gebhart/patrepeval huggingface dataset:
Neuronal activity-dependent membrane traffic at the neuromuscular junction (2002)

During development and also in adulthood, synaptic connections are modulated by neuronal activity. To follow such modifications in vivo, new genetic tools are designed. The nontoxic C-terminal fragment of tetanus toxin (TTC) fused to a reporter gene such as LacZ retains the retrograde and transsynaptic transport abilities of the holotoxin itself. In this work, the hybrid protein is injected intramuscularly to analyze in vivo the mechanisms of intracellular and transneuronal traffics at the neuromuscular junction (NMJ). Traffic on both sides of the synapse are strongly dependent on presynaptic neural cell activity. In muscle, a directional membrane traffic concentrates beta-galactosidase-TTC hybrid protein into the NMJ postsynaptic side. In neurons, the probe is sorted across the cell to dendrites and subsequently to an interconnected neuron. Such fusion protein, sensitive to presynaptic neuronal activity, would be extremely useful to analyze morphological changes and plasticity at the NMJ.
Identification and characterization of a novel agonistic anti-DR4 human monoclonal antibody (2010)

The tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and its functional receptors, DR4 and DR5, have been established as promising targets for cancer treatment. Therapeutics targeting TRAIL and its receptors are not only effective in killing many types of tumors, but they also synergize with traditional therapies and show efficacy against tumors that are otherwise resistant to conventional treatments. We describe here the identification and characterization of two human monoclonal antibodies, m921 and m922, that are specific for human DR4. Both antibodies competed with TRAIL for binding to DR4, but only m921 recognized cell surface-associated DR4 and inhibited the growth of ST486 cells. This antibody may have potential for further development as a candidate therapeutic and research tool.
A digitally programmable highly linear active-RC filter (2009)

A new approach providing the active RC inverting integrator with frequency tuning characteristics is proposed. An inherently linear current division network (CDN) preserving the high linearity property of the active RC technique is adopted. Experimental results, demonstrating the wide programmability and high linearity features, obtained from a 4th-order fully differential filter fabricated in a 0.18µm CMOS process are given.
Highly efficient on-chip integratable metasurface devices for polarimetric detection and imaging (Conference Presentation) (2019)

Optical metasurface refers to a kind of nanostructured material with sub-wavelength thickness and on-demand optical properties, which are not possible for natural materials. By rationally engineering the metasurface structures, one could achieve new capabilities for the manipulation of light, e.g., ultra-thin flat lenses, waveplates and holographic plates. Yet, the optical efficiency and performance of most metasurface-based devices are yet to improve to meet the requirements for real-world applications. In this talk, I will present our research on highly efficient on-chip integratable metasurface devices for ultra-compact polarimetric detection and imaging devices. I will discuss about our approach to realize highly efficient broadband hybrid metasurfaces (based on integrated dielectric and plasmonic metasurfaces) for phase and polarization control of light in near infrared wavelength (1.2-1.7 µm). We have theoretically investigated and experimentally demonstrated circular polarization (CP) detection with CP extinction ratio (defined as the ratio between the transmission of CP light with desired handedness and that of CP light with the other handedness) of 30 and transmission efficiency over 80%. I will also discuss about another approach of realizing highly efficient plasmonic metasurfaces for phase and polarization control of light in mid-infrared wavelength (2-12 µm). Despite the high ohmic loss of plasmonic metasurfaces, I will show that by rationally designing the metasurface structure, it is possible to realize highly efficient plasmonic devices with superior performance. As a proof-of-concept demonstration, we have designed and experimentally demonstrated CP polarization filters with transmission efficiency >85% and CP extinction ratio >50 at 4 µm (bandwidth > 600 nm for CP extinction ratio> 10). The total thickness of the metasurface structure is less than 1/10 of the operational wavelength. Last but not the least, I will present our recent progress on chip-integration of metasurface devices for full-stokes polarimetric detection and imaging.
Bioluminescence as the Basis for the Detection of Trichothecenes (1986)

The marine dinoflagellate, Pyrocystis lunula, luminesces strongly when subjected to a shear stress such as in stirring. The intensity of the luminescence reaches a maximum after approximately 2 hours of darkness. It was found that certain trichothecenes (popularly known as Yellow Rain compounds) inhibit the luminescence of Pyrocystis lunula; e.g. in the assay developed during this study, 2 micrograms of T-2 quench the luminescence of a test culture by 40%. The assay consists in preparing a suspension containing 100 cells/ml, storing it in the dark for 2 hours, then stirring mechanically for 1-1/2 minutes during which the output of a photometer absorbing the light produced is plotted on a strip chart recorder. Comparisons are then made of the displacement of the recorder pen with control cultures vs those containing a toxin. Because an epoxide group is a necessary component of the trichothecences, there was a possibility that the assay method was simply responding to the epoxide moiety. This is not the case, however, since a series of epoxide-containing compounds failed to inhibit the luminescence of the organism. It is recommended that further studies be conducted to determine the feasibility of adapting this assay to field use. Each assay requires less than two minutes, and no special workup of field samples is required. Keywords: Roridin; Verrucarin; and Weathering.
A target-selected <i>Apc</i> -mutant rat kindred enhances the modeling of familial human colon cancer (2007)

Progress toward the understanding and management of human colon cancer can be significantly advanced if appropriate experimental platforms become available. We have investigated whether a rat model carrying a knockout allele in the gatekeeper gene Adenomatous polyposis coli (Apc) recapitulates familial colon cancer of the human more closely than existing murine models. We have established a mutagen-induced nonsense allele of the rat Apc gene on an inbred F344/NTac (F344) genetic background. Carriers of this mutant allele develop multiple neoplasms with a distribution between the colon and small intestine that closely simulates that found in human familial adenomatous polyposis patients. To distinguish this phenotype from the predominantly small intestinal phenotype found in most Apc-mutant mouse strains, this strain has been designated the polyposis in the rat colon (Pirc) kindred. The Pirc rat kindred provides several unique and favorable features for the study of colon cancer. Tumor-bearing Pirc rats can live at least 17 months, carrying a significant colonic tumor burden. These tumors can be imaged both by micro computed tomography scanning and by classical endoscopy, enabling longitudinal studies of tumor genotype and phenotype as a function of response to chemopreventive and therapeutic regimes. The metacentric character of the rat karyotype, like that of the human and unlike the acrocentric mouse, has enabled us to demonstrate that the loss of the wild-type Apc allele in tumors does not involve chromosome loss. We believe that the Pirc rat kindred can address many of the current gaps in the modeling of human colon cancer.
Clinical Significance of Tissue Factor Pathway Inhibitor 2, a Serum Biomarker Candidate for Ovarian Clear Cell Carcinoma (2016)

TFPI2 is a useful serum biomarker for preoperative clinical diagnosis of CCC.
4H-SiC Epitaxial Growth on C-Face 150 mm SiC Substrate (2014)

The production of 150 mm-diameter SiC epitaxial wafers is the key to the spread of SiC power devices. We have developed production technology of the epitaxial growth for 4° off Carbon face (C-face) 4H-SiC epitaxial layers on 150 mm diameter substrates. Several growth parameters and hardware were optimized to obtain high uniformity wafers. We have succeeded in fabricating high quality C-face wafers with smooth surface and high uniformity.
<i>LaFA</i> (2009)

Although Regular Expressions (RegExes) have been widely used in network security applications, their inherent complexity often limits the total number of RegExes that can be detected using a single chip for a reasonable throughput. This limit on the number of RegExes impairs the scalability of today's RegEx detection systems. The scalability of existing schemes is generally limited by the traditional per character state processing and state transition detection paradigm. The main focus of existing schemes is in optimizing the number of states and the required transitions, but not the suboptimal character-based detection method. Furthermore, the potential benefits of reduced number of operations and states using out-of-sequence detection methods have not been explored. In this paper, we propose Looka-head Finite Automata (LaFA) to perform scalable RegEx detection using very small amount of memory. LaFA's memory requirement is very small due to the following three areas of effort described in this paper: (1) Different parts of a RegEx, namely RegEx components, are detected using different detectors, each of which is specialized and optimized for the detection of a certain RegEx component. (2) We systematically reorder the RegEx component detection sequence, which provides us with new possibilities for memory optimization. (3) Many redundant states in classical finite automata are identified and eliminated in LaFA. Our simulations show that LaFA requires an order of magnitude less memory compared to today's state-of-the-art RegEx detection systems. A single commodity Field Programmable Gate Array (FPGA) chip can accommodate up to twenty-five thousand (25k) RegExes. Based on the throughput of our LaFA prototype on FPGA, we estimated that a 34-Gbps throughput can be achieved.
Identification of two aptamers binding to Legionella pneumophila with high affinity and specificity (2020)

Legionella pneumophila (Lp) is a water borne bacterium causing Legionnaires' Disease (LD) in humans. Rapid detection of Lp in water system is essential to reduce the risk of LD outbreaks. The methods currently available require expert skills and are time intensive, thus delaying intervention. In situ detection of Lp by biosensor would allow rapid implementation of control strategies. To this end, a biorecognition element is required. Aptamers are considered promising biorecognition molecules for biosensing. Aptamers are short oligonucleotide sequence folding into a specific structure and are able to bind to specific molecules. Currently, no aptamer and thus no aptamer-based technology exists for the detection of Lp. In this study, Systemic Evolution of Ligands through EXponential enrichment (SELEX) was used to identify aptamers binding specifically to Lp. Ten rounds of positive selection and two rounds of counter-selection against two Pseudomonas species were performed. Two aptamers binding strongly to Lp were identified with K<sub>D</sub> of 116 and 135 nM. Binding specificity of these two aptamers to Lp was confirmed by flow cytometry and fluorescence microscopy. Therefore, these two aptamers are promising biorecognition molecules for the detection of Lp in water systems.
Engineering the thermostability of Bacillus neutral proteases (1991)

Protein engineering is multi-disciplinair onderzoek waarin de eigenschappen van eiwitten worden geanalyseerd met behulp van een combinatie van fysische, biochemische, wiskundige en genetische technieken. In de afgelopen jaren heeft protein engineering veel bijgedragen aan de toename in de kennis van de structuur-functie-stabiliteits relaties in eiwitten. Dit proefschrift beschrijf het gebruik van protein engineering voor de bestudering van de thermostabiliteit van neutrale proteases (NPr's) ,extra-cellulaire enzymen die worden geproduceerd door diverse leden van het bacteriële genus Bacillus. ... Zie: Samenvatting
Fractional moving blood volume: estimation with power Doppler US. (1995)

The power Doppler US technique has the potential to more accurately estimate alterations in blood flow and has the advantage of being a continuous parameter that can be depth normalized.
Attenuation of signaling pathways stimulated by pathologically activated FGF-receptor 2 mutants prevents craniosynostosis (2006)

Craniosynostosis, the fusion of one or more of the sutures of the skull vault before the brain completes its growth, is a common (1 in 2,500 births) craniofacial abnormality, approximately 20% of which occurrences are caused by gain-of-function mutations in FGF receptors (FGFRs). We describe a genetic and pharmacological approach for the treatment of a murine model system of Crouzon-like craniosynostosis induced by a dominant mutation in Fgfr2c. Using genetically modified mice, we demonstrate that premature fusion of sutures mediated by Crouzon-like activated Fgfr2c mutant is prevented by attenuation of signaling pathways by selective uncoupling between the docking protein Frs2alpha and activated Fgfr2c, resulting in normal skull development. We also demonstrate that attenuation of Fgfr signaling in a calvaria organ culture with an Fgfr inhibitor prevents premature fusion of sutures without adversely affecting calvaria development. These experiments show that attenuation of FGFR signaling by pharmacological intervention could be applied for the treatment of craniosynostosis or other severe bone disorders caused by mutations in FGFRs that currently have no treatment.
Ligand-Dependent Disorder of the Ω Loop Observed in Extended-Spectrum SHV-Type β-Lactamase (2011)

Among Gram-negative bacteria, resistance to β-lactams is mediated primarily by β-lactamases (EC 3.2.6.5), periplasmic enzymes that inactivate β-lactam antibiotics. Substitutions at critical amino acid positions in the class A β-lactamase families result in enzymes that can hydrolyze extended-spectrum cephalosporins, thus demonstrating an "extended-spectrum" β-lactamase (ESBL) phenotype. Using SHV ESBLs with substitutions in the Ω loop (R164H and R164S) as target enzymes to understand this enhanced biochemical capability and to serve as a basis for novel β-lactamase inhibitor development, we determined the spectra of activity and crystal structures of these variants. We also studied the inactivation of the R164H and R164S mutants with tazobactam and SA2-13, a unique β-lactamase inhibitor that undergoes a distinctive reaction chemistry in the active site. We noted that the reduced Ki values for the R164H and R164S mutants with SA2-13 are comparable to those with tazobactam (submicromolar). The apo enzyme crystal structures of the R164H and R164S SHV variants revealed an ordered Ω loop architecture that became disordered when SA2-13 was bound. Important structural alterations that result from the binding of SA2-13 explain the enhanced susceptibility of these ESBL enzymes to this inhibitor and highlight ligand-dependent Ω loop flexibility as a mechanism for accommodating and hydrolyzing β-lactam substrates.
Vaccination against δ-Retroviruses: The Bovine Leukemia Virus Paradigm (2014)

Bovine leukemia virus (BLV) and human T-lymphotropic virus type 1 (HTLV-1) are closely related d-retroviruses that induce hematological diseases. HTLV-1 infects about 15 million people worldwide, mainly in subtropical areas. HTLV-1 induces a wide spectrum of diseases (e.g., HTLV-associated myelopathy/tropical spastic paraparesis) and leukemia/lymphoma (adult T-cell leukemia). Bovine leukemia virus is a major pathogen of cattle, causing important economic losses due to a reduction in production, export limitations and lymphoma-associated death. In the absence of satisfactory treatment for these diseases and besides the prevention of transmission, the best option to reduce the prevalence of d-retroviruses is vaccination. Here, we provide an overview of the different vaccination strategies in the BLV model and outline key parameters required for vaccine efficacy.
<title>Frequency-domain flow cytometry: fluorescence-lifetime-based sensing technology for analyzing cells and chromosomes labeled with fluorescent probes</title> (1997)

A flow cytometer has been developed that combines flow cytometry (FCM) and fluorescence lifetime spectroscopy measurement principles to provide unique capabilities for making frequency-domain, excited-state lifetime measurements on cells/chromosomes labeled with fluorescent probes, while preserving conventional FCM capabilities. Cells are analyzed as they intersect a high-frequency, intensity-modulated (sine-wave) laser excitation beam. Fluorescence signals are processed by (1) low-pass filtering to obtain conventional FCM dc-excited signals and (2) phase-sensitive detection electronics to resolve heterogeneous fluorescence based on differences in lifetimes expressed as phase-shifts and to quantify fluorescence lifetimes in real time. Processed signals are displayed as frequency distribution histograms and bivariate contour diagrams. Recent examples of biological applications include: (1) lifetime histograms recorded on autofluorescent human lung fibroblasts, murine thymus cells labeled with antibodies conjugated to fluorophores for studying fluorescence quenching as a function of antibody dilution and F/P ratio, and on cultured cells, nuclei, and chromosomes stained with DNA-binding fluorochromes and (2) phase-resolved, fluorescence signal- intensity histograms recorded on autofluorescent HLFs labeled with immunofluorescence markers and on murine thymus cells labeled with Red 613-antiThy 1.2 and propidium iodide (PI positive `dead' cells) to demonstrate the resolution of signals from highly overlapping emission spectra. This technology will increase the number of fluorescent markers usable in multilabeling studies and lifetimes can be used as spectroscopic probes to study the interaction of markers with their targets, each other, and the surrounding microenvironment.© (1997) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Renin inhibitors containing .alpha.-heteroatom amino acids as P2 residues (1992)

A series of renin inhibitors having alpha-heteroatom amino acids as P2 substitutions has been prepared. Examples where the heteroatom is oxygen, sulfur, or nitrogen are described. Many of the compounds exhibit subnanomolar potency when tested in vitro against monkey renin. When selected compounds were tested orally in conscious, salt-depleted, normotensive, Cynomolgus monkeys, low to moderate blood pressure lowering was observed. At an oral dose of 30 mg/kg, compound 53a lowered blood pressure by a maximum of 18 mmHg at 2.5 h post-dose.
Improved superconducting magnet wire (1983)

This invention is directed to a superconducting tape or wire composed of alternating layers of copper and a niobium-containing superconductor such as niobium of NbTi, Nb/sub 3/Sn or Nb/sub 3/Ge. In general, each layer of the niobium-containing superconductor has a thickness in the range of about 0.05 to 1.5 times its coherence length (which for Nb/sub 3/Si is 41 A) with each copper layer having a thickness in the range of about 170 to 600 A. With the use of very thin layers of the niobium composition having a thickness within the desired range, the critical field (H/sub c/) may be increased by factors of 2 to 4. Also, the thin layers of the superconductor permit the resulting tape or wire to exhibit suitable ductility for winding on a magnet core. These compositions are also characterized by relatively high values of critical temperature and therefore will exhibit a combination of useful properties as superconductors.
Computer Science Reconsidered: The Invocation Model of Process Expression (2007)

Preface. Chapter 1. A Critical Review of the Notion of the Algorithm in Computer Science. Chapter 2. The Simplicity of Concurrency. Chapter 3. Dehumanizing Computer Science. Chapter 4. Transcending the Variable. Chapter 5. The Invocation Model. Chapter 6. Along the Spectrum. Chapter 7. Composing Boundaries. Chapter 8. Time and Memory. Chapter 9. Incidental Time. Chapter 10. Points of View. Chapter 11. Referential and Autonomous Process Expression. Chapter 12. The Invocation Language. Chapter 13. Reflections. Index.
Global Structural Changes in Hepatitis B Virus Capsids Induced by the Assembly Effector HAP1 (2006)

Hepatitis B virus (HBV) is a leading cause of liver disease and hepatocellular carcinoma; over 400 million people are chronically infected with HBV. Specific anti-HBV treatments, like most antivirals, target enzymes that are similar to host proteins. Virus capsid protein has no human homolog, making its assembly a promising but undeveloped therapeutic target. HAP1 [methyl 4-(2-chloro-4-fluorophenyl)-6-methyl-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate], a heteroaryldihydropyrimidine, is a potent HBV capsid assembly activator and misdirector. Knowledge of the structural basis for this activity would directly benefit the development of capsid-targeting therapeutic strategies. This report details the crystal structures of icosahedral HBV capsids with and without HAP1. We show that HAP1 leads to global structural changes by movements of subunits as connected rigid bodies. The observed movements cause the fivefold vertices to protrude from the liganded capsid, the threefold vertices to open, and the quasi-sixfold vertices to flatten, explaining the effects of HAP1 on assembled capsids and on the assembly process. We have identified a likely HAP1-binding site that bridges elements of secondary structure within a capsid-bound monomer, offering explanation for assembly activation. This site also interferes with interactions between capsid proteins, leading to quaternary changes and presumably assembly misdirection. These results demonstrate the plasticity of HBV capsids and the molecular basis for a tenable antiviral strategy.
Fiber-laser probe for near-field scanning microscopy (1994)

Recent advances in probe and feedback techniques have brought near-field scanning microscopy (NSOM) to the point where it can be routinely applied to a variety of systems.1 Although many efforts are directed at improving the current spatial resolution of ~12 nm of the current probe designs, the diversity of applications would be greatly increased by the development of a near-field probe with greatly improved photon flux.
Classification of Normal and Abnormal Heart Sound Recordings through Robust Feature Selection (2016)

We aim to develop a reliable and robust algorithm that accurately analyses a single short PCG recording (10-60s) from a single precordial location to determine the presence of heart abnormality for the Physionet/ Computing-in-Cardiology 2016 challenge.