Verifying OpenJDK’s LinkedList using KeY
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ABSTRACT:
SUBMITTER: Biere A
PROVIDER: S-EPMC7480693 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
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Project description:Background Colon cancer (CC) is one of the tumors with high morbidity and mortality in the world, and has a trend of younger generation. The molecular level of CC has not been fully elaborated. The purpose of this study is to screen and identify important genes with poor prognosis and their mechanisms at different levels. Methods GSE74602 and GSE10972 gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) database. There were 58 normal tissues and 58 CC tissues. Differentially expressed genes (DEGs) were screened out by using the GEO2R tool and Venn diagram. Then, the DAVID online database was used to perform the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Six hub genes with the highest correlation were screened out after the modular analysis of the protein-protein interaction (PPI) network by using Cytoscape’s MCODE plug-in. Finally, the overall survival of key hub genes and potential pathways were verified in GEPIA and UALCAN database. Results A total of 78 up-regulated DEGs were enriched in the mitotic nuclear division, cell division, cell proliferation, anaphase-promoting complex-dependent catabolic process and G2/M transition of the mitotic cell cycle. In total, 130 down-regulated DEGs were enriched in muscle contraction, bicarbonate transport, cellular response to zinc ion, negative regulation of growth, negative regulation of leukocyte apoptotic process and one-carbon metabolic process. CDK1, CCNB1, CDC20, AURKA, CCNA2 and TOP2A were the top six hub genes, mainly enriched in cell cycle pathways. Among them, CCNB1, CDK1, CDC20, CCNA2 were enriched in the G2/M phase. GEPIA and UALCAN database confirmed that CCNA2 and CCNB1 had a significant relationship with the poor prognosis of CC patients. Meanwhile, there was a positive correlation between the two. Conclusions Screening out genes with abnormal expression in CC help understand the initiation and progression of CC at the molecular level and explore candidate biomarkers for diagnosis, treatment and prognosis.
| S-EPMC8797306 | biostudies-literature
Project description:Heisenberg's uncertainty relations have played an essential role in quantum physics since its very beginning. The uncertainty relations in the modern quantum formalism have become a fundamental limitation on the joint measurements of general quantum mechanical observables, going much beyond the original discussion of the trade-off between knowing a particle's position and momentum. Recently, the uncertainty relations have generated a considerable amount of lively debate as a result of the new inequalities proposed as extensions of the original uncertainty relations. We report an experimental test of one of the new Heisenberg's uncertainty relations using a single 40Ca+ ion trapped in a harmonic potential. By performing unitary operations under carrier transitions, we verify the uncertainty relation proposed by Busch, Lahti, and Werner (BLW) based on a general error-trade-off relation for joint measurements on two compatible observables. The positive operator-valued measure, required by the compatible observables, is constructed by single-qubit operations, and the lower bound of the uncertainty, as observed, is satisfied in a state-independent manner. Our results provide the first evidence confirming the BLW-formulated uncertainty at a single-spin level and will stimulate broad interests in various fields associated with quantum mechanics.
| S-EPMC5566201 | biostudies-literature
Project description:BackgroundRespiration-gated radiotherapy (RGRT) can decrease treatment toxicity by allowing for smaller treatment volumes for mobile tumors. RGRT is commonly performed using external surrogates of tumor motion. We describe the use of time-integrated electronic portal imaging (TI-EPI) to verify the position of internal structures during RGRT deliveryMethodsTI-EPI portals were generated by continuously collecting exit dose data (aSi500 EPID, Portal vision, Varian Medical Systems) when a respiratory motion phantom was irradiated during expiration, inspiration and free breathing phases. RGRT was delivered using the Varian RPM system, and grey value profile plots over a fixed trajectory were used to study object positions. Time-related positional information was derived by subtracting grey values from TI-EPI portals sharing the pixel matrix. TI-EPI portals were also collected in 2 patients undergoing RPM-triggered RGRT for a lung and hepatic tumor (with fiducial markers), and corresponding planning 4-dimensional CT (4DCT) scans were analyzed for motion amplitude.ResultsIntegral grey values of phantom TI-EPI portals correlated well with mean object position in all respiratory phases. Cranio-caudal motion of internal structures ranged from 17.5-20.0 mm on planning 4DCT scans. TI-EPI of bronchial images reproduced with a mean value of 5.3 mm (1 SD 3.0 mm) located cranial to planned position. Mean hepatic fiducial markers reproduced with 3.2 mm (SD 2.2 mm) caudal to planned position. After bony alignment to exclude set-up errors, mean displacement in the two structures was 2.8 mm and 1.4 mm, respectively, and corresponding reproducibility in anatomy improved to 1.6 mm (1 SD).ConclusionTI-EPI appears to be a promising method for verifying delivery of RGRT. The RPM system was a good indirect surrogate of internal anatomy, but use of TI-EPI allowed for a direct link between anatomy and breathing patterns.
| S-EPMC2075522 | biostudies-literature
Project description:Cohn and Umans proposed a framework for developing fast matrix multiplication algorithms based on the embedding computation in certain groups algebras [9]. In subsequent work with Kleinberg and Szegedy, they connected this to the search for combinatorial objects called strong uniquely solvable puzzles (strong USPs) [8]. We begin a systematic computer-aided search for these objects. We develop and implement algorithms based on reductions to
| S-EPMC7326541 | biostudies-literature
Project description:This study utilizes process control techniques to identify action limits for TomoTherapy couch positioning quality assurance tests. A test was introduced to monitor accuracy of the applied couch offset detection in the TomoTherapy Hi-Art treatment system using the TQA "Step-Wedge Helical" module and MVCT detector. Individual X-charts, process capability (cp), probability (P), and acceptability (cpk) indices were used to monitor a 4-year couch IEC offset data to detect systematic and random errors in the couch positional accuracy for different action levels. Process capability tests were also performed on the retrospective data to define tolerances based on user-specified levels. A second study was carried out whereby physical couch offsets were applied using the TQA module and the MVCT detector was used to detect the observed variations. Random and systematic variations were observed for the SPC-based upper and lower control limits, and investigations were carried out to maintain the ongoing stability of the process for a 4-year and a three-monthly period. Local trend analysis showed mean variations up to ±0.5 mm in the three-monthly analysis period for all IEC offset measurements. Variations were also observed in the detected versus applied offsets using the MVCT detector in the second study largely in the vertical direction, and actions were taken to remediate this error. Based on the results, it was recommended that imaging shifts in each coordinate direction be only applied after assessing the machine for applied versus detected test results using the step helical module. User-specified tolerance levels of at least ±2 mm were recommended for a test frequency of once every 3 months to improve couch positional accuracy. SPC enables detection of systematic variations prior to reaching machine tolerance levels. Couch encoding system recalibrations reduced variations to user-specified levels and a monitoring period of 3 months using SPC facilitated in detecting systematic and random variations. SPC analysis for couch positional accuracy enabled greater control in the identification of errors, thereby increasing confidence levels in daily treatment setups.
| S-EPMC5874965 | biostudies-literature
Project description:Behavioural studies of elusive wildlife species are challenging but important when they are threatened and involved in human-wildlife conflicts. Accelerometers (ACCs) and supervised machine learning algorithms (MLAs) are valuable tools to remotely determine behaviours. Here we used five captive cheetahs in Namibia to test the applicability of ACC data in identifying six behaviours by using six MLAs on data we ground-truthed by direct observations. We included two ensemble learning approaches and a probability threshold to improve prediction accuracy. We used the model to then identify the behaviours in four free-ranging cheetah males. Feeding behaviours identified by the model and matched with corresponding GPS clusters were verified with previously identified kill sites in the field. The MLAs and the two ensemble learning approaches in the captive cheetahs achieved precision (recall) ranging from 80.1% to 100.0% (87.3% to 99.2%) for resting, walking and trotting/running behaviour, from 74.4% to 81.6% (54.8% and 82.4%) for feeding behaviour and from 0.0% to 97.1% (0.0% and 56.2%) for drinking and grooming behaviour. The model application to the ACC data of the free-ranging cheetahs successfully identified all nine kill sites and 17 of the 18 feeding events of the two brother groups. We demonstrated that our behavioural model reliably detects feeding events of free-ranging cheetahs. This has useful applications for the determination of cheetah kill sites and helping to mitigate human-cheetah conflicts.
| S-EPMC8398415 | biostudies-literature
Project description:BackgroundThe evaluation, verification and comparison of different numerical heart models are difficult without a commonly available database that could be utilized as a reference. Our aim was to compile an exemplary dataset.MethodsThe following methods were employed: Magnetic Resonance Imaging (MRI) of heart and torso, Body Surface Potential Maps (BSPM) and MagnetoCardioGraphy (MCG) maps. The latter were recorded simultaneously from the same individuals a few hours after the MRI sessions.ResultsA training dataset is made publicly available; datasets for blind testing will remain undisclosed.ConclusionsWhile the MRI data may provide a common input that can be applied to different numerical heart models, the verification and comparison of different models can be performed by comparing the measured biosignals with forward calculated signals from the models.
| S-EPMC3037925 | biostudies-literature
Project description:Many materials phenomena are governed by the interaction between chemistry and mechanics. However, it was only in the second half of the 20th century that the theory of open system elasticity by Francis Larché and John W. Cahn concatenated the fields of solid mechanics and alloy chemistry. As the theory's central materials descriptors, the open system elastic parameters describe how solids deform under stress when solute can rearrange at equilibrium while the chemical potential is held constant. Here, we report experiments verifying the predictions for these parameters. We study the elasticity of nanoporous Pd-H and Pd-Au-H during load cycles imposed by a dynamic mechanical analyzer. Short diffusion paths afford fast equilibration of H in the local strain gradients that carry the macroscopic elastic deformation. The experiment is in excellent agreement with the theory, confirming a central prediction of one of the key contributions to 20th-century thermodynamics.
| S-EPMC6205470 | biostudies-other
Project description:While single-molecule localization microscopy (SMLM) offers the invaluable prospect to visualize cellular structures below the diffraction limit of light microscopy, its potential has not yet been fully capitalized due to its inherent susceptibility to blinking artifacts. Particularly, overcounting of single molecule localizations has impeded a reliable and sensitive detection of biomolecular nanoclusters. Here we introduce a 2-Color Localization microscopy And Significance Testing Approach (2-CLASTA), providing a parameter-free statistical framework for the qualitative analysis of two-dimensional SMLM data via significance testing methods. 2-CLASTA yields p-values for the null hypothesis of random biomolecular distributions, independent of the blinking behavior of the chosen fluorescent labels. The method is parameter-free and does not require any additional measurements nor grouping of localizations. We validated the method both by computer simulations as well as experimentally, using protein concatemers as a mimicry of biomolecular clustering. As the new approach is not affected by overcounting artifacts, it is able to detect biomolecular clustering of various shapes at high sensitivity down to a level of dimers.
| S-EPMC7060173 | biostudies-literature
Project description:Hot and humid heat exposures challenge the health of outdoor workers engaged in occupations such as construction, agriculture, first response, manufacturing, military, or resource extraction. Therefore, government institutes developed guidelines to prevent heat-related illnesses and death during high heat exposures. The guidelines use Wet Bulb Globe Temperature (WBGT), which integrates temperature, humidity, solar radiation, and wind speed. However, occupational heat exposure guidelines cannot be readily applied to outdoor work places due to limited WBGT validation studies. In recent years, institutions have started providing experimental WBGT forecasts. These experimental products are continually being refined and have been minimally validated with ground-based observations. This study evaluated a modified WBGT hindcast using the historical National Digital Forecast Database and the European Centre for Medium-Range Weather Forecasts Reanalysis v5. We verified the hindcasts with hourly WBGT estimated from ground-based weather observations. After controlling for geographic attributes and temporal trends, the average difference between the hindcast and in situ data varied from -0.64°C to 1.46°C for different Köppen-Geiger climate regions, and the average differences are reliable for decision making. However, the results showed statistically significant variances according to geographical features such as aspect, coastal proximity, land use, topographic position index, and Köppen-Geiger climate categories. The largest absolute difference was observed in the arid desert climates (1.46: 95% CI: 1.45, 1.47), including some parts of Nevada, Arizona, Colorado, and New Mexico. This research investigates geographic factors associated with systematic WBGT differences and points toward ways future forecasts may be statistically adjusted to improve accuracy.
| S-EPMC8975719 | biostudies-literature