gebhart/patrepeval huggingface dataset:
Simulations of boundary layers and point defects in coupled VCSEL arrays (2005)

The inherent gain dependence on carrier depletion and on the lateral cavity interactions differentiates active photonic lattices from passively coupled models, employing a given complex gain profile. This paper addresses coupled vertical-cavity surface-emitting laser array effects due to finite boundaries and the possibility of individual bias failures, of interest for practical applications. The "cold-cavity" characteristic parameters are assumed identical, focusing on biasing defects and site vacancies. Analysis and numerical simulations based on the tight-binding approximation show that phase-locking persists in finite arrays. Self-regulation of the edge cavity density and power generate boundary layers of differentiated cavity operation values. The inter-cavity phase shift remains nearly uniform, with a small superimposed linear slope caused by cross-cavity reflection interference from distributed Bragg reflectors. Phase locking is robust against partial or complete failure to lase for individual cavity sites, or even entire rows, due to biasing errors.
Endosomal Proteolysis of Internalized Insulin at the C-terminal Region of the B Chain by Cathepsin D (2002)

The endosomal compartment of hepatic parenchymal cells contains an acidic endopeptidase, endosomal acidic insulinase, which hydrolyzes internalized insulin and generates the major primary end product A(1--21)-B(1--24) insulin resulting from a major cleavage at residues Phe(B24)-Phe(B25). This study addresses the nature of the relevant endopeptidase activity in rat liver that is responsible for most receptor-mediated insulin degradation in vivo. The endosomal activity was shown to be aspartic acid protease cathepsin D (CD), based on biochemical similarities to purified CD in 1) the rate and site of substrate cleavage, 2) pH optimum, 3) sensitivity to pepstatin A, and 4) binding to pepstatin A-agarose. The identity of the protease was immunologically confirmed by removal of greater than 90% of the insulin-degrading activity associated with an endosomal lysate using polyclonal antibodies to CD. Moreover, the elution profile of the endosomal acidic insulinase activity on a gel-filtration TSK-GEL G3000 SW(XL) high performance liquid chromatography column corresponded exactly with the elution profile of the immunoreactive 45-kDa mature form of endosomal CD. Using nondenaturating immunoprecipitation and immunoblotting procedures, other endosomal aspartic acid proteases such as cathepsin E and beta-site amyloid precursor protein-cleaving enzyme (BACE) were ruled out as candidate enzymes for the endosomal degradation of internalized insulin. Immunofluorescence studies showed a largely vesicular staining pattern for internalized insulin in rat hepatocytes that colocalized partially with CD. In vivo pepstatin A treatment was without any observable effect on the insulin receptor content of endosomes but augmented the phosphotyrosine content of the endosomal insulin receptor after insulin injection. These results suggest that CD is the endosomal acidic insulinase activity which catalyzes the rate-limiting step of the in vivo cleavage at the Phe(B24)-Phe(B25) bond, generating the inactive A(1--21)-B(1--24) insulin intermediate.
Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma (2013)

Tumor recurrence is a leading cause of cancer mortality. Therapies for recurrent disease may fail, at least in part, because the genomic alterations driving the growth of recurrences are distinct from those in the initial tumor. To explore this hypothesis, we sequenced the exomes of 23 initial low-grade gliomas and recurrent tumors resected from the same patients. In 43% of cases, at least half of the mutations in the initial tumor were undetected at recurrence, including driver mutations in TP53, ATRX, SMARCA4, and BRAF; this suggests that recurrent tumors are often seeded by cells derived from the initial tumor at a very early stage of their evolution. Notably, tumors from 6 of 10 patients treated with the chemotherapeutic drug temozolomide (TMZ) followed an alternative evolutionary path to high-grade glioma. At recurrence, these tumors were hypermutated and harbored driver mutations in the RB (retinoblastoma) and Akt-mTOR (mammalian target of rapamycin) pathways that bore the signature of TMZ-induced mutagenesis.
Mild hybrid technique using the automotive air-conditioning system (2016)

Among all the ancillary loads of a vehicle, the air-conditioning system accounts for the majority of fuel consumption, and its performance significantly affects the fuel economy of the vehicle. Topological similarities between the electrical system and the air-conditioning system can be utilized to formulate a new mild hybrid technique in which the compressor is treated as an energy conversion device and the evaporator as an energy storage device. Thus, the free kinetic energy during vehicle deceleration is harvestable by the air-conditioning system, provided that the on–off sequence of the clutch command is synchronized to the occurrence times of deceleration events. Motivated by this conceptualization, we are interested in three problems: first, the way in which the specific energy and the specific power of the evaporator can be measured; second, the types of new feature that the formulated optimization problem has; third, the method that is an appropriate mathematical tool for solving the problem. In order to solve these problems, energy-based models developed for air-conditioning systems with conventional evaporators and storage evaporators using a phase-change material are utilized, because they are physics based and have been validated against experimental data in previous work. A framework similar to that used in the energy management of a hybrid electric vehicle is established, and its unique characteristics are identified. The low-cost method using the air-conditioning system as an energy buffer, which is a very promising mild hybrid technique that has been demonstrated in conventional vehicles, is also applicable to hybrid electric vehicles.
Selective iodine imaging using K‐edge energies in computerized x‐ray tomography (1977)

Iodine is commonly used as a contrast material in computerized x-ray tomography. In some cases the determination of the iodine distribution in the image may be prevented by the presence of bone or tissue variations within the tomographic slice. This paper describes a method for quantitative selective imaging of the iodine concentration in the slice. The method employs scans using three heavily filtered x-ray beams, two having mean energies which straddle the iodine K edge (33 keV) and another at a slightly higher energy. The results are independent of tissue and bone over a broad range of projection path lengths. It is shown that, for separation of iodine from one other material, a two-beam K-edge approach requires less integral dose than a two-beam technique at conventional CT energies for slice diameters up to 30 cm. For selective iodine imaging in the presence of more than one other material, the three-spectrum K-edge technique is a necessity. Exposure requirements and beam-hardening corrections are discussed in detail and a computer-simulated CT image generated by the proposed scheme is presented.
Increasing the detection speed of an all-electronic real-time biosensor (2012)

Biosensor response time, which depends sensitively on the transport of biomolecules to the sensor surface, is a critical concern for future biosensor applications. We have fabricated carbon nanotube field-effect transistor biosensors and quantified protein binding rates onto these nanoelectronic sensors. Using this experimental platform we test the effectiveness of a protein repellent coating designed to enhance protein flux to the all-electronic real-time biosensor. We observe a 2.5-fold increase in the initial protein flux to the sensor when upstream binding sites are blocked. Mass transport modelling is used to calculate the maximal flux enhancement that is possible with this strategy. Our results demonstrate a new methodology for characterizing nanoelectronic biosensor performance, and demonstrate a mass transport optimization strategy that is applicable to a wide range of microfluidic based biosensors.
Generating Knock-Out and Complementation Strains of Neisseria meningitidis (2011)

The human-restricted pathogens Neisseria meningitidis and Neisseria gonorrhoeae are naturally competent for DNA uptake. This trait has been exploited extensively for genetic manipulation of these bacteria in the laboratory. Most transformation protocols were developed for N. gonorrhoeae, but appear to work also for N. meningitidis. In this chapter, we describe a number of protocols for genetic manipulation of N. meningitidis. Specifically, we describe how to (1) obtain knock-out mutants containing antibiotic-resistance markers, (2) generate markerless knock-out mutants, and (3) construct complementation strains. The generation of such mutants provides a valuable resource for studies of bacterial pathogenesis and vaccine development.
Spiral-CT-based assessment of tracheal stenoses using 3-D-skeletonization (2002)

LTT 3-D cross-sectional profiles permit objective, accurate and precise assessment of LTT caliber changes. Minor LTT caliber changes can be observed even in normals and, in case of an otherwise normal S-CT study, can be regarded as artifacts.
CSMA k-SIC &#x2014; A class of distributed MAC protocols and their performance evaluation (2015)

The CSMA/CA protocol is based on the “Interference as Noise” (IAN) paradigm i.e. it always gets rid of strong interference near a receiver to ensure quality of reception. However, it is well known from Multi-user Information Theory that treating Interference as Noise is not optimal. This paper proposes a class of protocols that employ the Successive Interference Cancellation (SIC) technique in a systematic fashion to move beyond always treating interference as noise. Such protocols allow one to pack more links than the classical CSMA. We describe the protocols along with their signaling mechanism to implement them in a distributed fashion. We then perform Monte Carlo simulations to evaluate the performance and show significant gains over the IAN based CSMA/CA protocol in large random networks.
New Functions of the Major Histocompatibility Complex Class II-Specific Transcription Factor RFXANK Revealed by a High-Resolution Mutagenesis Study (2005)

The transcription factors RFX and CIITA are major players in regulation of the expression of all classical and nonclassical major histocompatibility complex class II (MHC-II) genes. RFX nucleates the formation of a multiprotein complex, called the MHC-II enhanceosome, on MHC-II promoters. Assembly of this enhanceosome is an obligatory step for recruitment of the coactivator CIITA and thus for activation of MHC-II gene transcription. We have analyzed the function of the ankyrin repeat-containing protein RFXANK, which forms the heterotrimeric RFX complex together with RFX5 and RFXAP. We discovered that ANKRA2, the closest paralogue of RFXANK, can substitute for RFXANK in the activation of MHC-II genes and that this ability is mediated by its ankyrin repeat domain (ARD). This finding provided the basis for a high-resolution structure-function analysis of the ARD of RFXANK, which allowed us to map the RFX5 interaction domain and residues critical for assembly of the RFX complex. We also found that mutations in the fourth ankyrin repeat of RFXANK abolish assembly of the enhanceosome on MHC-II promoters in vivo but not in vitro, suggesting a new role of RFXANK in facilitating promoter occupation in the context of chromatin.
DNA Damage after Acute and Chronic Treatment with Malathion in Rats (2008)

Malathion is an insecticide widely used in agriculture and in public health programs that when used indiscriminately in large amounts can cause environmental pollution and risk to human health. However, it is possible that during the metabolism of malathion, reactive oxygen species can be generated, and malathion may produce oxidative stress in intoxicated rats that can be responsible for alterations in DNA molecules related in some studies. As a result, the present study aimed to investigate the DNA damage of cerebral tissue and peripheral blood in rats after acute and chronic malathion exposure. We used single cell gel electrophoresis (Comet assay) to measure early damage in hippocampus and peripheral blood and the Micronucleus test in total erythrocytes samples. Malathion was administered intraperitoneally once a day for one day (acute) or for 28 days (chronic) protocols (in both protocols, malathion was administered at 25, 50, 100, and 150 mg/kg). Our results showed that malathion (100 and 150 mg/kg) increased the DNA damage index in the peripheral blood and in the hippocampus after both chronic and acute treatment. Malathion increased the frequency of micronuclei only in chronic treatment at 150 mg/kg dose, and induced a cytotoxic dose-dependent decrease in the frequency of polychromatic erythrocytes in the peripheral blood of rats. In conclusion, since malathion increased both the peripheral blood and hippocampus DNA damage index using the Comet assay and increased the frequency of micronuclei in the total peripheral blood, it can be regarded as a potential mutagen/carcinogenic agent.
Antibody Responses to Plasmodium falciparum and Plasmodium vivax and Prospective Risk of Plasmodium spp. Infection Postpartum (2017)

AbstractPostpartum women may have an altered susceptibility to <i>Plasmodium falciparum</i> and <i>Plasmodium vivax</i>. The relationship between naturally acquired malarial immunity and susceptibility to malaria postpartum is yet to be determined. IgG levels were measured against <i>P. falciparum</i> and <i>P. vivax</i> antigens from delivery in 201 postpartum and 201 nonpregnant controls over 12 weeks. Associations between time-varying antibody levels and time to first microscopically confirmed species-specific infection were determined by Cox regression. Associations between antibody levels and prospective risk of <i>Plasmodium</i> infection were similar in postpartum and control women. A 2-fold increase in <i>P. falciparum</i> antibody levels was associated with increased prospective risk of <i>P. falciparum</i> infection (hazard ratio [HR] range = 1.37-1.94). Antibody levels against most <i>P. vivax</i> antigens displayed no association with prospective risk of <i>P. vivax</i> infection (HR range = 1.02-1.05) with the exception of <i>Pv</i>MSP1<sub>19</sub> antibodies that were weakly associated with prospective risk of <i>P. vivax</i> infection (HR = 1.14 (95% confidence interval = 1.02, 1.28) per 2-fold increase in levels). Associations between antibody levels and prospective risk of infection attenuated when adjusted for documented retrospective exposure. Serology may be a useful tool to predict and monitor women at increased risk of <i>P. falciparum</i> infection postpartum, particularly in the absence of a detailed history of retrospective infections.
wav2vec: Unsupervised Pre-Training for Speech Recognition (2019)

We explore unsupervised pre-training for speech recognition by learning representations of raw audio. wav2vec is trained on large amounts of unlabeled audio data and the resulting representations are then used to improve acoustic model training. We pre-train a simple multi-layer convolutional neural network optimized via a noise contrastive binary classification task. Our experiments on WSJ reduce WER of a strong character-based log-mel filterbank baseline by up to 36% when only a few hours of transcribed data is available. Our approach achieves 2.43% WER on the nov92 test set. This outperforms Deep Speech 2, the best reported character-based system in the literature while using two orders of magnitude less labeled training data.
Time series change detection using segmentation: A case study for land cover monitoring (2012)

Segmentation of a time series attempts to divide it into homogeneous subsequences, such that each of these segments are different from each other. A typical segmentation framework involves selecting a model that is used to represent the segment. In this paper, we investigate segmentation scores based on difference between models and propose two approaches for normalizing the difference based score. The first approach uses permutation testing to assign a p-value to model difference. The second approach builds on bootstrapping methodology used in statistics which estimates the null distribution of complex statistics whose standard errors are not analytically derivable by generating alternative versions of the data by a resampling strategy. More specifically, given a time series with either a single or two segments, we propose a method to estimate the distribution of model difference statistic for each segment. The proposed approach allows normalizing model difference statistic when complex models are being used in the segmentation algorithm. We study the strengths and weaknesses of the two normalizing approaches in the context of characteristics of land cover data such as seasonality and noise using synthetic and real data sets. We show that relative performance of normalization approaches can vary significantly depending on the characteristics of the data. We illustrate the utility of these approaches for detection of deforestation in Mato Grosso (Brazil).
Characterization of genome structure of amphotropic and ecotropic wild mouse retroviruses (1982)

We studied the RNA genomes of several wild mouse type C retroviruses by using RNase T1-oligonucleotide fingerprinting. The amphotropic and ecotropic viruses of field strain 1504 produced very similar oligonucleotide fingerprints, but each also had several unique oligonucleotides. All of these unique oligonucleotides were located in the env gene region and were probably responsible for the host range differences between these viruses, as well as the lymphomagenic and paralytogenic properties of the viruses. We obtained similar results with the amphotropic and ecotropic viruses of another field strain (4070), which was isolated from a mouse from a different trapping area. The amphotropic viruses of several field strains (strains 1504, 4070, and 1313) were more closely related than the ecotropic viruses of different strains (strains 1504, 4070, and 4996). These findings suggested that the genetic sequences of the amphotropic viruses are more conserved than those of ecotropic viruses isolated from the same wild mice.
Inter-view-predicted redundant pictures for viewpoint switching in multiview video streaming (2010)

Interactive selection of the desired viewpoint is one important feature in multiview video streaming. When receivers differ in the number of simultaneously displayed views, it is challenging to optimize the multiview coding structure particularly when it comes to the use of inter-view prediction and anchor picture frequency. This paper presents a coding and transmission scheme for streaming to clients of different display capabilities. The scheme saves transmission bandwidth by sending only those views that are displayed in a receiver. Furthermore, the scheme enables viewpoint switching through inter-view-predicted redundant pictures representing different sets of views being switched from and switched to. When switching happens at a switch point, an appropriate redundant picture is adaptively chosen based on which views were transmitted before and will be transmitted after the switch point. Experimental results show that the proposed scheme improves the rate-distortion (RD) performance compared to simple anchor picture insertion.
Rate Matrices for Analyzing Large Families of Protein Sequences (2001)

We propose and study a new approach for the analysis of families of protein sequences. This method is related to the LogDet distances used in phylogenetic reconstructions; it can be viewed as an attempt to embed these distances into a multidimensional framework. The proposed method starts by associating a Markov matrix to each pairwise alignment deduced from a given multiple alignment. The central objects under consideration here are matrix-valued logarithms L of these Markov matrices, which exist under conditions that are compatible with fairly large divergence between the sequences. These logarithms allow us to compare data from a family of aligned proteins with simple models (in particular, continuous reversible Markov models) and to test the adequacy of such models. If one neglects fluctuations arising from the finite length of sequences, any continuous reversible Markov model with a single rate matrix Q over an arbitrary tree predicts that all the observed matrices L are multiples of Q. Our method exploits this fact, without relying on any tree estimation. We test this prediction on a family of proteins encoded by the mitochondrial genome of 26 multicellular animals, which include vertebrates, arthropods, echinoderms, molluscs, and nematodes. A principal component analysis of the observed matrices L shows that a single rate model can be used as a rough approximation to the data, but that systematic deviations from any such model are unmistakable and related to the evolutionary history of the species under consideration.
Flame dynamics in the lean burnout zone of an RQL combustion chamber - response to primary zone velocity fluctuations (2022)

This study focuses on elucidating the flame dynamics of the lean burnout zone of an Rich-Quench-Lean (RQL) combustion chamber. With a new experimental approach of spatially separating the rich primary zone from the lean burnout zone, the latter can be investigated independently in terms of velocity fluctuations. Acoustically stiff mixing air ports in the lean burnout zone are ensured to prevent any acoustic interaction of the primary crossflow with the secondary mixing air jets. Therefore, defined boundary conditions at the mixing air inlets are used. Resulting no thermoacoustic interaction and additional flame dynamics are generated. In this specific case the lean burnout zone can be treated as a 2-port system allowing the application of existing evaluation methods e.g. acoustic determination of flame-transfer-functions (FTF) from the Rankine-Hugoniot (RH) equation or quantification of the heat release with chemiluminescence in combination with the Multi-Microphone-Method (MMM). Within this research, FTFs acoustically measured with the RH approach are presented and serve as a baseline for comparison with ones measured via a photomultiplier tube (PMT). It is found that the inverse diffusion flame in the burnout zone only reacts to fluctuations in the low frequency range and a clear low pass behavior is observed. The FTFs, calculated via the PMT match those from RH very well. Amplitude weighted phase images, recorded with a high-speed camera setup, visualize changes during excitation which complement and confirm the findings from the FTF.