gebhart/patrepeval huggingface dataset:
Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression (2011)

Serological studies of patients with pertussis and the identification of antigenic Bordetella pertussis proteins support the hypothesis that B. pertussis perceives an iron starvation cue and expresses multiple iron source utilization systems in its natural human host environment. Furthermore, previous studies using a murine respiratory tract infection model showed that several of these B. pertussis iron systems are required for colonization and persistence and are differentially expressed over the course of infection. The present study examined genome-wide changes in B. pertussis gene transcript abundance in response to iron starvation in vitro. In addition to known iron source utilization genes, we identified a previously uncharacterized iron-repressed cytoplasmic membrane transporter system, fbpABC, that is required for the utilization of multiple structurally distinct siderophores including alcaligin, enterobactin, ferrichrome, and desferrioxamine B. Expression of type III secretion system genes was also found to be upregulated during iron starvation in both B. pertussis strain Tohama I and Bordetella bronchiseptica strain RB50. In a survey of type III secretion system protein production by an assortment of B. pertussis laboratory-adapted and low-passage clinical isolate strains, iron limitation increased the production and secretion of the type III secretion system-specific translocation apparatus tip protein Bsp22 in all Bvg-proficient strains. These results indicate that iron starvation in the infected host is an important environmental cue influencing not only Bordetella iron transport gene expression but also the expression of other important virulence-associated genes.
Parallel XML Parsing Using Meta-DFAs (2007)

By leveraging the growing prevalence of multicore CPUs, parallel XML parsing(PXP) can significantly improve the performance of XML, enhancing its suitability for scientific data which is often dominated by floating-point numbers. One approach is to divide the XML document into equal-sized chunks, and parse each chunk in parallel. XML parsing is inherently sequential, however, because the state of an XML parser when reading a given character depends potentially on all preceding characters. In previous work, we addressed this by using a fast preparsing scan to build an outline of the document which we called the skeleton. The skeleton is then used to guide the parallel full parse. The preparse is a sequential phase that limits scalability, however, and so in this paper, we show how the preparse itself can be parallelized using a mechanism we call a meta-DFA. For each state q of the original preparser the meta-DFA incorporates a complete copy of the preparser state machine as a sub-DFA which starts in state q. The meta-DFA thus runs multiple instances of the preparser simultaneously when parsing a chunk, with each possible preparser state at the beginning of a chunk represented by an instance. By pursuing all possibilities simultaneously, the meta-DFA allows each chunk to be preparsed independently in parallel. The parallel full parse following the preparse is performed using libxml2, and outputs DOM trees that are fully compatible with existing applications that use libxml2. Our implementation scales well on a 30 CPU Sun E6500 machine.
ChemInform Abstract: Synthesis of (1,2,4)Triazoloquinazolinones and Imidazoquinazolinones. (1987)

Abstract The hydrazinoquinazolinones (I) are cyclized with the carbonyl derivatives (II) to give the triazoloquinazolinones (III).
Aspect: a formal specification language for detecting bugs (1992)

Aspect is a static analysis technique based on formal specifications. By trading expressive power for tractability, Aspect can offer efficient detection of a class of bugs that is not detectable by other static means. Since the specifications are partial, not all bugs can be caught. But there are never any spurious reports: an error message always indicates an error in the code or a flaw in the specification. Aspect can handle most of the features of modern imperative programming languages: side-effects and aliasing, exceptions, polymorphism and dynamic allocation. It takes advantage of strong typing and is designed for programs that are organized around procedures and abstract types. The checking mechanism is based on an enriched form of dependency analysis. Objects are divided into projections called 'aspects'; the dependencies of different aspects are then tracked individually. The analysis is comparable in complexity to the kinds of analysis already performed by optimizing compilers. A prototype checker has been implemented tor the CLU programming language. It runs almost as fast as the compiler, and has found a variety of bugs in real programs.
Detecting LSB steganography in color, and gray-scale images (2001)

We describe a reliable and accurate method for detecting least significant bit (LSB) nonsequential embedding in digital images. The secret message length is derived by inspecting the lossless capacity in the LSB and shifted LSB plane. An upper bound of 0.005 bits per pixel was experimentally determined for safe LSB embedding.
Electrokinetic Injection for Stacking Neutral Analytes in Capillary and Microchip Electrophoresis (2001)

An on-column mechanism for electrokinetically injecting long sample plugs with simultaneous stacking of neutral analytes in capillary electrokinetic chromatography is presented. On-column stacking methods allow for the direct injection of long sample plugs into the capillary, with narrowing of the analyte peak width to allow for an increase in the detected signal. Low-pressure injections (approximately 50 mbar) are commonly used to introduce sample plugs containing neutral analytes. We demonstrate that injection can be accomplished by applying an electric field from the sample vial directly into the capillary, with neutral analytes injected by electroosmotic flow at up to 1 order of magnitude faster than the corresponding pressure injections. Since stacking occurs simultaneously with electrokinetic injection, stacking is initiated at the capillary inlet, resulting in an increased length of capillary remaining for separation. Reproducibility obtained for peak height and peak area with electroosmotic flow injection is comparable to that obtained with the pressure injection mode, while reproducibility of analysis time is markedly improved. Electrokinetic stacking of neutral analytes utilizing electroosmotic flow is demonstrated with discontinuous (high conductivity, high mobility) as well as continuous (equal conductivity, equal mobility) sample electrolytes. Injecting neutral analytes by electroosmotic flow affords a 10-fold or greater decrease in analysis times when capillaries of 50-microm i.d. or smaller are used. This stacking method should be exportable to dynamic pH junction stacking and electrokinetic chromatography with capillary arrays. Equations describing this electrokinetic injection mode are introduced and stacking of a neutral analyte on a microchip by electrokinetic injection using a simple cross-T channel configuration is demonstrated.
Automatic classification of sleep apnea epochs using the electrocardiogram (2002)

This study investigated the automatic prediction of epochs of sleep apnea from the electrocardiogram. A large independently validated database of 70 single lead ECGs, each of approximately 8 hours in duration, was used throughout the study. Thirty five of these records were used for training and 35 retained for independent testing. After considering a wide variety of features the authors found that features based on the power spectral density estimates of the R-wave maxima and R-R intervals to be the most discriminating. Results show that a classification rate of approximately 89% is achievable.
Cyclo-((<i>S</i>)-leucyl-(<i>S</i>)-histidyl). A Catalyst for Asymmetric Addition of Hydrogen Cyanide to Aldehydes (1989)

Abstract Asymmetric addition of hydrogen cyanide to various aldehydes in the presence of a catalytic amount of cyclo-((S)-leucyl-(S)-histidyl) affords the corresponding cyanohydrins in moderate to good optical yields. The reaction of benzaldehyde with hydrogen cyanide gives (S)-2-hydroxy-2-phenylacetonitrile (85%, 55% ee) whose stereochemistry is found to be opposite to our previous result using cyclo-((S)-phenylalanyl-(S)-histidyl).
MR compatibility aspects of a silicon photomultiplier-based PET/RF insert with integrated digitisation (2014)

The combination of Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) into a single device is being considered a promising tool for molecular imaging as it combines the high sensitivity of PET with the functional and anatomical images of MRI. For highest performance, a scalable, MR compatible detector architecture with a small form factor is needed, targeting at excellent PET signal-to-noise ratios and time-of-flight information. Therefore it is desirable to use silicon photo multipliers and to digitize their signals directly in the detector modules inside the MRI bore. A preclinical PET/RF insert for clinical MRI scanner was built to demonstrate a new architecture and to study the interactions between the two modalities.The disturbance of the MRI's static magnetic field stays below 2 ppm peak-to-peak within a diameter of 56 mm (90 mm using standard automatic volume shimming). MRI SNR is decreased by 14%, RF artefacts (dotted lines) are only visible in sequences with very low SNR. Ghosting artefacts are visible to the eye in about 26% of the EPI images, severe ghosting only in 7.6%. Eddy-current related heating effects during long EPI sequences are noticeable but with low influence of 2% on the coincidences count rate. The time resolution of 2.5 ns, the energy resolution of 29.7% and the volumetric spatial resolution of 1.8 mm(3) in the PET isocentre stay unaffected during MRI operation. Phantom studies show no signs of other artefacts or distortion in both modalities. A living rat was simultaneously imaged after the injection with (18)F-Fluorodeoxyglucose (FDG) proving the in vivo capabilities of the system.
2.5D dictionary learning based computed tomography reconstruction (2016)

A computationally efficient 2.5D dictionary learning (DL) algorithm is proposed and implemented in the model- based iterative reconstruction (MBIR) framework for low-dose CT reconstruction. MBIR is based on the minimization of a cost function containing data-fitting and regularization terms to control the trade-off between data-fidelity and image noise. Due to the strong denoising performance of DL, it has previously been considered as a regularizer in MBIR, and both 2D and 3D DL implementations are possible. Compared to the 2D case, 3D DL keeps more spatial information and generates images with better quality although it requires more computation. We propose a novel 2.5D DL scheme, which leverages the computational advantage of 2D-DL, while attempting to maintain reconstruction quality similar to 3D-DL. We demonstrate the effectiveness of this new 2.5D DL scheme for MBIR in low-dose CT. By applying the 2D DL method in three different orthogonal planes and calculating the sparse coefficients accordingly, much of the 3D spatial information can be preserved without incurring the computational penalty of the 3D DL method. For performance evaluation, we use baggage phantoms with different number of projection views. In order to quantitatively compare the performance of different algorithms, we use PSNR, SSIM and region based standard deviation to measure the noise level, and use the edge response to calculate the resolution. Experimental results with full view datasets show that the different DL based algorithms have similar performance and 2.5D DL has the best resolution. Results with sparse view datasets show that 2.5D DL outperforms both 2D and 3D DL in terms of noise reduction. We also compare the computational costs, and 2.5D DL shows strong advantage over 3D DL in both full-view and sparse-view cases.
Configuring Cloud Admission Policies under Dynamic Demand (2013)

We consider the problem of admitting sets of, possibly heterogenous, virtual machines (VMs) with stochastic resource demands onto physical machines (PMs) in a Cloud environment. The objective is to achieve a specified quality-of-service related to the probability of resource over-utilization in an uncertain loading condition, while minimizing the rejection probability of VM requests. We introduce a method which relies on approximating the probability distribution of the total resource demand on PMs and estimating the probability of over-utilization. We compare our method to two simple admission policies: admission based on maximum demand and admission based on average demand. We investigate the efficiency of the results of using our method on a simulated Cloud environment where we analyze the effects of various parameters (commitment factor, coefficient of variation etc.) on the solution for highly variate demands.
Experimental parameters influencing surface-enhanced Raman scattering of bacteria (2007)

Surface-enhanced Raman scattering (SERS) is a powerful technique for the analysis of a variety of molecules and molecular structures. Due to its great complexity, the acquisition of detailed molecular information from biological organizations such as bacteria is still a challenging task. SERS can provide valuable information once silver or gold surfaces can be brought in close contact with the biological organization. Because several experimental parameters can affect SERS spectra of bacteria, the experimental conditions must be well defined for comparable and reproducible results. The influence of experimental parameters, such as the type of noble metal, size, and aggregation properties of nanoparticles, and the wavelength of the laser light on the SERS of E. coli and B. megaterium are examined. It is demonstrated that the impact of these parameters could be enormous and a standard protocol must be developed depending on the goal of the study.
Pyro (2017)

We present Pyro, a micro thumb-tip gesture recognition technique based on thermal infrared signals radiating from the fingers. Pyro uses a compact, low-power passive sensor, making it suitable for wearable and mobile applications. To demonstrate the feasibility of Pyro, we developed a self-contained prototype consisting of the infrared pyroelectric sensor, a custom sensing circuit, and software for signal processing and machine learning. A ten-participant user study yielded a 93.9% cross-validation accuracy and 84.9% leave-one-session-out accuracy on six thumb-tip gestures. Subsequent lab studies demonstrated Pyro's robustness to varying light conditions, hand temperatures, and background motion. We conclude by discussing the insights we gained from this work and future research questions.
LDPC code set for mmWave communication (2010)

A low-density parity-check (LDPC) code set is presented that is specifically designed for multi-gigabit throughput wireless communication in the 60GHz band. The code set is structured to enable low power decoder and encoder implementation while providing excellent coding gain over a wide variety of channels.
Optimistic transactional active replication (2008)

Critical database applications require 2-safe replication between at least two sites for disaster-tolerant services. At the same time, they must provide consistent and low-latency results to their clients in normal cases. In this paper, we propose Optimistic Transactional Active Replication (OTAR), which replicates the transaction logs with low latency and provides a consistent view to database applications. The latency of our replication is lower than Passive Replication, and guarantees the serializability of transaction isolation levels that cannot be supported by Active Replication. For our replication, each client sends a transaction request to all replicas and all of the replicas execute the request and optimistically return the result of the transaction to the client. Each replica generates a causality history of the transaction, sent to the client with the result. With the causality histories, the client can make sure that the requested transaction was executed in the same order at all of the replicas and eventually commit it. If the client cannot validate the order, then the client waits for the pessimistic result of the transaction from the replicas. This paper describes the algorithm and its properties.
Scintillation properties of Ce<sup>3&#x002B;</sup>-doped, Pr<sup>3&#x002B;</sup>-doped calcium orthoborate (2010)

To develop new scintillators for thermal neutron detection, we investigated optical and scintillation properties of Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> -doped, Pr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> -doped Ca <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (BO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> single crystals grown by the micro-pulling down (μ-PD) method. In optical transmission spectra, the absorption was observed around 275 and 345 nm correspond to the transition from the 4f ground state levels <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5/2</sub> , <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7/2</sub> to 5d excited state of Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> and Pr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> transition from the ground state <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> H to 5d state around 210-245 nm, respectively. The radioluminescence spectra showed intense peak around 400 nm (Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> :CBO) and 260-310 nm (Pr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> : CBO) under <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">241</sup> Am 5.5 MeV α-ray excitation due to the 5d-4f transition. The relative scintillation light yield of 0.5 % Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> : CBO crystal showed about 30 %, while that of 0.5 % Pr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> : CBO crystal showed about 10 % compared with that of reference Li-glass (GS20) scintillator under <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">252</sup> Cf neutron irradiation.
Demonstration of Low ON-Resistance CAVETS with Ammonia MBE Grown Active p-GaN Layer as the Current Blocking Layer for High Power Applications (2012)

Abstract not Available.
Novel 1,2,4-oxadiazoles and 1,2,4-thiadiazoles as dual 5-lipoxygenase and cyclooxygenase inhibitors (1992)

A series of 1,2,4-oxadiazoles and 1,2,4-thiadiazoles containing a 2,6-di-tert-butylphenol substituent were prepared and evaluated as dual inhibitors of 5-lipoxygenase and cyclooxygenase in rat basophilic leukemia (RBL-1) cells. Several of these compounds show oral efficacy in the rat carrageenan footpad edema (CFE) and mycobacterium footpad edema (MFE) antiinflammatory models, without concomitant gastric ulceration. Structure-activity relationships are discussed. The best compounds (ID40 values in MFE of 3-8 mg/kg po) contain guanidine-derived substituents on the heterocyclic ring.
CTH17-2: Energy-Efficient Cooperative Relaying over Fading Channels with Simple Relay Selection (2006)

We consider a cooperative wireless network where the source broadcasts data to relays, some or all of which cooperatively beamform to forward the data to the destination. The network is subject to an overall outage constraint. We generalize the standard approaches for cooperative communications in two respects: (i) we explicitly model and factor in the cost of acquiring channel state information (CSI), and (ii) we consider more general, yet simple, selection rules for the relays and compute the optimal one among them. These rules include as special cases several relay selection criteria proposed in the literature. We present analytical results for the homogeneous case, where the links have identical mean channel gains. For this case, we show that the optimal transmission scheme is simple and can be computed efficiently. Numerical results show that while the cost of training and feedback of CSI is significant, relay cooperation is still beneficial.
Identification of a missense mutation in the bovine <i>ABCG2</i> gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle (2005)

We previously localized a quantitative trait locus (QTL) on chromosome 6 affecting milk fat and protein concentration to a 4-cM confidence interval, centered on the microsatellite BM143. We characterized the genes and sequence variation in this region and identified common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL. Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires. The single nucleotide change capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 transporter was the only polymorphism corresponding to the segregation status of all 3 heterozygous and 15 homozygous sires for the QTL in the Israeli and U.S. Holstein populations. The allele substitution fixed effects on the genetic evaluations of 335 Israeli sires were -341 kg milk, +0.16% fat, and +0.13% protein (F-value = 200). No other polymorphism gave significant effect for fat and protein concentration in models that also included Y581S. The allele substitution effects on the genetic evaluations of 670 cows, daughters of two heterozygous sires, were -226 kg milk, 0.09% fat, and 0.08% protein (F-value = 394), with partial dominance towards the 581S homozygotes. We therefore propose that Y581S in ABCG2 is the causative site for this QTL.
Adaptive transition bias for robust low complexity speech recognition (2002)

The basis for all methods described in this paper is the application of an adaptive transition bias to the sequences of phoneme models that represent spoken utterances. This offers significantly improved accuracy in phoneme based speaker independent recognition, while adding very little overhead to the overall system complexity. The algorithms are tested using the low complexity hybrid recognizer denoted hidden neural networks (HNN) on US English and Japanese speaker independent name dialing tasks. Experimental results show that our approach provides a relative error rate reduction of up to 47% over the baseline system.