gebhart/patrepeval huggingface dataset:
Structural Basis for EarP-Mediated Arginine Glycosylation of Translation Elongation Factor EF-P (2017)

Glycosylation is a universal strategy to posttranslationally modify proteins. The recently discovered arginine rhamnosylation activates the polyproline-specific bacterial translation elongation factor EF-P. EF-P is rhamnosylated on arginine 32 by the glycosyltransferase EarP. However, the enzymatic mechanism remains elusive. In the present study, we solved the crystal structure of EarP from <i>Pseudomonas putida</i> The enzyme is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B). While dTDP-β-l-rhamnose is located within a highly conserved pocket of the C-domain, EarP recognizes the KOW-like N-domain of EF-P. Based on our data, we propose a structural model for arginine glycosylation by EarP. As EarP is essential for pathogenicity in <i>P. aeruginosa</i>, our study provides the basis for targeted inhibitor design.<b>IMPORTANCE</b> The structural and biochemical characterization of the EF-P-specific rhamnosyltransferase EarP not only provides the first molecular insights into arginine glycosylation but also lays the basis for targeted-inhibitor design against <i>Pseudomonas aeruginosa</i> infection.
Building a Foundation System for Producing Short Answers to Factual Questions. (2002)

In this paper we describe question answering research being pursued as a joint project between Columbia University and the University of Colorado at Boulder as part of ARDA&apos;s AQUAINT program. As a foundation for targeting complex questions involving opinions, events, and paragraph-length answers, we recently built two systems for answering short factual questions. We submitted results from the two systems to TREC&apos;s Q&amp;A track, and the bulk of this paper describes the methods used in building each system and the results obtained. We conclude by discussing current work aiming at combining modules from the two systems in a unified, more accurate system and adding capabilities for producing complex answers in addition to short ones.
Sputter etching mechanism and changes of surface structure of PTFE (1993)

Abstract Growth of microscopic cones on PTFE surface by RF sputter etching process are studied. The surface texm changes from initial submicron hillocks to large cones during sputter etching. The height of these cones is 33 to 45 percent of the etching depth calculated from etching rate. The direction of these cones is nearly equal to the ion incident angle. Boundary energy of sputtering and growth of cones are 100 eV and 150 eV, respectively. It is obtained that the redeposition ratio by back diffusion to sputtered molecule is 11 percent from the experiment using collector. It is concluded that redeposition and repolymerization process of sputtered material occurs in parallel with the ion etching process, and cones continue to grow partly during etching.
Classification of colon polyps in NBI endoscopy using vascularization features (2009)

The evolution of colon cancer starts with colon polyps. There are two different types of colon polyps, namely hyperplasias and adenomas. Hyperplasias are benign polyps which are known not to evolve into cancer and, therefore, do not need to be removed. By contrast, adenomas have a strong tendency to become malignant. Therefore, they have to be removed immediately via polypectomy. For this reason, a method to differentiate reliably adenomas from hyperplasias during a preventive medical endoscopy of the colon (colonoscopy) is highly desirable. A recent study has shown that it is possible to distinguish both types of polyps visually by means of their vascularization. Adenomas exhibit a large amount of blood vessel capillaries on their surface whereas hyperplasias show only few of them. In this paper, we show the feasibility of computer-based classification of colon polyps using vascularization features. The proposed classification algorithm consists of several steps: For the critical part of vessel segmentation, we implemented and compared two segmentation algorithms. After a skeletonization of the detected blood vessel candidates, we used the results as seed points for the Fast Marching algorithm which is used to segment the whole vessel lumen. Subsequently, features are computed from this segmentation which are then used to classify the polyps. In leave-one-out tests on our polyp database (56 polyps), we achieve a correct classification rate of approximately 90%.
Rapid on-chip genetic detection microfluidic platform for real world applications (2009)

The development of genetic detection protocols for field applications is an important aspect of modern medical diagnostic technology and environmental monitoring. In this paper, we report a rapid, portable, and inexpensive DNA hybridization technique using a bead-based microfluidic platform that functions by passing fluorescently labeled target DNA through a chamber packed with functionalized beads within a microfluidic channel. DNA hybridization is then assessed using a digital camera attached to a Clare Chemical DR-45M dark reader non-UV transilluminator that uses visible light as an excitation source and a blue and amber filter to reveal fluorescence. This microfluidic approach significantly enhances hybridization by reducing the diffusion time between target DNA and the silica surface. The use of probe-functionalized beads as solid support also enhances the sensitivity and limit of detection due to a larger surface area per unit volume. This platform could be adapted for use in medical applications and environmental monitoring, including the detection of harmful organisms in the ballast water of ships.
Development of a Structural Model for NF-κB Inhibition of Sesquiterpene Lactones Using Self-Organizing Neural Networks (2006)

A variety of sesquiterpene lactones (SLs) possess considerable anti-inflammatory activity. Several studies have shown that they exert this effect in part by inhibiting the activation of the transcription factor NF-κB. In the present study we elaborated on the investigation of a data set of 103 structurally diverse SLs for which we had previously developed several different QSAR equations dependent on the skeletal type. Use of 3D structure descriptors resulted in a single model for the entire data set. In particular, local radial distribution functions (L-RDF) were used that centered on the methylene−carbonyl substructure believed to be the site of attack of cysteine-38 of the p65/NF-κB subunit. The model was developed by using a counterpropagation neural network (CPGNN), attesting to the power of this method for establishing structure−activity-relationships. The investigations shed more light onto the influence of the chemical structure on NF-κB inhibitory activity.
Simultaneous Raman Spectroscopy and Electrochemical Studies of Corrosion Inhibiting Molecules on Copper (1985)

Surface‐enhanced Raman scattering (SERS) has been used as a complementary in situ technique for electrochemical measurements in order to investigate five structurally related N‐heterocyclic molecules on copper. Their different abilities to act as corrosion inhibitors are discussed in view of structural information obtained from SERS. It is concluded that the molecules investigated do not dissociate upon adsorption and that different functional groups result in different orientation of the adsorbed molecules on copper.
Alkylation of 3-Ethyl-2-methyl-4-oxo-4,5,6,7-tetrahydroindole with Bromoesters: Benzenesulfonyl as Convenient Nitrogen Protecting Group (1992)

a-Alkylation of 3 -e t h y l -2 -m e l h y l -4 -o l l o -l H 4 , 5 , 6 , 7 -t ~i d o l e (3) with bromoesters gives 3 -e t h y l -2 -m e t h y l -4 -a x o -I H 4 , 5 , 6 , 7 -t e l ~ (Sa), 3e t h y l -2 -m e t h y l 4 -o x o -I H 4 , 5 , 6 , 7 -t e t r a h y ~p i o n a t e (Sb), and 3-ethyl-2-methyl4-oxo-1H4,5.6,7-tetr~ydro-5-indol-3-ppiae(6).As part of our researchlJ on the synthesis and pharmacology of analogues of the well established antipsychotics molindone (l)3 and piquindone (2),4 we have investigated the preparation of 2-methyl-3-ethyl4axo4,5.6,7tetrabydmindoleacetic and propionic acids (7a, 7b and 8) by nlkylation of the carbanion of the 4motetrahydroindole
A Coordination Theory Approach to Organizational Process Design (1997)

An important practical problem for many managers is finding alternative processes for performing a desired task, for example, one that is more efficient, cheaper, or that is automated or enhanced by the use of information technology. Improving processes also poses theoretical challenges. Coordination theory provides an approach to the study of processes. In this view, the design of a process depends on the coordination mechanisms chosen to manage dependencies among tasks and resources involved in the process. In this paper, I use coordination theory to analyze the software change process of a large mini-computer manufacturer. Mechanisms analyzed include those for task assignment, resource sharing, and managing dependencies between modules of source code. For each, I suggest alternative mechanisms and thus alternative designs for the process. The organization assigned problem reports to engineers based on the module that appeared to be in error, since engineers only worked on particular modules. Alternative task assignment mechanisms include assignment to engineers based on workload or market-like bids. Modules of source code were not shared, but rather “owned” by one engineer, thus reducing the need for coordination. An alternative resource sharing mechanism would be needed to manage source code if multiple engineers could work on the same modules. Finally, engineers managed dependencies between modules informally, relying on their personal knowledge of which other engineers used their code; alternatives include formally defining the interfaces between modules and tracking their users. Software bug fixing provides a microcosm of coordination problems and solutions. Similar coordination problems arise in most processes and are managed by a similar range of mechanisms. For example, diagnosing bug reports and assigning them to engineers may have interesting parallels to diagnosing patients and assigning them to specialists. While the case presented does not formally test coordination theory, it does illustrate the potential of coordination theory for exploring the space of organizational processes. Future work includes developing more rigorous techniques for such analyses, applying the techniques to a broader range of processes, identifying additional coordination problems and mechanisms and developing tools for collecting and comparing processes and automatically suggesting potential alternatives.
Mapping Adverse Drug Reactions in Chemical Space (2009)

We present a novel method to better investigate adverse drug reactions in chemical space. By integrating data sources about adverse drug reactions of drugs with an established cheminformatics modeling method, we generate a data set that is then visualized with a systems biology tool. Thereby new insights into undesired drug effects are gained. In this work, we present a global analysis linking chemical features to adverse drug reactions.
Defragmentation of Resources in Virtual Desktop Clouds for Cost-Aware Utility-Optimal Allocation (2011)

Cloud Service Providers (CSPs) make virtual desktop cloud (VDC) resource provisioning decisions within desktop pools based on user groups and their application profiles. Such provisioning is aimed to satisfy acceptable user quality of experience (QoE) levels and is coupled with subsequent placement of VDs across distributed data centers. The placement decisions are influenced by session latency, load balancing and operation cost constraints. In this paper, we identify the resource fragmentation problem that occurs when placement is done opportunistically to minimize provisioning time and deliver satisfactory user QoE. To solve this problem, which inherently is an NP-Hard problem, we propose a defragmentation scheme that has fast convergence time and has three levels of complexity: (i) "utility fair provisioning" (UFP) to optimize resource provisioning within a data center - to achieve relative fairness between desktop pools, (ii) "static migration-free utility optimal placement and provisioning" (MUPP) to optimize resource provisioning between multiple data centers - to improve performance, and (iii) "dynamic global utility optimal placement and provisioning" (GUPP) to optimize resource provisioning using cost-aware and utility-maximal VD re-allocations and migrations - to increase scalability. We evaluate our defragmentation scheme against 'least latency', 'least load', and 'least cost' schemes using a novel "VDC-Sim" simulator that we have developed in this study. Our simulations leverage profiles of user groups and their applications within desktop pools, obtained from a real VDC test bed. Our simulation results demonstrate that defragmentation is an important optimization step that can enable CSPs to achieve fairness, substantially improve user QoE and increase VDC scalability.
Complex hydrophone calibrations using pseudo-Gaussian noise signals (1977)

A computer-based hydrophone calibration system has been developed for the measurement of complex receiving sensitivity over a wide frequency band in an open water acoustic tank. A pseudo-Gaussian number sequence is generated for transmission into the tank via a digital-to-analog coverter, filter, power amplifier and wide-band projector. A cross spectral analysis is performed between the sampled hydrophone output and the corresponding number sequence, averaging over several independent noise records. This process is carried out both for the “unknown” hydrophone and a “standard” hydrophone using the same pseudo-Gaussian noise records and the same hydrophone position in the noise field. The amplitude and phase response of the unknown is calculated relative to the standard, which may be one hydrophone of a group to be calibrated or may be a calibrated reference standard. The system is usable over the frequency range 20–9000 Hz.
Antibodies from patients with heparin-induced thrombocytopenia stimulate monocytic cells to express tissue factor and secrete interleukin-8 (2001)

Thrombosis is a life-threatening complication that occurs in a subset of patients with heparin-induced thrombocytopenia (HITT). The pathogenic mechanisms underlying the variable occurrence of thrombosis in HITT is poorly understood. It was hypothesized that monocyte activation leading to tissue factor expression may play a role in promoting a thrombogenic state in HITT. This study demonstrates that a human platelet factor 4 (PF4)/heparin-specific murine monoclonal antibody (KKO) binds to peripheral blood-derived human monocytes in a PF4-dependent manner. KKO and antibodies from patients with HITT induce monocytes to synthesize and secrete interleukin-8 and induce cell-surface procoagulant activity, which is abrogated following treatment with antihuman tissue factor antibody. The findings suggest a novel mechanism by which PF4/heparin antibodies may promote a hypercoagulable state in patients with HITT. (Blood. 2001;98:1252-1254)
High-Resolution <sup>19</sup>F MAS NMR Spectroscopy of Fluorocarbon Films from Pulsed PECVD of Hexafluoropropylene Oxide (1998)

Magic angle sample spinning with speeds of up to 25 kHz has been applied to obtain high-resolution solid-state 19F NMR spectra of fluorocarbon films deposited by pulsed plasma-enhanced chemical vapor deposition (PECVD) from hexafluoropropylene oxide. Compared to XPS, the common characterization method for fluorocarbon thin-film analysis, 19F NMR is demonstrated to provide greater structural information which is important in unraveling the complexity of plasma films. Seven fluorocarbon resonancesthree CF3 sequences, three CF2 sequences, and a CF resonancewere distinguished, based on differences in next nearest-neighbor bonding environment. Total CFx (x = 1−3) fractions, as quantified by NMR, agreed with independent XPS results. Line width variation of the assigned resonances resulted from isotropic shift dispersion, arising from connectivity permutation statistics and from the relative mobility of fluorocarbon moieties, which can be hindered by cross-links or branch junctions. With lower pulsed plasma deposition duty cycles, resulting films contained more linear CF2 chains. Cross-linking, branching, and irregular chain terminations, arising from plasma ion bombardment and excessive gas-phase fragmentation during film growth, are reduced. The thermal decomposition mechanism shifted from a loss of CF3 end groups to a loss of linear chain fragments as a result of changes in film structure with longer deposition pulse off-time. There is evidence to indicate thermal desorption of oligomers or radical-enhanced depolymerization for films deposited at lower duty cycles.
CD86 (B70/B7–2) on endothelial cells co-stimulates allogeneic CD4<sup>+</sup>T cells (1995)

In vascularized organ transplantation, vascular endothelial cells (EC) confronting recipient T cells are potentially significant APC initiating cellular immune responses that lead to rejection. In the present study, we studied the ability of human EC to stimulate allogeneic T cells and the co-stimulatory molecules involved in this response. On both human umbilical vein endothelial cells (HUVEC) and microvascular endothelial cells (MVEC), MHC class I, intercellular adhesion molecule (ICAM)-1 and CD86 were constitutively expressed as assessed by flow cytometry. After IFN-gamma treatment, MHC class II expression was induced, and MHC class I and ICAM-1 were up-regulated. In contrast, the expression of CD86 was unchanged and CD80 was undetectable even after IFN-gamma treatment. Highly purified CD4+ T cells proliferated in response to IFN-gamma-treated allogeneic HUVEC and MVEC, and this response was efficiently blocked by mAb to MHC class II, ICAM-1 and CD86. Furthermore, the addition of anti-CD86 mAb to the primary culture with allogeneic EC resulted in the induction of alloantigen-specific anergy. These results suggest that CD86 expressed on EC plays a critical role in initiating cellular immune responses to vascularized allografts and would be an important target for immune intervention.
The Accessory Genome of <i>Pseudomonas aeruginosa</i> (2010)

Pseudomonas aeruginosa strains exhibit significant variability in pathogenicity and ecological flexibility. Such interstrain differences reflect the dynamic nature of the P. aeruginosa genome, which is composed of a relatively invariable "core genome" and a highly variable "accessory genome." Here we review the major classes of genetic elements comprising the P. aeruginosa accessory genome and highlight emerging themes in the acquisition and functional importance of these elements. Although the precise phenotypes endowed by the majority of the P. aeruginosa accessory genome have yet to be determined, rapid progress is being made, and a clearer understanding of the role of the P. aeruginosa accessory genome in ecology and infection is emerging.
A pre-run-time scheduling algorithm for object-based distributed real-time systems (2002)

The most important goal in hard real-time systems is to guarantee that all timing constraints are satisfied. Even though object-based techniques (which contain reusable software components) are used to manage the complexity in the software development process of such systems, execution efficiency may have to be sacrificed, due to the large number of procedure calls and contention for accessing software components. These issues are addressed by the following parallelizing techniques: converting potentially inefficient procedure calls to a source of concurrency via asynchronous remote procedure calls (ARPC); and replicating (or cloning) software components to reduce the contention. The existing object-based scheduling algorithms construct an initial schedule and apply incremental parallelization techniques to modify the initial schedule until a feasible schedule is generated. These algorithms are applicable for scheduling only multiple independent tasks. This paper describes a pre-run-time scheduling algorithm for a set of periodic object-based tasks having precedence constraints among them. The algorithm employs parallelism exploitation techniques to guarantee timeliness in almost fully predictable environments such as factory automation, aerospace, and avionics. It allocates the components of object-based periodic tasks to the sites of a distributed system based on a clustering heuristic which takes into account the ARPC parallelism and load balancing, and schedules them on respective sites.
Common domain structure of Ca<sup>2+</sup> and lipid‐binding proteins (1986)

The phospholipase A2 inhibitor, lipocortin, shares common sequences with three abundant Ca2+-regulated membrane binding proteins of unknown function which are present in many cell and tissue types. A two-domain model for the structure of lipocortin is described and it is suggested that the new Ca2+-regulated proteins each contain at least one lipocortin domain. The structural and biochemical properties of each protein indicate that they all directly interact with phospholipids. Potential sites of interaction with the lipocortin domain are identified on the basis of homology with phospholipid transfer proteins and phospholipase A2.
Electromagnetic stirring in zone refining (1958)

The efficiency of the zone refining process can obviously be increased by stirring the molten zone to disperse the impurity-rich layer at the solid- liquid surface. Induction heating is sometimes preferred to radiant heat because it produces more convection, but no marked improvement has been reported. Pfann and Dorsi(1967) have described a method of stirring the melt by passing an electric current through the ingot and compressing a magnetic field across the molten zone. Preliminary results obtained by using a rotating magnetic field us the stirring agent during the purification of aluminum are described. (A.C.)
External cavity diode laser based upon an FBG in an integrated optical fiber platform (2016)

An external cavity diode laser is demonstrated using a Bragg grating written into a novel integrated optical fiber platform as the external cavity. The cavity is fabricated using flame-hydrolysis deposition to bond a photosensitive fiber to a silica-on-silicon wafer, and a grating written using direct UV-writing. The laser operates on a single mode at the acetylene P13 line (1532.83 nm) with 9 mW output power. The noise properties of the laser are characterized demonstrating low linewidth operation (< 14 kHz) and superior relative intensity noise characteristics when compared to a commercial tunable external cavity diode laser.
Development of an advanced dimensionally stable separator for rechargeable lithium-metal disulfide batteries (2003)

A unique separator which is AlN powder prefused to impart dimensional stability has been developed. Cell and battery design is based upon a bipolar configuration. Test samples each having 20-cm/sup 2/ area and having several porosities as well as highly uniform 200-cm/sup 2/ separators have been fabricated. Extensive pulse discharge characterization of the 20-cm/sup 2/ separators has verified excellent cycle life along with maintenance of dimensional stability over both time and deep discharge cycling, and complete inertness to the operating environment. Another added benefit is the separator structure's high thermal conductivity to aid with the thermal management of sealed modules. The physical and handling characteristics of these separators, pulse discharge and cycle data including comparisons to the standard MgO powder separator, and the status of the incorporation of the full size separators into bipolar modules are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>