gebhart/patrepeval huggingface dataset:
A graphics simulator for a robotic arm (1989)

A graphics robot simulator designed for an IBM PC/XT/AT or PS/2 personal computer is presented. The simulator is a terminate-and-stay resident (TSR) program that runs in the background and intercepts commands that would normally go to the robot controller through the COM1 serial communication device. With the use of the simulator, students can develop and test robot control programs offline without a physical robot present, using the language of their choice. The status of the simulated robot is available through a 3-D graphics display and a one-line text window, each of which can be activated from the keyboard or from within a user program. Data files are used to specify the robot to be simulated and the environment or workcell within which it is to operate. Currently supported robots include the Rhino XR-3 educational robot and the Adept One and Inteledex 660 industrial robots. The workcell features an overhead camera and objects that can be sensed by the camera and manipulated by the robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The bifunctional peptidoglycan lysin of Streptococcus agalactiae bacteriophage B30 (2004)

A group B streptococcal (GBS) bacteriophage lysin gene was cloned and expressed in Escherichia coli. The purified recombinant enzyme, calculated to have a molecular mass of 49 677 Da, lysed GBS cells. The susceptibility of GBS cells to lysis by the enzyme depended upon the growth stage at which they were harvested, with early exponential phase cells most sensitive. Calcium ions enhanced the activity of the enzyme. The enzyme also lysed other beta-haemolytic streptococci, including groups A, C, E and G streptococci, but not common oral streptococci, including Streptococcus mutans. The generation of both reducing activity and N-terminal alanine residues during lysis indicated that the lysin is a bifunctional enzyme, possessing both glycosidase and endopeptidase activities. This is consistent with the presence of two conserved sequence domains, an Acm (acetylmuramidase) domain associated with lysozyme activity, and a CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain associated with endopeptidase activity. Site-directed mutagenesis of conserved cysteine and histidine residues in the CHAP domain and conserved aspartate and glutamate residues in the Acm domain confirmed their importance for lysozyme and endopeptidase activity respectively.
Full-duplex communication systems using loudspeaker arrays and microphone arrays (2003)

For high-quality multimedia communication systems, such as teleconferencing, or tele-teaching (especially of music), multichannel sound reproduction is highly desirable. While current approaches still rely on a restrained listening area, the sweet spot, a volume solution for a large listening space is offered by the wave field synthesis (WFS) method, where arrays of loudspeakers generate a prespecified sound field. On the recording side of the two-way systems, the use of microphone arrays is an effective approach to cope with undesired signal components in the receiving room. However, before full-duplex communication can be deployed, efficient approaches to the acoustic echo cancellation (AEC) problem in this challenging scenario have to be found. We investigate different options for system integration, after a brief discussion of the current state of the art. We then present a first real-time solution on a regular PC platform, based on an efficient AEC for MIMO (multi-input and multi-output) systems in the frequency-domain.
Exosome separation using microfluidic systems: size‐based, immunoaffinity‐based and dynamic methodologies (2017)

Exosomes, nanovesicles secreted by most types of cells, exist in virtually all bodily fluids. Their rich nucleic acid and protein content make them potentially valuable biomarkers for noninvasive molecular diagnostics. They also show promise, after further development, to serve as a drug delivery system. Unfortunately, existing exosome separation technologies, such as ultracentrifugation and methods incorporating magnetic beads, are time-consuming, laborious and separate only exosomes of low purity. Thus, a more effective separation method is highly desirable. Microfluidic platforms are ideal tools for exosome separation, since they enable fast, cost-efficient, portable and precise processing of nanoparticles and small volumes of liquid samples. Recently, several microfluidic-based exosome separation technologies have been studied. In this article, the advantages of the most recent technologies, as well as their limitations, challenges and potential uses in novel microfluidic exosome separation and collection applications is reviewed. This review outlines the uses of new powerful microfluidic exosome detection tools for biologists and clinicians, as well as exosome separation tools for microfluidic engineers. Current challenges of exosome separation methodologies are also described, in order to highlight areas for future research and development.
Programmable polyproteams built using twin peptide superglues (2016)

Programmed connection of amino acids or nucleotides into chains introduced a revolution in control of biological function. Reacting proteins together is more complex because of the number of reactive groups and delicate stability. Here we achieved sequence-programmed irreversible connection of protein units, forming polyprotein teams by sequential amidation and transamidation. SpyTag peptide is engineered to spontaneously form an isopeptide bond with SpyCatcher protein. By engineering the adhesin RrgA from Streptococcus pneumoniae, we developed the peptide SnoopTag, which formed a spontaneous isopeptide bond to its protein partner SnoopCatcher with >99% yield and no cross-reaction to SpyTag/SpyCatcher. Solid-phase attachment followed by sequential SpyTag or SnoopTag reaction between building-blocks enabled iterative extension. Linear, branched, and combinatorial polyproteins were synthesized, identifying optimal combinations of ligands against death receptors and growth factor receptors for cancer cell death signal activation. This simple and modular route to programmable "polyproteams" should enable exploration of a new area of biological space.
Transcriptional regulation of the pyruvate kinase erythroid-specific promoter. (1993)

Mammal pyruvate kinases are encoded by two genes. The L gene produces the erythroid (R-PK) or the hepatic (L-PK) isozymes by the alternative use of two promoters. We report the characterization of the cis- and trans-acting elements involved in the tissue-specific activity of the L gene erythroid promoter. A R-PK DNA fragment extending from -870 to +54 relative to the cap site confers erythroid specificity to a reporter gene. Within this region, we define a minimal promoter (-62 to +54) that displays erythroid-specific activity and contains two DNA binding sites. One, located at -50, binds members of the CCACC/Sp1 family and the other, located at -20, binds the erythroid factor GATA-1. Although the -20 GATA binding site (AGATAA) is also a potential TFIID binding site, it does not bind TFIID. Furthermore, the substitution of this GATA binding site by a canonical TFIID binding site suppresses the promoter activity. Mutations and deletions of both sites indicate that only the association of CCACC/Sp1 and GATA binding sites can drive efficient and tissue-specific expression of this R-PK minimal promoter. Finally, by co-transfection experiments, we study the elements involved in the hGATA-1 transactivation of the R-PK promoter in HeLa cells.
A time digitizer CMOS gate-array with a 250 ps time resolution (1996)

A pipelined time digitizer CMOS gate-array has been developed using 0.5 /spl mu/m Sea-of-Gate technology. Precise timing signals which are used to sample input signals are generated from 32 taps of an asymmetric ring oscillator. The frequency of the oscillator is controlled by a phase-locked loop (PLL) circuit which runs in the 10-50 MHz frequency range. A test chip has been developed and tested; a time resolution of 250 ps rms at 40 MHz clock was measured. The chip has 4 channels and encoding circuits for both the rising and the falling edges of the input signals. The chip has 128-word dual-port memories, allowing the histories of the input signals to be stored and causing no deadtime for the conversion.
Integrated packet networks with quality of service constraints (2002)

The authors propose a QoS (quality of service) framework which strikes a balance between the quality criteria of the service providers and the quality requirement of the users. QoS is classified in terms of performance, resource, and priority constraints. The authors discuss how this framework fits into a connection-oriented fast packet environment. They also show how QoS negotiation is conducted in such a network, so that the QoS of the available network resources matches that needed by the users.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
SyDeR—System design for reusability (1998)

A fixed set of components with a fixed set of properties is often regarded as a defining characteristic of configuration design problems. In configuration design for larger and more complex systems (e.g., street cars), however, this often is not really true. The reason is that sometimes the component library offers no component that meets the actual requirements, so that a new component has to be added to the library. In general, configuration design for larger products must be interactive: interactive in the sense that the user controls the configuration process and in the sense that the phases of knowledge acquisition and configuration are partly mixed. This paper describes a method and a corresponding software tool (SyDeR, System Design for Reusability) that support the interactive configuration design of complex products, especially in the tendering phase. It combines three different technologies: [bull ] structural modeling of technical systems; [bull ] a library for technical solutions, which is based upon taxonomies and allows the reuse of the technical solutions; [bull ] constraint techniques to propagate design decisions and check designs for consistency to support interactive configuration design. This paper gives an overview of the functionality of the SyDeR tool and describes the main ideas behind the modeling language, which is especially oriented towards the requirements of system design problems. It also explains how we integrated structural modeling, taxonomies, and advanced constraint reasoning techniques into real-world applications.
Large-Scale Fabrication of Carbon Nanotube Probe Tips for Atomic Force Microscopy Critical Dimension Imaging Applications (2004)

We report an innovative approach that combines nanopatterning and nanomaterials synthesis with traditional silicon micromachining technologies for large-scale fabrication of carbon nanotube (CNT) probe tips for atomic force microscopy imaging applications. Our batch fabrication process has produced 244 CNT probe tips per 4-in. wafer with control over the CNT location, diameter, length, orientation, and crystalline morphology. CNT probe tips with diameters ranging between 40 and 80 nm and lengths between 2 and 6 μm are found to be functional probe tips with no need for shortening. This reliable and true bottom-up wafer scale integration and fabrication process provides a new class of high performance nanoprobes. Preliminary AFM imaging results show that the CNT probe tips are strong, wear-resistant, and capable of high-resolution and critical-dimension imaging.
Micro-LED arrays: a tool for two-dimensional neuron stimulation (2008)

Stimulating neuron cells with light is an exciting new technology that is revolutionizing the neurosciences. To date, due to the optical complexity that is involved, photostimulation has only been achieved at a single site using high power light sources. Here we present a GaN based micro-light emitting diode (LED) array that can open the way to multi-site photostimulation of neuron cells. The device is a two-dimensional array of micrometre size LED emitters. Each emitter has the required wavelength, optical power and modulation bandwidth to trigger almost any photosensitizer and is individually addressable. We demonstrate micrometre resolution photoactivation of a caged fluorophore and photostimulation of sensitized living neuron cells. In addition, a complete system that combines the micro-LED array with multi-site electrophysiological recording based on microelectrode array technology and/or fluorescence imaging is presented.
The highly conserved DAD1 protein involved in apoptosis is required for N‐linked glycosylation (1997)

tsBN7 cells have a defect in N-linked glycosylation caused by the loss of DAD1.
Recent developments in high integration multi-standard CMOS transceivers for personal communication systems (1998)

Issues associated with the integration of transceiver components on to a single silicon substrate are discussed. In particular, recently proposed receiver and transmitter architectures for high integration are examined on the promise of providing multistandard capability. In addition, existing barriers to lower power transceiver operation are examined as well as some proposed directions for future integrated transceiver research and development.
A new molecular mechanism for severe myoclonic epilepsy of infancy: Exonic deletions in SCN1A (2006)

We examined cases of severe myoclonic epilepsy of infancy (SMEI) for exon deletions or duplications within the sodium channel SCN1A gene by multiplex ligation-dependent probe amplification. Two of 13 patients (15%) who fulfilled the strict clinical definition of SMEI but without SCN1A coding or splicing mutations had exonic deletions of SCN1A.
Antibody specificity of human glomerular basement membrane type IV collagen NC1 subunits. Species variation in subunit composition. (1986)

NC1 subunits were purified from gel filtration pools of acid-extracted, collagenase-digested human glomerular basement membranes (hGBM). This methodology, which enriches 28-kDa monomers (M28) in the total digest, allowed purification of these monomers and 24-kDa (M24) and 26-kDa (M26) monomers free from dimers. Reactivity of these subunits with Goodpasture autoantibodies using immunoblotting of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and two-dimensional nonequilibrium pH gradient electrophoresis gels showed strong reactivity with the purified M28 subunits. Inhibition enzyme-linked immunosorbent assay, used to quantitate the reactivity of the purified NC1 subunits, indicated that M28 had a greater than 10-fold increase in ability to inhibit binding to NC1 than NC1 itself. Comparison of hGBM NC1 components were made with those obtained from collagenase digests of salt and acid-extracted bovine and sheep GBM and Englebreth-Holm-Swarm tumor similarly purified by gel filtration and reverse-phase high performance liquid chromatography. Two-dimensional gel analysis of these NC1 isolates revealed absence of the very cationic M28 monomers. Reactivity with antibodies eluted from diseased kidneys of sheep immunized with hGBM (Steblay nephritis) was compared with Goodpasture autoantibody reactivity by immunoblotting two-dimensional gels of hGBM NC1. We conclude that a very cationic M28 monomer (M28 ) found only in hGBM is the probable target in Goodpasture syndrome, that the epitope is present on most NC1 components from extracted and unextracted hGBM, and is exposed by urea denaturation which is enhanced by acid treatment. A weakly cationic M28 monomer (M28+) is present in GBM from other species and is the probable target in Steblay nephritis. Differential recognition of the two M28 components by these antibodies points to different genetic origins or possibly distinct post-translational modifications for these components. This is supported by their presence or absence in different species and tissues, as well as biochemical differences from the M24/26 monomers which presumably are derived from alpha 1(IV) and alpha 2(IV) collagen chains.
Hybrid nanofibrous membranes of PLGA/chitosan fabricated via an electrospinning array (2007)

Hybrid nanofibrous membranes of poly(lactic-co-glycolic acid) (PLGA) and chitosan with different chitosan amounts (32.3, 62.7, and 86.5%) were fabricated via a specially designed electrospinning setup consisting of two sets of separate syringe pumps and power supplies. After soaking in chloroform overnight to dissolve PLGA, the amount of chitosan in the hybrid membranes was determined. The structure, mechanical properties, water uptake, and cytocompatibilities of the nanofibrous membranes were investigated by scanning electron microscopy, tensile testing, incubation in phosphate buffer solution, and human embryo skin fibroblasts culturing. Results showed that the chitosan amount in PLGA/chitosan membranes could be well controlled by adjusting the number of syringe for electrospinning of PLGA or chitosan, respectively. Because of the introduction of chitosan, which is a naturally hydrophilic polymer, the hybrid PLGA/chitosan membranes after chitosan crosslinking exhibited good mechanical and water absorption properties. The cytocompatibility of hybrid PLGA/chitosan membranes was better than that of the electrospun PLGA membrane. The electrospun hybrid nanofibrous membranes of PLGA and chitosan appear to be promising for skin tissue engineering. The concept of using an electrospinning array to form multicomponent nanofibrous membranes will lead to the creation of novel scaffolds for tissue engineering applications.
An accurate numerical model for calculating the equilibration rate of a hanging-drop experiment (1999)

A numerical model of the equilibration of a hanging-drop experiment has been developed and tested. To obtain accurate calculations with a given precipitant, the vapor pressure of water over water/precipitant solutions must be known for various concentrations of the precipitant. The calculations of the model are in excellent agreement with all available experimental data on hanging-drop equilibration when the necessary vapor pressures are known (ammonium sulfate and sodium chloride). By varying each of the relevant rate constants in the model, the rate-limiting step in the equilibration of a hanging drop is determined. This analysis clearly shows that the rate-limiting step is the diffusion of water vapor from the drop to the reservoir, which agrees with experimental findings. Since the diffusion of water vapor is the rate-limiting step, there is virtually no precipitant concentration gradient in the drop during equilibration. As a result, there is no gravity-induced convection owing to the equilibration. Thus, whereas gravity might have an effect during crystal growth, gravity does not affect the equilibration rate of a hanging-drop experiment to a significant extent, and the diffusion of water vapor will remain the rate-limiting step in the absence of gravity. Finally, the effects of several of the parameters, such as initial drop volume, drop-to-reservoir distance and temperature, are considered quantitatively. The equilibration rate was found to vary nearly linearly with drop volume. The equilibration rate decreases roughly by a factor of three as the temperature decreases from 293 to 276 K. This decrease in the equilibration rate is greater than would be expected when just considering the change in the diffusion coefficient of water vapor in air. This large dependence can, however, be attributed to the change in water-vapor pressure. Most surprisingly, a linear dependence on drop-to-reservoir distance is found, a result that agrees very well with experiment.
SPECTROSCOPY WITH ELECTRONIC TERAHERTZ TECHNIQUES FOR CHEMICAL AND BIOLOGICAL SENSING (2003)

By illuminating the sample with a broadband 10-500 GHz stimulus and coherently detecting the response, we obtain reflection and transmission spectra of common powdered substances, and compare them as a starting point for distinguishing concealed threats in envelopes and on personnel. Because these samples are irregular and their dielectric properties cannot be modulated, the spectral information we obtain is largely qualitative. To show how to gain quantitative information on biological species at micro- and millimeter-wave frequencies, we introduce thermal modulation of a globular protein in solution, and show that changes in microwave reflections coincide with accepted visible absorption spectra, pointing the way toward gaining quantitative chemical and biological spectra from broadband terahertz systems.
Purification, Characterization and Biological Activities of a Garlic Oligosaccharide (2008)

A novel oligosaccharide was purified from garlic (Allium sativum L.) bulbs via hot water extraction, ammonium sulfate precipitation, gel filtration and ion exchange chromatography. The molecular weight of the oligosaccharide was determined to be 1800. A nuclear magnetic resonance (NMR) study showed that ten fructose molecules were connected by beta1-2 linkage to a terminal glucose. The oligosaccharide had cytotoxic activities against human malignant lymphoma cells (U937) and colon adenocarcinoma cells (WiDr) in vitro. Furthermore, this oligosaccharide significantly suppressed the growth of murine colon adenocarcinoma cells (colon 26) in vivo. The oligosaccharide also stimulated interferon-gamma production by human peripheral blood lymphocyte in vitro, indicating that it may activate the immunological pathways and suppress the growth of tumors in vivo.
A new kind of informational suppression in the nematode Caenorhabditis elegans. (1989)

Independent reversions of mutations affecting three different Caenorhabditis elegans genes have each yielded representatives of the same set of extragenic suppressors. Mutations at any one of six loci act as allele-specific recessive suppressors of certain allels of unc-54 (a myosin heavy chain gene), lin-29 (a heterochronic gene), and tra-2 (a sex determination gene). The same mutations also suppress certain alleles of another sex determination gene, tra-1, and of a morphogenetic gene, dpy-5. In addition to their suppression phenotype, the suppressor mutations cause abnormal morphogenesis of the male bursa and the hermaphrodite vulva. We name these genes smg-1 through smg-6 (suppressor with morphogenetic effect on genitalia), in order to distinguish them from mab (male abnormal) genes that can mutate to produce abnormal genitalia but which do not act as suppressors (smg-1 and smg-2 are new names for two previously described genes, mab-1 and mab-11). The patterns of suppression, and the interactions between the different smg genes, are described and discussed. In general, suppression is recessive and incomplete, and at least some of the suppressed mutations are hypomorphic in nature. A suppressible allele of unc-54 contains a deletion in the 3' noncoding region of the gene; the protein coding region of the gene is apparently unaffected. This suggests that the smg suppressors affect a process other than translation, for example mRNA processing, transport, or stability.