gebhart/patrepeval huggingface dataset:
Knowledge-based hierarchical sketch understanding (2005)

This article presents a knowledge-based framework for sketch understanding. Compared to traditional sketch understanding systems, it has two significant features: (1) knowledge-based. This makes the system independent of applied domain. Users can easily design an ontology-based domain knowledge base to guide the understanding process. (2) hierarchical approach. The sketch understanding process is divided into three phases: token recognition, salient symbol recognition and integral recognition. During all these phases, domain knowledge is used as a guider. In addition, a domain knowledge base of UML class diagram is presented as a case study of this framework, in which the details of how to design ontology-based knowledge base and how to implement a hierarchical recognition are given. Some UML class diagram sketches are used as experiments, which produce satisfactory results.
Phonetic recognition using hidden Markov models and maximum mutual information training (2003)

The application of maximum-mutual-information (MMI) training to hidden Markov models (HMMs) is studied for phonetic recognition. MMI training has been proposed as an alternative to standard maximum-likelihood (ML) training. In practice, MMI training performs better (produces models that are more accurate) than ML training. The fundamental notions of HMM, ML and MMI training are reviewed, and it is shown how MMI training can be applied easily to the case of phonetic models and phonetic recognition. Some computational heuristics are proposed to implement these computations practically. Some experiments (training and recognition) are detailed that show that the phonetic error rate decreases significantly when MMI training is used, as compared with ML training.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Array wide instantaneous bandwidth capability from using a distributed architecture approach (2002)

High range resolution waveforms are required in future shipboard radar systems to support TBM discrimination and target ID modes. These modes require significantly improved range resolution compared to existing shipboard radar system search and track waveforms. One potential antenna system approach for addressing this new requirement is to combine stretch pulse compression with phase/frequency beamsteering at the subarray level. A feasibility study of using this combination has been performed to assess this approach against a set of strawman TBM discrimination requirements. A simulation was developed to observe and quantify first-order performance trends due to various parameters of the system.
Group B <i>Streptococcus</i> suppression of phagocyte functions by protein-mediated engagement of human Siglec-5 (2009)

Group B Streptococcus (GBS) is a leading cause of invasive bacterial infections in human newborns. A key GBS virulence factor is its capsular polysaccharide (CPS), displaying terminal sialic acid (Sia) residues which block deposition and activation of complement on the bacterial surface. We recently demonstrated that GBS Sia can bind human CD33-related Sia-recognizing immunoglobulin (Ig) superfamily lectins (hCD33rSiglecs), a family of inhibitory receptors expressed on the surface of leukocytes. We report the unexpected discovery that certain GBS strains may bind one such receptor, hSiglec-5, in a Sia-independent manner, via the cell wall-anchored beta protein, resulting in recruitment of SHP protein tyrosine phosphatases. Using a panel of WT and mutant GBS strains together with Siglec-expressing cells and soluble Siglec-Fc chimeras, we show that GBS beta protein binding to Siglec-5 functions to impair human leukocyte phagocytosis, oxidative burst, and extracellular trap production, promoting bacterial survival. We conclude that protein-mediated functional engagement of an inhibitory host lectin receptor promotes bacterial innate immune evasion.
Innate Immunity SNPs are Associated with Risk for Severe Sepsis after Burn Injury (2006)

Carriage of variant alleles at immune response genes were associated with increased risk for severe sepsis after burn injury.
Adaptive Time-Frequency Analysis for Noise Reduction in an Audio Filter Bank With Low Delay (2016)

In this paper, an adaptive time-frequency analysis scheme is proposed along with a synthesis scheme using an asymmetric window. The proposed scheme is suitable for audio noise reduction with a low delay in the range of 0 to 4 ms. The main novelty of the paper is the adaptive analysis scheme that can adapt to the incoming signal independently in both time and frequency by employing a complex filter on a DFT modulated filter bank. A number of adaptive time-frequency schemes are described that are suitable for low delay and low computational complexity. The adaptive time-frequency scheme is used for the computation of noise reduction gain factors, which are then adopted in a nonadaptive analysis/synthesis scheme. The synthesis scheme uses an asymmetric window to achieve a good tradeoff between low delay and a sharp frequency response. Examples are given of the adaptive analysis and measurements of the synthesis scheme are given to show that the filter bank has a gain dependent nonlinear phase response. Finally, a noise reduction task is performed that shows good performance compared to reference implementations in terms of segmental SNR and PESQ.
Fast time series classification using numerosity reduction (2006)

Many algorithms have been proposed for the problem of time series classification. However, it is clear that one-nearest-neighbor with Dynamic Time Warping (DTW) distance is exceptionally difficult to beat. This approach has one weakness, however; it is computationally too demanding for many realtime applications. One way to mitigate this problem is to speed up the DTW calculations. Nonetheless, there is a limit to how much this can help. In this work, we propose an additional technique, numerosity reduction, to speed up one-nearest-neighbor DTW. While the idea of numerosity reduction for nearest-neighbor classifiers has a long history, we show here that we can leverage off an original observation about the relationship between dataset size and DTW constraints to produce an extremely compact dataset with little or no loss in accuracy. We test our ideas with a comprehensive set of experiments, and show that it can efficiently produce extremely fast accurate classifiers.
Formal techniques for an ITSEC-E4 secure gateway (2002)

We describe the method used to develop a gateway capable of meeting the ITSEC E4 requirements. The security policy was formally modelled and proven consistent with the functional specifications by means of an interactive theorem prover. The formalisms were used to assist in the design of the security architecture.
An introduction to NCEP SREF aviation project (2004)

NCEP’s Short Range (1-3-day) Ensemble Forecast (SREF) system provides mesoscale probabilistic forecast information, and has undergone several stages of development at the NCEP Environmental Modeling Center (EMC) since 1996 (Tracton et al 1998, Du and Tracton 2001, Du et al 2004). It has been well understood that the forecast skill of deterministic, computer-generated weather forecasts is limited by the chaotic processes in the atmosphere which bring either errors in the initial/boundary conditions or uncertainties in the model (Lorenz 1963). Generally, a single deterministic model will produce one possible solution to a weather system but may miss the actual situation. One approach called an Ensemble Forecast (EF) was proposed to try to capture a range of possible solutions and take into account the uncertainties in both the initial/boundary conditions and the models (Epstein 1969, Leith 1974, Palmer et al 1990). Since then, ensemble forecasts were launched and achieved significant progress at several weather centers in the world (NCEP, European Centre for Medium Range Weather Forecasts, US Navy, Japan Meteorological Agency, Canadian Meteorological Centre, etc). NCEP EMC is one of the pioneers in researching and developing EF systems, either on the global scale or mesoscale. The history of the NCEP Ensemble Prediction System (EPS) can be traced back to the early 1990s, when NCEP introduced and then implemented operationally its medium range global EPS (Tracton and Kalnay 1993, Toth and Kalnay, 1993, 1997). Motivated by the success of its global EPS, NCEP initiated the ensemble forecasting system for short range applications, using the Eta and the Regional Spectral Model (RSM) in the middle of 90s (Brooks, et al 1995, Tracton et al 1998). The Short Range Ensemble Forecast (SREF) system has undergone testing and forecast evaluation, and has shown promise in improving forecast skill for short-range forecasts (Hamill et al 1997, Du et al 1997, Stensrud, et al 2003). The SREF system was implemented operationally by NCEP in 2001, and is still being improved (Du and Tracton 2001, Du, et al 2004). In 2002, under FAA sponsorship, NCEP began its SREF Aviation Project in an effort to bring ensemble techniques to aviation forecasting by further postprocessing SREF generated output to create aviation-based forecast products for icing, turbulence and visibility, etc. This work is also applicable to the NCEP Aviation Weather Center (AWC) and NOAA Aviation Service Branch missions. This paper will present an overview of the SREF aviation project, including its configuration, post processing procedure, and product generation. Some concepts of verification and evaluation for the ensemble forecast are briefly discussed. Finally, the future plans for the SREF aviation project are presented.
Prothrombin complex concentrate in surgical patients: retrospective evaluation of vitamin K antagonist reversal and treatment of severe bleeding (2009)

Prothrombin complex concentrate application effectively reduced international normalized ratios in anticoagulation reversal, allowing surgical procedures and interventions without major bleeding. In bleeding patients, the improvement in coagulation after prothrombin complex concentrate administration was judged to be clinically significant.
Identification of a vitamin K‐dependent carboxylase in the venom duct of a <i>Conus</i> snail (1997)

Peptides from the venom ducts of cone snails (genus Conus) contain gamma-carboxyglutamate residues. The gamma-glutamyl carboxylase responsible for this post-translational modification is localized in the microsomal fraction, strictly dependent on vitamin K, activated by ammonium sulfate, and is associated with endogenous substrate. The K(m) of the enzyme for vitamin K is comparable to that for the bovine carboxylase. However, a propeptide containing substrate related to the blood coagulation protein factor IX, a highly efficient substrate for the bovine enzyme, was poorly carboxylated by the Conus enzyme, suggesting differences in gamma-carboxylase recognition signal sequences and/or structural requirements at the carboxylation site.
1-Ethoxyethylidene, a New Group for the Stepwise SPPS of Aminooxyacetic Acid Containing Peptides (2008)

For more than a decade, the oxime ether ligation has proven to be one of the most efficient technique for the preparation of various peptide conjugates. However, despite numerous reports, the preparation of aminooxy-containing peptides is still hampered by N-overacylation of the NH-O function either during its incorporation or through the peptide-chain elongation. This restricts the introduction of protected-NH-O function at the last acylation step and prevents the use of standard solid-phase peptide synthesis (SPPS) procedures for the preparation of more complex aminooxy-peptides. We have studied the coupling of modified Fmoc-lysine containing either N-Boc- or N,N'-bis-Boc-protected aminooxyacetic acids (Aoa) during the elongation of the peptide chain and found that none of them is adequate. To circumvent this limitation, we propose to protect the Aoa moiety with a 1-ethoxyethylidene group (Eei) to provide 2-(1-ethoxyethylideneaminooxy)acetic acid building block. We showed that the Eei group is fully compatible with standard SPPS conditions and safely allows the multiple incorporation of the aminooxy functionality into the growing peptide. Since Eei-protected Aoa remains as flexible as normal amino acids in peptide synthesis, it may become the rule for the straightforward preparation of aminooxy peptides.
Quantitation of cell-matrix adhesion using confocal image analysis of focal contact associated proteins and interference reflection microscopy (1997)

We have developed an approach for the quantitation of vinculin, a focal contact associated protein, based on a multimodal confocal microscopy and image analysis. Vinculin spot distribution was imaged in confocal fluorescence microscopy and the corresponding focal contacts were imaged in confocal interference reflection microscopy. These images were analyzed with a SAMBA image cytometer. The image analysis program provided 12 morphometric features describing cellular area, shape, and proportions of vinculin spots as well as six topographical features describing the distribution of vinculin and the relative overlap of vinculin and focal contacts. This approach was applied to the study of rat osteosarcoma cells submitted to mechanical stresses: successions of 2g and 0g accelerations during a series of parabolic flights. The measured features were assessed by means of correlation analysis and stepwise discriminant analysis. After correlation analysis, only ten parameters were retained. Quantitation of cell morphological parameters indicated that cell area was significantly affected by gravitational stresses as well as vinculin distribution. Cell area was reduced by 50% and vinculin spots were restricted to cell periphery. Cell adhesion measured by IRM decreased significantly in the first part of the flight and remained stable at the end of the flight. These results suggest that cell-matrix adhesion is affected by gravitational stresses. Image analysis provides useful tools to investigate focal adhesion re-organization under different physiological stimuli.
Feed Energy Evaluation for Growing Pigs&lt;xref rid="fn1-ajas-26-9-1205-1" ref-type="fn"&gt;&lt;sup&gt;*&lt;/sup&gt;&lt;/xref&gt; (2013)

Pigs require energy for maintenance and productive purposes, and an accurate amount of available energy in feeds should be provided according to their energy requirement. Available energy in feeds for pigs has been characterized as DE, ME, or NE by considering sequential energy losses during digestion and metabolism from GE in feeds. Among these energy values, the NE system has been recognized as providing energy values of ingredients and diets that most closely describes the available energy to animals because it takes the heat increment from digestive utilization and metabolism of feeds into account. However, NE values for diets and individual ingredients are moving targets, and therefore, none of the NE systems are able to accurately predict truly available energy in feeds. The DE or ME values for feeds are important for predicting NE values, but depend on the growth stage of pigs (i.e., BW) due to the different abilities of nutrient digestion, especially for dietary fiber. The NE values are also influenced by both environment that affects NE requirement for maintenance (NEm) and the growth stage of pigs that differs in nutrient utilization (i.e., protein vs. lipid synthesis) in the body. Therefore, the interaction among animals, environment, and feed characteristics should be taken into consideration for advancing feed energy evaluation. A more mechanistic approach has been adopted in Denmark as potential physiological energy (PPE) for feeds, which is based on the theoretical biochemical utilization of energy in feeds for pigs. The PPE values are, therefore, believed to be independent of animals and environment. This review provides an overview over current knowledge on energy utilization and energy evaluation systems in feeds for growing pigs.
Toward scaling hardware security module for emerging cloud services (2019)

The hardware security module (HSM) has been used as a root of trust for various key management services. At the same time, rapid innovation in emerging industries, such as container-based microservices, accelerates demands for scaling security services. However, current on-premises HSMs have limitations to afford such demands due to the restricted scalability and high price of deployment. This paper presents ScaleTrust, a framework for scaling security services by utilizing HSMs with SGX-based key management service (KMS) in a collaborative, yet secure manner. Based on a hierarchical model, we design a cryptographic workload distribution between HSMs and KMS enclaves to achieve both the elasticity of cloud software and the hardware-based security of HSM appliances. We demonstrate practical implications of ScaleTrust using two case studies that require secure cryptographic operations with low latency and high scalability.
Studies on semirigid tricyclic analogs of the nigrostriatal toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (1989)

The tetrahydro-beta-carboline derived from the condensation of N-methyltryptamine and formaldehyde, a semirigid tricyclic analogue of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) tha has been detected in the brains of normal laboratory rats, is biotransformed in a monoamine oxidase B (MAO-B) catalyzed reaction to the corresponding dihydro compound at a rate that is approximately 0.5% of that observed with MPTP. The corresponding tetrahydroindenopyridine in which the double bond beta,gamma to the nitrogen atom retains allylic character is a somewhat better MAO-B substrate. The steric bulk of the nitrogen and methylene bridges in addition to ring strain present in the proposed carbon-centered radical intermediates derived from these types of tricyclic structures may contribute to their relatively poor MAO-B substrate properties. Although no MPTP-like neurotoxic properties were observed following acute administration of the test compounds to mice, we speculate that the chronic accumulation of beta-carbolinium type metabolites could contribute to the rate of nigrostriatal cell loss associated with idiopathic Parkinson's disease.
Kinetics of an Intermittent-Flow, Continuous-Mix Anaerobic Reactor (2000)

A mathematicalmodeldescribingthe kinetics of an intermittent-flow, continuous-mix anaerobic reactor (IFCMAR) has been developed from the basic principles of mass balance. The model takes into consideration the effect of endogenous microbial decay on biogas production and effluent quality. The model has been tested using actual experimental data obtained from a digester operating on dairy manure at various temperatures (25 and 35°C) and retention times (5, 10, 15, 20, and 25 h). It predicted the treatment efficiency, methane yield, and volumetric methane productivity with R2 ranging from 0.97 to 0.99. Better predictions were observed at the longer hydraulic retention time (HRT) for the lower temperature (25°C) and at the shorter HRT for the higher temperature (35°C). There is a need for more accurate methods for estimating the biodegradability constant of animal waste, as well as the concentration of the active biomass in the reactor.
Analysis of eddy-current losses over conductive substrates with applications to monolithic inductors and transformers (2001)

In this paper, a closed-form integral representation for the eddy-current losses over a conductive substrate is presented. The results are applicable to monolithic inductors and transformers, especially when such structures are realized over an epitaxial CMOS substrate. The technique is verified against measured results from 100 MHz to 14 GHz for spiral inductors.
Protein microarray technology (2002)

This review summarizes the major activities in the field of protein microarray technology. A short summary of the theoretical concepts of miniaturized ligand binding assays explains why such microspot assays represent the most sensitive approaches for capture-target assays. The main focus of this review is centered on the applications using miniaturized and parallelized protein binding assays which rely on the product formation between immobilized capture molecules and their corresponding target molecules which are present in the sample. These types of ligand binding assays are useful tools for protein identification, quantification and protein affinity studies. Protein identification and quantification assays have a great potential in the field of diagnostics and proteomics where many different protein markers which are present in complex samples have to be analyzed in parallel. Protein affinity assays can be used to analyze interactions between proteins such as antibodies, receptors or enzymes with other proteins, peptides, low molecular weight compounds, oligosaccharides or DNA. Different applications of protein microarray-based assays and their huge potential for diagnostic and proteomic approaches will be discussed.
Endosulfine, an endogenous peptidic ligand for the sulfonylurea receptor: purification and partial characterization from ovine brain. (1992)

Antidiabetic sulfonylureas act through receptors coupled to ATP-dependent potassium channels. Using the binding of [3H]glibenclamide, a highly potent sulfonylurea, to rat brain membranes to follow the purification procedure, we extracted from ovine brain, purified, and partially characterized two peptides that are endogenous ligands for the central nervous system sulfonylurea receptors. These peptides, referred to as alpha and beta endosulfine, differ by their isoelectric points, the beta form being more basic. Each form of endosulfine is recognized equally by the sulfonylurea receptors from the central nervous system and from insulin-secreting beta cells. In the same concentration range that is active on the receptors, beta endosulfine releases insulin from a beta-cell line. Endosulfine is a good candidate for being implicated in the physiology of beta cells and their disorders (e.g., type II diabetes) and in certain pathologies related to modifications of ion fluxes.
<i>Alu</i> Evolution in Human Populations: Using the Coalescent to Estimate Effective Population Size (1997)

There are estimated to be approximately 1000 members of the Ya5 Alu subfamily of retroposons in humans. This subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLa-derived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of approximately 18,000 during the last one to two million years.