gebhart/patrepeval huggingface dataset:
Improved Antibiotic-Impregnated Catheters with Extended-Spectrum Activity against Resistant Bacteria and Fungi (2011)

Minocycline-rifampin-impregnated central venous catheters (M/R CVCs) have been shown to be efficacious in reducing catheter-related bloodstream infections (CRBSI) and inhibiting the biofilm adherence of resistant Gram-positive and Gram-negative pathogens, with the exception of Pseudomonas aeruginosa and Candida spp. To expand the spectrum of antimicrobial activity, a novel second-generation M/R catheter was developed by adding chlorhexidine (CHX-M/R). CVCs and peripherally inserted central catheters (PICCs) were impregnated with CHX-M/R and compared with first-generation M/R catheters, CHX-silver sulfadiazine-treated CVCs (CHX/SS-CVCs), chlorhexidine-treated PICCs, and uncoated catheters. A biofilm catheter colonization model was used to assess the efficacy of catheters against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium (VRE), P. aeruginosa, Candida albicans, and Candida glabrata. CHX-M/R-impregnated CVCs were the only antimicrobial catheters that completely inhibited the biofilm colonization of all resistant bacterial and fungal organisms tested at all time intervals, and they were significantly superior to uncoated catheters (all P values were ≤0.003). Furthermore, CHX-M/R-coated CVCs had a significantly more effective and prolonged (up to 3 weeks) antimicrobial activity against MRSA and P. aeruginosa than M/R, CHX/SS, and uncoated CVCs (P < 0.0001). Similarly, CHX-M/R-coated PICCs were also superior to M/R-coated and CHX-coated PICCs in preventing biofilms of MRSA, VRE, P. aeruginosa, and Candida species (P value = 0.003 for all). Our study shows that novel CHX-M/R-coated catheters have unique properties in completely inhibiting biofilm colonization of MRSA, VRE, P. aeruginosa, and fungi in a manner superior to that of M/R- and chlorhexidine-treated catheters.
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift (2020)

Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as "metabolic pathway drift," is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.
Ultra-High Sensitivity Surface-Micromachined Capacitive Differential Pressure Sensor for Low-Pressure Applications (2022)

An ultra-high sensitivity surface-micromachined capacitive differential pressure sensor and capacitance bridge readout circuit, with amplitude balancing for differential low-pressure gas measurement applications, was designed, fabricated, and characterized. The sensor membrane has a diameter of 800 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> with a thickness of 1 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> and the chip size is <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.5\times 2\times 0.6$ </tex-math></inline-formula> mm3. The characterized sensor pressure range is 0–2000 Pa, with a full-scale capacitance difference span of 0.95 pF. Typical pressure error within the pressure range of 0–2000 Pa is ±0.5%, and the temperature coefficient is 0.044%/°C, both respectively from the pressure reading. [2022-0017]
Transforming potential and growth stimulating activity of the v-fos and c-fos genes carried by avian retrovirus vectors. (1988)

To study transforming potential as well as growth stimulating activity of the fos genes on primary cells, we have developed avian retrovirus vectors by constructing derivatives of Rous sarcoma virus DNA in which the v-src gene was replaced by either the v-fos gene of FBJ-MuSV or the mouse c-fos gene. After each derivative was introduced into chicken embryo fibroblasts by transfection, replication-competent viruses that carry the v-fos gene (FJ2) or the c-fos gene (FM4) were recovered. FM4 and FJ2 introduced the fos genes into almost all chicken embryo fibroblasts within 3 days after infection, expressed their gene products, and induced morphological transformation and colony formation in soft agar. Results show that overproduction of the c-fos gene product is enough for cellular transformation not only of rat established fibroblasts as reported previously but also of avian primary fibroblasts. Using this vector system, we have further shown that the c-fos gene and the v-fos gene have biological activities that induce cellular proliferation of chicken neuroretinal cells, which normally stay in the resting stage of growth in monolayer culture.
Predicting the Phase Equilibria of Carbon Dioxide Containing Mixtures Involved in CCS Processes Using the PPR78 Model (2014)

Predicting the Phase Equilibria of Carbon Dioxide Containing Mixtures Involved in CCS Processes Using the PPR78 Model
Ultrasound Evaluation of the Magnitude of Pneumothorax: A New Concept (2000)

Pneumothorax is commonly seen in trauma patients; the diagnosis is usually confirmed by radiography. Use of ultrasound for this purpose, in environments such as space flight and remote terrestrial areas where radiographic capabilities are absent, is being investigated by NASA. In this study, the ability of ultrasound to assess the magnitude of pneumothorax in a porcine model was evaluated. Sonography was performed on anesthetized pigs (avg. wt. 50 kg) in both ground-based laboratory (n = 5) and micro gravity conditions (0 g) aboard the KC-135 aircraft during parabolic flight (n = 4). Aliquots of air (50-1 OOcc) were introduced into the chest through a catheter to simulate pneumothorax. Results were video-recorded and digitized for later interpretation by radiologists. Several distinct sonographic patterns of lung were noted, including the combination of a zone with a still zone, and a segmented zone. These partial lung sliding patterns exclude massive pneumothorax manifested by a complete separation of the lung from the parietal pleura. In 0 g, the sonographic picture was more diverse; 1 g differences between posterior and anterior aspects were diminished. CONCLUSIONS: Modest pneumothorax can be inferred by the ultrasound sign of partial lung sliding. This finding, which increases the negative predictive value of thoracic ultrasound, may be attributed to intermittent pleural contact, small air spaces, or alterations in pleural lubricant. Further studies of these phenomena are warranted.
Ultra-low-loss on-chip resonators with sub-milliwatt parametric oscillation threshold (2017)

On-chip optical resonators have the promise of revolutionizing numerous fields including metrology and sensing; however, their optical losses have always lagged behind their larger discrete resonator counterparts based on crystalline materials and flowable glass. Silicon nitride (Si3N4) ring resonators open up capabilities for optical routing, frequency comb generation, optical clocks and high precision sensing on an integrated platform. However, simultaneously achieving high quality factor and high confinement in Si3N4 (critical for nonlinear processes for example) remains a challenge. Here, we show that addressing surface roughness enables us to overcome the loss limitations and achieve high-confinement, on-chip ring resonators with a quality factor (Q) of 37 million for a ring with 2.5 {\mu}m width and 67 million for a ring with 10 {\mu}m width. We show a clear systematic path for achieving these high quality factors. Furthermore, we extract the loss limited by the material absorption in our films to be 0.13 dB/m, which corresponds to an absorption limited Q of at least 170 million by comparing two resonators with different degrees of confinement. Our work provides a chip-scale platform for applications such as ultra-low power frequency comb generation, high precision sensing, laser stabilization and sideband resolved optomechanics.
Sensing Mechanisms for Carbon Nanotube Based NH3 Gas Detection (2009)

There has been an argument on carbon nanotube (CNT) based gas detectors with a field-effect transistor (FET) geometry: do the response signals result from charge transfer between adsorbed gas molecules and the CNT channel and/or from the gas species induced Schottky barrier modulation at the CNT/metal contacts? To differentiate the sensing mechanisms, we employed three CNTFET structures, i.e., (1) the entire CNT channel and CNT/electrode contacts are accessible to NH(3) gas; (2) the CNT/electrode contacts are passivated with a Si(3)N(4) thin film, leaving the CNT channel open to the gas and, in contrast, (3) the CNT channel is covered with the film, while the contacts are open to the gas. We suggest that the Schottky barrier modulation at the contacts is the dominant mechanism from room temperature to 150 degrees C. At higher temperatures, the charge transfer process contributes to the response signals. There is a clear evidence that the adsorption of NH(3) on the CNT channel is facilitated by environmental oxygen.
Enhanced Dynamic Performance of Quantum Dot Semiconductor Lasers Operating on the Excited State (2014)

The modulation dynamics and the linewidth enhancement factor of excited-state (ES) lasing quantum dot (QD) semiconductor lasers are investigated through a set of improved rate equation model, in which the contribution of off-resonant states to the refractive index change is taken into account. The ES laser exhibits a broader modulation response associated with a much lower chirp-to-power ratio in comparison with the ground-state (GS) lasing laser. In addition, it is found that the laser emission in ES reduces the linewidth enhancement factor of QD lasers by about 40% than that in GS. These properties make the ES lasing devices, especially InAs/InP ones emitting at <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.55~\mu $ </tex-math></inline-formula> m, more attractive for direct modulation in high-speed optical communication systems.
A Variational Method for Dejittering Large Fluorescence Line Scanner Images (2018)

We propose a variational method dedicated to jitter correction of large fluorescence scanner images. Our method consists in minimizing a global energy functional to estimate a dense displacement field representing the spatially-varying jitter. The computational approach is based on a half-quadratic splitting of the energy functional, which decouples the realignment data term and the dedicated differential-based regularizer. The resulting problem amounts to alternatively solving two convex and nonconvex optimization subproblems with appropriate algorithms. Experimental results on artificial and large real fluorescence images demonstrate that our method is not only capable to handle large displacements but is also efficient in terms of subpixel precision without inducing additional intensity artifacts.
JITPR (2013)

The execution runtime usually is a headache for designers performing application mapping onto reconfigurable architectures. In this article we propose a methodology, as well as the supporting toolset, targeting to provide fast application implementation onto reconfigurable architectures with the usage of a Just-In-Time (JIT) compilation framework. Experimental results prove the efficiency of the introduced framework, as we reduce the execution runtime compared to the state-of-the-art approach on average by 53.5×. Additionally, the derived solutions achieve higher operation frequencies by 1.17×, while they also exhibit significant lower fragmentation ratios of hardware resources.
Side channels in deduplication: trade-offs between leakage and efficiency. (2016)

Deduplication removes redundant copies of files or data blocks stored on the cloud.Clientside deduplication, where the client only uploads the file upon the request of the server, provides major storage and bandwidth savings, but introduces a number of security concerns.Harnik et al. (2010) showed how cross-user client-side deduplication inherently gives the adversary access to a (noisy) side-channel that may divulge whether or not a particular file is stored on the server, leading to leakage of user information.We provide formal definitions for deduplication strategies and their security in terms of adversarial advantage.Using these definitions, we provide a criterion for designing good strategies and then prove a bound characterizing the necessary trade-off between security and efficiency.
Addition of bisulfite to α‐olefins: Synthesis of n‐alkane sulfonates and characterization of intermediates (1992)

The free radical‐catalyzed bisulfite addition to octene‐1, decene‐1, dodecene‐1 and tetradecene‐1 was studied under different conditions. The experimental conditions could be adjusted to yield different ratios of intermediate as well as final compounds. We have separated, purified and positively identified alkane‐1‐sodium sulfonates of general formula CH 3 ‐(CH 2 ) n ‐SO 3 Na (n=7,9,11 and 13), alkane‐1‐sodium sulfonate‐2‐sulfinic acids of general formula CH 3 ‐(CH 2 ) n ‐CHSO 2 H‐CH 2 ‐SO 3 Na (n=5,7,9 and 11) and alkane‐1,2‐disodium sulfonates of general formula CH 3 ‐(CH 2 ) n ‐CHSO 3 Na‐CH 2 ‐SO 3 Na (n=5,7,9 and 11). The solubilities and critical micelle concentrations of mono‐ and disodium alkane sulfonates were determined, and for definite identification 13 C nuclear magnetic resonance (NMR) and dispersive X‐ray crystallography were employed along with classical wet analytical procedures.
CARS measurements in a bluff-body stabilized diffusion flame (1979)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Gary L. Switzer, W. M. Roquemore, Royce B. Bradley, Paul W. Schreiber, and Won B. Roh, "CARS measurements in a bluff-body stabilized diffusion flame," Appl. Opt. 18, 2343-2345 (1979) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
The sectorial loop‐gap resonator for 31P NMR of the adult human liver at 1.5 t with surface tissue suppression (1986)

A new type of loop-gap resonator, which because of its topology is called a "sectorial resonator," is described in considerable analytical detail. It was used for 31P NMR of the livers of two human adult normal volunteers. An effective strategy for suppression of signals from surface tissue was developed. Depth selection was achieved using a separate excitation coil, permitting a reasonable degree of control of the shape of the sensitive region by adjustment of the dimensions of the excitation coil and of the type of pulse delivered. In addition a new principle for cancellation is described: the topology of the sectorial resonator leads to cancellation signals from tissue masses at the two openings of the structure. Using a phase-alternated repeated 90 degrees FID pulse sequence, good spectra were achieved in 2.5 min that are free from contamination by the phosphocreatine peak.
Influence of atorvastatin and carboxymethylated glucan on the serum lipoprotein profile and MMP activity of mice with lipemia induced by poloxamer 407 (2012)

The effects of atorvastatin and carboxymethylated β-glucan (CMG) on the lipoprotein-cholesterol (LP-C) and lipoprotein-triglyceride (LP-TG) fractions and subfractions at the early stage of murine hyperlipidemia, and its pleiotropic anti-inflammatory effects, were studied. Atorvastatin and CMG were administered in ICR male mice with acute lipemia induced with a single injection of poloxamer 407 (P-407). A novel small-angle X-ray scattering method for the determination of fractional and subfractional composition of LP-C and LP-TG was used. In P-407-treated animals, there was a drastic increase of total cholesterol and especially TG. Atorvastatin decreased both the total cholesterol and TG, but not to control levels. CMG primarily decreased TG and was not as potent as atorvastatin. P-407 increased atherogenic LDL-C (IDL-C and LDL(1-3)-C subfractions) and very low-density lipoprotein-C (VLDL-C) (VLDL(1-2)-C and VLDL(3-5)-C subfractions) fractions, with an increase of the total anti-atherogenic HDL-C fraction (HDL(2)-C subfraction). Atorvastatin treatment of lipemia was followed by a decrease in the total LP-C, total LDL-C (LDL(1-3)-C subfraction), and the LDL(1-3)-TG subfraction. Additionally, atorvastatin treatment resulted in an increase in the serum matrix metalloproteases activity both in control and P-407-treated mice. In general, high-dose atorvastatin therapy exerts its lipid-lowering and pleiotropic effects in the early stages of acute lipemia induced in mice by treatment with P-407.
(Invited) From MRTA to SMRTA: Improvements in Activating Implanted Dopants in GaN (2015)

The implantation and activation of dopants in GaN is a key enabling step for future devices requiring selective area doping. High temperatures (over 1300 ˚C) are required to activate p-type dopants in GaN. These high temperatures are above the decomposition temperature of GaN, which necessitates advanced annealing processes. One such process, the multicycle rapid thermal annealing (MRTA) process, has enabled the implantation and activation of p-type dopants in GaN. In this research, we demonstrate the symmetrical multicycle rapid thermal annealing (SMRTA) annealing process. The SMRTA annealing process includes an extra conventional annealing step after the rapid heating and cooling cycles and is shown to improve the crystalline structure of annealed GaN compared to the MRTA process.
Backscatter Modeling of Titan's Surface Features Using a Comprehensive Collection of Cassini Radar Data (2007)

The Cassini RADAR cycles between four modes (radiometry, scatterometry, altimetry, and synthetic aperture imaging) as it swings by Titan on a given orbit. Scatterometry uses the central antenna beam at 13.78-GHz (2.17-cm) in a real-aperture mode to produce regional-scale backscatter images across large areas of the surface. Raster scanning also achieves large angular coverage to properly sample the average backscatter response over the region. A backscatter function over a wide range of angles reveals much about the dielectric composition, surface and subsurface scattering properties. By modeling the backscatter response for individual features (e.g. crater ejecta and dune fields) rather than the average response over regional areas, we can constrain the composition and structure of specific units on Titan's heterogeneous surface, and thus the processes responsible for the feature's formation and evolution. Unfortunately, scatterometer-data alone does not provide adequate angular sampling of a specific feature's backscatter response. Of the 17 scatterometry scans acquired to-date, there are only eight distinct areas of overlap giving multi-angle coverage. But by applying the real-aperture processing techniques of the scatterometer to the other active radar modes, we can combine similarly calibrated datasets and complete the angular sampling. Altimetry provides the very low angle response (less than 1°), while SAR gives the mid-range response (10° to 40°). We separate the backscatter response into two different regimes: surface scatter dominates at low angles and volume scattering dominates at large angles. We use traditional facet scattering models (such as Hagfors' or Gaussian laws) to describe the quasi-specular scatter of the surface term, which yields the tightest constraints on dielectric constant and surface slopes. We consider two different approaches to model the diffuse volume term: an empirical cosine-law and a model that incorporates the radiometer emission measurements. We present the results of both models applied to specific features' backscatter curves.
Cell intrinsic role for MAVS in regulating CD8 T cell fitness during acute virus infection (P6113) (2013)

Abstract Mitochondrial antiviral Signaling molecule (MAVS) has been described in it’s role as an adaptor molecule that links viral RNA sensing by RIG-I-like receptors (RLR)s to type I IFN and inflammatory cytokine production. However it’s role in adaptive immune responses to viruses is not well defined. Using an adoptive cell transfer system we examined the requirement for MAVS directly in CD8 T cells during adaptive responses following acute Lymphocytic choriomeningitis virus (LCMV) infection. Here, we found that MAVS plays an RLR-independent role in determining CD8 effector T cell fitness. MAVS-deficient cells were deficient in virus-induced expansion and cytokine production. This deficiency correlated with altered cell size and granularity, differential mitochondrial membrane potential and reduced levels of steady-state intracellular calcium. We found cytokine production deficiencies were acute at earlier stages of CD8 cell expansion, suggesting that the requirement for MAVS is most critical when cellular need for mitochondrial metabolism is maximal. These results suggest that MAVS is required for metabolic support of CD8 effector cell expansion during acute virus infection. Our study therefore assigns a novel metabolic role to MAVS in adaptive CD8 T cell energetics. Defining the function of MAVS in enhancing T cell metabolism therefore has implications for vaccine strategies that aim to increase the quality and quality of the CD8 T cell response to virus infection.
A Streaming Multi-Threaded Model (2001)

We present SCORE (Stream Computations Organized for Reconfigurable Execution), a multi-threaded model that relies on streams to expose thread parallelism and to enable e#cient scheduling, low-overhead communication, and scalability. We present work to-date on SCORE for scalable reconfigurable logic, as well as implementation ideas for SCORE for processor architectures. We demonstrate that streams can be exposed as a clean architectural feature that supports forward compatibility to larger, more parallel hardware. 1. OVERVIEW For the past several decades, the predominant architectural abstraction for programmable computation systems has been the instruction set architecture (ISA). An ISA defines an instruction set and semantics for executing it. A key benefit of the ISA model is that those semantics decouple software from hardware development. A piece of software, written and compiled once, is guaranteed to run on any ISA-compatible device. This guarantee allows hardware to evolve...