gebhart/patrepeval huggingface dataset:
Recovering device drivers (2006)

This article presents a new mechanism that enables applications to run correctly when device drivers fail. Because device drivers are the principal failing component in most systems, reducing driver-induced failures greatly improves overall reliability. Earlier work has shown that an operating system can survive driver failures [Swift et al. 2005], but the applications that depend on them cannot. Thus, while operating system reliability was greatly improved, application reliability generally was not.To remedy this situation, we introduce a new operating system mechanism called a shadow driver . A shadow driver monitors device drivers and transparently recovers from driver failures. Moreover, it assumes the role of the failed driver during recovery. In this way, applications using the failed driver, as well as the kernel itself, continue to function as expected.We implemented shadow drivers for the Linux operating system and tested them on over a dozen device drivers. Our results show that applications and the OS can indeed survive the failure of a variety of device drivers. Moreover, shadow drivers impose minimal performance overhead. Lastly, they can be introduced with only modest changes to the OS kernel and with no changes at all to existing device drivers.
Functional diversity of E1A gene autoregulation among human adenoviruses (1992)

Autoregulation of the adenovirus E1A gene involves its constitutive expression and positively and negatively regulated transcription. Dissection of this process will identify basal-level cis elements and autoregulatory targets of the E1A promoter and functional domains within the trans-acting E1A gene products. In this report, the DNA sequence of the human subgroup B adenovirus type 3 (Ad3) E1A gene is presented and compared with that of the E1A genes of similar and distantly related human adenoviruses. The cDNA forms of the Ad3 E1A gene, corresponding to two major early mRNA species, are cloned, sequenced, and subcloned into plasmid expression vectors. Cotransfections of cell cultures are performed with Ad5 or Ad3 E1A gene expression plasmids and a reporter gene under control of the Ad5 or Ad3 E1A promoter. The Ad5 and Ad3 E1A promoters are similarly repressed by either serotype's 12S cDNA gene products. The Ad3 E1A promoter responds much more strongly than the Ad5 E1A promoter to transactivation by 13S cDNA gene products. In contrast, the 13S cDNA gene of Ad5 has greater transactivation activity than that of Ad3. Experiments with missense mutations of the Ad5 E1A gene indicate that transactivation of the Ad5 E1A promoter is weak, just reversing or balancing negative autorepression. Single amino acid substitutions in the conserved, repressive functional domain 2 of the E1A gene modulate transactivating activity that is usually associated with the separate and distal conserved functional domain 3. These results suggest a strong structure-function relationship influenced by the variable sequences separating these conserved domains.
Antithrombotic properties in rabbits of heparin and heparin fragments covalently coupled to human antithrombin III. (1985)

Clinical grade heparin is a very heterogeneous mucopolysaccharide, containing molecules with Mr ranging from 6,000 to 30,000 that have either a high affinity or a low affinity for antithrombin III (AT). In this study, the antithrombotic properties of intact high-affinity heparin (Mr = 15,000) and of two heparin fragments (h16, a 16-monosaccharide fragment, with Mr = 4,300, and h12, a 12-monosaccharide fragment, with Mr = 3,200) and of their functional covalent stoichiometric complexes with human AT were compared in a venous thrombosis stasis model in rabbits. Thrombosis was induced by injection of glass-activated human plasma and measured in a segment of the jugular vein that was isolated between two vascular clamps for 10 min. Injections of 55 micrograms/kg resulted in a clear antithrombotic effect for intact heparin, but not for the two fragments. Equivalent amounts (carbohydrate moiety) of covalent complexes of heparin or of both heparin fragments with human AT resulted in an antithrombotic effect lasting for 45-60 min. Injection of 110 micrograms/kg of heparin and of the heparin fragments yielded an antithrombotic effect, lasting 45-60 min; the corresponding amounts of covalent complexes caused an anti-thrombotic effect for 60-120 min. The free and conjugated fragments produced equal antithrombotic effects at equal plasma levels of anti-Factor Xa activity, but the specific antithrombotic activities of free and complexed intact heparin, on a molar basis, were 10-20-fold greater than those of the free and complexed heparin fragments. The plasma half-life of the covalent complexes of the heparin fragments with AT is, however, 10 times longer than that of the complex between intact heparin and AT and 30 times longer than that of free intact heparin. Covalent complexes between AT and heparin fragments could, therefore, be useful to maintain more stable levels of antithrombotic activity in plasma.
Excellent energy–power characteristics from a hybrid sodium ion capacitor based on identical carbon nanosheets in both electrodes (2016)

Sodium ion capacitor device fabricated by using peanut skin derived carbon nanosheets that has excellent electrochemical performance and promise for both low cost and environmentally friendliness.
A novel CAD system for local and global early diagnosis of Alzheimer's disease based on PIB-PET scans (2017)

This manuscript presents a Computer Aided Diagnosis (CAD) system to assist in the early diagnosis of Alzheimer's disease (AD) with the ability to provide a personalized diagnosis by visualizing the detected abnormality per brain regions (AAL atlas). The CAD system utilizes PiB-PET scans and consists of the following four essential stages-(1) a preprocessing step performs data reorientation, co-registration, and spatial normalization; (2) partitioning the brain into 116 labeled regions utilizing a brain atlas to facilitate local diagnosis; (3) extraction of features within each region using scale-invariant Laplacian of Gaussian (LoG) that detects the maximum or minimum of a radially symmetric intensity distribution; and (4) construction of two diagnosis layers (local and global) using a Support Vector Machine (SVM) classifier and its probabilistic variant (pSVM). The CAD system was tested on 84 PiB-PET scans (19 normal control (NC) and 65 mild cognitive impairment (MCI)) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The proposed system had a classification accuracy, sensitivity, and specificity of 100%.
A New Block-Based Method for HEVC Intra Coding (2016)

This paper presents a new block-based method for the High Efficiency Video Coding (HEVC) intra coding. First, we have found through analysis and test that the prediction errors on some pixels in each prediction block (PB) that are neighboring to the reference pixels would be no bigger than the corresponding coding errors. Based on this observation, the pixels in each PB are divided into two parts: half pixels are coded via a novel padding technique together with a constrained quantization algorithm (leading to around 3 dB gain under the same bit rate), whereas the other half are reconstructed by linear interpolations along a prediction direction by utilizing the neighboring reference pixels and the first half coded pixels. In the final implementation, a competition mechanism is employed between this new method and the original HEVC intra coding in order to choose the best mode for each PB. Experimental results show that about 2% BD-rate reduction has been achieved both for luma and chroma with respect to the original HEVC intra coding, whereas the encoder complexity increases by 130%, but the decoding time remains nearly unchanged.
Fabrication of Tetragonal Square Spiral Photonic Crystals (2001)

We present a simple, versatile technique for the fabrication of large, three-dimensional gap photonic crystals using glancing angle deposition (GLAD). A tetragonal lattice suitable for a large photonic band gap (PBG) can be synthesized by a regular array of square spiral structures grown from a simple, prepatterned substrate using physical vapor deposition and advanced substrate motion. Tetragonal square spiral crystals with a predicted PBG of up to 15% for a silicon structure can be produced in the visible, NIR, and IR spectrum. These PBG's exhibit good stability for large areas of parameter space that can be readily mapped out by the GLAD process through the variation of deposition parameters.
Wind profiling by a coherent Doppler lidar system VALIDAR with a subspace decomposition approach (2006)

The current nonlinear algorithm of the coherent Doppler lidar system VALIDAR at NASA Langley Research Center estimates wind parameters such as Doppler shift, power, wind velocity and direction by locating the maximum power and its frequency from the periodogram of the stochastic lidar returns. Due to the nonlinear nature of the algorithm, mathematically tractable parametric approaches to improve the quality of wind parameter estimates may pose a very little influence on the estimates especially in low signal-to-noise-ratio (SNR) regime. This paper discusses an alternate approach to accurately estimate the nonlinear wind parameters while preventing ambiguity in decision-making process via the subspace decomposition of wind data. By exploring the orthogonality between noise and signal subspaces expanded by the eigenvectors corresponding to the eigenvalues representing each subspace, a single maximum power frequency is estimated while suppressing erroneous peaks that are always present with conventional Fourier-transformbased frequency spectra. The subspace decomposition approach is integrated into the data processing program of VALIDAR in order to study the impact of such an approach on wind profiling with VALIDAR.
Response Selection for Multi-Party Conversations with Dynamic Topic Tracking (2020)

While participants in a multi-party multi-turn conversation simultaneously engage in multiple conversation topics, existing response selection methods are developed mainly focusing on a two-party single-conversation scenario. Hence, the prolongation and transition of conversation topics are ignored by current methods. In this work, we frame response selection as a dynamic topic tracking task to match the topic between the response and relevant conversation context. With this new formulation, we propose a novel multi-task learning framework that supports efficient encoding through large pretrained models with only two utterances at once to perform dynamic topic disentanglement and response selection. We also propose Topic-BERT an essential pretraining step to embed topic information into BERT with self-supervised learning. Experimental results on the DSTC-8 Ubuntu IRC dataset show state-of-the-art results in response selection and topic disentanglement tasks outperforming existing methods by a good margin. 1
Induction of Strain-Transcending Antibodies Against Group A PfEMP1 Surface Antigens from Virulent Malaria Parasites (2012)

Sequence diversity in pathogen antigens is an obstacle to the development of interventions against many infectious diseases. In malaria caused by Plasmodium falciparum, the PfEMP1 family of variant surface antigens encoded by var genes are adhesion molecules that play a pivotal role in malaria pathogenesis and clinical disease. PfEMP1 is a major target of protective immunity, however, development of drugs or vaccines based on PfEMP1 is problematic due to extensive sequence diversity within the PfEMP1 family. Here we identified the PfEMP1 variants transcribed by P. falciparum strains selected for a virulence-associated adhesion phenotype (IgM-positive rosetting). The parasites transcribed a subset of Group A PfEMP1 variants characterised by an unusual PfEMP1 architecture and a distinct N-terminal domain (either DBLα1.5 or DBLα1.8 type). Antibodies raised in rabbits against the N-terminal domains showed functional activity (surface reactivity with live infected erythrocytes (IEs), rosette inhibition and induction of phagocytosis of IEs) down to low concentrations (<10 µg/ml of total IgG) against homologous parasites. Furthermore, the antibodies showed broad cross-reactivity against heterologous parasite strains with the same rosetting phenotype, including clinical isolates from four sub-Saharan African countries that showed surface reactivity with either DBLα1.5 antibodies (variant HB3var6) or DBLα1.8 antibodies (variant TM284var1). These data show that parasites with a virulence-associated adhesion phenotype share IE surface epitopes that can be targeted by strain-transcending antibodies to PfEMP1. The existence of shared surface epitopes amongst functionally similar disease-associated P. falciparum parasite isolates suggests that development of therapeutic interventions to prevent severe malaria is a realistic goal.
Seismic Anisotropy Characterization in Heterogeneous Formations Using Borehole Sonic Data (2013)

Heterogeneity is a common phenomenon that needs to be taken into account when characterizing the elastic anisotropic properties of formations. Anisotropic elastic properties can be obtained from comprehensive borehole sonic datasets consisting of monopole compressional, dipole fast and slow shear, and Stoneley shear velocities. This can be done successfully through a methodology involving careful binning of the velocity data on the basis of independent, petrophysical information, followed by an inversion process that is carried out on each bin individually. The resulting table of anisotropic parameters per bin can then be used to derive, among other results, correlations between formation petrophysical and anisotropic properties. A new workflow was successfully applied to determine the elastic, transversely isotropic properties of heterogeneous sand-shale sequences. The results of the methodology have significant practical implications. One of these is that synthetics based on the anisotropy-corrected deviated well logs yield stronger and more apparent reflections, as well as a significantly different time-depth relation. Additional applications include the use of the inversion workflow results as inputs into anisotropic seismic velocity models and AVOs.
Peroxotitanate‐ and monosodium metal‐titanate compounds as inhibitors of bacterial growth (2011)

Sodium titanates are ion-exchange materials that effectively bind a variety of metal ions over a wide pH range. Sodium titanates alone have no known adverse biological effects but metal-exchanged titanates (or metal titanates) can deliver metal ions to mammalian cells to alter cell processes in vitro. In this work, we test a hypothesis that metal-titanate compounds inhibit bacterial growth; demonstration of this principle is one prerequisite to developing metal-based, titanate-delivered antibacterial agents. Focusing initially on oral diseases, we exposed five species of oral bacteria to titanates for 24 h, with or without loading of Au(III), Pd(II), Pt(II), and Pt(IV), and measuring bacterial growth in planktonic assays through increases in optical density. In each experiment, bacterial growth was compared with control cultures of titanates or bacteria alone. We observed no suppression of bacterial growth by the sodium titanates alone, but significant (p < 0.05, two-sided t-tests) suppression was observed with metal-titanate compounds, particularly Au(III)-titanates, but with other metal titanates as well. Growth inhibition ranged from 15 to 100% depending on the metal ion and bacterial species involved. Furthermore, in specific cases, the titanates inhibited bacterial growth 5- to 375-fold versus metal ions alone, suggesting that titanates enhanced metal-bacteria interactions. This work supports further development of metal titanates as a novel class of antibacterials.
The mass loading monitor—fundamental principles and proof of concept (2011)

The operating principle, and proof-of-concept data, for a physical device (the mass loading monitor) to alert plant operators when airborne dust approaches the minimum explosive concentration (MEC) level are presented. The MEC, stated as g m−3, is dependent upon the material and environmental factors. Values as low as 30 g m−3 must be evaluated. The measurement strategy, a temporal integration of the piston face pressure as the air-plus-dust charge is impulsively expelled from a cylinder compared with the same integral for an air-only sample, is shown to yield the mass loading (xx g m−3) of the airborne dust. This measurement strategy is demonstrated using a dedicated test apparatus. This demonstration establishes the proof of concept.
An Ontology-Aware Framework for Audio Event Classification (2020)

Recent advancements in audio event classification often ignore the structure and relation between the label classes available as prior information. This structure can be defined by ontology and augmented in the classifier as a form of domain knowledge. To capture such dependencies between the labels, we propose an ontology-aware neural network containing two components: feed-forward ontology layers and graph convolutional networks (GCN). The feed-forward ontology layers capture the intra-dependencies of labels between different levels of ontology. On the other hand, GCN mainly models interdependency structure of labels within an ontology level. The framework is evaluated on two benchmark datasets for single-label and multi-label audio event classification tasks. The results demonstrate the proposed solutions efficacy to capture and explore the ontology relations and improve the classification performance.
Discovery of Potent, Orally Bioavailable Inhibitors of Human Cytomegalovirus (2016)

A high-throughput screen based on a viral replication assay was used to identify inhibitors of the human cytomegalovirus. Using this approach, hit compound 1 was identified as a 4 μM inhibitor of HCMV that was specific and selective over other herpes viruses. Time of addition studies indicated compound 1 exerted its antiviral effect early in the viral life cycle. Mechanism of action studies also revealed that this series inhibited infection of MRC-5 and ARPE19 cells by free virus and via direct cell-to-cell spread from infected to uninfected cells. Preliminary structure-activity relationships demonstrated that the potency of compound 1 could be improved to a low nanomolar level, but metabolic stability was a key optimization parameter for this series. A strategy focused on minimizing metabolic hydrolysis of the N1-amide led to an alternative scaffold in this series with improved metabolic stability and good pharmacokinetic parameters in rat.
Image-derived second-order differential microphones (1994)

Second-order differential toroidal and unidirectional microphones derived using a bipolar first-order differential sensor and a reflecting plane are described. The bipolar first-order differential microphone is positioned with its axis perpendicular to and suspended a few centimeters from a large acoustically reflecting surface. The resulting sensor image is phase reversed resulting in a transducer that is a linear quadrupole. The linear quadrupole can be described by two dimensions, the distance corresponding to the dipole distance and twice the distance from the reflecting plane. If the reflecting surface is large enough or if the wall of a room is used, the resulting microphone becomes a second-order differential unidirectional microphone. The match between the sensor and its image from a good acoustic reflector results in a second-order differential microphone with 3-dB beamwidth of ±33° and no grating lobes below 3 kHz for a 2.5-cm spacing between the sensor and reflecting surface. A wall-mounted toroid can be formed by using two bipolar first-order sensors at right angles to each other and with the axis of each sensor at 45° to the reflecting surface and a spacing between transducers that is twice the height of the transducers from the reflecting plane. A table-mounted toroid can be realized by properly combining a filtered version of a suspended first-order sensor and an omnidirectional sensor flush mounted to the reflecting table top.
Efficient production of a bioactive, multiple disulfide‐bonded protein using modified extracts of <i>Escherichia coli</i> (2003)

In this report, we demonstrate that a complex mammalian protein containing multiple disulfide bonds is successfully expressed in an E.coli-based cell-free protein synthesis system. Initially, disulfide-reducing activities in the cell extract prevented the formation of disulfide bonds. However, a simple pretreatment of the cell extract with iodoacetamide abolished the reducing activity. This extract was still active for protein synthesis even under oxidizing conditions. The use of a glutathione redox buffer coupled with the DsbC disulfide isomerase and pH optimization produced 40 microg/mL of active urokinase protease in a simple batch reaction. This result not only demonstrates efficient production of complex proteins, it also emphasizes the control and flexibility offered by the cell-free approach.
A Review of Ground-Effect Diffuser Aerodynamics (2018)

The ground-effect diffuser has become a major aerodynamic device on open-wheel racing and sports cars. Accordingly, it is widely considered to be indispensable to their aerodynamic performance, largely due to its significant downforce contribution. However, the physics and characteristics that determine how it generates downforce and its application in the auto racing industry require an in-depth analysis to develop an understanding. Furthermore, research that could generate further performance improvement of the diffuser has not been defined and presented. For these reasons, this review attempts to create a systematic understanding of the physics that influence the performance of the ground-effect diffuser. As a means of doing this, the review introduces research data and observations from various relevant studies on this subject. It then investigates advanced diffuser concepts mainly drawn from the race car industry and also proposes a further research direction that would advance the aerodynamic performance of the diffuser. It is concluded that although the diffuser will continue to be paramount in the aerodynamic performance of racing cars, research is needed to identify means to further enhance its performance.
Channel and noise normalization using affine transformed cepstrum (2002)

The paper addresses the environmental mismatch problem that arises from noise and channel variabilities. A new feature mapping technique based on an optimal affine transform of the cepstrum is proposed to solve the mismatch problem observed over the speaker recognition systems. It is designed based on the fact that both the channel and noise interferences basically cause the cepstrum space to undergo an affine transformation. By taking an inverse transformation, one can easily decouple from the speech the effects of the channel and noise. Alternatively, one can take a forward transform of the training data to simulate the operating conditions.