gebhart/patrepeval huggingface dataset:
Comparison of Cyclosporine Measurement in Whole Blood by High-Performance Liquid Chromatography, Monoclonal Fluorescence Polarization Immunoassay, and Monoclonal Enzyme-Multiplied Immunoassay (1992)

Monitoring of cyclosporine concentrations in whole blood is used routinely as a guide to adjusting dose so as to achieve optimal therapeutic benefit with minimal adverse effects. In the present study, we have compared a specific high-performance liquid chromatography (HPLC) assay with a fluorescence polarization immunoassay (TDx) and an enzyme-multiplied immunoassay (Emit). Both Emit and TDx assays employ a monoclonal antibody to cyclosporin A and therefore have the potential for a high degree of specificity. Blood specimens (EDTA as anticoagulant) were obtained from 113 patients (71 renal transplants, 17 liver transplants, and 25 other categories) taking cyclosporine and analysed by all three methods. There were significant correlations between results for HPLC and Emit (Emit = 10.54 + 1.07 x HPLC; r2 = 0.82, p less than 0.001) and between results for HPLC and TDx (TDx = 9.16 + 1.42 x HPLC; r2 = 0.82, p less than 0.001). Compared to HPLC analysis, 74% and 96%, respectively, of Emit and TDx results were to the left of the line of identity. The TDx monoclonal antibody appears to have a lesser degree of specificity than that used in the Emit assay. Mean concentrations of cyclosporine measured by Emit and TDx were 17% and 51% higher, respectively, than those measured by HPLC. Because of this overestimation, we suggest that both Emit and TDx methods may find their most appropriate use in routine therapeutic monitoring of renal transplant patients in whom metabolite concentrations are less variable over time.
LAVEA: Latency-Aware Video Analytics on Edge Computing Platform (2017)

We present LAVEA, a system built for edge computing, which offloads computation tasks between clients and edge nodes, collaborates nearby edge nodes, to provide low-latency video analytics at places closer to the users. We have utilized an edge-first design to minimize the response time, and compared various task placement schemes tailed for inter-edge collaboration. Our results reveal that the client-edge configuration has task speedup against local or client-cloud configurations.
Synthesis of peptide analogs of prothrombin precursor sequence 5-9. Substrate specificity of vitamin K dependent carboxylase (1981)

Thirty-five analogues of Phe-Leu-Glu-Glu-Leu, the pentapeptide sequence 5-9 of bovine prothrombin precursor, were synthesized and assayed as potential substrates or inhibitors of rat liver vitamin K dependent carboxylase. Carboxylation of substrate was determined by measuring the incorporation of carbon-24 labeled bicarbonate into product. Changes in substrate carboxylation produced by changing peptide chain length, amino acid chirality, or the distance separating the peptide chain backbone from the carboxyl group were measured. The data suggest that the carboxylase carboxylates L-glutamic acid residues and does not carboxylate L-aspartic acid, L-homoglutamic acid, glutamine, or D-glutamic acid residues; tri-through pentapeptides are better substrates than mono- or bis(amino acid) derivatives, and hydrophobic groups added to the N-terminus can produce better substrates for the enzyme. None of the synthetic substrates is carboxylated as effectively as the endogenous protein substrates for the enzyme. The effect of structure on additional parameters affecting carboxylation is discussed.
Unique Opportunities for Microstructural Engineering with Duplex and Laminar Ceramic Composites (1992)

Duplex (two‐phase) microstructures and laminar composites offer some unique opportunities for improving the room‐temperature mechanical reliability (e.g., flaw tolerance) and the high‐temperature microstructural stability (e.g., resistance to grain growth and creep damage) of structural ceramic materials. Examples illustrating the approach to designing novel multiphase microstructures and laminar composites with enhanced structural reliability are given. These are based on current work on various alumina‐based ceramics as well as zirconia‐, silicon nitride‐, and silicon carbide‐containing ceramics. Critical issues and areas for future work are discussed.
Reverse time migration in tilted transversely isotropic media (2004)

This paper presents a reverse time migration (RTM) method for the migration of shot records in tilted transversely isotropic (TTI) media.It is based on the tilted TI acoustic wave equation that was derived from the dispersion relation.The RTM is a full depth migration allowing for velocity to vary laterally as well as vertically and has no dip limitations.The wave equation is solved by a tenth-order finite difference scheme.Using 2D numerical models, we demonstrate that ignoring the tilt angle will introduce both lateral and vertical shifts in imaging.The shifts can be larger than 0.5 wavelength in the vertical direction and 1.5 wavelength in the lateral direction.
Multiplex Mutagenically Separated Polymerase Chain Reaction Assay for Rapid Detection of Human Mitochondrial DNA Variations in Coding Area (2008)

Recently, it has been recognized that information in the mitochondrial DNA (mtDNA) coding region can provide additional forensic discrimination with respect to the standard typing of the D-loop region, increasing the forensic power of mtDNA testing, which is sometimes rather limited. In the present study, we simultaneously typed ten single nucleotide polymorphisms (SNP) in the coding region by use of mutagenically separated polymerase chain reaction (MS-PCR) in the Chinese Chengdu population. This technique, in which different-size allele-specific primers were used, specifically amplified both alleles of mtDNA in the same reaction. Subsequent gel electrophoresis showed ten of the allelic products of different loci. Using multiplex MS-PCR, 30 primers were added simultaneously into one reaction tube to identify ten SNPs. The mtDNA variations of 160 individuals from the Chinese Chengdu population were examined and classified into 18 haplotypes. The multiplex MS-PCR method is suitable for large-scale screening studies of mtDNA variability because it is both rapid and economical.
Consistency control for distributed interactive media (2001)

In this paper we present a generic consistency control service for distributed interactive media, i.e. media which allow a distributed group of users to interact with the medium itself. Consistency control is vital to these media since they typically require that a local copy of the medium's state be maintained by each user's application. Our service helps the applications to keep the local state copies consistent. The main characteristics of this service are as follows: a significant number of inconsistencies are prevented by using a mechanism called local lag. Inconsistencies that cannot be prevented are repaired by an improved timewarp algorithm that can be executed locally without burdening the network or the applications of other users. Exceptional situations and consistency during late-join situations are supported by a consistent state request mechanism. Moreover, the service also supports the application in detecting intention conflicts between the actions of distinct users. The major part of this functionality is based on a media model and the application level protocol for distributed interactive media (RTP/I) and can thus be reused by arbitrary RTP/I-based applications. In order to demonstrate the feasibility of our approach and to evaluate its performance we have integrated the generic consistency service into a shared whiteboard system.
Mix-and-Match Tuning for Self-Supervised Semantic Segmentation (2017)

Deep convolutional networks for semantic image segmentation typically require large-scale labeled data, e.g. ImageNet and MS COCO, for network pre-training. To reduce annotation efforts, self-supervised semantic segmentation is recently proposed to pre-train a network without any human-provided labels. The key of this new form of learning is to design a proxy task (e.g. image colorization), from which a discriminative loss can be formulated on unlabeled data. Many proxy tasks, however, lack the critical supervision signals that could induce discriminative representation for the target image segmentation task. Thus self-supervision's performance is still far from that of supervised pre-training. In this study, we overcome this limitation by incorporating a "mix-and-match" (M&M) tuning stage in the self-supervision pipeline. The proposed approach is readily pluggable to many self-supervision methods and does not use more annotated samples than the original process. Yet, it is capable of boosting the performance of target image segmentation task to surpass fully-supervised pre-trained counterpart. The improvement is made possible by better harnessing the limited pixel-wise annotations in the target dataset. Specifically, we first introduce the "mix" stage, which sparsely samples and mixes patches from the target set to reflect rich and diverse local patch statistics of target images. A "match" stage then forms a class-wise connected graph, which can be used to derive a strong triplet-based discriminative loss for fine-tuning the network. Our paradigm follows the standard practice in existing self-supervised studies and no extra data or label is required. With the proposed M&M approach, for the first time, a self-supervision method can achieve comparable or even better performance compared to its ImageNet pre-trained counterpart on both PASCAL VOC2012 dataset and CityScapes dataset.
Detecting anomalies in dynamic rating data (2014)

Rating data is ubiquitous on websites such as Amazon, TripAdvisor, or Yelp. Since ratings are not static but given at various points in time, a temporal analysis of rating data provides deeper insights into the evolution of a product's quality. In this work, we tackle the following question: Given the time stamped rating data for a product or service, how can we detect the general rating behavior of users as well as time intervals where the ratings behave anomalous? We propose a Bayesian model that represents the rating data as sequence of categorical mixture models. In contrast to existing methods, our method does not require any aggregation of the input but it operates on the original time stamped data. To capture the dynamic effects of the ratings, the categorical mixtures are temporally constrained: Anomalies can occur in specific time intervals only and the general rating behavior should evolve smoothly over time. Our method automatically determines the intervals where anomalies occur, and it captures the temporal effects of the general behavior by using a state space model on the natural parameters of the categorical distributions. For learning our model, we propose an efficient algorithm combining principles from variational inference and dynamic programming. In our experimental study we show the effectiveness of our method and we present interesting discoveries on multiple real world datasets.
Storage of Diffie-Hellman Keys in the Domain Name System (DNS) (1999)

A standard method for storing Diffie-Hellman keys in the Domain Name System is described which utilizes DNS KEY resource records.
Bacterial Production of the Tunicate-Derived Antitumor Cyclic Depsipeptide Didemnin B (2011)

Natural products obtained from marine invertebrates such as sponges and tunicates are attractive sources of drugs. However, a critical obstacle in the development of these compounds is the problem of supply. In most cases, neither chemical synthesis nor mariculture of invertebrates is economically feasible. Due to structural similarities, many marine natural products are suspected to be produced by associated microorganisms. A favorable strategy for the production of such compounds is to use culturable microorganisms. Here we report that didemnin B, a tunicate-derived depsipeptide, has been isolated from a culturable bacterium, Tistrella mobilis YIT 12409.
The Noncollagenous Domain 1 of Type X Collagen (1999)

In this study, we test the hypothesis that the carboxyl noncollagenous (NC1) domain of collagen X is sufficient to direct multimer formation without a triple helix. Two peptides containing the NC1 domain of avian collagen X have been synthesized using a bacterial expression system and their properties characterized. One peptide consists only of the NC1 domain, and the other is a chimeric molecule with a noncollagenous A domain of matrilin-1 fused to the N terminus of NC1. The NC1 peptide alone forms a 45-kDa trimer under native conditions, suggesting that NC1 contains all the information for trimerization without any triple helical residues. This trimeric association is highly thermostable without intermolecular disulfide bonds. This indicates that the NC1 domain contributes to the remarkable structural stability of collagen X. Chemical cross-linking of the NC1 trimer results in a series of varying sized multimers, the smallest of which is a trimer. Therefore the NC1 trimer is sufficient to form higher order multimers. The chimeric A-NC1 peptide forms a homotrimer by itself, and a series of heterotrimers with the NC1 peptide via the NC1 domain. Thus the NC1(X) domain directs multimer formation, even in a noncollagenous molecule.
Neural Engineering: Computation, Representation, and Dynamics in Neurobiological Systems (2004)

For years, researchers have used the theoretical tools of engineering to understand neural systems, but much of this work has been conducted in relative isolation. In Neural Engineering, Chris Eliasmith and Charles Anderson provide a synthesis of the disparate approaches current in computational neuroscience, incorporating ideas from neural coding, neural computation, physiology, communications theory, control theory, dynamics, and probability theory. This synthesis, they argue, enables novel theoretical and practical insights into the functioning of neural systems. Such insights are pertinent to experimental and computational neuroscientists and to engineers, physicists, and computer scientists interested in how their quantitative tools relate to the brain. The authors present three principles of neural engineering based on the representation of signals by neural ensembles, transformations of these representations through neuronal coupling weights, and the integration of control theory and neural dynamics. Through detailed examples and in-depth discussion, they make the case that these guiding principles constitute a useful theory for generating large-scale models of neurobiological function. A software package written in MatLab for use with their methodology, as well as examples, course notes, exercises, documentation, and other material, are available on the Web.
Velocity model building using migration to residual time (2006)

A new velocity model updating technique is presented which aims to focus the diffraction traveltime responses associated with locally coherent events in the zero‐offset poststack time domain. The method is a combination of tomographic inversion for the zero‐offset stationary point and residual traveltime tomography. Additionally, a criterion is derived which forces all migrated images to have the same dip at the depth points associated with the picks in the poststack time domain. Traveltime residuals are picked in common‐image gathers which are obtained by individual migration to residual time of each pick. There is no need to perform a complete prestack depth migration. Picking of residual moveout is not restricted to analytic moveout descriptions. Instead, residual moveout is picked by a cross‐correlation of the common‐image gather in residual time with the corresponding zero‐offset stacked trace. Migration to residual time is formulated in the angle domain and will be explained in detail. The applicability of the method is demonstrated by a data example.
Impact of mask alignment on the tunneling field effect transistor (TFET) (2005)

The tunneling field effect transistor (TFET) is a standard CMOS process flow compatible device which shows improved short channel characteristics and lower static power consumption. The device is generated by the p-implant layer overlapping the source extension. A test-structure is proposed to investigate the impact of the alignment of the p-implant mask on the device characteristics.
Markov edit distance (2004)

Edit distance was originally developed by Levenstein several decades ago to measure the distance between two strings. It was found that this distance can be computed by an elegant dynamic programming procedure. The edit distance has played important roles in a wide array of applications due to its representational efficacy and computational efficiency. To effect a more reasonable distance measure, the normalized edit distance was proposed. Many algorithms and studies have been dedicated along this line with impressive performances in recent years. There is, however, a fundamental problem with the original definition of edit distance that has remained elusive: its context-free nature. In determining the possible actions, i.e., insertion, deletion, and substitution, no systematic consideration was given to the local behaviors of the string/pattern in question that indeed encompass great amount of useful information regarding its content. In this paper, inspired by the success of the Markov Random Field theory, a new edit distance called Markov edit distance (MED) within the dynamic programming framework is proposed to take full advantage of the local statistical dependencies in the pattern in order to arrive at enhanced matching performance. Within this framework, two specialized distance measures are developed: The reshuffling MED to handle cases where a subpattern in the target pattern is the reshuffles of that in the source pattern, and the coherence MED which is able to incur local content based substitution, insertion, and deletion. The applications based on these two MEDs in string matching are then explored, whereof encouraging empirical results have been observed.
Morphology and Mechanical Properties of Crystalline Polyolefin Materials. (2001)

Structural factors controlling tensile deformation of crystalline polyolefins such as polyethylene (PE) and polypropylene (PP) as well as various polyolefin blends were investigated. It was found that the miscibility of the amorphous region of PP with rubbery polyolefin materials strongly affects the mechanical behavior. Furthermore, we introduced a new structural unit, i.e. the lamellar cluster, which is several stacked lamellae bound by some tie molecules to describe the yielding behavior of spherulitic polymers. It was shown that the tie molecules between the adjacent lamellar clusters plays a central role in tensile yielding process.
A Review of Eulerian Simulation of Geldart A Particles in Gas-Fluidized Beds (2009)

Although great progress has been made in modeling the gas fluidization of Geldart B and D particles and dilute gas−solid flow by standard Eulerian approach, researchers have shown that, because of the limitation of computational resources and the formation of subgrid-scale (SGS) heterogeneous structures, Eulerian model with a suitable SGS model for constitutive law is necessary to simulate the hydrodynamics of large-scale gas-fluidized beds containing Geldart A particles. In this article, a state-of-the-art review of Eulerian modeling of Geldart A particles in gas-fluidized beds is presented. The available methods for establishing SGS models are classified into six categories, that is, empirical correlation method, scaling factor method, structure-based method, modified Syamlal and O’Brien drag correlation method, EMMS-model-based method, and correlative multiscale method. The basic ideas of those methods, as well as their advantages and disadvantages, are reviewed. Finally, directions for future research are indicated.
A Novel Focal Tversky Loss Function with Improved Attention U-Net for Lesion Segmentation (2023)

<p>We propose a generalized focal loss function based on the Tversky index to address the issue of data imbalance in medical image segmentation. Compared to the commonly used Dice loss, our loss functionachievesa better trade offbetween precision and recall when training on small structures such as lesions. To evaluate our loss function, we improve the attention U-Net model by incorporating an image pyramid to preserve contextual features. We experiment on the BUS 2017 dataset and ISIC 2018 dataset where lesions occupy 4.84% and 21.4% of the images area and improve segmentation accuracy when compared to the standard U-Net by 25.7% and 3.6%, respectively.</p> <p><br></p>
Visible Photocatalytic Activity Of Vanadium Doped With Titanium Dioxide For Biomedical Applications (2015)

Infections are a common post-operative complication associated with high mortality rates after surgical procedures. Coating surgical instruments or implants with antibacterial or antifungal substances may reduce the occurrence rate of infections acquired during surgical operations. The high incidence rate of post-operative infections, caused for example by the implantation of biomedical devices and/or the general hospital environment, has a severe impact on patients' health. However, no studies have been reported on the prevalence of active species of fungal and bacteria. The present study systematically examines the antibacterial properties (against Staphylococcus, Bacillus, Serratia and Pseudomonas) of nanostructured thin films based on pure TiO2 and TiO2 with Vanadium as an additive, created using a simple and cost effective sol-gel process. The thin films were deposited on glass and Si substrates and their structural and morphological properties were investigated by standard spectroscopic techniques such as X-Ray Diffraction, Scanning Electron Microscopy and Atomic Force Microscopy. The drop test method was used to test for antifungal and antibacterial properties. Our results indicate that increased V concentrations are associated with increased antimicrobial activity in thin films based on TiO2:V.
Multiple sensor collision avoidance system for automotive applications using an IMM approach for obstacle tracking (2003)

In this paper a multi-sensor collision avoidance system is presented for automotive applications. For obstacle detection and tracking, millimeter wave (MMW) radar and a far infrared (FIR) camera are chosen in order to provide object lists to the sensors' trackers respectively. The algorithm for track management, data association, filtering and prediction for both sensors is also presented, focusing on Kalman filtering. Thus, an interacting multiple model (IMM) filter is designed for coping with all possible modes in which a car may be. Finally, a distributed fusion architecture using a central track file for the objects' tracks is adopted and described analytically. The results of the work will be used, among others, in the European co-funded project "EUCLIDE".