gebhart/patrepeval huggingface dataset:
An inducible lambdoid prophage encoding cytolethal distending toxin (Cdt-I) and a type III effector protein in enteropathogenic <i>Escherichia coli</i> (2007)

Cytolethal distending toxins (CDTs) are inhibitory cyclomodulins, which block eukaryotic cell proliferation and are produced by a diverse group of Gram-negative bacteria, including Escherichia coli strains associated with intestinal and extraintestinal infections. However, the mode of transmission of the toxin gene clusters among diverse bacterial pathogens is unclear. We found that Cdt-I produced by enteropathogenic E. coli strains associated with diarrhea is encoded by a lambdoid prophage, which is inducible and infectious. The genome of Cdt-I converting phage (CDT-1Phi) comprises 47,021 nucleotides with 60 predicted ORFs organized into six genomic regions encoding the head and tail, virulence, integrase, unknown functions, regulation, and lysis. The genomic organization of CDT-1Phi is similar to those of SfV, a serotype-converting phage of Shigella flexneri, and UTI89, a prophage identified in uropathogenic E. coli. Besides the cdtI gene cluster, the virulence region of CDT-1Phi genome contains sequences homologous to a truncated cycle inhibiting factor and a type 3 effector protein. Mutation analysis of susceptible E. coli strain C600 suggested that the outer membrane protein OmpC is a putative receptor for CDT-1Phi. CDT-1Phi genome was also found to integrate into the host bacterial chromosome forming lysogens, which produced biologically active Cdt-I. Furthermore, phage induction appeared to cause enhanced toxigenicity of the E. coli strains carrying lysogenic CDT-1Phi. Our results suggest that CDT-1Phi is the latest member of a growing family of lambdoid phages encoding bacterial cyclomodulins and that the phage may have a role in horizontal transfer of these virulence genes.
Parallax Player: a stereoscopic format converter (2003)

The Parallax Player is a software application that is, in essence, a stereoscopic format converter. Various formats may be inputted and outputted. In addition to being able to take any one of a wide variety of different formats and play them back on many different kinds of PCs and display screens. The Parallax Player has built into it the capability to produce ersatz stereo from a planar still or movie image. The player handles two basic forms of digital content - still images, and movies. It is assumed that all data is digital, either created by means of a photographic film process and later digitized, or directly captured or authored in a digital form. In its current implementation, running on a number of Windows Operating Systems, The Parallax Player reads in a broad selection of contemporary file formats.
Impedance-controlled ultrasound probe (2011)

An actuated hand-held impedance-controlled ultrasound probe has been developed. The controller maintains a prescribed contact state (force and velocity) between the probe and a patient's body. The device will enhance the diagnostic capability of free-hand elastography and swept-force compound imaging, and also make it easier for a technician to acquire repeatable (i.e. directly comparable) images over time. The mechanical system consists of an ultrasound probe, ball-screw-driven linear actuator, and a force/torque sensor. The feedback controller commands the motor to rotate the ball-screw to translate the ultrasound probe in order to maintain a desired contact force. It was found that users of the device, with the control system engaged, maintain a constant contact force with 15 times less variation than without the controller engaged. The system was used to determine the elastic properties of soft tissue.
Catalytic Hot-Gas Filtration with a Supported Heteropolyacid Catalyst for Preconditioning Biomass Pyrolysis Vapors (2019)

During ex situ catalytic fast pyrolysis (CFP) of biomass, the separation of reactive char and alkali/alkaline particulates from biomass pyrolysis vapors by hot-gas filtration (HGF) leads to improved vapor stability and quality. HGF in tandem with chemical tailoring (e.g., partial deoxygenation) of the clean pyrolysis vapors, denoted as catalytic hot-gas filtration (CHGF), has the potential to further improve vapor composition by removing reactive oxygen moieties and protect downstream upgrading catalysts from fouling. Downstream upgrading refers to both vapor phase upgrading (e.g., ex situ CFP) and condensed phase upgrading (e.g., hydrotreating). Consequently, CHGF (as a single unit operation) was evaluated for preconditioning pyrolysis vapors for downstream upgrading processes. In order to understand the effective operating conditions that successfully filter and partially deoxygenate pyrolysis vapors, a titania-supported molybdenum heteropolyacid (Mo-HPA/TiO2) catalyst was studied for use in CHGF. Here, pine pyrolysis vapors were generated in a small pilot-scale pyrolyzer and transferred to a CHGF unit via a continuous-flow slipstream. In the CHGF unit, the pyrolysis vapors were filtered and upgraded over a packed Mo-HPA/TiO2 catalyst bed. Real-time monitoring and identification of the products formed were achieved by molecular beam mass spectrometry. The results showed that under a hydrogen-rich environment, the pine vapors were partially deoxygenated and alkylated over the Mo-HPA/TiO2 catalyst. Reactivity studies revealed that an increase in hydrogen concentration and a reduction in weight-hourly space velocity enhanced deoxygenation and alkylation. Time-on-stream (TOS) studies showed stable product formation up to 1 h with little change in catalyst activity. Additionally, the liquid product was collected using a custom fractional condensation unit (built in-house) and analyzed by gas chromatography mass spectrometry to confirm that the product was partially deoxygenated and alkylated. The combination of CHGF and fractional condensation allowed for chemical and physical removal of both foulant and value-added compounds (e.g., phenols, alkylphenols, methoxyphenols, cyclopentenones) for additional enhancement of downstream upgrading processes. The pre- and postreaction catalysts were characterized using temperature-programmed desorption, N2 physisorption, and elemental analysis with results indicating some catalyst coking. A hydrogen-based catalyst regeneration procedure restored the reacted catalyst activity to that of fresh Mo-HPA/TiO2.
Surface modification of neural stimulating/recording electrodes with high surface area platinum-iridium alloy coatings (2011)

High-surface area platinum-iridium alloys were electrodeposited by on Pt and Au microelectrodes using a potential sweep technique. Detailed investigations of the structure and morphology and the electrochemical properties of the electrodeposited Pt-Ir alloy coatings were performed. Scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) were used for the determination of the surface morphology and the chemical composition of the Pt-Ir coatings, respectively. The elemental analysis by EDS showed a nearly 60-40% Pt-Ir composition of the coatings. The electrochemical properties of the Pt-Ir coatings were evaluated using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). CV and EIS measurements revealed that the Pt-Ir coated electrodes exhibit significantly increased charge storage capacity and real surface area compared to uncoated Pt electrodes. Charge injection experiments of the Pt-Ir coated microelectrodes revealed low potential excursions, indicating high charge injection capabilities within safe potential limits.
Well-Defined, Model Long Chain Branched Polyethylene. 1. Synthesis and Characterization (2000)

We describe the synthesis and characterization of a number of polymers with well-defined structures that serve as models for polyethylene with long chain branching. All of them have been made by using anionic polymerization techniques and controlled chlorosilane chemistry to give nearly monodisperse polybutadienes with precise control of the number, length, and placement of long (M̄w > 1500 g/mol) branches on each chain. This was followed by hydrogenation to give saturated polymers with the same well-defined long chain branching and the local structure of a typical linear low-density polyethylene. That is, both the backbones and the long branches had 17−25 ethyl branches per 1000 total carbons. Among the structures made were some with no long branches (“linears”), some with a single long branch (“stars”), others with exactly two branch points (the α−ω type, “H's”, “super-H's”, and “pom-poms”), and some with several long branches randomly distributed along the backbone (“combs”). Essentially all types of branching from a linear backbone can be made by the techniques described herein. While linear and symmetrical star models of polyethylene have been made previously, the other structures are the first examples of polyethylene models with multiple branches and precise control of the molecular architecture. We use the results given here to discuss how long chain branching can be detected in polyethylene. We also show how the branching structure controls chain dimensions. The Zimm−Stockmayer model works well to describe the sizes of the lightly branched molecules, but its predictions are too small for those with many long branches. This is presumably due to crowding of the branches. The rheological properties of these polymers will be described in subsequent publications.
Rhesus Macaque Theta Defensins Suppress Inflammatory Cytokines and Enhance Survival in Mouse Models of Bacteremic Sepsis (2012)

Theta-defensins (θ-defensins) are macrocyclic antimicrobial peptides expressed in leukocytes of Old World monkeys. The peptides are broad spectrum microbicides in vitro and numerous θ-defensin isoforms have been identified in granulocytes of rhesus macaques and Olive baboons. Several mammalian α- and β-defensins, genetically related to θ-defensins, have proinflammatory and immune-activating properties that bridge innate and acquired immunity. In the current study we analyzed the immunoregulatory properties of rhesus θ-defensins 1-5 (RTDs 1-5). RTD-1, the most abundant θ-defensin in macaques, reduced the levels of TNF, IL-1α, IL-1β, IL-6, and IL-8 secreted by blood leukocytes stimulated by several TLR agonists. RTDs 1-5 suppressed levels of soluble TNF released by bacteria- or LPS-stimulated blood leukocytes and THP-1 monocytes. Despite their highly conserved conformation and amino acid sequences, the anti-TNF activities of RTDs 1-5 varied by as much as 10-fold. Systemically administered RTD-1 was non-toxic for BALB/c mice, and escalating intravenous doses were well tolerated and non-immunogenic in adult chimpanzees. The peptide was highly stable in serum and plasma. Single dose administration of RTD-1 at 5 mg/kg significantly improved survival of BALB/c mice with E. coli peritonitis and cecal ligation-and-puncture induced polymicrobial sepsis. Peptide treatment reduced serum levels of several inflammatory cytokines/chemokines in bacteremic animals. Collectively, these results indicate that the anti-inflammatory properties of θ-defensins in vitro and in vivo are mediated by the suppression of numerous proinflammatory cytokines and blockade of TNF release may be a primary effect.
A Sensitivity-Based Pattern Search Algorithm for 3D Component Layout (2002)

This paper introduces the Sensitivity-based Pattern Search (SPS) algorithm for 3D component layout. Although based on the pattern search algorithm, SPS differs in that at any given step size the algorithm does not necessarily perturb the search space along all possible search dimensions. Instead all possible perturbations, or moves are ranked in decreasing order of their effect on the objective function and are applied in that order. The philosophy behind this algorithm is that moves that affect the objective function more must be applied before the moves that affect the objective function less. We call this effect on the objective function the sensitivity of the objective function to a particular move and present a simple method to quantify it. This algorithm performs better than the previous Extended Pattern Search algorithm with decrease in run time of up to 28%.
Algorithmic modeling of TES processes (1995)

TES (transform-expand-sample) is a versatile class of stationary stochastic processes which can model arbitrary marginals, a wide variety of autocorrelation functions, and a broad range of sample path behaviors. TES parameters are of two kinds: the first kind is used for the exact fitting of the empirical distribution (histogram), while the second kind is used for approximating the empirical autocorrelation function. Parameters of the first kind are easy to determine algorithmically, but those of the second kind require a hard heuristic search on a large parametric function space. This paper describes an algorithmic procedure which can replace the heuristic search, thereby largely automating TES modeling. The algorithm is cast in nonlinear programming setting with the objective of minimizing a weighted sum of squared differences between the empirical autocorrelations and their candidate TES model counterparts. It combines a brute-forte search with steepest-descent nonlinear programming using Zoutendijk's feasible direction method. Finally, we illustrate the efficacy of our approach via three examples: two from the domain of VBR (variable bit rate) compressed video and one representing results from a laser intensity experiment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Janus Kinase 2 Inhibitors. Synthesis and Characterization of a Novel Polycyclic Azaindole (2009)

The synthesis and characterization of a novel polycyclic azaindole based derivative is disclosed, and its binding to JAK2 is described. The compound is further evaluated for its ability to block the EPO/JAK2 signaling cascade in vitro and in vivo.
Alternating phase-shifting masks: phase determination and impact of quartz defects--theoretical and experimental results (2002)

In optical lithography balancing the aerial image of an alternating phase shifting mask (alt. PSM) is a major challenge. For the exposure wavelengths (currently 248nm and 193nm) an optimum etching method is necessary to overcome imbalance effects. Defects play an important role in the imbalances of the aerial image. In this contribution defects will be discussed by using the methodology of global phase imbalance control also for local imbalances which are a result of quartz defects. The effective phase error can be determined with an AIMS-system by measuring the CD width between the images of deep- and shallow trenches at different focus settings. The AIMS results are analyzed in comparison to the simulated and lithographic print results of the alternating structures. For the analysis of local aerial image imbalances it is necessary to investigate the capability of detecting these phase defects with state of the art inspection systems. Alternating PSMs containing programmed defects were inspected with different algorithms to investigate the capture rate of special phase defects in dependence on the defect size. Besides inspection also repair of phase defects is an important task. In this contribution we show the effect of repair on the optical behavior of phase defects. Due to the limited accuracy of the repair tools the repaired area still shows a certain local phase error. This error can be caused either by residual quartz material or a substrate damage. The influence of such repair induced phase errors on the aerial image were investigated.
Terahertz-Range Weak Reflection Fiber Optic Structures for Sensing Applications (2016)

This paper describes a series of terahertz-range weak reflection fiber optic structures engineered for distributed temperature and strain sensing applications. Four specific structures are described: an intrinsic Fabry-Perot interferometer, a terahertz-range fiber Bragg grating, a phase-shifted terahertz-range fiber Bragg grating, and a terahertz-range fiber Bragg grating fabricated with an intact optical fiber buffer coating. All four structures were fabricated using a femtosecond laser micromachining system, which inscribed the structures within the core of a single-mode silica optical fiber. Interrogation technique, signal processing, fabrication method, and experimental investigation of each structure are described. The results presented demonstrate that these structures specifically, and terahertz-range optical fiber sensors more generally, hold substantial utility as methods of distributed temperature and strain sensing.
Frequency-Domain Optical Tomographic Imaging of Arthritic Finger Joints (2011)

We are presenting data from the largest clinical trial on optical tomographic imaging of finger joints to date. Overall we evaluated 99 fingers of patients affected by rheumatoid arthritis (RA) and 120 fingers from healthy volunteers. Using frequency-domain imaging techniques we show that sensitivities and specificities of 0.85 and higher can be achieved in detecting RA. This is accomplished by deriving multiple optical parameters from the optical tomographic images and combining them for the statistical analysis. Parameters derived from the scattering coefficient perform slightly better than absorption derived parameters. Furthermore we found that data obtained at 600 MHz leads to better classification results than data obtained at 0 or 300 MHz.
Deposition of diamondlike films by electron cyclotron resonance microwave plasmas (1990)

Hard a-C:H films have been deposited through electron cyclotron resonance (ECR) microwave plasma decomposition of CH4 diluted with H2 gas. It has been found that hard diamondlike films could only be produced under a rf-induced negative self-bias of the substrate stage. Raman spectra indicate the deposition of two distinct film types: one film type exhibiting well-defined bands at 1360 and 1580 cm−1 (the graphitic D and G bands) and another displaying a broad Raman peak centered at approximately 1500 cm−1. The optical gaps of these films are from 1.0 to 1.6 eV, respectively, with resistivities &gt;1012 Ω cm. Variation of the mirror magnetic-field profile of the ECR system was examined, demonstrating the manipulation of film morphology through the extraction of different ion energies.
Evidence That Sea State Bias is Different for Ascending and Descending Tracks (2004)

Jason-1 and TOPEX/Poseidon (T/P) measured sea-surface heights (SSHs) are compared for five regions during the verification tandem phase. The five regions are of similar latitude and spatial extent and include the Gulf of Mexico, Arabian Sea, Bay of Bengal, and locations in the Pacific and Atlantic Oceans away from land. In all five regions, a bias, defined as Jason SSH—TOPEX-B SSH, exists that is different for ascending and descending tracks. For example, in the Gulf of Mexico the bias for ascending tracks was −0.13 cm and the bias for descending tracks was 2.19 cm. In the Arabian Sea the bias for ascending tracks was −2.45 cm and the bias for descending tracks was −1.31 cm. The bias was found to depend on track orientation and significant wave height (SWH), indicating an error in the sea state bias (SSB) model for one or both altimeters. The bias in all five regions can be significantly reduced by calculating separate corrections for ascending and descending tracks in each region as a function of SWH. The correction is calculated by fitting a second-order polynomial to the bias as a function of SWH separately for ascending and descending tracks. An additional constraint is required to properly apply the correction, and we chose to minimize the sum of the TOPEX-B and Jason-1 root-mean-square (rms) crossover differences to be consistent with present SSB models. Application of this constraint shows that the correction, though consistent within each region, is different for each region and that each satellite contributes to the bias. One potential source that may account for a portion of the difference in bias is the leakage in the wave forms in TOPEX-B due to differing altitude rates for ascending and descending tracks. Global SSB models could be improved by separating the tracks into ascenders and descenders and calculating a separate SSB model for each track.
Expanding the molecular recognition repertoire of antifreeze polypeptides: effects on nucleoside crystal growth (2012)

Despite differences in the crystal structures of ice and nucleosides, antifreeze polypeptides (AFPs) have been demonstrated to inhibit nucleation of 5-methyluridine, cytidine, and inosine and modify the crystal growth of the nucleosides efficiently. The molecular recognition repertoire of AFPs has been expanded to non-ice-like crystalline solids.
An Approach to Flux Control of Induction Motors Operated with Variable-Frequency Power Supply (1980)

A new speed control system for induction motors has been developed which is capable of controlling with quick field weakening and superior response and stability. This method is to control the stator current as a vector quantity on the basis of slip frequency control. More specifically, it is designed to calculate the commanded stator current of the induction motor by corresponding to flux and torque commands on the basis of motor constants and use the calculated commands to control the stator current.
A Fluorescent Lamp with Integral Proximity Sensor for Building Energy Management (2007)

We have developed a proximity sensor that can be integrated with a fluorescent lamp ballast. This sensor measures disturbances in the electric field around the lamp in order to detect the presence and motion of people. Range test data from our preliminary experiments showed detection ranges of 11 ft. between the lamp and the closest edge of a human target. The detector enables fine-grain occupancy measurements in spaces, promising to improve energy efficiency by reducing wasted lighting of unoccupied spaces.
Syntheses of 23-deoxy-23-N-ethyl-23-(2-fluoro-, 2,2-difluoro-, and 2,2,2-trifluoroethyl)amino derivatives of mycaminosyl tylonolide and 4'-deoxymycaminosyl tylonolide. (1984)

Derivatives of mycaminosyl tylonolide (1) and 4'-deoxymycaminosyl tylonolide (2) containing N-ethyl-2-fluoro-, 2,2-difluoro- and 2,2,2-trifluoroethylamino groups at their C-23 have been prepared by treating 23-deoxy-23-ethylaminomycaminosyl tylonolide diethyl acetal (14) and its 4'-deoxy analog 15 with 2-fluoro-, 2,2-difluoro- and 2,2,2-trifluoroethyl trifluoromethanesulfonates. The relationship between the antibacterial activity and the numbers of the fluorine atoms introduced in the final products is discussed.
Bi-directional gas pump driven by a thermoelectric material (2010)

The paper describes the first use of a thermoelectric material to create a thermally driven, bi-directional pump with no moving parts using the thermal transpiration effect (called a Knudsen pump). The use of a thermoelectric material to create the temperature gradient increases the efficiency of the pump and enables the design of a bi-directional pump. Pumps using thermal transpiration reported in earlier publications were all uni-directional. This pump achieves high flow rates in both directions, is easy to fabricate, and generates a continuous pneumatic pressure. The measured pump efficiency, 0.035 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> /min/W, is the highest reported to date for a Knudsen pump.
Priming with intranasal lactobacilli prevents Pseudomonas aeruginosa acute pneumonia in mice (2021)

These results demonstrate that intranasal priming with lactobacilli acts as a prophylaxis, and avoids fatal complications caused by Pseudomonas aeruginosa pneumonia in mice. These results were independent of in vitro anti-Pseudomonas aeruginosa activity on QS-dependent virulence factors. Further experiments are required to identify the immune mechanism before initiating clinical trials.