A high-reproducibility and high-accuracy method for automated topic classification

Much of human knowledge sits in large databases of unstructured text. Leveraging this knowledge requires algorithms that extract and record metadata on unstructured text documents. Assigning topics to documents will enable intelligent search, statistical characterization, and meaningful classification. Latent Dirichlet allocation (LDA) is the state-of-the-art in topic classification. Here, we perform a systematic theoretical and numerical analysis that demonstrates that current optimization techniques for LDA often yield results which are not accurate in inferring the most suitable model parameters. Adapting approaches for community detection in networks, we propose a new algorithm which displays high-reproducibility and high-accuracy, and also has high computational efficiency. We apply it to a large set of documents in the English Wikipedia and reveal its hierarchical structure. Our algorithm promises to make "big data" text analysis systems more reliable.Comment: 23 pages, 24 figure

Smad2 and Smad4 gene mutations in hepatocellular carcinoma

TGF-β is a negative regulator of liver growth. Smad family of genes, as mediators of TGF-β pathway, are candidate tumor suppressor genes in hepatocellular carcinoma (HCC). We studied 35 HCC and non-tumour liver tissues for possible mutations in Smad2 and Smad4 genes. Three tumours displayed somatic mutations; two in Smad4 (Asp332Gly and Cys401Arg) and one in Smad2 (Gln407Arg) genes. All three mutations were A:T → G:C transitions suspected to result from oxidative stress as observed in mitochondrial DNA. These observation demonstrate that TGF-β pathway is altered in hepatocellular carcinoma

Standardized ASCE Penman-Monteith: Impact of sum-of-hourly vs. 24-hour timestep computations at reference weather station sites

ABSTRACT. The standardized ASCE Penman-Monteith (ASCE-PM) model was used to estimate grass-reference evapotran-spiration (ETo) over a range of climates at seven locations based on hourly and 24 h weather data. Hourly ETo computations were summed over 24 h periods and reported as sum-of-hourly (SOH). The SOH ASCE-PM ETo values (ETo,h,ASCE) were compared with the 24 h timestep ASCE-PM ETo values (ETo,d) and SOH ETo values using the FAO Paper 56 Penman-Monteith (FAO56-PM) method (ETo,h,FAO). The ETo,h,ASCE values were used as the basis for comparison. The ETo,d estimated higher than ETo,h,ASCE at all locations except one, and agreement between the computational timesteps was best in humid regions. The greatest differences between ETo,d and ETo,h,ASCE were in locations where strong, dry, hot winds cause advective increases in ETo. Three locations showed considerable signs of advection. Some of the differences between the timesteps was attributed to uncertainties in predicting soil heat flux and to the difficulty of ETo,d to effectively account for abrupt diurnal changes in wind speed, air temperature, and vapor pressure deficit. The ETo,h,FAO values correlated well with ETo,h,ASCE values (r2> 0.997), but estimated lower than ETo,h,ASCE at all locations by 5 % to 8%. This was due to the impact of higher surface resistance during daytime periods. Summing the ETo values over a weekly, monthly, or annual basis generally reduced the differences between ETo,d and ETo,h,ASCE. Summing the ETo,d values over multiple days and longer periods for peak ETo months resulted in inconsistent differences between the two timesteps. The results suggest a potential improvement in accuracy when using the standardized ASCE-PM procedure applied hourly rather than daily. The hourly application helps to account for abrupt changes in atmospheric conditions on ETo estimation in advective and other environments when hourly climate data are available

Loss of Axial Symmetry in Hypersonic Flows over Conical Shapes

The assumption of axial symmetry for hypersonic flows over conically shaped geometries is ubiquitous in both experiments and numerical simulations. Yet depending on the free stream conditions, many of these flows are unsteady and their transition from laminar to turbulent is a three-dimensional phenomena. Combining triple deck theory/linear stability analysis with the kinetic direct simulation Monte Carlo method we analyze the azimuthal eigenmodes of flows over single and double-cone configurations. For Mach 16 flows we find that the strongest amplification rate occurs for the non-axisymmetric azimuthal wavenumber of n = 1. This occurs in regions quite close to the tip of the cone due to the proximity of the conical shock to the viscous shear layer where non-axisymmetric modes are amplified through linear mechanisms. Comparison of triple deck linear stability predictions shows that in addition to the azimuthal wavenumber, both the temporal content and amplification rate of these non-axisymmetric disturbances agree well with the time accurate DSMC flowfield. In addition to the loss of axial symmetry observed at the conical shock, the effect of axial symmetry assumptions on the more complex shock-shock and shock-boundary layer interactions of a flow over a double cone are considered. The results for the separation region show that axisymmetric and three dimensional simulations differ in almost all of the main flow structures. Three dimensional flowfields result in a smaller separation bubble with weaker shocks and three dimensional effects were manifest in the variation in surface parameters in the azimuthal direction as well. Interestingly, the DSMC simulations show that the loss of axial symmetry in the separation region, begins near the cone tip.Comment: 27 pages, 8 figure

A practical method using a network of fixed infrared sensors for estimating crop canopy conductance and evaporation rate

The authors regret that there is an error in the published Fig. 4 (d)of this paper where the line for T dry (energy balance) was originally plotted incorrectly. A corrected version of this figure, and caption, which also now includes values for the air temperature (T a ) and surface temperature (T s ) in order to aid comparisons, follows. The authors would like to apologise for any inconvenience caused. </p

On linear stability of supersonic flow over a short compression corner at large ramp angles

Linear stability of supersonic flow over a short compression corner with ramp angles 30 and 42 is investigated using Direct Simulation Monte Carlo (DSMC) and Linear Stability Theory (LST) at Mach number 3, Reynolds number 11,200 and low Knudsen number, O(10$^{-4}$). The two-dimensional base flows feature nonzero velocity slip and temperature jump and were found to be steady and laminar at both ramp angles. Modal analysis revealed a previously unknown traveling three-dimensional global mode, the amplitude functions of which peak at the leading-edge and separation shocks and extend within the shear layer of the large laminar separation bubble formed on the short compression corner. This mode is linearly unstable at the higher ramp angle and stable at the lower one, while the known stationary three-dimensional global mode which peaks at the laminar separation is also present in the spectrum, but is (strongly) damped at both ramp angles. Three-dimensional DSMC simulations have fully confirmed the LST results, underlined (again) the significance of modeling the shock contribution in linear stability analyses of high-speed flow, and predicted the nonlinear evolution of the flow up to the generation of lambda vortices on the ramp, for the first time in the context of kinetic theory simulations.Comment: 22 pages, 14 figure

TIME-DOMAIN AND FREQUENCY-DOMAIN REFLECTOMETRY TYPE SOIL MOISTURE SENSOR PERFORMANCE AND SOIL TEMPERATURE EFFECTS IN FINE- AND COARSE-TEXTURED SOILS

The performances of six time-domain reflectometry (TDR) and frequency-domain reflectometry (FDR) type soil moisture sensors were investigated for measuring volumetric soil-water content (θv) in two different soil types. Soil-specific calibration equations were developed for each sensor using calibrated neutron probe-measured θv. Sensors were also investigated for their performance response in measuring θv to changes in soil temperature. The performance of all sensors was significantly different (P\u3c0.05) than the neutron probe-measured θv, with the same sensor also exhibiting variation between soils. In the silt loam soil, the 5TE sensor had the lowest root mean squared error (RMSE) of 0.041 m3/m3, indicating the best performance among all sensors investigated. The performance ranking of the other sensors from high performance to low was: TDR300 (High Clay Mode), CS616 (H) and 10HS, SM150, TDR300 (Standard Mode), and CS616 (V) (H: horizontal installation and V: vertical installation). In the loamy sand, the CS616 (H) performed best with an RMSE of 0.014 m3/m3 and the performance ranking of other sensors was: 5TE, CS616 (V), TDR300 (S), SM150, and 10HS. When θv was near or above field capacity, the performance error of most sensors increased. Most sensors exhibited a linear response to increase in soil temperature. Most sensors exhibited substantial sensitivity to changes in soil temperature and the θv response of the same sensor to high vs. normal soil temperatures differed significantly between the soils. All sensors underestimated θv in high temperature range in both soils. The ranking order of the magnitude of change in θv in response to 1°C increase in soil temperature (from the lowest to the greatest impact of soil temperature on sensor performance) in silt loam soil was: SM150, 5TE, TDR300 (S), 10HS, CS620, CS616 (H), and CS616 (V). The ranking order from lower to higher sensitivity to soil temperature changes in loamy sand was: 10HS, CS616 (H), 5TE, CS616 (V), SM150, and TDR300 (S). When the data from all sensors and soils are pooled, the overall average of change in θv for a 1°C increase in soil temperature was 0.21 m3/m3 in silt loam soil and -0.052 m3/m3 in loamy sand. When all TDR- and FDR-type sensors were pooled separately for both soils, the average change in θv for a 1°C increase in soil temperature for the TDR- and FDR-type sensors was 0.1918 and -0.0273 m3/m3, respectively, indicating that overall TDR-type sensors are more sensitive to soil temperature changes than FDR-type sensors when measuring θv

The role of climatic elements in public tendency towards alternative tourism: a sample of Turkey.

In recent years, there has been an apparent alteration in tourists’ destination preferences. The reasons for this are, of course, very diverse. Due to discomforting environment of the coastal regions, people may prefer to spend their holidays in bioclimatologically more comfortable areas, such as mountain or plateau resorts. The aim of this study is to determine the effect of climate and weather on tourism and recreational activities via a questionnaire survey in the city of Erzurum, Turkey. It was found that although people who participated the survey live in a city, which is a well-known winter sports center and where extreme climatic features in winter are prevalent and have to experience, at least, an eight-month cold period (from late October to late May), they would still prefer summer season for recreation and tourism even if they were given full year recreation opportunities. This condition was thought to result from the lack of efficient winter recreation facilities and it was suggested that this kind of facilities should be constructed.EN AÑOS RECIENTES HA OCURRIDO UNA APARENTE MODIFICACIÓN EN LOS DESTINOS PREFERENTES DE LOS TURISTAS. LAS RAZONES PARA ESTO SON, DESDE LUEGO, MUY DIVERSAS. DEBIDO AL AMBIENTE INCÓMODO DE LAS REGIONES COSTERAS, MUCHAS PERSONAS PREFIEREN PASAR SUS VACACIONES EN ÁREAS BIOCLIMATOLÓGICAMENTE MÁS CONFORTABLES, COMO LOS CENTROS TURÍSTICOS DE MONTAÑA O MESETAS. EL OBJETIVO DE ESTE ESTUDIO ES DETERMINAR EL EFECTO DEL CLIMA Y EL TIEMPO EN LAS ACTIVIDADES RECREATIVAS POR MEDIO DE UN CUESTIONARIO DE INVESTIGACIÓN EN LA CIUDAD DE ERZURUM, EN TURQUÍA. SE ENCONTRÓ QUE AUNQUE LA GENTE QUE PARTICIPÓ EN LA INVESTIGACIÓN VIVE EN UNA CIUDAD QUE ES UN CONOCIDO CENTRO DE DEPORTES INVERNALES, CON CARACTERÍSTICAS EXTREMAS DE UN PERÍODO DE FRÍO DE AL MENOS OCHO MESES (DEL FINAL DE OCTUBRE AL DE MAYO), PREFIEREN EL VERANO PARA RECREACIÓN Y TURISMO AUNQUE SE LES DIERA LA OPORTUNIDAD DE UN AÑO COMPLETO DE ACTIVIDADES RECREATIVAS. SE PIENSA QUE ESTO ES RESULTADO DE LA FALTA DE INSTALACIONES RECREATIVAS ADECUADAS PARA EL INVIERNO Y SE SUGIERE QUE ÉSTAS DEBERÍAN CONSTRUIRS

Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma

Background: Proteomic discovery of cancer biomarkers in body fluids is challenging because of their low abundance in a complex background. Altered gene expression in tumours may not reflect protein levels in body fluids. We have tested combining gene expression profiling of tumours with proteomic analysis of cancer cell line secretomes as a strategy to discover urinary biomarkers for bladder cancer. Methods: We used shotgun proteomics to identify proteins secreted by three bladder cancer cell lines. Secreted proteins with high mRNA levels in bladder tumours relative to normal urothelium were assayed by ELISA in urine samples from 642 patients. Results: Midkine and HAI-1 were significantly increased in bladder cancer patients, with the highest levels in invasive disease (area under the receiver operating characteristic curve 0.89 vs non-cancer). The urinary concentration of both proteins was too high to be explained by bladder cancer associated haematuria and most likely arises by direct tumour secretion. Conclusions: This ‘dual-omic’ strategy identified tumour secreted proteins whose urine concentrations are increased significantly by bladder cancer. Combined secretome-transcriptome analysis may be more useful than direct proteomic analysis of body fluids for biomarker discovery in both bladder cancer and other tumour type