gebhart/patrepeval huggingface dataset:
Real-time stereo matching: A cross-based local approach (2009)

We propose an area-based local stereo matching algorithm that yields accurate disparity estimates, while achieving the real-time speed completely on the graphics processing unit (GPU). For a local stereo method, the key challenge is to decide an appropriate support window for the pixel under consideration. Our stereo method starts with computing an upright local cross adaptively for each anchor pixel, which defines a per-pixel support skeleton. Next, based on this compact local cross representation, we aggregate the matching costs in a shape adaptive full support region using two orthogonal integration steps. Approximating scene structures accurately, the proposed method is among the best-performing real-time stereo methods according to the benchmark Middlebury stereo evaluation. Additionally, our method is very easy to implement, memory efficient, and hence it is promising for many practical applications.
Analysis of protein-protein interaction networks using random walks (2005)

Genome wide protein networks have become reality in recent years due to high throughput methods for detecting protein interactions. Recent studies show that a networked representation of proteins provides a more accurate model of biological systems and processes compared to conventional pair-wise analyses. Complementary to the availability of protein networks, various graph analysis techniques have been proposed to mine these networks for pathway discovery, function assignment, and prediction of complex membership. In this paper, we propose using random walks on graphs for the complex/pathway membership problem. We evaluate the proposed technique on three different probabilistic yeast networks using a benchmark dataset of 27 complexes from the MIPS complex catalog database and 10 pathways from the KEGG pathway database. Furthermore, we compare the proposed technique to two other existing techniques both in terms of accuracy and running time performance, thus addressing the scalability issue of such analysis techniques for the first time. Our experiments show that the random walk technique achieves similar or better accuracy with more than 1,000 times speed-up compared to the best competing technique.
Update on Antiplatelet Therapy for Stroke Prevention (2000)

The high rates of mortality and long-term disability associated with ischemic stroke, coupled with its prevalence, necessitate good, long-term preventive strategies. Risk-factor management is effective for individuals with preclinical and clinical cerebrovascular disease. Patients suffering from a transient ischemic attack or stroke are particularly vulnerable to subsequent stroke. Most of these individuals are candidates for antiplatelet treatment to prevent a recurrence. Available antiplatelet therapies include aspirin, ticlopidine, and clopidogrel. The combination of low-dose aspirin plus extended-release dipyridamole has been shown to offer safe, effective antiplatelet therapy for appropriate patients. In the second European Stroke Prevention Study, the combination was found to be significantly more effective than either drug alone, at the cost of relatively few treatment-related adverse effects. This combination is currently recommended as one of the first-line treatments for stroke prevention after first transient ischemic attack or stroke.
Recent trends in the treatment of testosterone deficiency syndrome (2007)

Testosterone deficiency syndrome (TDS) is defined as a clinical and biochemical syndrome associated with advancing age and is characterized by typical symptoms and deficiency in serum testosterone levels. TDS is a result of the interaction of hypothalamo-pituitary and testicular factors. Now, treatment of TDS with testosterone is still controversial due to a lack of large, controlled clinical trials on efficacy. The risks of treatment with testosterone appear to be minimal, although long-term studies on the safety of testosterone therapy are lacking. The aim of the therapy is to establish a physiological concentration of serum testosterone in order to correct the androgen deficiency, relieve its symptoms and prevent long-term sequelae. All of the available products, despite their varying pharmacodynamic and pharmacokinetic profiles, are able to reach this goal. Newer testosterone patches seem not to cause severe skin irritation. Testosterone gels minimize the skin irritation while providing flexibility in dosing and a low discontinuation rate. Oral testosterone undecanoate (TU) is free of liver toxicity. Recent formulation of oral TU markedly increased shelf-live, a major drawback in the older preparation. Producing swings in testosterone levels rising rapidly to the supraphysiological range is not the case with the new injectable long-acting preparation of TU. To be able to rapidly react and stop treatment in cases where side-effects and contraindications are detected, the short-acting transdermal and oral delivery modes have certain advantages. However, there is no evidence that the use of an injectable long-acting TU in men with TDS has limitations in clinical application for this reason. The use of dehydroepiandrosterone is still controversial because of a lack of well designed long-term trials, although some recent studies suggest positive effects on various body systems. Only a few studies have been carried out to investigate the effect of hCG (human chorionic gonadotropin) in TDS with some positive results on various body systems.
Making RCU safe for deep sub-millisecond response realtime applications (2004)

Linux TM has long been used for soft realtime applications. More recent work is preparing Linux for more aggressive realtime use, with scheduling latencies in the small number of hundreds of microseconds (that is right, microseconds, not milliseconds). The current Linux 2.6 RCU implementation both helps and hurts. It helps by removing locks, thus reducing latency in general, but hurts by causing large numbers of RCU callbacks to be invoked all at once at the end of the grace period. This batching of callback invocation improves throughput, but unacceptably degrades realtime response for the more discerning realtime applications. This paper describes modifications to RCU that greatly reduce its effect on scheduling latency, without significantly degrading performance for non-realtime Linux servers. Although these modifications appear to prevent RCU from interfering with realtime scheduling, other Linux kernel components are still problematic. We are therefore working on tools to help identify the remaining problematic components and to definitively determine whether RCU is still an issue. In any case, to the best of our knowledge, this is the first time that anything resembling RCU has been modified to accommodate the needs of realtime applications. 1
Biopharmaceutical Classification System in <i>Invitro/ In-vivo</i> Correlation: Concept and Development Strategies in Drug Delivery (2012)

Drug development is a very laborious and expensive process. One of the major reasons for failure during the clinical phases of drug development is inadequate pharmacokinetic data on the drug candidate. Therefore, it would be advantageous if the pharmacokinetic properties of drug candidates be predicted beforehand. One major obstacle in making such&nbsp; predictions is the inability to appropriately scale the in-vitro data to the in-vivo situation. Results from in-vitro in-vivo correlation (IVIVC) studies have been used to select the appropriate excipients and optimize the manufacturing processes for quality control purposes, and for characterizing the release patterns of newly formulated immediate release, and modified-release products relative to the references. In recent years, the concept and application of the IVIVC for pharmaceutical dosage forms have been a major focus of attention in the pharmaceutical industry, academia and regulatory agencies. Hence, this article highlights the importance of appropriate selection of IVIVC level with respect to the Biopharmaceutical Classification System (BCS) and also covers examples of BCS-based IVIVCs of drugs/products with different types of release profiles.Keywords: In vitro/In vivo correlation, Biopharmaceutical Classification System, Drug Delivery.
Correction of the Anemia of End-Stage Renal Disease with Recombinant Human Erythropoietin (1987)

We administered recombinant human erythropoietin to 25 anemic patients with end-stage renal disease who were undergoing hemodialysis. The recombinant human erythropoietin was given intravenously three times weekly after dialysis, and transfusion requirements, hematocrit, ferrokinetics, and reticulocyte responses were monitored. Over a range of doses between 15 and 500 units per kilogram of body weight, dose-dependent increases in effective erythropoiesis were noted. At 500 units per kilogram, changes in the hematocrit of as much as 10 percentage points were seen within three weeks, and increases in ferrokinetics of three to four times basal values, as measured by erythron transferrin uptake, were observed. Of 18 patients receiving effective doses of recombinant human erythropoietin, 12 who had required transfusions no longer needed them, and in 11 the hematocrit increased to 35 percent or more. Along with the rise in hematocrit, four patients had an increase in blood pressure, and a majority had increases in serum creatinine and potassium levels. No organ dysfunction or other toxic effects were observed, and no antibodies to the recombinant hormone were formed. These results demonstrate that recombinant human erythropoietin is effective, can eliminate the need for transfusions with their risks of immunologic sensitization, infection, and iron overload, and can restore the hematocrit to normal in many patients with the anemia of end-stage renal disease.
Nucleoid Structure and Partition in Methanococcus jannaschii: An Archaeon With Multiple Copies of the Chromosome (1999)

We measured different cellular parameters in the methanogenic archaeon Methanococcus jannaschii. In exponential growth phase, the cells contained multiple chromosomes and displayed a broad variation in size and DNA content. In most cells, the nucleoids were organized into a thread-like network, although less complex structures also were observed. During entry into stationary phase, chromosome replication continued to termination while no new rounds were initiated: the cells ended up with one to five chromosomes per cell with no apparent preference for any given DNA content. Most cells in stationary phase contained more than one genome equivalent. Asymmetric divisions were detected in stationary phase, and the nucleoids were found to be significantly more compact than in exponential phase.
Digital Tapestry (2005)

This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov random field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with "almost" metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented.
MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III (1990)

The mutY gene of Escherichia coli, which codes for an adenine glycosylase that excises the adenine of a G-A mispair, has been cloned and sequenced. The mutY gene codes for a protein of 350 amino acids (Mr = 39,123) and the clone genetically complements the mutY strain. The protein shows significant sequence homology to E. coli endonuclease III, an enzyme that has previously been shown to have glycosylase activity on damaged base pairs. Sequence analysis suggests that, like endonuclease III, MutY is an iron-sulfur protein with a [4Fe-4S]2+ cluster.
A pairwise key predistribution scheme for wireless sensor networks (2005)

To achieve security in wireless sensor networks, it is important to be able to encrypt and authenticate messages sent between sensor nodes. Before doing so, keys for performing encryption and authentication must be agreed upon by the communicating parties. Due to resource constraints, however, achieving key agreement in wireless sensor networks is nontrivial. Many key agreement schemes used in general networks, such as Diffie-Hellman and other public-key based schemes, are not suitable for wireless sensor networks due to the limited computational abilities of the sensor nodes. Predistribution of secret keys for all pairs of nodes is not viable due to the large amount of memory this requires when the network size is large.In this paper, we provide a framework in which to study the security of key predistribution schemes, propose a new key predistribution scheme which substantially improves the resilience of the network compared to previous schemes, and give an in-depth analysis of our scheme in terms of network resilience and associated overhead. Our scheme exhibits a nice threshold property: when the number of compromised nodes is less than the threshold, the probability that communications between any additional nodes are compromised is close to zero. This desirable property lowers the initial payoff of smaller-scale network breaches to an adversary, and makes it necessary for the adversary to attack a large fraction of the network before it can achieve any significant gain.
Distributed sensor fusion for object position estimation by multi-robot systems (2002)

We present a method for representing, communicating and fusing distributed, noisy and uncertain observations of an object by multiple robots. The approach relies on re-parameterization of the canonical two-dimensional Gaussian distribution that corresponds more naturally to the observation space of a robot. The approach enables two or more observers to achieve greater effective sensor coverage of the environment and improved accuracy in object position estimation. We demonstrate empirically that, when using our approach, more observers achieve more accurate estimations of an object's position. The method is tested in three application areas, including object location, object tracking, and ball position estimation for robotic soccer. Quantitative evaluations of the technique in use on mobile robots are provided.
Design of Position Estimation Strategy of Sensorless Interior PMSM at Standstill Using Minimum Voltage Vector Injection Method (2017)

This paper presents a new initial rotor position estimation method for an interior permanent magnet synchronous motor. The proposed method includes two steps. First, the minimum voltage vectors are injected to estimate the rotor position. Second, in order to identify the magnet polarity accurately, two opposite voltage pulses are injected on the estimated d-axis. In the proposed method, no filter is needed to draw the high frequency current signal for position estimation and no low-pass filter is required in the current control loop for extracting the fundamental current component for field-oriented control. The fast and reliable feature of this proposed method allows starting the motor with 100% load torque. The effectiveness of the proposed method is verified experimentally and the maximum position estimation error is around 6 electrical degrees.
The application of Tet repressor in prokaryotic gene regulation and expression (2007)

Inducible gene expression based upon Tet repressor (tet regulation) is a broadly applied tool in molecular genetics. In its original environment, Tet repressor (TetR) negatively controls tetracycline (tc) resistance in bacteria. In the presence of tc, TetR is induced and detaches from its cognate DNA sequence tetO, so that a tc antiporter protein is expressed. In this article, we provide a comprehensive overview about tet regulation in bacteria and illustrate the parameters of different regulatory architectures. While some of these set-ups rely on natural tet-control regions like those found on transposon Tn10, highly efficient variations of this system have recently been adapted to different Gram-negative and Gram-positive bacteria. Novel tet-controllable artificial or hybrid promoters were employed for target gene expression. They are controlled by regulators expressed at different levels either in a constitutive or in an autoregulated manner. The resulting tet systems have been used for various purposes. We discuss integrative elements vested with tc-sensitive promoters, as well as tet regulation in Gram-negative and Gram-positive bacteria for analytical purposes and for protein overproduction. Also the use of TetR as an in vivo biosensor for tetracyclines or as a regulatory device in synthetic biology constructs is outlined. Technical specifications underlying different regulatory set-ups are highlighted, and finally recent developments concerning variations of TetR are presented, which may expand the use of prokaryotic tet systems in the future.
CONCEPTUAL DESIGN AND COMPARISON OF FOUR-PRODUCTS DIVIDING WALL COLUMNS FOR SEPARATION OF A MULTICOMPONENT AROMATICS MIXTURE (2010)

Preliminary evaluations using a simple but reliable short-cut method indicated that a 15 component aromatic’s mixture can be separated very efficiently into four fractions according to given product specifications employing either a single or a multiple partition wall dividing wall column (DWC). The obtained results have been used to initiate rigorous simulations, to determine the number of stages required in different sections, as well as to obtain internal flows of vapour and liquid necessary for dimensioning and adequate (actual delivery prices) cost estimation. Comparison of total annualized costs indicates that more energy efficient complex configuration with three partition walls is a viable option in present case.
Learning data augmentation for consumer devices and services (2018)

Transferring the success of deep learning models to consumer electronic devices requires the construction of deep learning models that are small enough to fit on resource constrained hardware. Since embedded and mobile devices lack the resources in terms of power consumption requirements, processing speed, and available memory of the latest GPU technology, it is desirable to create neural networks that are significantly smaller without sacrificing accuracy. A new technique for data augmentation called “Smart Augmentation” has recently been introduced that has been experimentally shown to be effective at this task. In this paper, we show how Smart Augmentation can be used to train models that are significantly smaller than their equivalently performant counterparts, and thus more viable for deployment on consumer devices.
Conservation of Amino Acids in Human Rhinovirus 3C Protease Correlates with Broad-Spectrum Antiviral Activity of Rupintrivir, a Novel Human Rhinovirus 3C Protease Inhibitor (2005)

The picornavirus 3C protease is required for the majority of proteolytic cleavages that occur during the viral life cycle. Comparisons of published amino acid sequences from 6 human rhinoviruses (HRV) and 20 human enteroviruses (HEV) show considerable variability in the 3C protease-coding region but strict conservation of the catalytic triad residues. Rupintrivir (formerly AG7088) is an irreversible inhibitor of HRV 3C protease with potent in vitro activity against all HRV serotypes (48 of 48), HEV strains (4 of 4), and untyped HRV field isolates (46 of 46) tested. To better understand the relationship between in vitro antiviral activity and 3C protease-rupintrivir binding interactions, we performed nucleotide sequence analyses on an additional 21 HRV serotypes and 11 HRV clinical isolates. Antiviral activity was also determined for 23 HRV clinical isolates and four additional HEV strains. Sequence comparison of 3C proteases (n = 58) show that 13 and 11 of the 14 amino acids that are involved in side chain interactions with rupintrivir are strictly conserved among HRV and HEV, respectively. These sequence analyses are consistent with the comparable in vitro antiviral potencies of rupintrivir against all HRV serotypes, HRV isolates, and HEV strains tested (50% effective concentration range, 3 to 183 nM; n = 125). In summary, the conservation of critical amino acid residues in 3C protease and the observation of potent, broad-spectrum antipicornavirus activity of rupintrivir highlight the advantages of 3C protease as an antiviral target.
Replication of Modified Vaccinia Virus Ankara in Primary Chicken Embryo Fibroblasts Requires Expression of the Interferon Resistance Gene E3L (2003)

Highly attenuated modified vaccinia virus Ankara (MVA) serves as a candidate vaccine to immunize against infectious diseases and cancer. MVA was randomly obtained by serial growth in cultures of chicken embryo fibroblasts (CEF), resulting in the loss of substantial genomic information including many genes regulating virus-host interactions. The vaccinia virus interferon (IFN) resistance gene E3L is among the few conserved open reading frames encoding viral immune defense proteins. To investigate the relevance of E3L in the MVA life cycle, we generated the deletion mutant MVA-DeltaE3L. Surprisingly, we found that MVA-DeltaE3L had lost the ability to grow in CEF, which is the first finding of a vaccinia virus host range phenotype in this otherwise highly permissive cell culture. Reinsertion of E3L led to the generation of revertant virus MVA-E3rev and rescued productive replication in CEF. Nonproductive infection of CEF with MVA-DeltaE3L allowed viral DNA replication to occur but resulted in an abrupt inhibition of viral protein synthesis at late times. Under these nonpermissive conditions, CEF underwent apoptosis starting as early as 6 h after infection, as shown by DNA fragmentation, Hoechst staining, and caspase activation. Moreover, we detected high levels of active chicken alpha/beta IFN (IFN-alpha/beta) in supernatants of MVA-DeltaE3L-infected CEF, while moderate IFN quantities were found after MVA or MVA-E3rev infection and no IFN activity was present upon infection with wild-type vaccinia viruses. Interestingly, pretreatment of CEF with similar amounts of recombinant chicken IFN-alpha inhibited growth of vaccinia viruses, including MVA. We conclude that efficient propagation of MVA in CEF, the tissue culture system used for production of MVA-based vaccines, essentially requires conserved E3L gene function as an inhibitor of apoptosis and/or IFN induction.