Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Key Physio-Biochemical and Ultrastructural Attributes after Synergistic Application of Zinc and Silicon on Rice under Cadmium Stress

Excessive industrialization and the usage of pesticides plague the farming soils with heavy metals, reducing the quality of arable land. Assessing phytoavailability of cadmium (Cd) from growth medium to plant system is crucial and necessitates precise and timely monitoring of Cd to ensure food safety. Zinc (Zn) and silicon (Si) have singularly demonstrated the potential to ameliorate Cd toxicity and are important for agricultural production, human health, and environment in general. However, Zn-Si interaction on Cd toxicity alleviation, their effects and underlying mechanisms are still fragmentarily understood. Seven treatments were devised besides control to evaluate the single and combined effects of Zn and Si on the physio-biochemical attributes and ultrastructural fingerprints of Cd-treated rice genotypes, i.e., Cd tolerant “Xiushui-110” and Cd sensitive “HIPJ-1”. Supplementation of both Zn and Si promoted plant biomass, photosynthetic parameters, ionic balance, and improved chloroplast ultrastructure with minimized Cd uptake and malondialdehyde (MDA) content due to the activation of antioxidant enzymes in Cd stressed plants. The combined effects of 10 μM Zn and 15 μM Si on 15 μM Cd displayed a greater reduction in Cd uptake and root-leaf MDA content, while enhancing photosynthetic activity, superoxide dismutase (SOD) activity and root-leaf ultrastructure particularly in HIPJ-1, whilst Xiushui-110 had an overall higher leaf catalase (CAT) activity and a higher root length and shoot height was observed in both genotypes compared to the Cd 15 µM treatment. Alone and combined Zn and Si alleviation treatments reduced Cd translocation from the root to the stem for HIPJ-1 but not for Xiushui-110. Our results confer that Zn and Si singularly and in combination are highly effective in reducing tissue Cd content in both genotypes, the mechanism behind which could be the dilution effect of Cd due to improved biomass and competitive nature of Zn and Si, culminating in Cd toxicity alleviation. This study could open new avenues for characterizing interactive effects of simultaneously augmented nutrients in crops and provide a bench mark for crop scientists and farmers to improve Cd tolerance in rice.
Field scale patterns of soil water storage from non-contacting measurements of bulk electrical conductivity.

Soil water storage (0–1.7 m) was measured every 10 m in a 660-m-long transect using a neutron probe and compared to bulk electrical conductivity, ECA, measurements obtained using noncontacting electomagnetic induction meters. Coherency analysis indicated a lack of correlation at scales less than 40 m. At scales greater than 40 m, ECA explained more than 80% of the variation of soil water storage. Measurement of ECA should be a simple and fast method of determining general field patterns of soil water storage. Key words: Spatial variability, soil water, coherency, electromagnetic induction
Pandemic of the aging society - sporadic cerebral small vessel disease.

ABSTRACT Age-related sporadic cerebral small vessel disease (CSVD) has gained increasing attention over the past decades because of its increasing prevalence associated with an aging population. The widespread application of and advances in brain magnetic resonance imaging in recent decades have significantly increased researchers' understanding in the in vivo evolution of CSVD, its impact upon the brain, its risk factors, and the mechanisms that explain the various clinical manifestation associated with sporadic CSVD. In this review, we aimed to provide an update on the pathophysiology, risk factors, biomarkers, and the determinants and spectrum of the clinical manifestation of sporadic CSVD.
Roseomonas coralli sp. nov., a heavy metal resistant bacterium isolated from coral.

A Gram-stain-negative, aerobic, mesophilic, non-motile bacterium, designated M0104T, was isolated from a gorgonian coral collected from Xieyang island, Guangxi Province, PR China. Colonies of the strain were non-motile cocci and pink. The strain grew at 15-34 °C (optimum, 28 °C), pH 4.5-8.0 (optimum, pH 7.0) and with 0-4% (w/v) NaCl (optimum, 0-2 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M0104T was closely related to Roseomonas deserti JCM 31275T (96.2 %), Roseomonas vastitatis KCTC 62043T (96.0 %), Roseomonas aerofrigidensis JCM 31878T (95.9 %) and Roseomonas oryzae KCTC 42542T (95.7 %). The strain had an assembly size of 5.0 Mb and a G+C content of 71.0mol%. Genes involved in copper, cadmium, lead, arsenic and zinc resistance were identified in the genome of strain M0104T. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain M0104T and those of closely related type strains were 19.4-24.9 % and 74.3-81.8 %, respectively. Strain M0104T contained C18:1 ω7c, C18:3 ω3c, anteiso C11:0 and C16:0 as the major fatty acids (>7 %) and ubiquinone Q-10 as the sole isoprenoid quinone. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were its major polar lipids. Based on its phenotypic, phylogenetic and chemotaxonomic properties, strain M0104T is proposed to represent a novel species within the genus Roseomonas, for which the name Roseomonas coralli sp. nov. is proposed. The type strain is M0104T (=KCTC 62359T=MCCC 1K03632T).
Rewinding extinction in the northern white rhinoceros: Genetically diverse induced pluripotent stem cell bank for genetic rescue.

Extinction rates are rising, and current conservation technologies may not be adequate for reducing species losses. Future conservation efforts may be aided by the generation of induced pluripotent stem cells (iPSCs) from highly endangered species. Generation of a set of iPSCs from multiple members of a species can capture some of the dwindling genetic diversity of a disappearing species. We generated iPSCs from fibroblasts cryopreserved in the Frozen Zoo: nine genetically diverse individuals of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni) and two from the closely related southern white rhinoceros (Ceratotherium simum simum). We used a non-integrating Sendai virus reprogramming method and developed analyses to confirm the cells' pluripotency and differentiation potential. This work is the first step of a long-term interdisciplinary plan to apply assisted reproduction techniques to the conservation of this highly endangered species. Advances in iPSC differentiation may enable generation of gametes in vitro from deceased and non-reproductive individuals that could be used to repopulate the species.
Characteristic Analysis and Structural Design of Hollow-Core Photonic Crystal Fibers with Band Gap Cladding Structures

Due to their flexible structure and excellent optical characteristics hollow-core photonic crystal fibers (HC-PCFs) are used in many fields, such as active optical devices, communications, and optical fiber sensing. In this paper, to analyze the characteristics of HC-PCFs, we carried out finite element analysis and analyzed the design for the band gap cladding structure of HC-PCFs. First, the characteristics of HC19-1550 and HC-1550-02 in the C-band were simulated. Subsequently, the structural optimization of the seven-cell HC-1550-02 and variations in characteristics of the optimized HC-1550-02 in the wavelength range 1250–1850 nm were investigated. The simulation results revealed that the optimal number of cladding layers is eight, the optimal core radius is 1.8 times the spacing of adjacent air holes, and the optimal-relative thickness of the core quartz-ring is 2.0. In addition, the low confinement loss bandwidth of the optimized structure is 225 nm. Under the transmission bandwidth of the optimized structure, the core optical power is above 98%, the confinement loss is below 9.0 × 10−3 dB/m, the variation range of the effective mode field area does not exceed 10 μm2, and the relative sensitivity is above 0.9570. The designed sensor exhibits an ultra-high relative sensitivity and almost zero confinement loss, making it highly suitable for high-sensitivity gas or liquid sensing.
Long‐Term Effects of Natural Enclosure: Carbon Stocks, Sequestration Rates and Potential for Grassland Ecosystems in the Loess Plateau

The aim of this study was to better understand the effects of grassland restoration on carbon sequestration at the total carbon stock (plant and soil) scale. The objective of the study was to investigate the temporal carbon sink and sequestration dynamics of grassland ecosystems with five different succession communities, namely, Stipa grandis, Stipa bungeana, Artemisia sacrorum, Thymus mongolicus, and cropland succession in the hilly-gully region of the Loess Plateau, China. Twenty-four research papers were analyzed to form the basis of the subsequent field survey conducted at the Yunwu Observatory for Vegetation Protection and Eco-environment in Ningxia. Following the conversion of cropland to grassland, carbon sequestration values all increased at deeper soil depths of 40–100 cm; carbon stocks within the 0–40 cm profile were largely unchanged. Five time intervals, 0 (cropland) 23, 35, 58, and 78 years yielded carbon stocks of 7.69, 14.58, 16.25, 19.22, and 19.95 kg/m2 at the total carbon stock scale. The main finding indicates that the conversion of cropland to grassland results in significant changes to ecosystem carbon pool properties. This finding has broad implications for the anthropogenic management of terrestrial carbon sequestration at the regional scale.
Automatic Evaluation of the Lung Condition of COVID-19 Patients Using X-ray Images and Convolutional Neural Networks

COVID-19 represents one of the greatest challenges in modern history. Its impact is most noticeable in the health care system, mostly due to the accelerated and increased influx of patients with a more severe clinical picture. These facts are increasing the pressure on health systems. For this reason, the aim is to automate the process of diagnosis and treatment. The research presented in this article conducted an examination of the possibility of classifying the clinical picture of a patient using X-ray images and convolutional neural networks. The research was conducted on the dataset of 185 images that consists of four classes. Due to a lower amount of images, a data augmentation procedure was performed. In order to define the CNN architecture with highest classification performances, multiple CNNs were designed. Results show that the best classification performances can be achieved if ResNet152 is used. This CNN has achieved AUCmacro¯ and AUCmicro¯ up to 0.94, suggesting the possibility of applying CNN to the classification of the clinical picture of COVID-19 patients using an X-ray image of the lungs. When higher layers are frozen during the training procedure, higher AUCmacro¯ and AUCmicro¯ values are achieved. If ResNet152 is utilized, AUCmacro¯ and AUCmicro¯ values up to 0.96 are achieved if all layers except the last 12 are frozen during the training procedure.
Ecological Characteristic of Pesticide Tomb in the Warmia Region on the Basis of Index Numbers of Vascular Plants

An ecological characteristic of the surrounding of the pesticide tomb in the Warmia Region was prepared on the basis of index numbers of Poland’s vascular plants in May and June 2002. The results lead to the conclusion that indicators of tropism, the organic matter content of the soil and nitrophylity denote high soil poverty, which are inconsistent with the history of this location. This area used to be a waste disposal site of residues generated in the process of managing post-slaughter waste and carcasses. Presumably some other factor determines such low values of the indicators mentioned above. The indicators analyzed were: lower than expected tropism indicator and a low indicator of organic matter content and particularly the dispersion of values of the nitrophylity indicator denote the existence of a new factor, which modifies the content of species in the communities that we analyzed. The humidity indicator and the indicator of soil mechanical composition confirm the presumed direction of rainwater flow and probable leakage from the pesticide tomb. The flow stays in agreement with the topographic features and the characteristics of the soils that occur in the analyzed area. Soil acidity ranges from: 5.5 to 6.5 pH. Climatic indicators are quite stable, the continentality indicator in particular, and they are typical of North-Eastern Poland. The diversity of the thermal indicator is caused by surface features. A large participation of weeds from the upper plant layer and topographic diversity, both influence the diversity of the luminous indicator. Further research is recommended in order to exclude or confirm the emerging hypothesis of the modifying influence of pesticides deposited in the tomb on the characteristics of the flora and the fauna of the nearby ecosystems.
Evaluation of Commercially Available Anthelminthics in Laboratory Models of Human Intestinal Nematode Infections.

Drug repurposing from veterinary to human medicine has been the main strategy to develop the four recommended human anthelminthics, albendazole, mebendazole, levamisole, and pyrantel pamoate, for the treatment of soil-transmitted helminthiasis. A systematic, head-to-head comparison of the anthelminthic activity profile of derivatives of these drugs and other anthelminthics developed in succession has not been conducted to date. We studied eight benzimidazoles, five macrocyclic lactones, tribendimidine, levamisole, and pyrantel pamoate in laboratory models of human intestinal nematode infections. In vitro studies were performed on Trichuris muris L1 larval stage and adults, as well as Ancylostoma ceylanicum, Necator americanus, Heligmosomoides polygyrus, and Strongyloides ratti L3 larvae and adults. The benzimidazoles showed pronounced differences against larval and adult stages, with low activity against larvae and the highest activity observed against adult N. americanus (IC50 of flubendazole 1.1 μM). The macrocyclic lactones, on the other hand, revealed a higher activity on the larval stages, with the lowest IC50 values observed against N. americanus L3 (IC50 values of 0.03-3 μM). In vivo studies were performed in the T. muris and H. polygyrus mice models, with moxidectin and milbemycin oxime showing the highest activity against H. polygyrus (ED50 values of 0.009 and 0.006 mg/kg, respectively) and moxidectin and abamectin being the most effective drugs against T. muris (ED50 values of 0.2 and 0.5 mg/kg, respectively). Laboratory models for soil-transmitted helminthiasis can assist characterizing potential drug candidates. Drugs should be evaluated against different species, and both the adult and larval stages as activities could differ considerably.
Geography as non-genetic modulation factor of chicken cecal microbiota

The gastrointestinal tract of chickens harbors a highly diverse microbiota contributing not only to nutrition, but also to the physiological development of the gastrointestinal tract. Microbiota composition depends on many factors such as the portion of the intestine as well as the diet, age, genotype, or geographical origin of birds. The aim of the present study was to demonstrate the influence of the geographical location over the cecal microbiota from broilers. We used metabarcoding sequencing datasets of the 16S rRNA gene publicly available to compare the composition of the Argentine microbiota against the microbiota of broilers from another seven countries (Germany, Australia, Croatia, Slovenia, United States of America, Hungary, and Malaysia). Geographical location played a dominant role in shaping chicken gut microbiota (Adonis R2 = 0.6325, P = 0.001; Mantel statistic r = 0.1524, P = 4e-04) over any other evaluated factor. The geographical origin particularly affected the relative abundance of the families Bacteroidaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. Because of the evident divergence of microbiota among countries we coined the term “local microbiota” as convergent feature that conflates non-genetic factors, in the perspective of human-environmental geography. Local microbiota should be taken into consideration as a native overall threshold value for further appraisals when testing the production performance and performing correlation analysis of gut microbiota modulation against different kind of diet and/or management approaches. In this regard, we described the Argentine poultry cecal microbiota by means of samples both from experimental trials and commercial farms. Likewise, we were able to identify a core microbiota composed of 65 operational taxonomic units assigned to seven phyla and 38 families, with the four most abundant taxa belonging to Bacteroides genus, Rikenellaceae family, Clostridiales order, and Ruminococcaceae family.
Effect of Surface pH on Electrodeposited Ni Films

Ni metal was potentiostatically electrodeposited on a vertical plane cathode in a Watts bath in order to determine the effect of the cathode surface pH on the Ni film microstructure. Polarization curves and current efficiencies were measured at pH values of 1.5, 3.4, and 5.5. The surface pH value (pH s ) was estimated from the measured partial current density for hydrogen gas evolution based on a steady-state one-dimensional mass transfer model. Any species relating to the buffering function through the dissociation reactions (HSO - 4 , H 3 BO 3 , Ni 4 (OH) 4+ 4 , H 3 O + , OH - ) were taken into account. The pH s abruptly rose to above 6 as the partial current density for H 2 gas evolution increased. The preferred orientation of electrodeposited Ni thin film was plotted in electrode potential-pH s diagram. It was found that the transition boundary between {110} and {100} preferred orientations was located along a ridge 500 mV below the H + /H 2 equilibrium potential line. This relationship suggests that the dissolved hydrogen atoms in Ni metal are partly responsible for the evolution of structural texture of the Ni films.
Genetical, Biochemical and Technological Parameters Associated with Biscuit Quality. II. Prediction Using Storage Proteins and Quality Characteristics in a Soft Wheat Population

Abstract The present research aims to study the genetic, biochemical and technological characteristics of the Portuguese soft wheat landrace «Barbela» population. Several new HMW-GS and ω-gliadins that characterise this population were identified. The potential of this local variety for biscuit production was evaluated using 150 derived pure lines cultivated over three consecutive years. The use of various indirect tests and storage protein analysis allowed us to select 98 lines to study biscuit value (sweet-biscuit). The sweet-biscuit parameters studied were the speed and energy of dough extrusion, cooking time, dough temperature, and biscuit mass before and after cooking, length, thickness, width, density and surface appearance of the biscuit. These parameters were related to the technological characteristics as evaluated by mixograph and alveograph analysis as well as grain hardness, starch damage levels, protein content, relative viscosity of the pentosans, storage protein alleles, Zeleny test, flour yield and thousand kernel weight of grains. As the «Barbela» lines were all of the soft type, our study demonstrated that grain hardness did not significantly influence the parameters of the biscuit test. Multiple regression analysis showed that protein content was the main variable accounting for the quality potential of the soft wheats selected for biscuit value. Protein content was negatively correlated with machinability (the ratio of extrusion speed/energy of dough extrusion), length and surface appearance of the biscuit. Moreover, the relative viscosity of the water-soluble pentosans was important for several biscuit parameters such as surface appearance and extrusion time. The variables of the mixograph generally correlated well with several biscuit parameters. Conversely, alveograph parameters did not show any significant correlation with the biscuit test. The variation observed in «Barbela» lines for extrusion energy, length, density and surface appearance in the biscuit test were significantly influenced by the Glu-1 locus. This study allowed us to define additional criteria for predicting sweet biscuit value in a soft wheat progeny.
Productivity and Chemical Composition of Tomato and Cucumber Plants Growing in Natural Soils Fertilized with Biona‐312

This study was carried out to evaluate the effect of small additions of ion exchange substrate, Biona‐312, to soil on the yield and mineral composition of cherry tomato cv. ‘Koralik’ and cucumber cv. ‘Hermes F1. ’ The test plants were grown under greenhouse conditions and subjected to 0, 2, and 5% (mass) Biona‐312 doses introduced into the soil. The study results showed that Biona‐312 introduced into soil significantly increased the yield of the test species at the flowering and fruiting stage. Soil enrichment with 2 and 5% Biona additions generally increased the nitrogen–phosphorus–potassium (N‐P‐K) content in tomato and cucumber organs at the flowering and fruiting stage with parallel magnesium (Mg) and calcium (Ca) content decrease. Introduction of nutrients together with the ion exchange substrate did not cause negative effects of overfertilization, and thus the ion exchange substrate can be recommended as a fertilizer in tomato and cucumber cultivation.
Nitrogen spiraling in streams: Comparisons between stable isotope tracer and nutrient addition experiments

A common method to quantify stream nutrient uptake length is to enrich the stream at an upstream point and monitor the downstream decline in the concentration of the added nutrient. However, increasing the nutrient concentration of the stream alters nutrient uptake, and uptake length quantified using this amendment approach does not necessarily reflect uptake length under ambient conditions. We conducted a series of 15NO3− tracer and 14NO3− nutrient amendment experiments to (1) assess the overestimation of amendment‐derived uptake length in streams spanning a gradient of ambient nitrogen concentration, and (2) evaluate a technique to estimate ambient uptake length using data from multiple amendments conducted at different concentrations. Single amendment‐derived uptake lengths were consistently longer than ambient uptake lengths quantified using the stableisotope tracer. The ratio of single amendment‐derived to ambient uptake length ranged more than sixfold across streams but was not related to ambient stream water nitrogen concentration or amendment concentration. Estimated ambient uptake length calculated from the multiple amendment technique was a better predictor of ambient uptake length than single amendment‐derived uptake length in three of five experiments. However, with this technique, calculated uptake length was negative in two streams. Our results suggest that nitrogen limitation was weak in these two streams and that the multiple amendment technique may be ineffective in streams where the nutrient of study is not limiting.
A Flory–Huggins thermodynamic approach for predicting sorption equilibrium in ternary polymer systems

The Flory–Huggins theory as modified by Pouchlý has been applied to calculate preferential (λ) and total (Y) sorption coefficients for a ternary polymer system. The ternary interaction function (ϕ1ϕ2ϕ3GT(u1, ϕ3)) is described as the product of three independent binary functions. This expression allows prediction of λ and Y from binary interaction parameters χ, χ, g, g, and g12(ϕ10). Three ternary polymer systems are used to check the validity of the expression. Moreover for polymer systems in which the parameters g and/or g are unknown, a procedure to evaluate them has been developed and verified on systems for which sufficient experimental information is available.