gebhart/patrepeval huggingface dataset:
Continuous and Efficient Lock Profiling for Java on Multicore Architectures (2015)

Today, the processing of large dataset is generally parallelised and performed on computers with many cores. However, locks can serialize the execution of these cores and hurt the latency and the processing throughput. Spotting theses lock contention issues in-vitro (i.e. during the development phase) is complex because it is difficult to reproduce a production environment, to create a realistic workload representative of the context of use of the software and to test every possible configuration of deployment where will be executed the software. This thesis introduces Free Lunch, a lock profiler that diagnoses phases of high lock contention due to locks in-vivo (i.e. during the operational phase). Free Lunch is designed around a new metric, the Critical Section Pressure (CSP), which aims to evaluate the impact of lock contention on overall thread progress. Free Lunch is integrated in Hotpost in order to minimize the overhead and regularly reports the CSP during the execution in order to detect temporary issues due to locks. Free Lunch is evaluated over 31 benchmarks from Dacapo 9.12, SpecJVM08 and SpecJBB2005, and over the Cassandra database. We were able to pinpoint the phases of lock contention in 6 applications for which some of these were not detected by existing profilers. With this information, we have improved the performance of Xalan by 15% just by rewriting one line of code and identified a phase of high lock contention in Cassandra during the replay of transactions after a crash of a node. Free Lunch has never degraded performance by more than 6%, which makes it suitable to be deployed continuously in an operational environment.
Interlaminar Performance of Waterproof and Cohesive Materials for Concrete Bridge Deck under Specific Test Conditions (2018)

The performance of waterproof and cohesive material significantly affects the service life of concrete bridge deck pavement. In this paper, six kinds of waterproof and cohesive materials including epoxy asphalt, AMP-100, styrene-butadiene-styrene (SBS)–modified asphalt, and asphalt rubber (dosages of rubber power are 17, 19, and 21% respectively) were measured via oblique shear test, pull-off test, and shear test after loading under different test conditions. The impermeability and the influence of aging on material performance were studied. The viscosity and strength characteristics of epoxy asphalt were also studied at different curing times and temperature conditions. Results show that the optimum dosages of epoxy asphalt, AMP-100, SBS-modified asphalt, and asphalt rubber with 17, 19, and 21% rubber powder are 0.9, 0.3, 0.5, 1.0, 0.5, and 0.5 kg/m2, respectively. The shear strength value of epoxy asphalt is the largest at 25°C, followed by SBS-modified asphalt. The shear strength and pull-off strength of several materials decline at different levels under the condition of high temperatures or being soaked in water. The order of shear failure life of the selected waterproof and cohesive materials is epoxy asphalt > SBS-modified asphalt > asphalt rubber (19%) >AMP-100. In various waterproof and cohesive materials, the shear strength and pull-off strength of epoxy asphalt after the aging of a specimen are the largest. Epoxy asphalt shows a good waterproof property under traffic load after the asphalt mixture has been paved. The viscosity change characteristic of epoxy asphalt is closely related to the temperature and curing time. The pull-off strength reaches its peak value after curing for 30 min, which is earlier than shear strength. The epoxy asphalt has a significant performance advantage as a waterproof and cohesive material for a concrete bridge deck.
Development of cell-laden hydrogels with high mechanical strength for tissue engineering applications (2013)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Materials Science and Engineering, February 2014.
Approaches to Software Fault Tolerance (1993)

A personal and rather discursive account is given of the background to the start of work in the early 1970s at Newcastle on software fault tolerance, and of how work has developed to encompass forward as well as backward error recovery, and parallel and distributed software as well as sequential programs. A major theme of the paper is that of the links between this work and that carried out elsewhere in connection with the topic of objectoriented programming, in particular on concepts such as generic classes and functions, exception-handling, delegation and reflection.
Three‐stage doherty amplifier with uneven input splitter (2013)

Abstract This article presents a new high‐efficiency three‐stage Doherty power amplifier (DPA) using a simple uneven power splitter. The proposed three‐way uneven power splitter, which was designed based on a multiway Wilkinson power divider, was applied to the three‐stage DPA. Also, the proposed structure is much simpler and uses fewer lumped components than the conventional one. Using the uneven input splitter, each individual amplifier in the DPA has an appropriate input power level. It results in a proper load modulation of the three‐stage Doherty amplifier. The proposed three‐stage DPA has been implemented for the E‐UTRA‐13 band of from 746 to 756 MHz. For the LTE‐frequency‐division duplexing release 9 downlink signal with a peak‐to‐average power ratio of 10 dB and a signal bandwidth of 5 MHz, a high power‐added efficiency of 42.3% and an adjacent channel leakage power ratio of −37 dBc at an offset of 2.7 MHz were experimentally achieved at an average output power of 30 dBm. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:1405–1409, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.27581
Surface plasmon polariton compression through radially and linearly polarized source (2012)

We report on the possibility of realizing a radial mode on a metallic conical structure by means of a linearly polarized incident wave. This result is utilized for observing surface plasmon polaritons adiabatic compression on a tapered conical nanostructure. The ingredients for radial mode generation are described in terms of phase-matching of the components of the electromagnetic field. We conclude by showing the robustness of this approach, explaining the polaritonic behavior as a function of the device geometry.
Autoaggregation and adhesion ability in a Bifidobacterium suis strain (1998)

On the basis of autoaggregation ability, two different phenotypes (Agg + and Agg -) were selected from a strain (BSu895) of Bifidobacterium suis. The relationship between autoaggregation and adhesion of bacteria to intestinal tissue was investigated by observing the adhesivity of the two phenotypic variants to ileum and colon tissue pieces collected from six new-born piglets. The results suggest that there is a good relationship between autoaggregation and adhesion as variant Agg + (autoaggregating) has a stronger adhesion ability than Agg - (non-autoaggregating).
<title>Vertebral surface extraction from ultrasound images for technology-guided therapy</title> (1999)

The use of intra-operative spinal ultrasound (US) for surgical navigation of the spine has been proposed as a novel extension of interactive image-guided surgery (IIGS) procedures. For the proposed spinal applications, a surface-based registration of US images to preoperative CT or MR scans will be applied. This type of registration requires the extraction of numerous vertebral surface points from each slice in a series of US images. A plastic spine phantom immersed in a water tank was scanned posteriorly with one of several US transducers -- at frequencies 3.5, 4.5, and 7.5 MHz. Images from the lumbar region of the spine were captured in the transverse plane and were processed for surface detection of the spinous process, transverse processes and laminae. Steps in image processing included application of a morphological open operator, a linear threshold, a ray-tracing algorithm, and a 3-D point identifier. Despite the generally noisy environment of US, the three regions of interest from the lumbar vertebrae were successfully extracted from all three sets of images. With a successful segmentation of corresponding CT or MR images, registration of these modalities to intra-operative US images will provide surgeons with a step towards a less invasive method of spinal therapy.
Event-based estimation and control for remote robot operation with reduced communication (2015)

An event-based communication framework for remote operation of a robot via a bandwidth-limited network is proposed. The robot sends state and environment estimation data to the operator, and the operator transmits updated control commands or policies to the robot. Event-based communication protocols are designed to ensure that data is transmitted only when required: the robot sends new estimation data only if this yields a significant information gain at the operator, and the operator transmits an updated control policy only if this comes with a significant improvement in control performance. The developed framework is modular and can be used with any standard estimation and control algorithms. Simulation results of a robotic arm highlight its potential for an efficient use of limited communication resources, for example, in disaster-response scenarios such as the DARPA Robotics Challenge.
Pyrrolizidine Alkaloids from Crotalaria laburnifolia subspec. australis (1992)

Seeds of Crotaloria laburnifolia L. subspec. australis (Bak. f.) Polhill were investigated for pyrrolizidine alkaloids. Anacrotine and madurensine were found, and their structures confirmed by spectroscopic methods.
Development of carbon dioxide removal system from the flue gas of coal fired power plant (2011)

Post-combustion carbon dioxide capture is the technique that can be rapidly and safely employed for substantially reducing carbon dioxide emissions from existing and near future power plants. The key question of the absorption/desorption technique for carbon dioxide removal is process economics. Toshiba is pushing through the post-combustion carbon dioxide capture because it can be employed in rather short period and applied for both retrofit and new power plants. In this work, we evaluated the seven amine-based absorbents as new solvents, which was selected from about 900 amines, in terms of energy consumption for CO2 desorption using a thermodynamic absorption and desorption cycle simulation. We estimated the consumed energy in the stripper when the flue gas contains 12 % CO2 and the capture ratio of CO2 from the flue gas is 90 %. It was found that the lowest energy consumption in the stripper was about 2.5 GJ/t- CO2 when one mixed amine-based aqueous solution (Toshiba Solvent 2, TS-2) was used as the solvent. The value was much lower than that for the general 30 wt.% monoethanolamine (MEA) aqueous solution. And it is lower than our former solvent (Toshiba Solvent 1, TS-1) which was presented at GHGT-9. Then we evaluated the new solvent TS-2 using the bench-scale test facility which contains a complete absorption/desorption process with the absorber and the stripper. At this test TS-2 showed lower consumed energy, less than 2.5 GJ/t- CO2, by optimizing the space velocity of the simulated flue gas and so on, while TS-1 showed about 2.7 GJ/t- CO2 which is nearly equal of the value of the thermodynamic simulation. Parallel to these activities the pilot plant of 10 t- CO2 /day recovery was constructed and commenced in September 2009 with a complete absorption/desorption supplied with the flue gas of a coal fired power plant. In the demonstration tests CO2 capture ratio and captured CO2 rate exceeded the planning values of 90% and 10t- CO2 /day each during continuous 3,000 hour operation. Furthermore the energy consumption for CO2 recovery at the stripper had been kept between 3.2 and 3.3 GJ/t- CO2. These results prove that Toshiba CO2 capture system using TS-1 solvent is a promising system which has been realizing good and stable performances. Toshiba will utilize the results of these studies to further improve and optimize the performance of the system, towards implementation and integration of the system to a larger scale thermal power plant system.
BRAF mutations may identify a clinically distinct subset of glioblastoma (2021)

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Prior studies examining the mutational landscape of GBM revealed recurrent alterations in genes that regulate the same growth control pathways. To this regard, ~ 40% of GBM harbor EGFR alterations, whereas BRAF variants are rare. Existing data suggests that gain-of-function mutations in these genes are mutually exclusive. This study was designed to explore the clinical, pathological, and molecular differences between EGFR- and BRAF-mutated GBM. We reviewed retrospective clinical data from 89 GBM patients referred for molecular testing between November 2012 and December 2015. Differences in tumor mutational profile, location, histology, and survival outcomes were compared in patients with EGFR- versus BRAF-mutated tumors, and microarray data from The Cancer Genome Atlas was used to assess differential gene expression between the groups. Individuals with BRAF-mutant tumors were typically younger and survived longer relative to those with EGFR-mutant tumors, even in the absence of targeted treatments. BRAF-mutant tumors lacked distinct histomorphology but exhibited unique localization in the brain, typically arising adjacent to the lateral ventricles. Compared to EGFR- and IDH1-mutant tumors, BRAF-mutant tumors showed increased expression of genes related to a trophoblast-like phenotype, specifically HLA-G and pregnancy specific glycoproteins, that have been implicated in invasion and immune evasion. Taken together, these observations suggest a distinct clinical presentation, brain location, and gene expression profile for BRAF-mutant tumors. Pending further study, this may prove useful in the stratification and management of GBM.
PML is a ROS sensor activating p53 upon oxidative stress (2017)

Promyelocytic leukemia (PML) nuclear bodies (NBs) recruit partner proteins, including p53 and its regulators, thereby controlling their abundance or function. Investigating arsenic sensitivity of acute promyelocytic leukemia, we proposed that PML oxidation promotes NB biogenesis. However, physiological links between PML and oxidative stress response in vivo remain unexplored. Here, we identify PML as a reactive oxygen species (ROS) sensor. <i>Pml<sup>-/-</sup></i> cells accumulate ROS, whereas PML expression decreases ROS levels. Unexpectedly, <i>Pml<sup>-/-</sup></i> embryos survive acute glutathione depletion. Moreover, <i>Pml<sup>-/-</sup></i> animals are resistant to acetaminophen hepatotoxicity or fasting-induced steatosis. Molecularly, <i>Pml<sup>-/-</sup></i> animals fail to properly activate oxidative stress-responsive p53 targets, whereas the NRF2 response is amplified and accelerated. Finally, in an oxidative stress-prone background, <i>Pml<sup>-/-</sup></i> animals display a longevity phenotype, likely reflecting decreased basal p53 activation. Thus, similar to p53, PML exerts basal antioxidant properties but also drives oxidative stress-induced changes in cell survival/proliferation or metabolism in vivo. Through NB biogenesis, PML therefore couples ROS sensing to p53 responses, shedding a new light on the role of PML in senescence or stem cell biology.
Genome editing technology and applications with the type I CRISPR system (2022)

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, which are representative genome editing technologies, are classified into class 1 and class 2 in terms of evolutionary biology and are further classified into several subtypes. Class 2 CRISPR systems, including type II Cas9 and type V Cas12a, are the most commonly used for genome editing in eukaryotic cells, while type I CRISPR systems within Class 1 are also becoming available. Type I CRISPR recognizes longer target sequences than CRISPR-Cas9 and can induce large deletion mutations of several kilobases. These features demonstrate its potential as a novel and unique genome editing tool that can induce genetic disruption safely and reliably. Thus, it is expected to be utilized for gene therapy and industrial applications. Recently, the DNA cleavage mechanism of type I CRISPR has also revealed details from protein-complex analyses with X-ray crystallography, cryo-electron microscopy, and high-speed atomic force microscopy. The single-strand DNA trans-cleavage activity of type I CRISPR, called collateral activity, has broadened the potential application for CRISPR diagnostics, especially in the development of point-of-care testing methods for COVID-19. In this review, we present an overview of the type I CRISPR system, its application to genome editing, and genetic diagnosis using CRISPR-Cas3.
Basic studies on controlled transdermal delivery of nicardipine hydrochloride using ethylene-vinyl acetate and ethylene-vinyl alcohol copolymer membranes. (1988)

The permeability of a model drug, nicardipine hydrochloride (NC), through ethylene-vinyl acetate copolymer (EVAc) or ethylene-vinyl alcohol copolymer (EVAl) membrane as a rate controlling layer was examined as one step in the development of a well-designed membrane permeation-controlled transdermal therapeutic system (TTS). The membrane permeability of NC from various suspensions in ethanol (EtOH)-methyl ethyl ketone (MEK)-water mixed solvents was affected by the solvent composition as well as the membrane composition. The NC permeation through EVAc membrane increased with increase in the MEK content in the solvent, whereas that through the EVAl membrane showed a convex curve against MEK content. As solvent penetration into the membranes may be important for the NC permeation, the extent of swelling of EVAc or EVAl beads was determined as an index of solvent pentration. The relationship between the solvent composition and degree of swelling of the copolymer was similar to that between the solvent composition and the logarithm of the product of the steady-state permeation rate of NC through EVAc or EVAl membrane and thickness of the membrane. It was found from the results of the permeation and swelling experiments that the permeability of NC through EVAc or EVAl membrane is mainly affected by the solvent penetration into the membrane. Finally, the effect of EVAll membrane on the permeation of NC through the intact or damaged skin was measured. The NC permation through a piled layer of EVAl membrane and full-thickness skin was similar to that through a piled layer of EVAl membrane and damaged skin. This result suggests that the application of these membranes would be useful in making a well-designed TTS which shows little inter- and/or intra-subject variation in skin permeation of NC.
Supplementary Table 1 from Mutations in the Ras–Raf Axis Underlie the Prognostic Value of CD133 in Colorectal Cancer (2023)

&lt;p&gt;PDF file, 179KB, CSC marker CD133 as prognostic marker in CRC.&lt;/p&gt;
Primary Hodgkin's disease of the CNS in an immunocompetent patient: A case study and review of the literature (2000)

Primary Hodgkin's disease limited to the CNS is exceedingly rare.Little is known regarding etiologic risk factors, optimal management, and prognosis.A case of Hodgkin's disease con ned to the CNS, with cerebrospinal uid negative for cytology, is described in an immunocompetent patient previously treated for hyperthyroidism with 131 I.The patient underwent craniotomy, with resection of two lesions in close proximity within the parenchyma of the temporoparietal lobe.Histopathology revealed classic nodular sclerosing Hodgkin's disease, without evidence of Epstein-Barr viral infection.Treatment included radiation to the whole brain with a boost to the tumor bed.The patient made a full neurologic recovery and remains free of disease recurrence 21 months after treatment.A literature review has identi ed only 9 additional cases.Seven of 8 evaluable patients remain alive and free of recurrence with a median follow-up of 13 months.The risk factors for this presentation remain unde ned.Although followup is short, radiotherapy alone appears to provide excellent disease-free survival.Chemotherapy may be reserved for patients with positive cerebrospinal uid, extracranial disease, or subsequent relapse.
Severity and Characteristics of Developmental Delay Can Be Assessed Using Variability Measures of Sitting Posture (2010)

Our method of evaluating sitting postural control could be an objective tool to help describe distinctive features of motor delay in an individual infant and could lead in the design of selective therapeutic interventions for improving postural control of infants with motor delays.
Alkyl, hydrido, and tetrahydroaluminato complexes of manganese with 1,2-bis(dimethylphosphino)ethane (dmpe). X-Ray crystal structures of Mn2(µ-C6H11)2(C6H11)2(µ-dmpe), (dmpe)2Mn(µ-H)2AlH(µ-H)2AlH(µ-H)2-Mn(dmpe)2, and Li4{MnH(C2H4)[CH2(Me)PCH2CH2PMe2]2}2·2Et2O (1985)

Alkylation of MnBr2dmpe)2[dmpe = 1,2-bis(dimethylphosphino)ethane] with MgBut2 leads to the t-butyl complex MnBut2(dmpe); alkylation with Mg(C6H11)2 gives the cyclohexyl-bridged dimer Mn2(µ-C6H11)2(C6H11)2(µ-dmpe)(2). By contrast, alkylation with MgEt2 leads to the diamagnetic manganese(I) species, trans-MnH (C2H4)(dmpe)2. Interaction of the latter with LiBut leads to deprotonation of the dmpe ligand and formation of a complex, (4), of stoicheiometry Li2(MnH(C2H4)[CH2(Me)PCH2CH2PMe2]2}·Et2O. A reduction of MnII to MnI also occurs in the interaction of MnBr2(dmpe)2 with LiAlH4 when the tetrahydroaluminate complex [Mn(AlH4)(dmpe)2]2(5) is formed. Hydrolysis of (5) gives the volatile diamagnetic hydride MnH3(dmpe)2. The X-ray crystal structures of the complexes (2), (4), and (5) have been determined. In (2), the molecule, which has two-fold symmetry, has two manganese atoms each bound to one terminal related cyclohexyl group [Mn–C = 2.118(10)Å] and bridged asymmetrically by two symmetry related cyclohexyls [Mn–C = 2.256(9), 2.327(9)Å]. The Mn ⋯ Mn distance is quite short at 2.616(5)Å and the manganese atoms have a distorted tetrahedral co-ordination. In complex (4), two MnH(C2H4)(dmpe)2 units [Mn–H 1.44(4),Mn–C (av.) 2.121(5), Mn–P 2.213(3)–2.274(3)Å] have each lost two hydrogen atoms, one from each of two dmpe methyls, and the resulting four CH2 groups form multicentre alkyl bridges to a central Li4 tetrahedron [C ⋯ Li 2.20–2.36(I), Li ⋯ Li 2.46(1)–2.69(1)Å]. Two of the lithiums are co-ordinated by diethyl ether [ Li–O 2.053(8)Å]. The complex as a whole has C2 symmetry and the manganese(I) centre has a pseudo-octahedral geometry, although pentagonal bipyramidal is an alternative description if the ethylene is considered to occupy two co-ordination sites. Complex (5) is a centrosymmetric dimer in which two cis-octahedral MnH2(dmpe)2 units are bridged by a AlH-(µ-H)2AlH moiety via Al(µ-H)2Mn linkages. The two H atoms in the AlH2Mn bridge are closer to the Mn atoms [Mn–H = 1.61(3), 1.63(3)Å] than to the Al atoms [Al–H = 1.81(3), 1.81(3)Å]. The Al–H distances in the AlH2Al unit are 1.64(3) and 1.80(3)Å, while the terminal Al–H distance is 1.51(3)Å. The aluminium has trigonal bipyramidal co-ordination with one terminal hydrogen in an equatorial position.