gebhart/patrepeval huggingface dataset:
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors (2011)

Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions.
A thin film indium gallium arsenide focal plane array for visible and near infrared hyperspectral imaging (2003)

Indium gallium arsenide (InGaAs) focal plane arrays (FPAs) have proven useful in a wide variety of scientific, commercial, and military applications ranging from near infrared spectroscopy to night vision imaging. In a two-dimensional InGaAs FPA, an InGaAs photodiode array is hybrid-integrated to a silicon CMOS readout integrated circuit using indium bump-bonding techniques. The array is backside-illuminated with a long wavelength cutoff at 1.7 /spl mu/m due to the bandgap of the In/sub 0.57/Ga/sub 0.53/As active layer and a 0.9 /spl mu/m "cut-on" due to absorption in the indium phosphide (InP) substrate. We report a novel heteroepitaxial structure and process technology in which a thin (/spl les/ 0.3 /spl mu/m) InP "common cathode" is inserted under the InGaAs active layer. The InP substrate is removed after the FPA has been hybrid-integrated. The result is a thin (< 5 /spl mu/m) photodiode array membrane supported on a two-dimensional matrix of indium columns. The FPA exhibits photoresponse from 0.5 /spl mu/m in the visible to the 1.7 /spl mu/m InGaAs cutoff and is ideal for broad-band imaging spectroscopy or hyperspectral imaging.
Reconstitution of DNA Segregation Driven by Assembly of a Prokaryotic Actin Homolog (2007)

Multiple unrelated polymer systems have evolved to partition DNA molecules between daughter cells at division. To better understand polymer-driven DNA segregation, we reconstituted the three-component segregation system of the R1 plasmid from purified components. We found that the ParR/parC complex can construct a simple bipolar spindle by binding the ends of ParM filaments, inhibiting dynamic instability, and acting as a ratchet permitting incorporation of new monomers and riding on the elongating filament ends. Under steady-state conditions, the dynamic instability of unattached ParM filaments provides the energy required to drive DNA segregation.
Molecular Weight Distribution in Emulsion Polymerization:  Role of Active Chain Compartmentalization (1998)

A comparison of the results of two models with different levels of complexity has shown that errors can be made in the calculation of the polydispersity ratio of a polymer, produced in emulsion in the presence of termination by combination, if compartmentalization is not taken into account by properly considering the distribution of the lengths of the pairs of chains belonging to the same particle. These errors have been shown to be significant for values of the average number of free radicals per particle between about 0.4 and 2, which are typical of many emulsion systems. Accounting correctly for compartmentalization becomes crucial when the termination by combination mechanism is responsible for gelation, as in the case where branching through chain transfer to polymer is present in the system. The nature of the effects of compartmentalization on molecular weight has been analyzed both from a physical and a mathematical point of view. The importance of using a detailed model has been discussed for three polymerization systems: styrene, methyl methacrylate, and vinyl acetate.
A simple method for designing high-quality prototype filters for M-band pseudo QMF banks (1995)

Discusses a new method for designing the prototype filters necessary to implement M-band pseudo QMF banks. This method does not rely on the traditional nonlinear optimization used in past work but rather optimizes a single parameter on a convex error surface, consistently delivering the best equiripple filter possible while minimizing the overlapped passband distortion. A very simple algorithm for designing lowpass prototype filters suitable for use in pseudo QMF banks is described. To illustrate the applicability of this algorithm, two different filters are designed, both for such applications as wideband audio coding that require high quality reconstructed signals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Development of UWB microwave array radar for concealed weapon detection (2010)

This paper describes two approaches to short-range microwave imaging by means of ultra-wideband (UWB) technology. The first approach deals with synthetic aperture radar (SAR) that employs a transmit-receive antenna pair on mechanical scanner. The second one represents a multiple input multiple output (MIMO) antenna array that scans electronically in the horizontal plane and mechanically, installed on the scanner, in the vertical plane. The mechanical scanning in only one direction reduces significantly the measurement time. Two respective prototypes have been built and compared. Both systems comprise the same 10–18 GHz antennas and multichannel video impulse electronics while the same focusing based on Kirchhoff migration is applied to acquired data for radar imaging. The study has been carried out for an application of concealed weapon detection.
An approach for simulating the transport of spherical particles in a rarefied gas flow via the direct simulation Monte Carlo method (2001)

An approach is presented for computing the force on and heat transfer to a spherical particle from a rarefied flow of a monatomic gas that is computed using the direct simulation Monte Carlo (DSMC) method. The particle concentration is taken to be dilute, and the gas flow around the particle (but not necessarily throughout the flow domain) is taken to be free-molecular. Green’s functions for the force and heat transfer are determined analytically, are verified by demonstrating that they yield certain well-known results, and are implemented numerically within a DSMC code. Simulations are performed for the case of gas confined between two parallel plates at different temperatures for broad ranges of pressures and particle velocities. The simulation results agree closely with analytical results, where applicable. A simple approximate expression relating the thermophoretic force to the gas-phase heat flux is developed, and the drag and thermophoretic forces are found to be almost decoupled for a wide range of particle velocities.
Automatic Cell Detection and Tracking (1979)

Algorithms for the automatic detection and tracking of precipitation cells have been developed for the processing of digital weather radar data. The basic premise of the processing procedure is to represent the essential information in the weather radar data with a significantly smaller data set that describes the characteristics of the radar echo cells and their surrounding echo regions. Radar echo cells are defined by contours 3 dB below enclosed reflectivity peaks which do not enclose other cells. Attributes such as reflectivity, area, and location are tallied for each detected cell. Similar attributes are also tallied for the larger echo regions enclosed by preselected reflectivity value contours that encompass the cells. The attributes are used to extablish and maintain cell tracks within a tilt scan sequence and from one scan sequence to the next. Detected cells persist and produce tracks which last an average of 15 min. The detected cells are relatively small, typically 3 km in diameter, and often occur in clusters. The automatic detection and tracking programs provide a new tool for the analysis of large volumes of weather radar data.
Retargeting Polyomavirus-Like Particles to Cancer Cells by Chemical Modification of Capsid Surface (2016)

Virus-like particles based on polyomaviruses (PVLPs) are promising delivery devices for various cargoes, including nucleic acids, imaging probes, and therapeutic agents. In biological environments, the major coat protein VP1 interacts with ubiquitously distributed sialic acid residues, and therefore PVLPs show a broad tropism. For selective targeting, appropriate engineering of the PVLP surface is needed. Here, we describe a chemical approach to retarget PVLPs to cancer cells displaying abnormally high levels of transferrin receptor. We created an array of transferrin molecules on the surface of PVLPs by combining a high-yielding bioconjugation approach with specific point modification of transferrin. This artificial surface protein architecture enables (i) suppression of natural VP1-specific interactions by blocking the surface conformational epitope on the VP1 protein, (ii) unusually high cellular uptake efficiency, and (iii) selective retargeting of PVLPs to osteosarcoma (U2OS) and lymphoblastoid leukemia (CCRF-CEM) cells.
An embedded DRAM module using a dual sense amplifier architecture in a logic process (2002)

A dual sense amplifier array architecture (DSSA) amenable to a logic-process-compatible 1T DRAM eliminates the penalty that can be imposed by any two-bank-architecture-based DRAM. A 32k/spl times/16 eDRAM test chip is used to verify the architecture. The chip is implemented in a 0.5 /spl mu/m single-poly, triple-metal CMOS process. The DRAM array cell capacitance and bitline parasitic capacitance are 23 fF and 550 fF, respectively. The DRAM cell is 33 /spl mu/m/sup 2/ (7.38/spl times/4.5 /spl mu/m/sup 2/).
Domain orientation in polycrystalline BaTiO<sub>3</sub> (1949)

X-ray diffraction patterns of polycrystalline BaTiO3 show that, below the Curie temperature, the c axes of some of the individual crystallites can be oriented by large electric fields into a direction normal to their original direction and more nearly parallel to the applied field. For a field of 24 kV.cm.−1 applied 35° C. below the Curie temperature about 80% of the material was oriented so that the c axis made an angle of less than 45° to the electric field. At temperatures considerably above the Curie temperature the electric field had no effect; but at temperatures just above the average cubic–tetragonal transition temperature, the electric field appeared to increase the number of non-isometric crystals.
MIMO radio signals over fiber in picocells for increased WLAN coverage (2008)

We show that separating base station antennas in an optically-fed 2×3 MIMO WLAN system increases the overall coverage area in picocells. A peak throughput of 130 Mb/s was measured for antenna spacings of both 16 cm and 7 m.
Effect of Synthetic Human Atrial Natriuretic Peptide on Aldosterone Secretion by Dispersed Aldosterone-Producing Adenoma Cells<i>in Vitro</i>* (1985)

The effect of synthetic alpha-human atrial natriuretic peptide (alpha hANP), a potent natriuretic and vasorelaxant polypeptide recently isolated from human atria, on aldosterone secretion was studied in vitro in collagenase-dispersed adrenal adenoma cells from a patient with primary aldosteronism. alpha hANP (3.2 X 10(-7) M) significantly inhibited both basal and potassium (16 mM)-stimulated aldosterone secretion, whereas it had little or no effect on aldosterone secretion submaximally or maximally stimulated by ACTH (3.4 X 10(-10)-3.4 X 10(-9) M) or angiotensin II (10(-8)-10(-9) M). The less potent effect of alpha hANP on aldosterone secretion by dispersed human adrenal tumor cells compared to that in in vitro animal studies may reflect decreased affinity and/or number of specific receptors for ANP on the tumor cells. Whether ANP plays a physiological role in regulation of aldosterone secretion in humans in vivo remains to be determined.
Improving witness search using orders on states (2003)

We present a method for constructing concrete executions or witnesses to abstract behaviour specifications. The key concept is the use of an ordering on states which preserves containment of behaviours seen from the states. We present a modified depth-first search algorithm which uses the ordering to prune the requisite search paths and the memory needed for the history of the search. We apply the search to a model of a superscalar pipeline.
Identification of Novel Hexapeptides Bioactive against Phytopathogenic Fungi through Screening of a Synthetic Peptide Combinatorial Library (2002)

The purpose of the present study was to improve the antifungal activity against selected phytopathogenic fungi of the previously identified hexapeptide PAF19. We describe some properties of a set of novel synthetic hexapeptides whose D-amino acid sequences were obtained through screening of a synthetic peptide combinatorial library in a positional scanning format. As a result of the screening, 12 putative bioactive peptides were identified, synthesized, and assayed. The peptides PAF26 (Ac-rkkwfw-NH(2)), PAF32 (Ac-rkwhfw-NH(2)), and PAF34 (Ac-rkwlfw-NH(2)) showed stronger activity than PAF19 against isolates of Penicillium digitatum, Penicillium italicum, and Botrytis cinerea. PAF26 and PAF32, but not PAF34, were also active against Fusarium oxysporum. Penicillium expansum was less susceptible to all four PAF peptides, and only PAF34 showed weak activity against it. Assays were also conducted on nontarget organisms, and PAF26 and PAF32 showed much-reduced toxicity to Escherichia coli and Saccharomyces cerevisiae, demonstrating selectivity towards certain filamentous fungi. Thus, the data showed distinct activity profiles for peptides differentiated by just one or two residue substitutions. Our conclusion from this observation is that a specificity factor is involved in the activity of these short peptides. Furthermore, PAF26 and PAF32 displayed activities against P. digitatum, P. italicum, and B. cinerea similar to that of the hemolytic 26-amino acid melittin, but they did not show the high toxicity of melittin towards bacteria and yeasts. The four peptides acted additively, with no synergistic interactions among them, and PAF26 was shown to have improved activity over PAF19 in in vivo orange fruit decay experiments.
Definition of a Behavior-Driven Model for Requirements Specification and Testing of Interactive Systems (2016)

In a user-centered development process, artifacts are aimed to evolve in iterative cycles until they meet users' requirements and then become the final product. Every cycle gives the opportunity to revise the design and to introduce new requirements which might affect the specification of artifacts that have been set in former development phases. Testing the consistency of multiple artifacts used to develop interactive systems every time that a new requirement is introduced it is a cumbersome and time consuming activity, especially if it should be done manually. For that we propose an approach based on Behavior-Driven Development (BDD) to support the automated assessment of artifacts along the development process of interactive systems. In order to prevent that test should be written to every type of artifact, we investigate the use of ontologies for specifying the test once and then run it in all artifacts sharing the ontological concepts.
P2X7 Receptor-Stimulated Secretion of MHC Class II-Containing Exosomes Requires the ASC/NLRP3 Inflammasome but Is Independent of Caspase-1 (2009)

We recently reported that P2X7 receptor (P2X7R)-induced activation of caspase-1 inflammasomes is accompanied by release of MHC class II (MHC-II) protein into extracellular compartments during brief stimulation of murine macrophages with ATP. Here we demonstrate that MHC-II containing membranes released from macrophages or dendritic cells (DCs) in response to P2X7R stimulation comprise two pools of vesicles with distinct biogenesis: one pool comprises 100- to 600-nm microvesicles derived from direct budding of the plasma membrane, while the second pool is composed of 50- to 80-nm exosomes released from multivesicular bodies. ATP-stimulated release of MHC-II in these membrane fractions is observed within 15 min and results in the export of approximately 15% of the total MHC-II pool within 90 min. ATP did not stimulate MHC-II release in macrophages from P2X7R knockout mice. The inflammasome regulatory proteins, ASC (apoptosis-associated speck-like protein containing a caspase-recruitment domain) and NLRP3 (NLR family, pyrin domain containing 3), which are essential for caspase-1 activation, were also required for the P2X7R-regulated release of the exosome but not the microvesicle MHC-II pool. Treatment of bone marrow-derived macrophages with YVAD-cmk, a peptide inhibitor of caspase-1, also abrogated P2X7R-dependent MHC-II secretion. Surprisingly, however, MHC-II release in response to ATP was intact in caspase-1(-/-) macrophages. The inhibitory actions of YVAD-cmk were mimicked by the pan-caspase inhibitor zVAD-fmk and the serine protease inhibitor TPCK, but not the caspase-3 inhibitor DEVD-cho. These data suggest that the ASC/NLRP3 inflammasome complexes assembled in response to P2X7R activation involve protease effector(s) in addition to caspase-1, and that these proteases may play important roles in regulating the membrane trafficking pathways that control biogenesis and release of MHC-II-containing exosomes.
Work in progress: 252Cf neutron brachytherapy for hemispheric malignant glioma. (1982)

It has been shown that 252Cf neutron brachytherapy of hemispheric malignant glioma can be readily carried out and may be combined with external, whole brain photon beam therapy of 6,000 rad (60 Gy) administered over a five-week to seven-week period. The ten patients who were studied tolerated both procedures well. There was improvement in performance status, and a decrease in tumor size was observed upon computed tomographic scanning.
1971 - J.J.A. Mooij: Aspecten van redelijkheid. Rede uitgesproken bij de aanvaarding van het ambt van gewoon hoogleraar in de analytische wijsbegeerte aan de Rijksuniversiteit te Groningen op dinsdag 11 mei 1971. Groningen, Wolters-Noordhoff (2012)

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Identification of the <scp>l</scp> -Aspartate Transporter in <i>Bacillus subtilis</i> (2003)

YveA of Bacillus subtilis, a putative transporter of the amino acid/polyamine/organocation (APC) superfamily, is shown to mediate uptake of both L-aspartate and L-glutamate as well as having sensitivity to L-aspartate hydroxamate. This 14 TMS protein is the primary aspartate uptake system in B. subtilis and serves as the prototype for a new family within the APC superfamily.
G Protein-Coupled Receptor 43 Is Essential for Neutrophil Recruitment during Intestinal Inflammation (2009)

Molecular danger signals attract neutrophilic granulocytes (polymorphonuclear leukocytes (PMNs)) to sites of infection. The G protein-coupled receptor (GPR) 43 recognizes propionate and butyrate and is abundantly expressed on PMNs. The functional role of GPR43 activation for in vivo orchestration of immune response is unclear. We examined dextrane sodium sulfate (DSS)-induced acute and chronic intestinal inflammatory response in wild-type and Gpr43-deficient mice. The severity of colonic inflammation was assessed by clinical signs, histological scoring, and cytokine production. Chemotaxis of wild-type and Gpr43-deficient PMNs was assessed through transwell cell chemotactic assay. A reduced invasion of PMNs and increased mortality due to septic complications were observed in acute DSS colitis. In chronic DSS colitis, Gpr43(-/-) animals showed diminished PMN intestinal migration, but protection against inflammatory tissue destruction. No significant difference in PMN migration and cytokine secretion was detected in a sterile inflammatory model. Ex vivo experiments show that GPR43-induced migration is dependent on activation of the protein kinase p38alpha, and that this signal acts in cooperation with the chemotactic cytokine keratinocyte chemoattractant. Interestingly, shedding of L-selectin in response to propionate and butyrate was compromised in Gpr43(-/-) mice. These results indicate a critical role for GPR43-mediated recruitment of PMNs in containing intestinal bacterial translocation, yet also emphasize the bipotential role of PMNs in mediating tissue destruction in chronic intestinal inflammation.
High-dose immunosuppressive therapy and autologous peripheral blood stem cell transplantation for severe multiple sclerosis (2003)

There were 26 patients enrolled in a pilot study of high-dose immunosuppressive therapy (HDIT) for severe multiple sclerosis (MS). Median baseline expanded disability status scale (EDSS) was 7.0 (range, 5.0-8.0). HDIT consisted of total body irradiation, cyclophosphamide, and antithymocyte globulin (ATG) and was followed by transplantation of autologous, granulocyte colony-stimulating factor (G-CSF)-mobilized CD34-selected stem cells. Regimen-related toxicities were mild. Because of bladder dysfunction, there were 8 infectious events of the lower urinary tract. One patient died from Epstein-Barr virus (EBV)-related posttransplantation lymphoproliferative disorder (PTLD) associated with a change from horse-derived to rabbit-derived ATG in the HDIT regimen. An engraftment syndrome characterized by noninfectious fever with or without rash developed in 13 of the first 18 patients and was associated in some cases with transient worsening of neurologic symptoms. There were 2 significant adverse neurologic events that occurred, including a flare of MS during mobilization and an episode of irreversible neurologic deterioration after HDIT associated with fever. With a median follow-up of 24 (range, 3-36) months, the Kaplan-Meier estimate of progression (>/= 1.0 point EDSS) at 3 years was 27%. Of 12 patients who had oligoclonal bands in the cerebrospinal fluid at baseline, 9 had persistence after HDIT. After HDIT, 4 patients developed new enhancing lesions on magnetic resonance imaging of the brain. The estimate of survival at 3 years was 91%. Important clinical issues in the use of HDIT and stem cell transplantation for MS were identified; however, modifications of the initial approaches appear to reduce treatment risks. This was a heterogeneous high-risk group, and a phase 3 study is planned to fully assess efficacy.