Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context

Genomic selection has been utilized for genetic improvement in both plant and animal breeding and is a favorable technique for quantitative trait development. Within this study, genomic selection was evaluated within a breeding program, using novel validation methods in addition to plant materials and data from a commercial soybean (Glycine max) breeding program. A total of 1501 inbred lines were used to test multiple genomic selection models for multiple traits. Validation included cross‐validation, inter‐environment, and empirical validation. The results indicated that the extended genomic best linear unbiased prediction (EGBLUP) model was the most effective model tested for yield, protein, and oil in cross‐validation with accuracies of 0.50, 0.68, and 0.64, respectively. Increasing marker number from 1000 to 3000 to 6000 single nucleotide polymorphism markers leads to statistically significant increases in accuracy. Cross‐environment predictions were statistically lower than cross‐validation with accuracies of 0.24, 0.54, and 0.42 for yield, protein, and oil, respectively, using the extended genomic BLUP model. Empirical validation, predicting the yield of 510 soybean lines, had a prediction accuracy of 0.34, with the inclusion of a maturity covariate leading to a notable increase in accuracy. Genomic selection identified high‐performance lines in inter‐environment predictions: 34% of lines within the upper quartile of yield, and 51% and 48% of the highest quartile protein and oil lines, respectively. Statistically similar results occurred comparing rankings in empirical validation and selection for advancements in yield trials. These results indicate that genomic selection is a useful tool for selection decisions.
Longitude dependences of Saturn's ultraviolet aurora

Based on periodicities in the kilometric radio emissions, the Saturn Longitude System 4 (SLS4) was used to organize the far ultraviolet (120–150 nm) aurora observed by the Ultraviolet Imaging Spectrograph on the Cassini spacecraft. Individual Ultraviolet Imaging Spectrograph pixels were projected onto the ionosphere of Saturn, transformed into the SLS4 north and SLS4 south longitude systems, accumulated over all over auroral observations from 2007 to early 2009, and binned into 1°×1° bins of colatitude. The intensity of the northern aurora showed little variation in its SLS4 north system, but the intensity of the southern aurora exhibited an enhancement of over ~10 kR between ~140–280° SLS4 south longitude. This enhancement may represent the auroral signature of a southern ionospheric vortex proposed in MHD models of Saturn's magnetosphere to explain its periodicities. The loci of the northern intensity peaks and the 3 kR boundaries varied little over 360° of longitude, while the equatorward boundary of the southern aurora varied by ~5° in SLS4 south longitude, reaching its most equatorward location of ~23° colatitude between 100° and 180° longitude. The polygonal centroids of the aurora in both north and south were consistent with offsets of no more than ~1° in both hemispheres.
Soil moisture dynamics at high temporal resolution in a semiarid Mediterranean watershed with scattered tree cover

Subsurface water flows play a key role in the distribution of water and solutes and thereby in the water availability for plants. However, the characterization of different flow processes (i.e. matrix and preferential flow), the frequency and factors that cause them, is relatively rare. This characterization enables a better understanding of spatio‐temporal variability of water resources and allows for the design of models to be improved. Using a method based on the time derivative of soil moisture variation known as maximum wetting slope, types of soil wetting processes were classified and quantified. For this, capacitance sensors, which registered the volumetric water content at high temporal resolution (30 min) for more than two hydrological years, were installed at different depths and placed in soil moisture stations with different vegetation covers, lithology and topographic position. Results indicated that there is a general behaviour or pattern of soil moisture dynamics in the catchment with a dominant occurrence of slower soil wetting processes (>50%), caused by matrix flows, and a low occurrence of those faster processes (<30%), originated by preferential flows. Nevertheless, when the total volume of water is considered, preferential flow becomes the dominant process, so that the ecological role of both flow types becomes prominent in water‐limited environments. Statistical multivariate analyses based on data‐mining techniques proved that although both flow types depend on variables associated with precipitation and antecedent soil moisture conditions, faster soil wetting processes are mainly related to variables such as rainfall intensity and topography, while slower soil wetting processes are related to flow velocity, soils or vegetation. Copyright © 2015 John Wiley & Sons, Ltd.
Effects of soil spatial resolution on quantifying CH4 and N2O emissions from rice fields in the Tai Lake region of China by DNDC model

Fourteen grid data sets of different cell resolutions were generated, from 0.5 × 0.5 km to 64 × 64 km, to estimate CH4 and N2O emissions from paddy soils in the Tai Lake region of China using the Denitrification‐Decomposition (DNDC) model. The grids were derived from a polygon‐based data set (1:50,000 digital soil map/database), which was the most detailed soil database for the region. Comparison of simulated CH4 and N2O concentrations from input of the 14 grid data sets with the original polygon data demonstrated (1) no distinct variability (relative errors <5%) of the results when grid data sets of cell size ≤2 km were used as input for the DNDC model; (2) slight variability (<10%) in the results when grid data sets with cell size in the range of 2 to 8 km were used as input; and (3) distinct variability (>10%) in the results when grid data sets with cell size of >8 km were applied as input. A grid data set with a cell size of 8 km was found to be optimal based on accuracy and computational efficiency of DNDC simulations. The results can be used as a guideline for optimizing field sampling strategies for locations where there is a lack of or insufficient soil data, whereby soil data can be collected through sampling in cell centers of designed grid frames.
Efficacy of stored grain insecticides against 2 pest beetles in rough rice

Insecticidal grain protectants can provide control of pest insects during grain storage, but studies which directly compare the efficacy of insecticides in rough rice are few. We examined methoprene, deltamethrin, commercial formulations of methoprene + deltamethrin, β-cyfluthrin, and diatomaceous earth applied to rough rice over a 6-month period for control of lesser grain borers, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), and rice weevils, Sitophilus oryzae (L.) (Coleoptera: Curculionidae). We found that methoprene, deltamethrin, or a combination of the 2 were the most effective controls of both beetles in 22.7-liter metal containers. Damage mass and beetle mass in methoprene-treated rice were reduced by 38% and 55%, respectively, when compared to the nontreated control. Similarly, the mixture of deltamethrin and methoprene reduced damage mass by 32% and total beetle mass by 45% below that of the nontreated control. Deltamethrin reduced total beetle mass by 38% relative to the nontreated rice. In vial assays, only the combination of deltamethrin and methoprene provided control of R. dominica. Diatomaceous earth had the greatest impact upon S. oryzae, but it did not affect R. dominica. Based on these results, a commercial formulation of deltamethrin and methoprene is likely to provide the best overall control of stored grain beetles, though diatomaceous earth may be effective when use of chemical insecticides is undesirable or when S. oryzae is the sole pest present.
Evaluation of factors affecting treatment and mortality in patients over 65 years of age and without chronic disease, followed in the Intensive Care Unit due to COVID-19.

OBJECTIVE In this study, demographic, clinical, and laboratory data of patients aged 65 and over who are followed on mechanical ventilators due to COVID-19 in intensive care clinics will be useful in terms of strategies to be developed in the fight against COVID-19 and other infectious agents. PATIENTS AND METHODS Our study included 299 patients aged 65 years and older, who were not chronically ill, and who were followed up on mechanical ventilators due to COVID-19 in intensive care clinics in the period between 2020 and 2022. Our study was designed as a retrospective cross-sectional study. The demographic characteristics of the patients included in the study, their complaints during hospitalization, the time between the beginning of the complaint and the admission to the hospital, the vital signs at the time of admission to the hospital, the lung computed tomography findings during hospitalization, and the treatments given were examined. RESULTS 55.9% of all patients were males, and the mean age was 75.45±7.47 years. While there was no significant difference in terms of mean age between the groups of patients with/without a higher risk of mortality, there was a significant difference in gender (p=0.025). There was a statistically significant difference between the COVID-19 intensive care (p=0.001) and renal failure (p=0.014) and mortality groups. The mean nutric score, Procalcitonin (PCT), Lactate Dehydrogenase (LDH), Blood Urea Nitrogen (BUN), Phosphorus, and lactate values, which are important parameters, were statistically higher in the group with a higher risk of mortality (p<0.001). In addition, there was a statistically significant difference in terms of sepsis, neuromuscular blocker (Nmb), vasopressor, and intubation between the groups of patients with/without a higher risk of mortality (p<0.001). In the group with high mortality, 34.2% (n=55) had plasmapheresis treatment, and 14.2% had hemodiafiltration treatment (p<0.001). According to the results of the multivariate logistic regression model in determining the factors associated with a higher risk of mortality, those who were males (p=0.001), those with kidney failure (p<0.001), those with organ failure (p=0.006), increased in alanine aminotransferase (ALT) values (p=0.019), those with sedation (p=0.001) and those with vasopressors (p<0.001) were found to have an increased risk of mortality. CONCLUSIONS We think that our study is valuable in terms of determining the most appropriate treatment strategies by following the patients in terms of parameters that are significant in the findings during their follow-up period in the Intensive Care Unit.
Spatial and temporal variability of Arctic ice thickness

A numerical model is used to study the spatial and temporal variability of ice thickness in the Arctic. The model is run to cyclo-stationary equilibrium, forced with daily varying geostrophic winds and monthly varying surface air temperatures from 1951 to 1990. Decadal-average winter ice-thickness fields exhibit a trend of increasing ice thickness in the East Siberian Sea and somewhat thicker ice overall in the 1980s. Inter-annual variability was largest in the Beaufort and East Siberian Seas and generally lower in the Laptev Sea and central Arctic. Spatial correlation patterns show that ice thickness at a point is correlated with ice thickness over a surrounding area of roughly 4 × 105 km2 with a correlation coefficient of 0.7. Temporal auto-correlation functions indicate that the total ice volume has a correlation time-scale of roughly 7 years, while the volume of ice between 2 and 5 m thick and the volume of ice less than 1 m thick have correlation times of roughly 2 years and 2 months, respectively.
The metabolic profile of the synthetic cannabinoid receptor agonist ADB-HEXINACA using human hepatocytes, LC–QTOF-MS and synthesized reference standards

Abstract Synthetic cannabinoid receptor agonists (SCRAs) remain a major public health concern, with their use implicated in intoxications and drug-related deaths worldwide. Increasing our systematic understanding of SCRA metabolism supports clinical and forensic toxicology casework, facilitating the timely identification of analytical targets for toxicological screening procedures and confirmatory analysis. This is particularly important as new SCRAs continue to emerge on the illicit drug market. In this work, the metabolism of ADB-HEXINACA (ADB-HINACA, N-[1-amino-3,3-dimethyl-1-oxobutan-2-yl]-1-hexyl-1H-indazole-3-carboxamide), which has increased in prevalence in the United Kingdom and other jurisdictions, was investigated using in vitro techniques. The (S)-enantiomer of ADB-HEXINACA was incubated with pooled human hepatocytes over 3 hours to identify unique and abundant metabolites using liquid chromatography–quadrupole time-of-flight mass spectrometry. In total, 16 metabolites were identified, resulting from mono-hydroxylation, di-hydroxylation, ketone formation (mono-hydroxylation then dehydrogenation), carboxylic acid formation, terminal amide hydrolysis, dihydrodiol formation, glucuronidation and combinations thereof. The majority of metabolism took place on the hexyl tail, forming ketone and mono-hydroxylated products. The major metabolite was the 5-oxo-hexyl product (M9), while the most significant mono-hydroxylation product was the 4-hydroxy-hexyl product (M8), both of which were confirmed by comparison to in-house synthesized reference standards. The 5-hydroxy-hexyl (M6) and 6-hydroxy-hexyl (M7) metabolites were not chromatographically resolved, and the 5-hydroxy-hexyl product was the second largest mono-hydroxylated metabolite. The structures of the terminal amide hydrolysis products without (M16, third largest metabolite) and with the 5-positioned ketone (M13) were also confirmed by comparison to synthesized reference standards, along with the 4-oxo-hexyl metabolite (M11). The 5-oxo-hexyl and 4-hydroxy-hexyl metabolites are suggested as biomarkers for ADB-HEXINACA consumption.
Cover effect in bedrock abrasion : A new derivation and its implications for the modeling of bedrock channel morphology

The sediment load of a bedrock river plays an important role in the fluvial incision process by providing tools for abrasion (the tools effect) and by covering and thereby protecting the bed (the cover effect). We derive a new formulation for the cover effect, in which the fraction of exposed bed area falls exponentially with increasing sediment flux or decreasing transport capacity, and explore its consequences for the model of bedrock abrasion by saltating bed load. Erosion rates predicted by the model are higher than those predicted by earlier models. In a closed system, the maximum erosion rate is predicted to occur when sediment supply is equal to transport capacity for a flat bed. By optimizing the channel geometry to minimize the potential energy of the stream and using representative values for both discharge and grain size, we derive equations for the geometry of a bedrock river and explore how predictions for width, slope, and bed cover vary as functions of drainage area, rock uplift rate, and rock strength. The equations predict a dependence of channel width on drainage area similar to the relations using a simple shear stress incision law. The slope-area relationship is predicted to be concave up in a log-log regime, with a curvature dependent on uplift rate. However, this curvature does not deviate sufficiently from a straight line to allow discrimination between models using empirical data. Dependence of channel width and slope on rock uplift rate can be separated into two domains: for low uplift rates, channel geometry is largely insensitive to uplift rate due to a threshold effect. At high uplift rates, there is a power law dependence. Bed cover is predicted to increase progressively downstream and to increase with increasing uplift rate. In our model, the width-to-depth ratio is a function of both tectonic and climatic forcing. This indicates that the scaling between channel width and bed slope is neither a unique indicator of tectonic forcing at steady state nor a signature of transience or steady state. We conclude that sediment effects need to be taken into account when modeling bedrock channel morphology.
Regional climatic warming and associated twentieth century land-cover changes in north-western North America

Twentieth century (1900 to 1990) changes in annual surface air temperature (SAT) are compared with contemporaneous changes in annual ground surface temperature (GST) over an area extending from east of the Cordillera in north-western Canada, to Texas in the south-central United States. One of the largest SAT increases over the past century has occurred in the north-western por- tion of this study area. It also coincides (spatial regression coefficient r = 0.70) with the largest positive GST anomaly in northern North America. However, there are large areas of Alberta, Saskatchewan, Manitoba and southern Northwest Territories that exhibit spatially coherent patterns of differences between SAT and GST warming. These differences appear to be related to twentieth century land-use and land-cover changes. The highest GST warming has been observed in large areas where extensive land-cover changes, such as the clearing of forests, increased forest fire activity, and conversion of prairie grassland to agricultural land, have occurred. It is hypothesized that land-cover change dra- matically alters surface characteristics affecting the radiation budget and energy balance. The parti- tioning between sensible and latent fluxes is altered and the potential for land drying is increased. Cal- culated flux changes associated with land-cover change are comparable in magnitude with greenhouse gas radiative forcing. It therefore appears that through a step change in GST, land-cover changes have contributed to a portion of the observed SAT warming in this region.
Histone post-translational modifications in the nuclei of striatal D1 and D2 neurons : development of a novel method of study and effects of cocaine

The aim of this work is to determine the protein modifications contributing to epigenetic changes in the nuclei of striatal neurons in response to cocaine, and, thus, to progress in our understanding of the long-term plasticity underlying behavioral modifications. In the striatum, 95% of neurons are medium-sized spiny neurons (MSNs) subdivided mainly in two populations: the D1 dopamine receptor (D1)-expressing neurons participating in the direct pathway and the D2 dopamine receptor (D2)- expressing neurons participating in the indirect pathway. This segregation confers to dopamine the ability to exert opposite functional modulation of the two pathways. With this heterogeneous neuronal composition, analyzing lysates from pooled neuronal populations would average the responses. Taking this into consideration, we developed an assay, using flow cytometric analysis, to quantify the cocaine-induced changes in histone acetylation and methylation, and the enzyme controlling them, in the isolated D1 and D2 MSNs subpopulations. We found that D1 and D2 MSNs displayed remarkable epigenetic specificities dynamically regulated by acute and chronic cocaine. In particular, we showed that H3K14, H4K5, H4K12 acetylation and H3K9 methylation exhibit opposite regulation between the two cell types underlying the differential gene expression occurring in D1 and D2 MSNs. Finally, we showed that there is complex correlation between histone PTMs that is altered by cocaine and is cell-type dependent. We propose an original approach in neuroscience that allows to explore nuclear protein changes from virtually all neurons in basal, drug-altered or pathological conditions
Effect of Lipid‐Lowering Drugs on Renal and Cardiovascular Outcomes in Patients with Chronic Kidney Disease and Dyslipidemia: A Retrospective Cohort Study

The effects of lipid‐lowering drugs (LLDs) on cardiovascular and renal outcomes in patients with advanced chronic kidney disease (CKD) and dyslipidemia are not completely understood. We conducted a retrospective cohort study to evaluate the effect of LLDs on end‐stage kidney disease (ESKD), major adverse cardiovascular events (MACEs), and mortality in adult patients with CKD stage 3b, 4, or 5, and dyslipidemia. Participants were recruited between January 1, 2008, and December 31, 2018, and classified as LLD or non‐LLD users; the final follow‐up date was December 31, 2020. The primary outcome was time to ESKD or death due to renal failure. Sub‐distribution hazard regression models adjusted for multivariables, including time‐varying lipid profile covariates, were used for the analysis. Among the 6,740 participants, 4,280 patients with CKD and dyslipidemia, including 872 using LLDs and 3,408 not using LLDs, completed the primary analysis. The multivariable analyses showed that LLD users had a significantly lower risk of time to the composite renal outcome (adjusted hazard ratio [aHR], 0.76, 95% confidence interval [CI], 0.65–0.89), and MACE incidence (aHR, 0.75, 95% CI, 0.62–0.93) than did non‐LLD users. After adjusting for time‐varying covariates of the lipid profile, there was a significant difference in the composite renal outcome (aHR, 0.78, 95% CI, 0.65–0.93) and MACEs (aHR, 0.77, 95% CI, 0.60–0.98). Among adult patients with advanced CKD and dyslipidemia, LLD users had a significantly lower risk of composite renal outcomes and MACEs than non‐LLD users. In addition to reducing lipid profile, the use of LLD is associated with renal and cardiovascular protective effects.
Dependence of magnetopause erosion on southward interplanetary magnetic field

On May 4, 1998, the Wind and ACE satellites observed a period of extremely strong southward interplanetary magnetic field (IMF) followed by a period of highly variable IMF. The magnetopause moved inside the geosynchronous orbit, exposing Los Alamos National Laboratory (LANL) geosynchronous satellites and Polar to the magnetosheath. In a simple model the magnetopause erosion may be linearly proportional to the magnitude of southward IMF. A careful comparison of the predictions derived from various magnetopause location models to the in situ observations indicates a nonlinear dependence of the magnetopause erosion on IMF Bz. The observations from the Wind and ACE satellites are significantly different in the period of highly variable IMF. The predictions based on the ACE solar wind data are more consistent with the LANL observations than those based on the Wind solar wind data. The positions of the satellites show that ACE and LANL were mainly on the same side of the Sun-Earth meridian plane. However, for the Polar observations the predictions based on the Wind data are better than those based on the ACE data. Wind and Polar were on the same side of the equatorial plane. These results suggest that we choose a solar wind monitor that is on the same side of the meridian or equatorial plane as the magnetospheric satellite for better predictions.