyme function, whereas the mutation of Arg-51 to His or Lys provides a fully active recombinant protein. The mutations Y59F, Y97F, Y93F, N55A, V49F, and A52S increase the Km of the recombinant microsomal enzyme for GSH. The mutation Y93F also markedly reduces enzyme function and increases the optimum for pH-dependent activity. The deletion of the third hydrophobic domain with the carboxyl terminus abolishes the enzyme activity, and function is restored by the substitution of the third hydrophobic domain and carboxyl terminus of 5-lipoxygenase-activating protein for that of LTC4S. Mutations of C56S and C82V alone or together and the deletion of Lys-2 and Asp-3 of LTC4S do not alter enzyme function. The direct linkage of two LTC4S monomers by a 12-amino acid bridge provides an active dimer, and the same bridging of inactive R51I with a wild-type monomer creates an active pseudo-dimer with function similar to that of the wild-type enzyme. These results suggest that in the catalytic function of LTC4S, Arg-51 probably opens the epoxide ring and Tyr-93 provides the thiolate anion of GSH. Furthermore, the monomer has independent conjugation activity, and dimerization of LTC4S maintains the proper protein structure.
Identification of novel cell migration‐promoting genes by a functional genetic screen (2009)

Here we describe the identification of novel cell migration-promoting genes based on an unbiased functional genetic screen in cultured cells. After the introduction of the retroviral mouse brain cDNA library into NIH3T3 mouse fibroblast cells, migration-promoted cells were selected by a 3-dimensional migration assay using cell culture inserts. After 5 rounds of enrichment, cDNAs were retrieved from the cells with a selected phenotype. Cell migration-promoting activity was confirmed by independent migration assays for the retrieved cDNAs, among which further investigation was focused on coiled-coil-helix-coiled-coil-helix domain-containing protein 2 (chchd2). Whereas overexpression of chchd2 promoted cell migration, knockdown of endogenous chchd2 expression reduced cell migration. Chchd2-induced cell migration was associated with augmented formation of actin stress fibers and focal adhesion, which was mediated through Akt, RhoA/ROCK, and Jnk pathways. CHCHD2 protein directly interacted with hyaluronic acid-binding protein 1 (HABP1) that possessed migration-suppressing activity. Intracellular localization and further functional studies suggested that CHCHD2 and HABP1 may mutually regulate each other to balance cell migration. Thus, chchd2 is a novel cell migration determinant identified by an in vitro functional genetic selection strategy. The selection method can also be useful for the isolation of genes that give other phenotypes of interest.
Fabrication of quartz microchips with optical slit and development of a linear imaging UV detector for microchip electrophoresis systems (2001)

We have developed quartz microchips for electrophoresis and a linear imaging UV detector along with the microchip. The microchips have an optical slit, which cut off the stray light in order to improve the sensitivity of UV absorption detection on the chip, at the bonding interface. They have been successfully fabricated on synthesized quartz glass substrates using the hydrofluoric acid (HF) solution bonding method. The signal level of UV absorption detection was effectively improved by applying microchips with the "on-chip" optical slit. It is also possible to improve the signal-to-noise ratio by repetitive scanning of linear photodiode array located along the separation channel, and signal averaging during elimination of the potential. Furthermore, the analysis may be performed until the separation of the target component is complete, because the real-time migration pattern of each component in the sample can be seen just as in a slab-gel electrophoresis, thus enabling a shorter analysis time.
Combining the hok/sok, parDE, and pnd postsegregational killer loci to enhance plasmid stability (1997)

To enhance plasmid segregational stability in bacterial cells, two pairs of independent postsegregational killing loci (genes which induce host killing upon plasmid loss) isolated from plasmids R1, R483, or RP4 (hok+/sok+ pnd+ or hok+/sok+ parDE+) were cloned into a common site of the beta-galactosidase expression vector pMJR1750 (ptac::lacZ+) to form a series of plasmids in which the effect of one or two stability loci on segregational plasmid stability could be discerned. Adding two antisense killer loci (hok+/sok+ pnd+) decreased the specific growth rate by 50% though they were more effective at reducing segregational instability than hok+/sok+ alone. With the ptac promoter induced fully (2.0 mM isopropyl-beta-D-thiogalactopyranoside) and no antibiotic selection pressure, the combination of a proteic killer locus (parDE+) with antisense killer loci (hok+/sok+) had a negligible impact on specific growth rate, maintained high beta-galactosidase expression, and led to a 30 and 190% increase in segregational stability (based on stable generations) as compared to plasmids containing either hok+/sok+ or parDE+ alone, respectively. Use of hok+/sok+ or parDE+ alone with high cloned-gene expression led to ninefold and fourfold increases in the number of stable generations, respectively. Two convenient cloning cassettes have been constructed to facilitate cloning the dual hok+/sok+ parDE+ and hok+/sok+ pnd+ killer systems.
Molecular characterization of an IgA receptor from group B streptococci: sequence of the gene, identification of a proline‐rich region with unique structure and isolation of N‐terminal fragments with IgA‐binding capacity (1991)

Abstract Certain strains of group B streptococci express a cell surface protein that binds IgA and acts as a virulence factor. This IgA receptor is referred to here as protein Bac. The gene for protein Bac was cloned and expressed in Escherichia coli , and the complete nucleotide sequence was determined. The deduced amino acid sequence of 1134 residues includes a signal sequence of 37 amino acids and a putative membrane anchor region at the C‐terminal end. The processed form of the receptor, 1097 residues, has a calculated molecular weight of 123 786. There are no cysteines in protein Bac, suggesting a fibrillar structure. The C‐terminal half of the protein includes a 90 residues long region with a novel type of periodic structure, the “XPZ motif”, in which every third amino acid is proline. Unlike other bacterial immunoglobulin‐binding proteins, there are no long repeats in protein Bac. Clones which express only part of the protein Bac gene were used to show that IgA‐binding takes place in the N‐terminal part of the molecule. Protein Bac was originally described as an antigen called β, but N‐terminal fragments that bind IgA do not react with a reference serum against the β antigen. These and other data indicate that protein Bac can be divided into two regions with different functions: an N‐terminal IgA‐binding region and a C‐terminal region corresponding to the β antigen. The IgA‐binding region of protein Bac does not show any homology to protein Arp, the IgA receptor from group A streptococci, although these receptors have similar binding properties. This indicates that convergent evolution has favored the appearance of these two structurally different streptococcal IgA receptors.
A new class of oxidosqualene cyclases directs synthesis of antimicrobial phytoprotectants in monocots (2001)

Many plants synthesize antimicrobial secondary metabolites as part of their normal program of growth and development, often sequestering them in tissues where they may protect against microbial attack. These include glycosylated triterpenoids (saponins), natural products that are exploited by man for a variety of purposes including use as drugs [Hostettmann, K. & Marston, A. (1995) Saponins (Cambridge Univ. Press, Cambridge, U.K.)]. Very little is known about the genes required for the synthesis of this important family of secondary metabolites in plants. Here we show the novel oxidosqualene cyclase AsbAS1 catalyzes the first committed step in the synthesis of antifungal triterpenoid saponins that accumulate in oat roots. We also demonstrate that two sodium azide-generated saponin-deficient mutants of oat, which define the Sad1 genetic complementation group, are defective in the gene encoding this enzyme and provide molecular genetic evidence indicating a direct link between AsbAS1, triterpenoid saponin biosynthesis, and disease resistance. Orthologs of AsbAS1 are absent from modern cereals and may have been lost during selection, raising the possibility that this gene could be exploited to enhance disease resistance in crop plants.
Intracellular generation of reactive oxygen species during nonhypoxic lung ischemia (1997)

Surface fluorometry with 40 microM hydroethidine (HE) as a probe was used to detect oxidant generation in isolated, ventilated rat lungs during lung ischemia. Ethidium fluorescence due to HE oxidation was continuously monitored with 470 nm excitation and 610 nm emission. Fluorescence increased with ischemia in O2-ventilated lungs [0.98 +/- 0.08 arbitrary fluorescence units (AFU)/min vs. 0.58 +/- 0.07 with control perfusion]. HE oxidation during ischemia was prevented by N2 ventilation but was unaltered by preperfusion with superoxide dismutase. Ethidium fluorescence in homogenate prepared from lungs subjected to 1 h of nonhypoxic ischemia was increased (16.8 +/- 1.5 vs. 9.8 +/- 0.4 AFU/mg protein in control) but was unchanged in lungs that had been N2 ventilated. Microfluorographs of HE perfused and fixed lung sections demonstrated marked generalized increases in ethidium fluorescence with ischemia compared with control perfusion. Ischemia resulted in significant increases in tissue thiobarbituric acid reactive substance (176 +/- 13 vs. 44 +/- 3 pmol/mg protein for control) and in lung conjugated dienes (0.90 +/- 0.07 vs. 0.48 +/- 0.06 U/mg protein for control), indicating peroxidation of lung lipids. These results indicate that lung ischemia leads to intracellular oxidant generation that can be continuously monitored by surface fluorometry.
Effects of platelet growth factors on human mesenchymal stem cells and human endothelial cells in vitro. (2004)

The aim of the present in vitro study has been to investigate the effects of a enriched platelet derived growth factors on proliferation and migration of human endothelial and mesenchymal stem cells and on osteogenic differentiation of stem cells. Platelet rich plasma has been produced, yielding a four time higher number of thrombocytes than normal plasma. Degranulation of platelets has been performed by means of calcium and thrombin. Plasma has served as a control, whereas plasma in combination with calcium and thrombin was used to distinguish the difference between calcium and/or thrombin mediated effects and growth factor induced effects on the cells. The observed enhanced proliferation and migration of endothelial cells towards the platelet derived growth factors was driven by the plasma component of these preparations. However PDGF solely stimulated the migration and proliferation of mesenchymal stem cells. The increased osteogenic differentiation of growth factor treated mesenchymal stem cells was mostly driven by the high level of calcium used for the platelets degranulation. In summery, the different components of platelet derived growth factors work together to influence human endothelial and mesenchymal stem cells. This is of special clinically interest regarding the stimulation of bone healing in orthopaedic and traumatic surgery.
Erythropoietin Induces Glycosylphosphatidylinositol Hydrolysis (1999)

We showed that erythropoietin induced rapid glycosylphosphatidylinositol (GPI) hydrolysis and tyrosine phosphorylation of phospholipase C (PLC)-gamma(2) in FDC-P1 cells transfected with the wild-type erythropoietin-receptor. Erythropoietin-induced tyrosine phosphorylation of PLC-gamma(2) was time- and dose-dependent. By using FDC-P1 cells transfected with an erythropoietin receptor devoid of tyrosine residues, we showed that both effects required the tyrosine residues of intracellular domain on the erythropoietin receptor. Erythropoietin-activated PLC-gamma(2) hydrolyzed purified [(3)H]GPI indicating that GPI hydrolysis and PLC-gamma(2) activation under erythropoietin stimulation were correlated. Results obtained on FDC-P1 cells transfected with erythropoietin receptor mutated on tyrosine residues suggest that tyrosines 343, 401, 464, and/or 479 are involved in erythropoietin-induced GPI hydrolysis and tyrosine phosphorylation of PLC-gamma(2), whereas tyrosines 429 and/or 431 seem to be involved in an inhibition of both effects. Thus, our results suggest that erythropoietin regulates GPI hydrolysis via tyrosine phosphorylation of its receptor and PLC-gamma(2) activation.
Resting heart rate as a low tech predictor of coronary events in women: prospective cohort study (2009)

<b>Objective</b> To evaluate resting heart rate as an independent predictor of cardiovascular risk in women. <b>Design</b> Prospective cohort study. <b>Setting</b> The Women’s Health Initiative was undertaken at 40 research clinics in the United States. <b>Participants</b> 129 135 postmenopausal women. <b>Main outcome measure</b> Clinical cardiovascular events. <b>Results</b> During a mean of 7.8 (SD 1.6) years of follow up, 2281 women were identified with myocardial infarction or coronary death and 1877 with stroke. We evaluated associations between resting heart rate and cardiovascular events in Cox regression models adjusted for multiple covariates. Higher resting heart rate was independently associated with coronary events (hazard ratio 1.26, 95% confidence interval 1.11 to 1.42 for highest [&gt;76 beats per minute] <i>v</i> lowest quintile [≤62 beats per minute]; P=0.001), but not with stroke. The relation between heart rate and coronary events did not differ between white women and women from other ethnic groups (P for interaction=0.45) or between women with and without diabetes (P for interaction=0.31), but it was stronger in women aged 50-64 at baseline than in those aged 65-79 (P for interaction=0.009). <b>Conclusion</b> Resting heart rate, a low tech and inexpensive measure of autonomic tone, independently predicts myocardial infarction or coronary death, but not stroke, in women. <b>Trial registration</b> ClinicalTrials.gov NCT00000611.
A SU-8-Based Fully Integrated Biocompatible Inductively Powered Wireless Neurostimulator (2012)

A fully integrated minimally invasive compact polymer-based wireless neurostimulator was designed, fabricated, and characterized both in open air and in vivo. The neurostimulator <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$(3.1 \times 1.6 \times 0.3\ \hbox{mm})$</tex></formula> consists of a planar spiral coil for wireless power supply through inductive coupling, two Schottky diodes for full-wave rectification, an application-specific integrated circuit neurostimulator circuit chip for stimulus spike signal generation, and two biphasic platinum–iridium (PtIr) stimulation electrodes. The device is fully integrated and completely embedded in biocompatible SU-8 packaging. For in vivo testing, the wireless neurostimulator was implanted subcutaneously in a rat hind limb. At the coupling power of 21 dBm (125 mW) at 394-MHz resonant frequency, stable and robust cortical responses during extended periods of wireless stimulation were recorded. <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hfill$</tex></formula> [2012-0085]