gebhart/patrepeval huggingface dataset:
Topological leakage detection and freeze-and-grow propagation for improved CT-based airway segmentation (2018)

Numerous large multi-center studies are incorporating the use of computed tomography (CT)-based characterization of the lung parenchyma and bronchial tree to understand chronic obstructive pulmonary disease status and progression. To the best of our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. A failure in even a fraction of segmentation results necessitates manual revision of all segmentation masks which is laborious considering the thousands of image data sets evaluated in large studies. In this paper, we present a novel CT-based airway tree segmentation algorithm using topological leakage detection and freeze-and-grow propagation. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity-based connectivity and a freeze-and-grow propagation algorithm to iteratively grow the airway tree starting from an initial seed inside the trachea. It begins with a conservative parameter and then, gradually shifts toward more generous parameter values. The method was applied on chest CT scans of fifteen subjects at total lung capacity. Airway segmentation results were qualitatively assessed and performed comparably to established airway segmentation method with no major visual leakages.
Online cache modeling for commodity multicore processors (2010)

Modern chip-level multiprocessors (CMPs) contain multiple processor cores sharing a common last-level cache, memory interconnects, and other hardware resources. Workloads running on separate cores compete for these resources, often resulting in highlyvariable performance. It is generally desirable to co-schedule workloads that have minimal resource contention, in order to improve both performance and fairness. Unfortunately, commodity processors expose only limited information about the state of shared resources such as caches to the software responsible for scheduling workloads that execute concurrently. To make informed resourcemanagement decisions, it is important to obtain accurate measurements of per-workload cache occupancies and their impact on performance, often summarized by utility functions such as miss-ratio curves (MRCs) In this paper, we first introduce an efficient online technique for estimating the cache occupancy of individual software threads using only commonly-available hardware performance counters. We derive an analytical model as the basis of our occupancy estimation, and extend it for improved accuracy on modern cache configurations, considering the impact of set-associativity, line replacement policy, and memory locality effects. We demonstrate the effectiveness of occupancy estimation with a series of CMP simulations in which SPEC benchmarks execute concurrently on multiple cores. Leveraging our occupancy estimation technique, we also introduce a lightweight approach for online MRC construction, and demonstrate its effectiveness using a prototype implementation in the VMware ESX Server hypervisor. We present a series of experiments involving SPEC benchmarks, comparing the MRCs we construct online with MRCs generated offline in which various cache sizes are enforced via static page coloring
A high proportion of novel mutations in BRCA1 with strong founder effects among Dutch and Belgian hereditary breast and ovarian cancer families (2020)

We have identified 79 mutations in BRCA1 in a set of 643 Dutch and 23 Belgian hereditary breast and ovarian cancer families collected either for research or for clinical diagnostic purposes. Twenty-eight distinct mutations have been observed, 18 of them not previously reported and 12 of them occurring more than once. Most conspicuously, a 2804delAA mutation has been found 19 times and has never been reported outside the Netherlands. A common haplotype spanning > or = 375 kb could be identified for each of the nine examined recurrent mutations, indicating the presence of multiple BRCA1 founder mutations in the Dutch population. The 2804delAA mutation has been estimated to have originated approximately 32 generations ago. No specific breast or ovarian cancer phenotype could be assigned to any of the common mutations, and the ovarian cancer incidence among 18 families with the 2804delAA mutation was heterogeneous.
Mechanism of (111) Silicon Etching in  HF  ‐ Acetonitrile (1995)

The electrochemical oxidation‐dissolution of (111) silicon has been investigated in solutions. Four electrons per silicon were observed per oxidized silicon. Current doubling (quantum efficiency of 2.2) was observed for the photo‐oxidation of n‐Si. Unlike the etching of (111) silicon in aqueous solutions, no pores were formed in. The etching of (111) silicon in resulted in the formation of triangular pits defined by the {111} planes. A mechanism for the etching is proposed where steric hindrance of the surface terminated hydrogens induces bond strain and enhances the chemical reactivity. The mechanism also accounts for the formation of pores in (100) silicon, and the formation of a highly branched microporous structure when silicon is etched in an aqueous solution.
Systemic and pulmonary antibody responses of calves to Pasteurella haemolytica after intrapulmonary inoculation (1992)

Systemic and pulmonary antibody responses of calves to Pasteurella haemolytica were evaluated by measuring immunoglobulin production in blood for 9 days and in pulmonary lavage fluid for 7 days after intrapulmonary inoculation. Clinical signs, pulmonary lesions, pulmonary and systemic inflammatory response, and amount of antigen in lavage fluid were used to evaluate the response of calves to challenge with P haemolytica. The pulmonary response consisted of production of IgG, IgE, and IgM antibodies to P haemolytica antigens and a 17- to 68-fold increase of cells in lavage fluid 8 hours after inoculation, with a gradual decrease toward normal. Antibodies of the IgM isotype to P haemolytica were demonstrated as early as 8 hours through 7 days after inoculation in 3 of 3 calves. Of the anti-P haemolytica isotypes, IgM was found in the highest concentration. In all of the inoculated calves, IgE was found 1 to 2 days after inoculation, and IgG was found in 2 of 3 inoculated calves from day 1 through 7 after inoculation. Detection of IgG correlated with smaller pulmonary lesions. Immunoglobulin A was not detected in lavage fluid. Serum was evaluated for IgG and IgM antibody response to P haemolytica. Specific IgM was detectable 5 days after inoculation, and IgG was detectable 7 days after inoculation. Pasteurella haemolytica antigens were not detected in serum or plasma. A transient increase in neutrophil count was found 8 hours after inoculation, with return to baseline values by 24 hours after inoculation.(ABSTRACT TRUNCATED AT 250 WORDS)
On the regularization of sense and space-rip in parallel MR imaging (2005)

Parallel imaging methods provide accelerated multiple coil MR image acquisitions via reconstruction of sub-sampled k-space data. Currently, analytic comparison between different reconstruction approaches has been hampered by use of different phase encoding paradigms and regularization approaches, historically unique to each method. We present an analysis of the Space-RIP image reconstruction problem that demonstrates the ability to recast the problem in a decoupled form when uniform down-sampling is employed. We show that this decoupled problem is equivalent to the SENSE image reconstruction approach. This approach enables a clear analytic comparison between SENSE and Space-RIP, and we demonstrate the effect of different regularization approaches on image formation in low coil sensitivity regions.
Creation of Dystrophin Expressing Chimeric Cells of Myoblast Origin as a Novel Stem Cell Based Therapy for Duchenne Muscular Dystrophy (2018)

Over the past decade different stem cell (SC) based approaches were tested to treat Duchenne Muscular Dystrophy (DMD), a lethal X-linked disorder caused by mutations in dystrophin gene. Despite research efforts, there is no curative therapy for DMD. Allogeneic SC therapies aim to restore dystrophin in the affected muscles; however, they are challenged by rejection and limited engraftment. Thus, there is a need to develop new more efficacious SC therapies. Chimeric Cells (CC), created via ex vivo fusion of donor and recipient cells, represent a promising therapeutic option for tissue regeneration and Vascularized Composite Allotransplantation (VCA) due to tolerogenic properties that eliminate the need for lifelong immunosuppression. This proof of concept study tested feasibility of myoblast fusion for Dystrophin Expressing. Chimeric Cell (DEC) therapy through in vitro characterization and in vivo assessment of engraftment, survival, and efficacy in the mdx mouse model of DMD. Murine DEC were created via ex vivo fusion of normal (snj) and dystrophin-deficient (mdx) myoblasts using polyethylene glycol. Efficacy of myoblast fusion was confirmed by flow cytometry and dystrophin immunostaining, while proliferative and myogenic differentiation capacity of DEC were assessed in vitro. Therapeutic effect after DEC transplant (0.5 × 10<sup>6</sup>) into the gastrocnemius muscle (GM) of mdx mice was assessed by muscle functional tests. At 30 days post-transplant dystrophin expression in GM of injected mdx mice increased to 37.27 ± 12.1% and correlated with improvement of muscle strength and function. Our study confirmed feasibility and efficacy of DEC therapy and represents a novel SC based approach for treatment of muscular dystrophies.
Conversion of Waste Plastic to Lubricating Base Oil (2005)

A new process has been developed for the conversion of waste plastic to lubricating base oil. It has also been demonstrated that waste plastic and Fischer−Tropsch (FT) wax can be co-processed to produce lube range molecules. The process uses a thermal, noncatalytic, atmospheric pressure pyrolysis process that converts high-molecular-weight molecules to lower-molecular-weight molecules in the lube oil range. Hydroisomerization is then used to convert this product to low-pour-point oils of unconventional base oil (UCBO) quality. The major byproduct is diesel, with little production of C4− gas. Initial experiments in bench-scale laboratory pyrolysis units were followed by tests in a 1 gal/day pilot plant. The feedstocks that were tested consisted of polyethylene (PE), 96% PE−4% poly(ethylene terephthalate) (PET), FT wax, and a 50/50 mixture of PE and FT wax. The product distribution and lube quality showed surprisingly little variation for these feedstocks. The pyrolysis yields of 385 °C+ product were in the range of 37−57 wt %, whereas the potential lube yields were 60−70 wt %, assuming all the olefins (almost all 1-olefins) could be upgraded to lube by oligomerization. Hydroisomerization of the pyrolysis bottoms yielded oil with a viscosity of 3.4−5.4 cSt, pour points between −13 to −37 °C, and a viscosity index in the range of 150−160.
DNA Enzymology above 100 °C. (1995)

The widespread application of polymerase chain reaction and related techniques in biology and medicine has led to a heightened interest in thermophilic enzymes of DNA metabolism. Some of these enzymes are stable for hours at 100 degrees C, but no enzymatic activity on duplex DNA at temperatures above 100 degrees C has so far been demonstrated. Recently, we isolated topoisomerase V from the hyperthermophile Methanopyrus kandleri, which grows up to 110 degrees C. This novel enzyme is similar to eukaryotic topoisomerase I and acts on duplex DNA regions. We now show that topoisomerase V catalyzes the unlinking of double-stranded circular DNA at temperatures up to 122 degrees C. In this in vitro system, maximal DNA unlinking occurs at 108 degrees C and corresponds to complementary strands being linked at most once. These results further imply that in the presence of sufficient positive supercoiling DNA can exist as a double helix even at 122 degrees C.
NPLIC: A Machine Learning Approach to Piecewise Linear Interface Construction (2020)

Volume of fluid (VOF) methods are extensively used to track fluid interfaces in numerical simulations, and many VOF algorithms require that the interface be reconstructed geometrically. For this purpose, the Piecewise Linear Interface Construction (PLIC) technique is most frequently used, which for reasons of geometric complexity can be slow and difficult to implement. Here, we propose an alternative neural network based method called NPLIC to perform PLIC calculations. The model is trained on a large synthetic dataset of PLIC solutions for square, cubic, triangular, and tetrahedral meshes. We show that this data-driven approach results in accurate calculations at a fraction of the usual computational cost, and a single neural network system can be used for interface reconstruction of different mesh types.
Two Additional Loci underlying Durable Field Resistance to Soybean Sudden Death Syndrome (SDS) (1996)

Severe losses of soybean [ Glycine max (L.) Merr.] grain yield occur as a result of the disease sudden death syndrome (SDS), caused by Fusarium solani (Mart.) Sacc. f. sp. phaseoli (Burk.) Snyd. & Hans., type A. Selection for resistance to SDS is currently the most efficient means of yield protection. This study was undertaken within adapted soybean germplasm to identify and characterize loci underlying useful field resistance to SDS. One hundred eleven polymorphic DNA markers were compared with SDS disease response among 100 recombinant inbred lines derived from a cross between a durably SDS resistant cultivar, ‘Forrest’, and a SDS susceptible cultivar, ‘Essex’. SDS disease incidence (DI) and disease severity (DS) were determined in replicated, F. solani infested field‐test sites during 4 yr encompassing five locations. Four separate chromosomal segments were strongly associated with mean SDS DI across 5 locations ( P < 0.001). In a previous report using the same genetic materials tested in the same environments two of these quantitative trait loci (QTL) had been identified. With the further analysis with 40 additional markers, two more QTL were detected. The two new QTL were stably associated with SDS resistance within each of five F. solani infested locations ( P < 0.007). These two loci were identified by RAPD markers OI03 450 and OG13 490 and by OE04 450 and OE02 1000 . The alleles that conferred resistance were both derived from Forrest. Jointly, the four QTL accounted for about 65% of total phenotypic variability in mean DI and 50% in mean DS. DNA markers can be used to define alleles conferring resistance to SDS. Selection for the SDS resistance QTL may allow efficient selection of resistant genotypes with good yield potential in F. solani infested fields.
LMS-based calibration of an RF digitally controlled oscillator for mobile phones (2006)

We propose a least-mean square based gain calibration technique of an RF digitally controlled oscillator (DCO) in an all-digital phase-locked loop (ADPLL). The DCO gain of about 12-kHz/least significant bit is subject to process, voltage and temperature variations, but is tracked and compensated in real time. Precise setting of the inverse DCO gain in the ADPLL modulating path allows direct wide-band frequency modulation that is independent from the ADPLL loop bandwidth. The technique is part of a single-chip fully compliant Global System for Mobile Communications (GSM)/EDGE transceiver in 90-nm digital CMOS.
Electromagnetic time reversal applied to fault detection: The issue of losses (2015)

Electromagnetic time reversal (EMTR) has recently been applied to the problem of fault location in AC and DC power grids. In this paper, we present an analysis of the effect of losses on the application of EMTR to locate faults. Three models for the back propagation are proposed and discussed. We show that a back-propagation model in which the losses are included results in a perfect estimation of the fault location, even though in this case the telegrapher's equations are not strictly time-reversal invariant.
Non-Iterative Holographic Image Reconstruction and Phase Retrieval Using a Deep Convolutional Neural Network (2018)

We demonstrate a non-iterative holographic image reconstruction and phase retrieval framework based on deep learning. After its training, a deep convolutional neural network rapidly recovers phase and amplitude images of specimen from a single hologram.
Reconstruction implementation based on a flat panel detector cone beam breast CT (2006)

Flat panel detector based cone beam breast imaging CT can provide 3-D image of the scanned breast with 3-D isotropic spatial resolution, overcoming the disadvantage of the superimposition of structure associated with X-ray projection mammography that makes a small carcinoma (a few millimeters in size) difficult to detect when it is occult or in dense breast, which leads to a high false-positive biopsy rate. Circular scan CBBCT is the most desirable mode due to its simple geometrical configuration and potential applications in functional imaging. Only circular scan, however, can't provide the sufficient information for nearly exact reconstruction, and thus resulting in the reconstructed image artifacts, such as density drop and geometrical deformation when the cone angle becomes large. In order to combat this drawback, a circle plus sparse helical line scan scheme is proposed. Computer simulation on mathematic breast phantom testifies the practical feasibility of the new scheme and correction of those artifacts to a certain degree.
Probabilistic estimation-based data mining for discovering insurance risks (1999)

IBM's underwriting profitability analysis application mines property and casualty insurance policy and claims data to construct predictive models for insurance risks. UPA uses the ProbE data-mining kernel to discover risk-characterization rules by analyzing large, noisy data sets.
Fatty Acid SNP Interaction Analysis in Angus Sired Beef Cattle (2015)

The triacylglyceride (TAG) fatty acid content in meat from Angus-sired cattle was analyzed for non-additive genetic effects. A total of 11,482 significant DNA marker interactions (false discovery rate [FDR] < 0.05) were detected across thirty-seven different TAG fatty acids. Interactions were not evenly distributed amongst all fatty acids analyzed, and types of interactions (additive-by-additive, additive-by-dominance, and dominance-by-dominance) varied within each individual fatty acid. These results indicate that it may be possible to account for additional genetic variance amongst TAG fatty acids over and above individual markers.
Regeneration of spine disc and joint cartilages under temporal and space modulated laser radiation (2009)

The effect of laser radiation on the generation of hyaline cartilage in spine disc and joints has been demonstrated. The paper considers physical processes and mechanisms of laser regeneration, presents results of investigations aimed to optimize laser settings and to develop feedback control system for laser reconstruction of spine discs. Possible mechanisms of laser-induced regeneration include: (1) Space and temporary modulated laser beam induces nonhomogeneous and pulse repetitive thermal expansion and stress in the irradiated zone of cartilage. Mechanical effect due to controllable thermal expansion of the tissue and micro and nano gas bubbles formation in the course of the moderate (up to 45-50 oC) heating of the NP activate biological cells (chondrocytes) and promote cartilage regeneration. (2) Nondestructive laser radiation leads to the formation of nano and micro-pores in cartilage matrix. That promotes water permeability and increases the feeding of biological cells. Results provide the scientific and engineering basis for the novel low-invasive laser procedures to be used in orthopedics for the treatment cartilages of spine and joints. The technology and equipment for laser reconstruction of spine discs have been tested first on animals, and then in a clinical trial. Since 2001 the laser reconstruction of intervertebral discs have been performed for 340 patients with chronic symptoms of low back or neck pain who failed to improve with non-operative care. Substantial relief of back pain was obtained in 90% of patients treated who returned to their daily activities. The experiments on reparation of the defects in articular cartilage of the porcine joints under temporal and spase modulated laser radiation have shown promising results.
Microwave And Video Sensor Fusion For The Shape Extraction Of 3D Space Objects (1987)

In order for robots to perform meaningful operations in space, some type of sophisticated vision system is required. Such a system should provide the robot with three dimensional (3D) information about its surrounding work space and the objects to be operated on. The problem of remotely determining an object's 3D shape is difficult in any situation, but the space environment presents special problems due to the ambient illumination and lack of atmosphere. The most common imaging systems, visual sensors, are able to accurately determine the boundary of an object's two-dimensional projection onto the image plane. The exact shape of an object can be determined through the analysis of shading in an optical image, but frequently, shading details are obscured by the high intensity specular reflections which occur in space images. An alternate sensor for robotic applications is microwave radar. Some 3D information is available from time-domain radar imaging, but high resolution radar is prohibitively expensive and complex. We would like to integrate the information available from T .V . images and low-resolution radar scattering cross-sections to reconstruct an object's 3D shape. We present a new system for the fusion of optical image data and polarized radar scattering cross-sections. The radar data is used in an iterative procedure which generates successive approximations to the target shape by minimizing the error between the computed scattering cross-sections, and the observed radar returns. The image data is incorporated by supplying an initial estimate of shape through knowledge of the two-dimensional silhouette and shading models. These components are assembled into a larger iterative process designed to refine the estimate of 3D shape and obtain the best possible description of the attitude and motion of the target.
<scp>l</scp>-Arginine enhances aerobic exercise capacity in association with augmented nitric oxide production (2001)

We tested whether supplementation with L-arginine can augment aerobic capacity, particularly in conditions where endothelium-derived nitric oxide (EDNO) activity is reduced. Eight-week-old wild-type (E(+)) and apolipoprotein E-deficient mice (E(-)) were divided into six groups; two groups (LE(+) and LE(-)) were given L-arginine (6% in drinking water), two were given D-arginine (DE(+) and DE(-)), and two control groups (NE(+) and NE(-)) received no arginine supplementation. At 12-16 wk of age, the mice were treadmill tested, and urine was collected after exercise for determination of EDNO production. NE(-) mice demonstrated a reduced aerobic capacity compared with NE(+) controls [maximal oxygen uptake (VO(2 max)) of NE(-) = 110 +/- 2 (SE) vs. NE(+) = 122 +/- 3 ml O(2). min(-1). kg(-1), P < 0.001]. This decline in aerobic capacity was associated with a diminished postexercise urinary nitrate excretion. Mice given L-arginine demonstrated an increase in postexercise urinary nitrate excretion and aerobic capacity in both groups (VO(2 max) of LE(-) = 120 +/- 1 ml O(2). min(-1). kg(-1), P < 0.05 vs. NE(-); VO(2 max) of LE(+) = 133 +/- 4 ml O(2). min(-1). kg(-1), P < 0.01 vs. NE(+)). Mice administered D-arginine demonstrated an intermediate increase in aerobic capacity in both groups. We conclude that administration of L-arginine restores exercise-induced EDNO synthesis and normalizes aerobic capacity in hypercholesterolemic mice. In normal mice, L-arginine enhances exercise-induced EDNO synthesis and aerobic capacity.