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

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

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

Variability Analyses of Alfalfa-Reference to Grass-Reference Evapotranspiration Ratios in Growing and Dormant Seasons

Alfalfa-reference evapotranspiration (ETr) values sometimes need to be converted to grass-reference ET (ETo), or vice versa, to enable crop coefficients developed for one reference surface to be used with the other. However, guidelines to make these conversions are lacking. The objectives of this study were to: (1) develop ETr to ETo ratios (Kr values) for different climatic regions for the growing season and nongrowing (dormant) seasons; and (2) determine the seasonal behavior of Kr values between the locations and in the same location for different seasons. Monthly average Kr values from daily values were developed for Bushland, (Tex.), Clay Center, (Neb.), Davis, (Calif.), Gainesville, (Fla.), Phoenix (Ariz.), and Rockport, (Mo.) for the calendar year and for the growing season (May– September). ETr and ETo values that were used to determine Kr values were calculated by several methods. Methods included the standardized American Society of Civil Engineers Penman–Monteith (ASCE-PM), Food and Agriculture Organization Paper 56 (FAO56) equation (68), 1972 and 1982 Kimberly-Penman, 1963 Jensen-Haise, and the High Plains Regional Climate Center (HPRCC) Penman. The Kr values determined by the same and different methods exhibited substantial variations among locations. For example, the Kr values developed with the ASCE-PM method in July were 1.38, 1.27, 1.32, 1.11, 1.28, and 1.19, for Bushland, Clay Center, Davis, Gainesville, Phoenix, and Rockport, respectively. The variability in the Kr values among locations justifies the need for developing local Kr values because the values did not appear to be transferable among locations. In general, variations in Kr values were less for the growing season than for the calendar year. Average standard deviation between years was maximum 0.13 for the calendar year and maximum 0.10 for the growing season. The ASCE-PM Kr values had less variability among locations than those obtained with other methods. The FAO56 procedure Kr values had higher variability among locations, especially for areas with low relative humidity and high wind speed. The 1972 Kim-Pen method resulted in the closest Kr values compared with the ASCE-PM method at all locations. Some of the methods, including the ASCE-PM, produced potentially unrealistically high Kr values (e.g., 1.78, 1.80) during the nongrowing season, which could be due to instabilities and uncertainties that exist when estimating ETr and ETo in dormant season since the hypothetical reference conditions are usually not met during this period in most locations. Because simultaneous and direct measurements of the ETr and ETo values rarely exist, it appears that the approach of ETr to ETo ratios calculated with the ASCE-PM method is currently the best approach available to derive Kr values for locations where these measurements are not available. The Kr values developed in this study can be useful for making conversions from ETr to ETo, or vice versa, to enable using crop coefficients developed for one reference surface with the other to determine actual crop water use for locations, with similar climatic characteristics of this study, when locally measured Kr values are not available

Cover crop planting practices determine their performance in the U.S. Corn Belt

Cover crop growing periods in the western U.S. Corn Belt could be extended by planting earlier. We evaluated both pre-harvest broadcast interseeding and post-harvest drilling of the following cover crops: (a) cereal rye (Secale cereale L.) [RYE]; (b) a mix of rye + legumes + brassicas [MIX1], (c) a mix of rye + oat [Avena sativa L.] + legumes + brassicas (MIX2), (d) legumes [LEGU]) and (e) a no cover crop control. These were tested in continuous corn (Zea mays L.) [corn–corn] and soybean [Glycine max (L.) Merr.]–corn systems [soybean–corn] at three sites in Nebraska for their effect on cover crop productivity, soil nutrients, and subsequent corn performance. At the sites with wet fall weather, pre-harvest broadcasting increased cover crop biomass by 90%, to 1.29 Mg ha−1 for RYE and 0.87 Mg ha−1 for MIX1 in soybean–corn, and to 0.56 Mg ha−1 and 0.39 Mg ha−1 in corn–corn, respectively. At the drier site, post-harvest drilling increased biomass of RYE and MIX1 by 95% to 0.80 Mg ha−1 in soybean–corn. Biomass N uptake was highest in pre-harvest RYE and MIX1 at two sites in soybean–corn (35 kg ha−1). RYE and sometimes mixes reduced soil N, but effects on P, K, and soil organic C were inconsistent. In soybean–corn, corn yields decreased by 4% after RYE, and in corn–corn, by 4% after pre-harvest cover crops. Site-specific selection of cover crops and planting practices can increase their performance while minimizing impacts on corn

Cover crop productivity and subsequent soybean yield in the western Corn Belt

Cover crops (CC) in corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotations may prevent N loss and provide other ecosystem services but CC productivity in the western Corn Belt is limited by the short growing season. Our objective was to assess CC treatment and planting practice effects on CC biomass, spring soil nitrate concentrations, and soybean yield at two rainfed sites in eastern and one irrigated site in south-central Nebraska over 4 yr. Cover crop treatments (cereal rye [Secale cereale L.] [RYE] and a mix of rye, legume, and brassica species [MIX]) were planted by broadcast interseeding into corn stands in September (pre-harvest broadcast) or drilling after corn harvest (post-harvest drilled) and terminated 2 wk before planting soybean. Cover crop biomass and N uptake varied between years, but generally at the eastern sites, pre-harvest broadcasting produced more biomass than post-harvest drilling (1.64 and 0.79 Mg ha−1, respectively) and had greater N uptake (37 and 24 kg ha−1, respectively). At the south-central site, post-harvest drilling produced more than pre-harvest broadcasting (1.44 and 1.20 Mg ha−1, respectively). RYE had more biomass than MIX (1.41 and 1.09 Mg ha−1, respectively), but the same N uptake. Soil nitrate reductions after CC were small. In 3 of 12 site-years, soybean yielded less after pre-harvest CC. Yield reductions were not correlated to CC biomass, but were likely due to greater weed pressure. High CC productivity is necessary for high N uptake, and requires site-specific selection of planting practice and CC treatments

Cover Crops have Negligible Impact on Soil Water in Nebraska Maize–Soybean Rotation

One perceived cost of integrating winter cover cropping in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotation systems is the potential negative impact on soil water storage available for primary crop production. The objective of this 3-yr study was to evaluate the effects of winter cover crops on soil water storage and cover crop biomass production following no-till maize and soybean rotations. Locations were near Brule (west-central), Clay Center (south-central), Concord (northeast), and Mead (east-central), NE. Treatments included crop residue only (no cover crop) and a multi-species cover crop mix, both broadcast-seeded before primary crop harvest and drilled following harvest. Pre-harvest broadcast-seeded cereal rye (Secale cereale L.) was also included in the last year of the study because rye was observed to be the dominant component of the mix in spring biomass samples. Soil water content was monitored using neutron probe or gravimetric techniques. Mean aboveground cover crop biomass ranged from practically 0 to ~3,200 kg ha–1 across locations and cover crop treatments. Differences in the change in soil water storage between autumn and spring among treatments occurred in 4 of 20 location–rotation phase–years for the top 0.3 m of soil and 3 of 20 location–rotation phase–years for the 1.2-m soil profile. However, these differences were small (profile). In conclusion, winter cover crops did not have an effect on soil water content that would impact maize and soybean crop production

Phenotypic and Genotypic Analysis of Hereditary Ataxia Patients in Sakarya City, Turkey

Conclusion: Hereditary ataxias are rare neurodegenerative disorders. Large genetic pool, ethnic and local differences complicate diagnosing even further. Our study contributes to the literature by reflecting phenotypic and genotypic characteristics of hereditary SCA patients in our region and reporting rare hereditary ataxia genotypes