Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between Aluminum in Soils and Soil Water in Mineral Horizons of a Range of Acid Forest Soils

Previous studies suggest that the solubility of Al in acid forest soils may be expressed as the log Al 3+ activity = -n pH + log K H-Al + log Al P /C P concentration ratio, with Al and C P representing pyrophosphate-extractable Al and C, respectively, and K H-Al is is the binding constant of Al to protonated complexation sites on soil organic matter (SOM). We show that a slightly modified model, in which Al is replaced by Al org (= Al P - KCl-extractable Al), successfully describes the concentration ofAl in A and B horizons of a wide range of acid forest soils (Typic Dystochrepts) developed in different parent materials from a large number of spruce [Picea abies (L.) Karst. ] and mixed forest stands in southern Poland. Analysis of the data suggests a reaction stoichiometry of n = 1.27 and log K H-Al = 1.98 with R 2 = 0.76. Furthermore, statistical analysis of a large set of published data, in addition to our own data from the Polish soils, indicates that log[Al org /C P ] is significantly correlated with soil pH measured in 1 mol L -1 KCl (pH KCl ), suggesting that the Al binding to SOM is less at small pH KCl due to increased competition with H + : log[Al org /C P ] = 0.82 pH KCl - 4.16 (R 2 = 0.77, n = 276). Combining the two equations gives a simple Al solubility model for mineral horizons in acid forest soils: log Al = -1.27pH + 0.82pH KCl - 2.18 (R 2 = 0.82, n = 127). In this equation, pH KCl relates to chemical soil properties, whereas the pH of soil water also depends on solution characteristics like ionic strength. The equation may be applied to acid forest soils having a soil solution pH in the range of 3.0 to 4.2. Such conditions are rather common in surface horizons (A, E, and upper B) of acid forest soils of the temperate and boreal zones.
Antifreeze Proteins and Their Practical Utilization in Industry, Medicine, and Agriculture

Antifreeze proteins (AFPs) are specific proteins, glycopeptides, and peptides made by different organisms to allow cells to survive in sub-zero conditions. AFPs function by reducing the water’s freezing point and avoiding ice crystals’ growth in the frozen stage. Their capability in modifying ice growth leads to the stabilization of ice crystals within a given temperature range and the inhibition of ice recrystallization that decreases the drip loss during thawing. This review presents the potential applications of AFPs from different sources and types. AFPs can be found in diverse sources such as fish, yeast, plants, bacteria, and insects. Various sources reveal different α-helices and β-sheets structures. Recently, analysis of AFPs has been conducted through bioinformatics tools to analyze their functions within proper time. AFPs can be used widely in various aspects of application and have significant industrial functions, encompassing the enhancement of foods’ freezing and liquefying properties, protection of frost plants, enhancement of ice cream’s texture, cryosurgery, and cryopreservation of cells and tissues. In conclusion, these applications and physical properties of AFPs can be further explored to meet other industrial players. Designing the peptide-based AFP can also be done to subsequently improve its function.
Ambient Fine and Ultrafine Particle Measurements and Their Correlations with Particulate PAHs at an Elementary School Near a Highway

Ambient particulate matter (PM) and particle-bound polycyclic aromatic hydrocarbon (PAH) concentrations were measured continuously for 70 days at a Korean elementary school located near a highway. The PM10, PM2.5, and PM1 values were measured with a light-scattering, multi-channel, aerosol spectrometer (Grimm, Model 1.107). The number concentrations of the particles were measured using a scanning mobility particle sizer and counter (SMPS+C) which counted particles from 11.1 to 1083.3 nm classified in 44 channels. Particle-bound PAHs were measured with a direct reading, photoelectric aerosol sensor. The daily NO2, SO2, and CO concentrations were obtained from a national air-monitoring station located near the school. The average concentrations of PM10, PM2.5, and PM1 were 75.3, 59.3, and 52.1 μg/m3, respectively. The average number concentration of the ultrafine particles (UFPs) was 46,307/cm3, and the averaged particle-bound PAHs concentration was 17.9 ng/m3 during the study period. The ambient UFP variation was strongly associated with traffic intensity, particularly peak concentrations during the traffic rush hours. Particles <100 nm corresponded to traffic-related pollutants, including PAHs. Additional long-term monitoring of ambient UFPs and high-resolution traffic measurements should be carried out in future studies. In addition, transient variations in the ambient particle concentration should be taken into consideration in epidemiology studies in order to examine the short-term health effects of urban UFPs.
Development of Monoclonal Antibody-Based Enzyme-Linked Immunosorbent Assay for Detecting Tetrodotoxin

This study aimed to develop a method for the detection of tetrodotoxin (TTX) based on monoclonal antibody (McAb). The hapten TTX was linked to carrier protein keyhole limpet hemocyanin (KLH) as immunogen, and linked to ovalbumin (OVA) as coating antigen by the Mannich method. Then the 6~8 weeks Babl/c mice were immunized. After cell amalgamation, a cell line with high specificity and sensitivity was obtained, and McAb was produced. The indirect competitive enzyme-linked immunosorbent assay (icELISA) was developed for detecting TTX. The optimized working conditions of the icELISA were 4.0 μg/mL coating antigen, 0.75 μg/mL McAb, 45 min competitive time, at room temperature (20~25 °C). The IC50 value of this method was 24.0 ng/mL, the working ranges were 5.2~107.6 ng/mL, the intra-assay and inter-assay coefficient of variation (CV %) were 4.2 and 4.5, respectively. This investigation will benefit the assay kit development for detecting TTX.
Leakage and spillover effects of forest management on carbon storage: theoretical insights from a simple model

Leakage (spillover) refers to the unintended negative (positive) consequences of forest carbon (C) management in one area on C storage elsewhere. For example, the local C storage benefit of less intensive harvesting in one area may be offset, partly or completely, by intensified harvesting elsewhere in order to meet global timber demand. We present the results of a theoretical study aimed at identifying the key factors determining leakage and spillover, as a prerequisite for more realistic numerical studies.We use a simple model of C storage in managed forest ecosystems and their wood products to derive approximate analytical expressions for the leakage induced by decreasing the harvesting frequency of existing forest, and the spillover induced by establishing new plantations, assuming a fixed total wood production from local and remote (non-local) forests combined.We find that leakage and spillover depend crucially on the growth rates, wood product lifetimes and woody litter decomposition rates of local and remote forests. In particular, our results reveal critical thresholds for leakage and spillover, beyond which effects of forest management on remote C storage exceed local effects. Order of magnitude estimates of leakage indicate its potential importance at global scales.
Impacts of Milking and Housing Environment on Milk Microbiota

Simple Summary Microbiota can enter and persist in raw milk at several stages of the farming chain. The development of culture-independent methods and high-throughput DNA sequencing techniques have improved the approach to study microbiota communities in milk and milk products. This work aimed to determine the effects of farming environments on milk microbiota using the high-throughput DNA sequencing technique, and to elucidate the relationship among the microbiota. The effects of the farming environment on the microbiota in milk can guide farm and management practices to ensure that the milk is not contaminated with bacteria during milking and processing, thereby improving the quality of the milk. Abstract The aim of the present study was to determine the effects of farming environments on microbiota in raw milk and to assess the relationship among microbes by 16S rRNA sequencing methods. Samples of raw milk, cow trough water, teat dip cup, teat, teat liner, dairy hall air, cowshed air, feces, feed, and bedding from two farms were collected. The two highest abundant bacterial groups of Moraxellaceae and Staphylococcaceae were found in milk and teat liner samples, respectively, at Zhengzhou farm, Henan Province. Moreover, the two highest abundant bacterial groups of Enterobacteriaceae and Moraxellaceae were found in milk and teat dip cup samples, respectively, at Qiqihar farm, Heilongjiang Province. Source Tracker analysis revealed that the teat liner and teat dip cup were the most important contributors of microbes in milk samples at Zhengzhou farm and Qiqihar farm, respectively, which could be attributed to the management level of the farm. Therefore, disinfection and cleaning procedures should be developed to improve the quality of raw milk.
Long-term effects of mini-screw-assisted rapid palatal expansion on airway.

OBJECTIVES To evaluate the long-term effects on airway in patients with mini-screw-assisted rapid palatal expansion (MARPE), rapid palatal expansion (RPE), and controls with three-dimensional cone-beam computed tomography (CBCT) analysis. MATERIALS AND METHODS A total of 180 CBCTs of 60 patients were analyzed at different time points, such as pretreatment, postexpansion, and posttreatment. Patients were divided into three groups: mini-screw assisted rapid palatal expansion (MARPE), rapid palatal expansion (RPE), and controls. The nasal cavity, nasopharyngeal, oropharyngeal, and laryngopharyngeal airway volume and area were measured. Changes in total airway volume, total airway area, minimal cross-sectional area, maxillary intermolar width, external maxillary width, and palatal width were also evaluated. RESULTS Both MARPE and RPE caused a statistically significant increase in the airway after expansion as compared with the control group, but there was no statistically significant difference in the change in airway between MARPE, RPE, and the control group at posttreatment, except for nasopharyngeal volume, which was significantly increased in the MARPE group. There was no correlation between the amount of expansion and increase in total airway volume. CONCLUSIONS There was a significant increase in total airway volume, total airway area, and minimal cross-sectional area with MARPE and RPE immediately after expansion, but at posttreatment, the changes in the MARPE and RPE groups were similar to the change in the control group. However, MARPE led to a significant long-term increase in nasopharyngeal volume. The amount of expansion did not correlate with the increase in pharyngeal airway volume.
Bistability in the redox chemistry of sediments and oceans

Significance Changes in ocean redox chemistry are frequently observed in Earth’s history and have fundamental implications for the evolution of marine life. These transitions are commonly ascribed to large changes in the supply of iron, sulfur, or organic carbon in the deeper ocean. We propose that small variations in carbon input flux can drive nonreversible redox changes of the ocean interior and other anoxic systems, such as marine sediments. Nonlinear interactions in the iron and sulfur cycles create tipping points where regime shifts can occur between alternative stable states that are either iron dominated or sulfide dominated. The recognition that the biogeochemistry of sediments and oceans embeds intrinsic bistability provides a conceptual framework for understanding past and present anoxic marine systems. For most of Earth’s history, the ocean’s interior was pervasively anoxic and showed occasional shifts in ocean redox chemistry between iron-buffered and sulfide-buffered states. These redox transitions are most often explained by large changes in external inputs, such as a strongly altered delivery of iron and sulfate to the ocean, or major shifts in marine productivity. Here, we propose that redox shifts can also arise from small perturbations that are amplified by nonlinear positive feedbacks within the internal iron and sulfur cycling of the ocean. Combining observational evidence with biogeochemical modeling, we show that both sedimentary and aquatic systems display intrinsic iron–sulfur bistability, which is tightly linked to the formation of reduced iron–sulfide minerals. The possibility of tipping points in the redox state of sediments and oceans, which allow large and nonreversible geochemical shifts to arise from relatively small changes in organic carbon input, has important implications for the interpretation of the geological rock record and the causes and consequences of major evolutionary transitions in the history of Earth’s biosphere.
Assessing Effects of Salinity on the Performance of a Low-Cost Wireless Soil Water Sensor

Low-cost, accurate soil water sensors combined with wireless communication in an internet of things (IoT) framework can be harnessed to enhance the benefits of precision irrigation. However, the accuracy of low-cost sensors (e.g., based on resistivity or capacitance) can be affected by many factors, including salinity, temperature, and soil structure. Recent developments in wireless sensor networks offer new possibilities for field-scale monitoring of soil water content (SWC) at high spatiotemporal scales, but to install many sensors in the network, the cost of the sensors must be low, and the mechanism of operation needs to be robust, simple, and consume low energy for the technology to be practically relevant. This study evaluated the performance of a resistivity–capacitance-based wireless sensor (Sensoterra BV, 1018LE Amsterdam, Netherlands) under different salinity levels, temperature, and soil types in a laboratory. The sensors were evaluated in glass beads, Oso Flaco sand, Columbia loam, and Yolo clay loam soils. A nonlinear relationship was exhibited between the sensor measured resistance (Ω) and volumetric soil water content (θ). The Ω–θ relationship differed by soil type and was affected by soil solution salinity. The sensor was extremely sensitive at higher water contents with high uncertainty, and insensitive at low soil water content accompanied by low uncertainty. The soil solution salinity effects on the Ω–θ relationship were found to be reduced from sand to sandy loam to clay loam. In clay soils, surface electrical conductivity (ECs) of soil particles had a more dominant effect on sensor performance compared to the effect of solution electrical conductivity (ECw). The effect of temperature on sensor performance was minimal, but sensor-to-sensor variability was substantial. The relationship between bulk electrical conductivity (ECb) and volumetric soil water content was also characterized in this study. The results of this study reveal that if the sensor is properly calibrated, this low-cost wireless soil water sensor has the potential of improving soil water monitoring for precision irrigation and other applications at high spatiotemporal scales, due to the ease of integration into IoT frameworks.
Platelet-activating factor induces the stemness of ovarian cancer cells via the PAF/PAFR signaling pathway.

BACKGROUND Cancer stem cells (CSCs) play an important role in tumor recurrence, metastasis, and chemoresistance. CSCs can shift between non-CSC and CSC states in certain tumor microenvironments. The mechanisms of this shift are not well understood. We previously demonstrated that platelet-activating factor (PAF), a lipid mediator of inflammation in the tumor microenvironment, can promote ovarian cancer progression and induce chemoresistance via PAF/PAFR-mediated inflammatory signaling pathways. Here, we investigated the role of PAF/PAFR signaling in the stemness of ovarian cancer cell. METHODS The effects of PAF and PAFR antagonists on the stemness of SKOV3 and A2780 cells were evaluated using sphere-formation assays, FACS analysis and real-time PCR in vitro and a SKOV3 tumor-formation experiment in nude mice in vivo. The potential mechanism of the PAF effect on the stemness of ovarian cancer cells was evaluated by human cytokine antibody microarray analysis. RESULTS PAF can promote spheroid formation and inhibit the transition of quiescent ovarian cancer cells into the cell cycle. The percentage of cancer stem cells increased significantly, and the expression of stemness genes increased in PAF-treated group. These effects could be blocked by PAFR inhibitors. Ginkgolide B (GB) inhibited tumor growth and decreased the CSC percentage in vivo. Human cytokine antibody microarray analysis showed that some stemness-maintaining proteins increased in PAF-treated group. CONCLUSION Our results suggest that PAF can regulate the stemness of ovarian cancer cells through the PAF/PAFR pathway, suggesting a new target for the treatment of ovarian cancer.
Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiomes of Sorghum bicolor

While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, very little has been published on how the corresponding crop plant microbiome is impacted. ABSTRACT Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California’s San Joaquin Valley that is under long-term cultivation with (i) standard (ST) or no tilling (NT) and (ii) cover cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal versus bacterial communities. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. In addition, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops. IMPORTANCE While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, very little has been published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover cropping or fallow fields, shape soil, and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, we demonstrate here the significance of agronomic practice in modulating plant-microbe interactions, as well as encourage future work on the mechanisms involved in community assemblages supporting similar crop outcomes.
Temperature and hydration dependence of low-frequency spectra of poly-L-glutamic acid with different secondary structures studied by terahertz time-domain spectroscopy

We have investigated low-frequency spectra of poly-L-glutamic acid (polyE) in the powder state by terahertz time-domain spectroscopy (THz-TDS). Samples with three different secondary structures (α-helix, β-sheet, and random-coil) and different chain lengths were prepared to investigate the dependence of the THz spectra on temperature and hydration. The temperature dependence of the THz absorption spectra clearly shows that polyE, regardless of its secondary structure, undergoes dynamical transition between 190 and 240 K. We have estimated the apparent activation energy and transition temperature by phenomenological spectral analysis. We also have estimated the effective dipole moment of the amino acid residue from the real part of the dielectric permittivity at zero frequency. Both results show that the transition temperature is lower when the secondary structure undergoes a transition from a random-coil structure to an α-helix or β-sheet structure. Furthermore, both hydrating water molecules and peptide hydrogen bonds contribute to induce anharmonicity in the low-frequency vibrational motions. Meanwhile, hydration, not peptide hydrogen bonds, is crucial for the dynamical transition to occur because the onset of anharmonicity was observed only when the polypeptide is hydrated. An apparent intermolecular vibrational mode in the β-sheet structure, which suggests a highly ordered structure in the sample, did not exhibit anharmonicity at the tested temperatures and humidity levels. This result suggests that short-range or inter-strand hydrogen bonds of the α-helix or low-ordered β-sheet structures gave rise to the lower transition temperatures and the smaller effective activation energies compared with those of the random-coil structure.
Predictors of Plasma Fluoride Concentrations in Children and Adolescents

Despite increasing concerns about neurotoxicity of fluoride in children, sources of fluoride exposure apart from municipal water fluoridation are poorly understood. We aimed to describe the associations of demographics, drinking water characteristics, diet, and oral health behaviors with plasma fluoride concentrations in U.S. children. We used data from 3928 6–19-year-olds from the 2013–2016 National Health and Nutrition Examination Survey. We used a 24-h dietary recall to estimate recent consumption of fluoridated tap water and select foods. We estimated the associations of fluoridated tap water, time of last dental visit, use of toothpaste, and frequency of daily tooth brushing with plasma fluoride concentrations. The participants who consumed fluoridated (≥0.7 mg/L) tap water (n = 560, 16%) versus those who did not had 36% (95% CI: 22, 51) higher plasma fluoride. Children who drank black or green tea (n = 503, 13%) had 42% higher plasma fluoride concentrations (95% CI: 27, 58) than non-tea drinkers. The intake of other foods and oral health behaviors were not associated with plasma fluoride concentrations. The consumption of fluoridated tap water and tea substantially increases plasma fluoride concentrations in children. Quantifying the contribution of diet and other sources of fluoride is critical to establishing safe target levels for municipal water fluoridation.