gebhart/patrepeval huggingface dataset:
Speeding Up Algorithms on Compressed Web Graphs (2009)

A variety of lossless compression schemes has been proposed to reduce the storage requirements of web graphs. One successful approach is virtual-node compression [Buehrer and Chellapilla 08], in which often-used patterns of links are replaced by links to virtual nodes, creating a compressed graph that succinctly represents the original. In this paper, we show that several important classes of web graph algorithms can be extended to run directly on virtual-node-compressed graphs, such that their running times depend on the size of the compressed graph rather than on that of the original. These include algorithms for link analysis, estimating the size of vertex neighborhoods, and a variety of algorithms based on matrix-vector products and random walks. Similar speedups have been obtained previously for classical graph algorithms such as shortest paths and maximum bipartite matching. We measure the performance of our modified algorithms on several publicly available web graph data sets, and demonstrate significant empirical speedups that nearly match the compression ratios.
Expression of unglycosylated mutated prion protein facilitates PrPSc formation in neuroblastoma cells infected with different prion strains (2000)

Prion replication involves conversion of the normal, host-encoded prion protein PrP(C), which is a sialoglycoprotein bound to the plasma membrane by a glycophosphatidylinositol anchor, into a pathogenic isoform, PrP(Sc). In earlier studies, tunicamycin prevented glycosylation of PrP(C) in scrapie-infected mouse neuroblastoma (ScN2a) cells but it was still expressed on the cell surface and converted into PrP(Sc); mutation of PrP(C) at glycosylation consensus sites (T182A, T198A) produced low steady-state levels of PrP that were insufficient to propagate prions in transgenic mice. By mutating asparagines to glutamines at the consensus sites, we obtained expression of unglycosylated, epitope-tagged MHM2PrP(N180Q,N196Q), which was converted into PrP(Sc) in ScN2a cells. Cultures of uninfected neuroblastoma (N2a) cells transiently expressing mutated PrP were exposed to brain homogenates prepared from mice infected with the RML, Me7 or 301V prion strains. In each case, mutated PrP was converted into PrP(Sc) as judged by Western blotting. These findings raise the possibility that the N2a cell line can support replication of different strains of prions.
Selection and Properties of Streptococcus thermophilus Mutants Deficient in Urease (2004)

Natural variations of the urea content of milk have a detrimental effect on the regularity of acidification by Streptococcus thermophilus strains used in dairy processes. The aim of the present study was to select urease-deficient mutants of S. thermophilus and to investigate their properties. Using an improved screening medium on agar plates, mutants were selected from 4 different parent strains after mutagen treatment and by spontaneous mutation. Most mutants were stable and had a phage sensitivity profile similar to that of their parent strain. Some of them contained detrimental secondary mutations, as their acidifying activity was lower than that of the parent strain cultivated in the presence of the urease inhibitor flurofamide. The proportion of this type of mutant was much lower among spontaneous mutants than among mutants selected after mutagen treatment. Utilization of urease-deficient mutants in dairy processes may have several advantages, such as an increase in acidification, an improved regularity of acidification, and a lower production of ammonia in whey.
Check‐hybrid GLDPC codes: Systematic elimination of trapping sets and guaranteed error correction capability (2016)

ABSTRACT In this paper, we propose a new approach to construct a class of check‐hybrid generalized low‐density parity‐check (CH‐GLDPC) codes, which are free of small trapping sets. The approach is based on converting some selected check nodes involving a trapping set into super checks corresponding to a 2‐error‐correcting component code. Specifically, we follow 2 main purposes to construct the check‐hybrid codes; first, on the basis of the knowledge of trapping sets of an LDPC code, single parity checks are replaced by super checks to disable the trapping sets. We show that by converting specified single check nodes, denoted as critical checks, to super checks in a trapping set, the parallel bit flipping decoder corrects the errors on a trapping set. The second purpose is to minimize the rate loss through finding the minimum number of such critical checks. We also present an algorithm to find critical checks in a trapping set of a column‐weight 3 LDPC code of girth 8 and then provide upper bounds on the minimum number of such critical checks such that the decoder corrects all error patterns on elementary trapping sets. Guaranteed error correction capability of the CH‐GLDPC codes is also studied. We show that a CH‐GLDPC code in which each variable node is connected to 2 super checks corresponding to a 2‐error‐correcting component code corrects up to 5 errors. The results are also extended to column‐weight 4 LDPC codes of girth 6. Finally, we investigate eliminating of trapping sets of a column‐weight 3 LDPC code of girth 8 using the Gallager B decoding algorithm.
Comparison of several control standard endotoxins to the National Reference Standard Endotoxin--an HIMA collaborative study (1985)

A collaborative study, initiated under the auspices of the Health Industry Manufacturers Association (HIMA), was designed to establish the relationship of Escherichia coli O55:B5 endotoxin (the control standard endotoxin of HIMA and the Food and Drug Administration's Office of Medical Devices) to the U.S. National Reference Standard Endotoxin and to two internationally used control standard endotoxins. By using two Limulus amoebocyte lysate test systems, it was established that the E. coli O55:B5 endotoxin lot originally used by HIMA and the Office of Medical Devices to establish Limulus amoebocyte lysate release test criteria for pyrogen testing of medical devices contains approximately 4.5 endotoxin units (EU) per ng. Thus, the 1.0-ng/kg endotoxin dose limit currently established for medical devices is approximately the same as the 5.0-EU/kg endotoxin limit (on an activity basis) established by several other Food and Drug Administration agencies for human and animal parenteral drugs and biological products.
Automated Quantitation of Choroidal Neovascularization: A Comparison Study Between Spectral-Domain and Swept-Source OCT Angiograms (2017)

The automated algorithm measurements of CNV were in agreement with the hand-drawn measurements. On average, automated SS-OCTA measurements were larger than SD-OCTA measurements and consistent with the results from using hand-drawn measurements.
Development of MS<sup>n</sup> in Digitally Operated Linear Ion Guides (2014)

This publication demonstrates the use of digital waveform manipulation in linear ion guides to trap isolated ions and fragment them before mass analysis by time-of-flight mass spectrometry (TOF-MS). Ion trapping and collection was performed by waveform duty cycle manipulation to create a negative axial potential between the rods and the end-cap electrodes. Ion isolation can be performed by duty cycle manipulation to narrow the range of stable masses while continuing to axially trap the ions. Further ion isolation can then be performed by jumping the quadrupole frequency to each side of the stability zone to eliminate ions above and below the isolated ion mass. Collision-induced dissociation was demonstrated by duty cycle manipulation to either axially or radially excite the ions. The methods for performing these types of excitations are discussed and demonstrated. These techniques can be combined or used separately for MS(n) analysis. The use of frequency and duty cycle manipulation of the applied waveforms simplifies the hardware while greatly increasing the capabilities of linear ion guides and quadrupole time-of-flight mass spectrometers (Q-TOF-MS). Linear quadrupoles can now be used as high efficiency ion traps for collection, isolation, and tandem mass spectrometry at any value of m/z when operated digitally.
Enhancement of Measurement Efficiency for Electrical Capacitance Tomography (2011)

This paper presents a new sensing method to improve the efficiency of electrical capacitance tomography. Instead of applying one excitation signal to one electrode at a time, the multiple excitation capacitance polling (MECaP) method progressively applies an increasing number of multiple excitations to multiple electrodes and simultaneously measures the capacitance values, thereby significantly increasing the image scanning speed. The performance of a MECaP-based sensor system is numerically simulated and analyzed using the finite element method. Experimental evaluation of the numerical results demonstrates the effectiveness and efficiency of the new sensing technique and its applicability to a broad range of commercial and industrial applications where permittivity determination through capacitance measurement provides an effective means for noninvasive dynamic processes monitoring in an enclosed environment.
The Calculation of Regeneration Limits of Diesel Particulate Traps for Different Regeneration Methods (1984)

<div class="htmlview paragraph">Using known approaches to describe the reaction kinetics of soot, simple models are formulated to calculate regeneration limits and describe the interaction between engine and filter. <ul class="list disc"> <li class="list-item"> <span class="li-label">-</span> <div class="htmlview paragraph">Insulation of exhaust ports and manifold reduces the lower limit of automatic filter regeneration by approx. 0.5 bar bmep.</div></li> <li class="list-item"> <span class="li-label">-</span> <div class="htmlview paragraph">Intake throttling extends the range of automatic regeneration to within medium load.</div></li> <li class="list-item"> <span class="li-label">-</span> <div class="htmlview paragraph">The combination of intake throttling with a small constant output burner enables regeneration for all engine operating conditions.</div></li> <li class="list-item"> <span class="li-label">-</span> <div class="htmlview paragraph">Fuel additives can lower the limit for filter regeneration through lowering the activation energy to within the lower part load without additional measures.</div></li></ul></div>
Detecting salient motion by accumulating directionally-consistent flow (1999)

Motion detection can play an important role in many vision tasks. Yet image motion can arise from "uninteresting" events as well as interesting ones. In this paper, salient motion is defined as motion that is likely to result from a typical surveillance target (e.g., a person or vehicle traveling with a sense of direction through a scene) as opposed to other distracting motions (e.g., the scintillation of specularities on water, the oscillation of vegetation in the wind). We propose an algorithm for detecting this salient motion that is based on intermediate-stage vision integration of optical flow. Empirical results are presented that illustrate the applicability of the proposed methods to real-world video. Unlike many motion detection schemes, no knowledge about expected object size or shape is necessary for rejecting the distracting motion.
Multizone/multipass photorefractive keratectomy: Six month results (1995)

A multizone/multipass photorefractive keratectomy (MP-PRK) technique was used to treat 315 eyes with the 193 nm VISX 20/20 excimer laser. Algorithms were developed to treat the full range of myopia, including 170 low myopic eyes (-1.0 to -6.0 diopters [D]), 105 moderately myopic eyes (-6.0 to -10.0 D), and 40 highly myopic eyes (-10.0 to -27.0 D). Preoperative mean myopia was -6.69 D; astigmatism equal to or greater than -0.5 D (mean -1.18 D) was present in 193 eyes. At one month postoperatively, most eyes were slightly hyperopic (mean +0.8 D); this regressed to a mean of -0.16 D. At six months, 95.5% of low myopes, 84.8% of moderate myopes, and 59.5% of high myopes were within 1.0 D of emmetropia; 78.4% of high myopes were within 2.0 D of the intended correction. There was no loss of 20/40 best corrected visual acuity (BCVA) at six months; a significant gain in 20/25 BCVA was seen in the moderate and high myopia groups (P < .05). At six months, uncorrected visual acuity was 20/25 in 89.4% of low myopes, 75.0% of moderate myopes, and 25.7% of high myopes. Mean haze value was 0.48 at one month and was not significantly different among the three groups (0.44, 0.52, 0.51, respectively). A control group treated with the one-pass multizone technique had a significantly higher amount of haze: 1.05 (P < .01). The data presented compare favorably with those obtained from other centers. Based on these results, we believe that MP-PRK is a safe, reliable technique to correct most low, moderate, and high myopia.
277 ENERGY REQUIREMENT DURING DEVELOPMENT TO THE BLASTOCYST STAGE OF PORCINE EMBRYOS PRODUCED IN VITRO (2004)

A successful in vitro production (IVP) of porcine blastocysts, which enables piglet production after transfer to recipients, was reported (Kikuchi et al., 2002 Biol. Reprod. 66, 1033–1041). Generally, in the IVP system, both glucose and glutamine as energy sources were included in vitro culture (IVC) medium from Day 2 (Day 0 = the day of in vitro fertilization) until Day 6. However, the exact requirement of these substances for the development to the blastocyst stage of IVP embryos has not yet been clarified. The objective of the present study was to evaluate whether these two substances are necessary for embryonic development to the blastocyst stage in culture during the period. Porcine cumulus-oocyte complexes were matured for 46 h and fertilized in vitro as reported by Kikuchi et al. (see above). After removal of cumulus cells and spermatozoa, the oocytes were cultured subsequently in NCSU-37 supplemented with pyruvate and lactate (IVC-PyrLac) for 2 days. Then they were cultured until Day 6 in other IVC medium prepared as follows (1–6); Basic IVC medium (BM) was a modified NCSU-37 consisting of 108.7 mM NaCl, 4.8 mM KCl, 1.7 mM CaCl2, 1.2 mM KH2PO4, 1.2 mM MgSO4, 25.1 mM NaHCO3 and 4 mg mL-1 fatty acid-free BSA. Then one or more of the following energy sources were supplemented to BM;; (1) 12 mM sorbitol (SigmaUltra), 5.55 mM glucose (Wako special grade) and 1.0 mM glutamine (Sigma) (NCSU-37/Gln+), (2) 19.2 mM sorbitol and 1.0 mM glutamine (IVC-Sorbitol/Gln+); (3) 19.2 mM mannitol (SigmaUltra) and 1.0 mM glutamine (IVC-Mannitol/Gln+), (4) 12 mM sorbitol and 5.55 mM glucose (NCSU-37/Gln-); 5) 19.2 mM sorbitol (IVC-Sorbitol/Gln-); and 6) 19.2 mM mannitol (IVC-Mannitol/Gln-). The osmolarity of these media was adjusted to 283–285 osmol g-1. All embryos were fixed as whole mounts, stained and evaluated. The rate of blastocysts in NCSU-37/Gln+ (26.8%) was significantly higher (P &lt; 0.05; by analysis of variance and Duncan’s multiple range test) than those in IVC-Sorbitol/Gln+, IVC-Mannitol/Gln+ and NCSU-37/Gln- (19.0%, 17.0% and 15.5%, respectively). A remarkable decrease in the rates in IVC-Sorbitol/Gln- and IVC-Mannitol/Gln- (P &lt; 0.05; 1.4% and 2.0%, respectively) was observed. The cell numbers of NCSU-37/Gln+, IVC-Sorbitol/Gln+, IVC-Mannitol/Gln+ and NCSU-37/Gln- (55.5, 52.0, 49.6 and 58.7, respectively) had a tendency to be higher than those of IVC-Sorbitol/Gln- and IVC-Mannitol/Gln- (38.0 and 35.2, respectively). These results confirm that the supplementation of maturation medium with at least one energy source (glucose or glutamine) promotes embryonic development in vitro to the blastocyst stage, that the combination of both sources improves the chance of the embryonic survival, and that porcine embryos do not utilize sorbitol or mannitol as an energy source. The importance of glucose and glutamine is suggested for the development to the blastocyst stage of porcine IVP embryos.
Automated femoral version estimation without the distal femur (2018)

Femoral version impacts the long-term functioning of the femoroacetabular joint. Accurate measurements of version are thus required for success in total hip arthroplasties and hip reconstructive surgeries. These are impossible to obtain without visualization of the distal femur, which is often unavailable preoperatively as the majority of imaging scans are isolated to the pelvis and proximal femur. We developed an automated algorithm for identifying the major landmarks of the femur. These landmarks were then used to identify proximal axes and create a statistical shape model of the proximal femur across 144 asymptomatic femora. With six proximal axes selected, and 200 parameters (distances and angles between points) from the shape model measured, the best-fitting linear correlation was found. The difference between true version and version predicted by this model was 0.00 ± 5.13° with a maximum overestimation and underestimation of 11.80 and 15.35°, respectively. The mean absolute difference was 4.14°. This model and its prediction of femoral version are a substantial improvement over pre-operative 2D or intra-operative visual estimation measures. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:3161-3168, 2018.
Two Birds with One Network: Unifying Failure Event Prediction and\n Time-to-failure Modeling (2018)

One of the key challenges in predictive maintenance is to predict the\nimpending downtime of an equipment with a reasonable prediction horizon so that\ncountermeasures can be put in place. Classically, this problem has been posed\nin two different ways which are typically solved independently: (1) Remaining\nuseful life (RUL) estimation as a long-term prediction task to estimate how\nmuch time is left in the useful life of the equipment and (2) Failure\nprediction (FP) as a short-term prediction task to assess the probability of a\nfailure within a pre-specified time window. As these two tasks are related,\nperforming them separately is sub-optimal and might results in inconsistent\npredictions for the same equipment. In order to alleviate these issues, we\npropose two methods: Deep Weibull model (DW-RNN) and multi-task learning\n(MTL-RNN). DW-RNN is able to learn the underlying failure dynamics by fitting\nWeibull distribution parameters using a deep neural network, learned with a\nsurvival likelihood, without training directly on each task. While DW-RNN makes\nan explicit assumption on the data distribution, MTL-RNN exploits the implicit\nrelationship between the long-term RUL and short-term FP tasks to learn the\nunderlying distribution. Additionally, both our methods can leverage the\nnon-failed equipment data for RUL estimation. We demonstrate that our methods\nconsistently outperform baseline RUL methods that can be used for FP while\nproducing consistent results for RUL and FP. We also show that our methods\nperform at par with baselines trained on the objectives optimized for either of\nthe two tasks.\n
NURR1 activation in skeletal muscle controls systemic energy homeostasis (2019)

Skeletal muscle plays a central role in the control of metabolism and exercise tolerance. Analysis of muscle enhancers activated after exercise in mice revealed the orphan nuclear receptor NURR1/NR4A2 as a prominent component of exercise-responsive enhancers. We show that exercise enhances the expression of NURR1, and transgenic overexpression of NURR1 in skeletal muscle enhances physical performance in mice. NURR1 expression in skeletal muscle is also sufficient to prevent hyperglycemia and hepatic steatosis, by enhancing muscle glucose uptake and storage as glycogen. Furthermore, treatment of obese mice with putative NURR1 agonists increases energy expenditure, improves glucose tolerance, and confers a lean phenotype, mimicking the effects of exercise. These findings identify a key role for NURR1 in governance of skeletal muscle glucose metabolism, and reveal a transcriptional link between exercise and metabolism. Our findings also identify NURR1 agonists as possible exercise mimetics with the potential to ameliorate obesity and other metabolic abnormalities.
CO<sub>2</sub>-Free Production of Hydrogen by Catalytic Pyrolysis of Hydrocarbon Fuel (1998)

All conventional options of hydrogen production from hydrocarbon fuel (primarily natural gas, NG), e.g., steam reforming (SR), partial oxidation, and autothermal reforming, involve CO2 production at some point in the technological chain of the process. Therefore, the main problem remains: how to produce hydrogen from hydrocarbon fuels without CO2 emission. The capture of CO2 from the SR process streams and its sequestration (underground or ocean disposal) are actively discussed in the literature. However, this method is energy intensive, poses uncertain ecological consequences, and still does not completely eliminate CO2 emission. Another approach is to decompose hydrocarbon fuels into hydrogen and carbon. The thermal decomposition of NG is a technologically simple one-step process without energy and material intensive gas separation stages and shows the potential to be a CO2-free hydrogen production process. The experimental results of the thermocatalytic decomposition of gaseous (methane and propane) and liquid (hexane, gasoline and diesel fuel) hydrocarbons over metal-oxide and carbon-based catalysts are presented. Although transition metal catalysts produce gas with high initial hydrogen concentration, their activity rapidly drops because of the surface deposition of carbon. Carbon-based catalysts offer certain advantages over metal catalysts, since there is no need for the carbon separation from the catalyst. Catalytic pyrolysis of light liquid hydrocarbons, including gasoline, over activated carbon yields hydrogen-rich gas (40−50 vol % H2). The decomposition of methane in binary mixtures with saturated and unsaturated hydrocarbons was also studied. It was found that the addition of small amounts of unsaturated hydrocarbons (e.g., acetylene) to methane noticeably increases the steady-state concentration of hydrogen in the effluent gas. The studied process can be the basis for the development of compact catalytic units for on-site production of hydrogen/methane blends from NG and liquid hydrocarbon fuels at gas refueling stations. The concept can also be used for a CO2-free production of hydrogen for fuel cell applications.