Miracle-dz/UniFAR-FTUs huggingface dataset:
Possible Misidentification of Mycobacterium yongonense

To the Editor: Tortoli et al. (1) reported pulmonary disease caused by M. yongonense strains isolated from patients in Italy; these strains were identified by sequencing the 16S rRNA, hsp65, rpoB, and sodA genes and the internal transcribed spacer 1 (ITS1) region. The 16S rRNA gene sequence of these isolates showed 100% similarity with those of M. yongonense and M. marseillense. The isolates were more closely related to M. yongonense than to M. marseillense in terms of the hsp65 gene and ITS1 region; however, the rpoB gene sequence showed a higher degree of similarity to that of M. intracellulare (99.4%) than to that of M. marseillense (97.4%). The authors did not mention the similarity of the isolates with M. intracellulare in these sequences except for the rpoB gene. However, because these sequences showed high similarity to M. yongonense, a high degree of similarity to M. intracellulare could be inferred. The initial description of M. yongonense highlighted its unique molecular character (2). The 16S rRNA and hsp65 genes and ITS1 region are closely related to those of M. intracellulare ATCC 13950T; however, the rpoB gene is closely related to that of M. parascrofulaceum ATCC BAA-614T (99.4%). No consensus guidelines are available for mycobacterial identification, but the rpoB gene has been used widely as a target gene; multilocus sequence analysis also has been used recently (3,4). Although the authors suggest that a variant of M. yongonense preceded the acquisition of the rpoB gene from M. parascrofulaceum by a lateral gene transfer event (3), the isolates described are more similar to M. intracellulare than to M. yongonense on the basis of the rpoB gene sequence and multilocus sequence analysis. It is also possible that the isolates are a M. yongonense strain that preceded the acquisition of the rpoB gene but that are not the same as the initially described M. yongonense.
Use of the ranking distance as an index for assessing the accuracy and precision of equations for the bearing capacity of piles and at-rest earth pressure coefficient

In many geotechnical design situations, a number of different calculation models have been developed to predict the value of a particular quantity required for use in design calculations, for example, the bearing capacities of driven and root piles, and K0, the at-rest earth pressure coefficient. In this paper the authors show how the dependability of different calculation methods can be compared and assessed using a synthetic probabilistic approach and the ranking distance (RD) index. Measured values, Qmeas, are compared with calculated values, Qcalc, using the "bias factor," defined as the ratio Qmeas/Qcalc. The bias factor values obtained using a particular calculation method are processed to evaluate the "accuracy" and "precision" by calculating a central tendency and a variability statistical parameter, respectively, from the values. The RD index is a comprehensive statistical parameter for assessing the dependability of a particular calculation method and is based on the central tendency and variabi.
MODELING INFILTRATION INTO A SEALING SOIL

Rain infiltration is often controlled by a less permeable layer known as a seal. Infiltration through this layer was modeled numerically by continuously updating the seal properties as a function of rainfall characteristics. The seal remains unchanged until the surface has reached incipient ponding. Subsequently, a rapid change in the hydraulic properties of the seal is imposed to reflect the effect of raindrop impact. Finally, an equilibrium state develops between seal formation due to raindrop impact and seal erosion due to the rainstorm intensity effects. Model-predicted infiltration was similar to that observed during simulated rainstorms having various combinations of intensities and kinetic energy rates per millimeter of rain. A sensitivity analysis was performed to determine the effects of changes in seal and bulk soil properties, as well as simulation parameters, on infiltration. Seal formation was dependent on cumulative rainfall energy and the rainstorm intensity.
Estimating the evolution of vegetation cover and its hydrological impact in the Mekong River basin in the 21st century

The terrestrial biosphere plays a key role in regional energy and water cycles. Thus, for long‐term hydrological predictions, possible future changes in vegetation cover must be understood. This study examined the evolution of vegetation cover in the 21st century and its estimated impact on river discharge in the Mekong River basin. Based on climatic predictions (TYN SC 2·03) under the Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios (IPCC SRES) A1FI, A2, B1, and B2, changes in vegetation type and the leaf area index (LAI) were simulated using a Lund‐Potsdam‐Jena‐Dynamic Global Vegetation Model (LPJ‐DGVM) and Terrestrial Biogeochemical Cycle Model (BIOME‐BGC). The estimated LAI was then used in the rainfall‐runoff analysis in the Yamanashi Distributed Hydrological Model (YHyM).
Inversion of diurnally varying synthetic CO2: Network optimization for an Australian test case

Hourly CO2 fluxes, generated from a biosphere model applied to the Australian region, are used to produce synthetic CO2 atmospheric concentration data. The concentration data are inverted using a Bayesian synthesis method, to test whether the CO2 fluxes can be successfully retrieved at monthly temporal resolution. The inversion is performed globally (with a base network of about 100 sites), but the tests focus on the Australian continent, subdivided into 12 regions. The inversion is tested using dense networks of approximately 40 new sites in and around Australia. Land‐based and offshore networks are compared. The land‐based network produces biased source estimates, for regions with large diurnal source variability, if the inversion only solves for a constant flux throughout the month. The bias is eliminated when we solve for two fluxes for each region, a constant monthly flux and a daytime‐only flux. The offshore network gives large uncertainties and biases for inland regions of Australia. These latter biases are not significantly improved by solving for the daytime flux. The inversion that includes daytime fluxes is used to design a network to minimize the average annual mean uncertainty for Australian sources. Networks designed using incremental optimization are compared with some reference networks. Site locations are found to be sensitive to the data uncertainty applied to each site. The incremental optimization method appears to be most effective for networks of fewer sites than about half the number of regions being solved for.
Validation of Next Generation Sequencing Technologies in Comparison to Current Diagnostic Gold Standards for BRAF, EGFR and KRAS Mutational Analysis

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.
Stress changes along the Sunda trench following the 26 December 2004 Sumatra‐Andaman and 28 March 2005 Nias earthquakes

The 26 December 2004 Mw = 9.2 and 28 March 2005 Mw = 8.7 earthquakes on the Sumatra megathrust altered the state of stress over a large region surrounding the earthquakes. We evaluate the stress changes associated with coseismic and postseismic deformation following these two large events, focusing on postseismic deformation that is driven by viscoelastic relaxation of a low‐viscosity asthenosphere. Under Coulomb failure stress (CFS) theory, the December 2004 event increased CFS on the future hypocentral zone of the March 2005 event by about 0.25 bar, with little or no contribution from viscous relaxation. Coseismic stresses around the rupture zones of the 1797 and 1833 Sunda trench events are negligible, but postseismic stress perturbations since December 2004 are predicted to result in CFS increases of 0.1 to 0.2 bar around these rupture zones between 2 and 8 years after the December 2004 event. These are considerable stress perturbations given that the 1797 and 1833 rupture zones are likely approaching the end of a complete seismic cycle.
Cryptic sequence boundaries in braided fluvial successions

In braided fluvial deposits, consisting of monotonous successions of sandstone or conglomerate, it may be difficult to distinguish regionally significant bounding surfaces (sequence boundaries) from autogenic channel‐scour surfaces. Major surfaces may be characterized by erosional relief and draped by lag deposits, but not all sequence boundaries show these characteristics. Other clues to the presence of a major surface are sharp changes in detrital composition, shifts in regional palaeocurrent trends and evidence of early diagenesis of the sandstones immediately below the sequence boundary. Examples of these attributes of cryptic sequence boundaries are illustrated from three Mesozoic units in the Colorado Plateau area of the United States. In the Chinle Formation (Triassic), near Moab, Utah, angular intraformational unconformities overlie sandstones showing evidence of early diagenesis. In the Castlegate Sandstone (Upper Cretaceous) of east‐central Utah, a cryptic sequence boundary can be discriminated from other erosion surfaces by the evidence of detrital petrography and early diagenesis. Palaeocurrent data indicate changes in regional palaeoslope at two sequence boundaries within this unit. Evidence of early diagenesis is also present at a sequence boundary in the Kayenta Formation (Jurassic) of westernmost Colorado.
Plant enhancement of indigenous soil micro-organisms: a low-cost treatment of contaminated soils

Abstract The United States has more than 1000 individual areas of petroleum-contaminated soil at formerly used defense (FUD) sites located in cold regions. This paper investigates biotreatment systems based on exploiting naturally occurring phenomena in the rhizosphere — the soil adjacent to and influenced by plant roots. Rhizosphere-based remediation systems would be inexpensive to implement and maintain and would be applicable to remote or permafrost sites. Herein, this paper provides the rationale for using rhizosphere-based biotreatment systems and some initial results. In both laboratory and field studies, successful plant germination, plant growth, and root intrusion into and through contaminated soil are demonstrated. Using a Captina silt loam in a 10-week laboratory study, the effects of vegetation and contamination on microbial numbers were compared. The vegetation treatments included an unvegetated control and a vegetated treatment seeded with bahiagrass (Paspalum notatum). The contamination treatments included an uncontaminated control and a treatment with 2000 mg pyrene kg-1 soil added. Microbial numbers at 10 weeks were not significantly influenced by the contaminant level of 2000 mg pyrene kg-1 soil compared to the control. However, microbial numbers were greater in the rhizosphere of the bahiagrass-vegetated soil compared to the unvegetated soil. In a 34-week field study, total petroleum hydrocarbon (TPH) concentrations of a diesel-contaminated soil decreased significantly more in the rhizosphere+nutrient treatment compared to the control that was not vegetated or fertilized. Bacterial numbers in the field study were 287 times greater in the rhizosphere+nutrient treated soils than in the control treatments. Measurable TPH compounds in the plant tissue were insignificant. The data demonstrated that rhizosphereenhanced treatment of organic-contaminated soils can be effective in reducing soil petroleum concentrations and may be a cost-effective strategy particularly suited for treating cold-region sites where remediation options are limited by cost, remoteness of the site, and/or brevity of the treatment season.
Viscous constitutive relations of solid‐liquid composites in terms of grain boundary contiguity: 2. Compositional model for small melt fractions

[1] We develop a compositional model for the grain boundary (GB) diffusion creep of melt-bearing polycrystalline aggregates. This model is an extension of the GB diffusion control model by taking into account the effects of finite liquid diffusivity and finite reaction rates, which are important at small melt fractions (ϕ). For shear viscosity η, there exists a critical melt fraction ϕcη below which the rate-limiting process changes from diffusion through GB to diffusion through the liquid, and for bulk viscosity ξ, there exists a critical melt fraction ϕcξ below which the rate-limiting process changes from diffusion through GB to reaction at the pore surface. The implication of the model results is that different processes may limit the kinetics of bulk and shear viscosities at small ϕ. The model also predicts that stress can cause compositional and hence volumetric asymmetry in pores. As melt fraction increases from zero to the critical melt fractions, rapid decreases occur in η, from ηcc to 0. 2ηcc, and in ξ, from ∞ to 0. 4ηcc, where ηcc represents η for Coble creep. In the GB diffusion control model, these decreases occur discontinuously at zero melt fraction, but this singularity is removed in the compositional model. For a typical grain size in the mantle (3 mm), the critical melt fractions are estimated semiquantitatively as ϕcη = 10−4 and ϕcξ < 6 × 10−8, demonstrating the significant effect of very small amount of melt on the viscosities in the mantle.
Influence of land use change on hydrology of shallow water table environments

Land development through urbanization plays a significant role in changing the hydrology of a watershed. A two-dimensional finite element variable saturation flow model is coupled with a digital terrain analysis to quantify the impacts of urbanization on the hydrology of shallow water table environments. The ground surface is sealed to infiltration for a fraction of the surface corresponding to urbanized land. A 75% increase in urbanization reduces the cumulative transpiration by 86.4%, cumulative infiltration by 76.4% and base flow by 55.5%. Simulations to assess the influences of slope on local hydrology indicated that landscapes with mild slopes have less base flow than landscapes with steep slopes. Effect of surface slope on infiltration is found to be negligible due to the presence of high porosity sandy soil at this site.
Optimizing geochemical threshold selection while evaluating exploration techniques using a minimum hypergeometric probability method

Hypergeometric statistics have recently been used to establish a quantitative measure of performance for geochemical exploration techniques over known mineral occurrences. Using this method, the effectiveness of new exploration techniques can be compared objectively with conventional approaches. Sample site classification is the basis on which survey results are compared. This performance measure requires prior knowledge of the location of mineralization and a model for element dispersion from the primary into the secondary environment. This information allows assignment of sample sites that should give ‘anomalous’ (e.g. those overlying mineralized zones) or ‘background’ results to be identified prior to the orientation survey. Previous application of hypergeometric statistics requires that a high contrast exists between ‘anomalous’ and ‘background’ subpopulations in the geochemical orientation data so that there is no uncertainty in the classification of samples. In this paper, a refinement is developed that allows consideration of geochemical variables that do not exhibit this required high level of geochemical contrast, that is, where ‘anomalous’ and ‘background’ subpopulations exhibit significant overlap. This refinement involves determining the hypergeometric probabilities of obtaining the same result at random (P(x)) for a range of geochemical thresholds, instead of only one threshold (i.e. the one used to classify anomalous and background samples in cases with high geochemical contrast). At each threshold, different numbers of samples will be classified as ‘anomalous’ and different numbers of ‘anomalous’ samples will occur at ‘anomalous’ sites. As a consequence, the resulting random hypergeometric probabilities will change with threshold level. Using a range of thresholds to classify the geochemical orientation survey results allows identification of the minimum hypergeometric probability (MHP) for the dataset. Using this threshold, the classification of anomalies will bear the least resemblance to what would be expected if the survey results were generated at random. Employing this refined MHP approach, one can simultaneously evaluate the effectiveness of an exploration method, and select the threshold that optimally classifies anomalous and background samples.
Therapeutic Potential of small Activating RNAs (saRNAs) in Human Cancers

Background: RNA is increasingly recognized as a powerful molecule that can be used to control gene expression. Sophisticated, well-engineered RNA-based regulators are being developed as oligotherapeutics. Methods: In particular, small activating RNAs (saRNAs) are promising therapeutic options for targeting human diseases. Numerous saRNAs targeting multiple cancers have been developed in preclinical models. One saRNA targeting C/EBPα is currently undergoing clinical trials in liver cancer. Results and Conclusion: In this review, we describe the current working model of the intracellular mechanism of saRNA, discuss the recent progress of saRNA therapeutics in preclinical and clinical trials, and current advances in targeted delivery using aptamers in detail.
A new technique for measuring tidal currents by using a two‐site HF Doppler radar system

We have measured surface currents by using a newly developed high-frequency (HF) Doppler radar technique. The system was operated in lower Cook Inlet, Alaska, in July 1977. During one particular day, July 13, we analyzed the radar data collected every 30 min for 24 hours. By least squares fitting these data to two of the dominant tidal periods, 12.31 and 24.6 hours, we determined the spatial distribution of the tidal currents for each of these two periods. In addition, we determined the spatial distribution of the mean surface currents for this 24-hour period. Our analysis of this data shows that near Kachemak Bay there is a distinct difference of the east-west component of tidal flow in comparison with regions further from Kachemak. In addition, we observed longer period components for which we cannot determine the period. These components exhibited gyrelike spatial patterns. Our results demonstrate the use of HF radar techniques for resolving spatial and temporal currents which affect the nearshore environment.
Wildland Fire Use: A Wilderness Perspective on Fuel Management

Current federal wildland fire policy recognizes wildland fire as an impor- tant natural process and emphasizes the need to reintroduce fire into ecosystems. The policy also recognizes that hazardous fuel accumulations may need to be re- duced on vast acreages of land before fire can safely be returned to wildland ecosystems. Wildland fire and fuel managers have a variety of options for reducing fuels including wildland fire use, management-ignited prescribed fires, thinning, and other mechanical methods. All of these options will need to be exploited to accom- plish the task of reducing hazardous fuels and restoring healthy fire-dependent ecosystems. Wildland fire use, while focusing primarily on restoring fire as a natural process and maintaining ecosystems, has the potential to be very effective for man- aging fuels. It may be the most appropriate strategy in wilderness and in other remote unroaded areas. To effectively implement wildland fire use, wildland fire managers will need to rely on comprehensive fire management plans. The development of these plans should include analyses needed to support the wildland fire use decision and should consider the potential benefits from wildland fire, long-term consequences of manage- ment decisions, and impacts of decisions across large landscapes.
The use of multi-temporal MODIS images with ground data to distinguish cotton from maize and sorghum fields in smallholder agricultural landscapes of Southern Africa

In this study, we test whether we can significantly (p < 0.05) distinguish cotton (Gossypium hirsutum L.) fields from maize (Zea mays L.) and sorghum (Sorghum bicolor) fields in smallholder agricultural landscapes of the Mid-Zambezi Valley, Zimbabwe, using a temporal series of 16-day Moderate Resolution Imaging Spectroradiometer – normalized difference vegetation index (MODIS NDVI) data. We test this hypothesis at different phenological stages over the growing season, that is, early green-up onset, late green-up onset, green-peak, early senescence and late senescence. We also statistically compare the rate of change in the greenness of the three crops at the three phenological stages. Results show that we can significantly (p < 0.05) distinguish cotton fields from maize and sorghum fields using 16-day MODIS NDVI data during the late green-up onset as well as during the green-peak stage of the three crops. Our results indicate that cotton can successfully be distinguished from maize and sorghum in spatially heterogeneous smallholder agricultural landscapes using temporal MODIS NDVI.
Physical Activity Attenuates the Influence of FTO Variants on Obesity Risk: A Meta-Analysis of 218,166 Adults and 19,268 Children

Ruth Loos and colleagues report findings from a meta-analysis of multiple studies examining the extent to which physical activity attenuates effects of a specific gene variant, FTO, on obesity in adults and children. They report a fairly substantial attenuation by physical activity on the effects of this genetic variant on the risk of obesity in adults.