Miracle-dz/UniFAR-FTUs huggingface dataset:
Cocoa Industrial Debris Composting in Soil and Earthworm Breeding

Toasted husk, the main cocoa (Theobroma cacao L.) industrialization by-product, was added to pots in different husk doses with 1 kg of topsoil from a cocoa plantation (Umbrisol) and then treated with 5 earthworms (Pontoscolex corethrurus) during 60 days, in a greenhouse experiment. Amendment enhanced (p < 0.5) soil organic matter, water retention, bulk density. Best dose for earthworms breeding was 63.3 g·kg−1 (1,840 g·m−2). Husk was used to feed 10 earthworms•m−2 in an Eutric Fluvisol at Villahermosa, Tabasco, Mexico; in 67 days, produced 58 worms on husk 920 g·m−2, or 54 worms on 1150 g·m−2 husk. Husk was then subjected to a conventional pile composting, and the compost was used to feed 10 earthworms m−2 in the Eutric Fluvisol; those fed with 920 g·m−2 yielded 300 worms·m−2. The product of this last experiment was used as amendment (dose 920 g·m−2) in a 30,000 plants·ha−1 maize crop on a highland Mollisol: yields were 954 kg·ha−1 without amendment, 1137 kg·ha−1 amended. As for humification, the main quality parameters from the materials and soils studied, and purified fractions of humic and fulvic acids were studied by visible and infrared (FTIR) spectroscopy. The major changes observed in the humic acid fraction suggest that the improvement in soil organic matter properties could be related to the increase in aromatic, oxygen-containing and amide functional groups, as could correspond to selective biodegradation process concomitant to incorporation of microbial products into oxidized, altered husk lignin fractions.
Turn-on mode diarylethenes for bioconjugation and fluorescence microscopy of cellular structures

Significance In superresolution fluorescence microscopy, employing synthetic dyes that can be reversibly photoswitched between a nonfluorescent (“dark”) and a fluorescent (“bright”) state has been an attractive alternative to using photoswitchable fluorescent proteins. However, employing such synthetic dyes has been elusive because they have defied reliable attachment to proteins and required UV light for photoswitching. Here we prepared “turn-on mode” fluorescent diarylethenes (fDAEs) that are switchable with visible rather than UV light and blink between a bright fluorescent and a dark state in aqueous buffers. Moreover, our thienyl-substituted fDAEs effectively labeled two thiol groups on nanobodies bearing a single maleimide tag. With these small-sized probes, we acquired superresolution images of vimentin filaments in cells by applying just yellow (561 nm) light. The use of photoswitchable fluorescent diarylethenes (fDAEs) as protein labels in fluorescence microscopy and nanoscopy has been limited by labeling inhomogeneity and the need for ultraviolet light for fluorescence activation (on-switching). To overcome these drawbacks, we prepared “turn-on mode” fDAEs featuring thienyl substituents, multiple polar residues, and a reactive maleimide group in the core structure. Conjugates with antibodies and nanobodies displayed complete on-switching and excitation with violet (405 nm) and yellow-green (<565 nm) light, respectively. Besides, they afforded high signal-to-noise ratios and low unspecific labeling in fluorescence imaging. Irradiation with visible light at 532 nm or 561 nm led to transient on-off switching (“blinking”) of the fDAEs of double-labeled nanobodies so that nanoscale superresolution images were readily attained through switching and localization of individual fluorophores.
Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria).

The use of high-throughput sequencing technologies to produce genome-scale datasets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these datasets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch support metrics to an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published UCE data and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was lower for interfamilial relationships (except the SH-like aLRT and aBayes methods) regardless of the type of marker used. Several nodes that were highly supported with bootstrap had very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths in the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic datasets.
12-month results from the real-life observational treat-to-target and tight-control therapy NOR-Gout study: achievements of the urate target levels and predictors of obtaining this target

Objectives Gout is often not adequately treated, and we aimed to apply urate lowering treatment (ULT) combined with individual information to achieve target serum urate (sUA) in clinical practice, and to identify predictors of achievement of this sUA target. Methods Patients with a recent gout flare and sUA >360 µmol/L (>6 mg/dL) were consecutively included in a single-centre study and managed with a treat-to-target approach combining nurse-led information about gout with ULT. All patients were assessed with tight controls at baseline, 1, 2, 3, 6, 9 and 12 months including clinical examination, information on demographics, lifestyle, self-efficacy and beliefs about medicines. The treatment target was sUA <360 µmol/L and multivariable logistic regression was used to identify predictors of target attainment with ORs and 95% CIs. Results Of 211 patients (mean age 56.4 years, disease duration 7.8 years, 95% males), 186 completed the 12-month study. Mean sUA levels decreased from baseline mean 500 to 311 µmol/L at 12 months with 85.5% achieving the treatment target. Alcohol consumption at least weekly versus less frequently (OR 0.14; 95% CI 0.04 to 0.55) as well as beliefs in overuse of medicines (OR per unit 0.77; 95 CI 0.62 to 0.94) decreased the chance of reaching the treatment target, while higher self-efficacy for arthritis symptoms (OR 1.49 per 10 units; 95% CI 1.09 to 2.05) increased the likelihood. Conclusions This study shows that target sUA can be achieved with ULT in most patients. Less self-reported alcohol consumption, low beliefs in overuse of medicines and higher self-efficacy are associated with treatment success.
Preparation of Nanotextured and Nanofibrous Hydroxyapatite through Dicalcium Phosphate with Gelatin

Organized nanostructures of hydroxyapatite (HAp) were produced using a novel preparation route through the topotactic transition of dicalcium phosphate dihydrate (DCPD) containing gelatin molecules. A nanoscale texture of dicalcium phosphate (DCP) was formed by the dehydration of DCPD prepared in gelatin gel containing phosphate ions. A three-dimensionally oriented framework of HAp consisting of ca. 20 nm grains was prepared by a rapid hydrolysis of the nanotextured DCP with a sodium hydroxide solution. Nanoscale HAp fibers elongated along the c axis with a diameter of ca. 50 nm were also obtained by a moderate hydrolysis with ammonia water. The hierarchical architectures of the nanostructured HAp were successfully achieved by the phase transition associated with the specific interaction of the organic molecules.
Molecular changes of Arabidopsis thaliana plastoglobules facilitate thylakoid membrane remodeling under high light stress.

Plants require rapid responses to adapt to environmental stresses. This includes dramatic changes in the size and number of plastoglobule lipid droplets within chloroplasts. Although the morphological changes of plastoglobules are well-documented, little is known about the corresponding molecular changes. To address this gap, we have compared the quantitative proteome, oligomeric state, prenyl-lipid content, and kinase activities of A. thaliana plastoglobules under unstressed and 5-day light-stressed conditions. Our results show a specific recruitment of proteins related to leaf senescence and jasmonic acid biosynthesis under light stress and identify nearly half of the plastoglobule proteins in high native molecular weight masses. Additionally, a specific increase in plastoglobule carotenoid abundance under the light stress was consistent with enhanced thylakoid disassembly and leaf senescence, supporting a specific role for plastoglobules in senescence and thylakoid remodeling as an intermediate storage site for photosynthetic pigments. In-vitro kinase assays of isolated plastoglobules demonstrated kinase activity towards multiple target proteins, which was more pronounced in the plastoglobules of unstressed than light stressed leaf tissue and which was diminished in plastoglobules of the abc1k1/abc1k3 double mutant. These results strongly suggest that plastoglobule-localized ABC1 kinases hold endogenous kinase activity, as these were the only known or putative kinases identified in the isolated plastoglobules by deep bottom-up proteomics. Collectively, our study reveals targeted changes to the protein and prenyl-lipid composition of plastoglobules under light stress that present strategies by which plastoglobules appear to facilitate stress adaptation within chloroplasts.
Homeostatic sleep and body temperature responses to acute sleep deprivation are preserved following chronic sleep restriction in rats

Chronic sleep insufficiency is common in our society and has negative cognitive and health impacts. It can also alter sleep regulation, yet whether it affects subsequent homeostatic responses to acute sleep loss is unclear. We assessed sleep and thermoregulatory responses to acute sleep deprivation before and after a ‘3/1’ chronic sleep restriction protocol in adult male Wistar rats. The 3/1 protocol consisted of continuous cycles of wheel rotations (3 h on/1 h off) for 4 days. Sleep latency in a 2‐h multiple sleep latency test starting 26 h post‐3/1 was unchanged, whereas non‐rapid eye movement sleep (NREMS) and associated electroencephalogram delta power (a measure of sleep need) over a 24‐h period beginning 54 h post‐3/1 were reduced, compared to respective pre‐3/1 baseline levels. However, in response to acute sleep deprivation (6 h by ‘gentle handling’) starting 78 h post‐3/1, the compensatory rebounds in NREMS and rapid eye movement sleep (REMS) amounts and NREMS delta power were unaltered. Body temperature increased progressively across the 3/1 protocol and returned to baseline levels on the second day post‐3/1. The acute sleep deprivation also increased body temperature, followed by a decline below baseline levels, with no difference between before and after 3/1 sleep restriction. Non‐sleep‐restricted control rats showed responses to acute sleep deprivation similar to those observed in the sleep‐restricted animals. These results suggest that the process of sleep homeostasis is altered on the third recovery day after a 4‐day 3/1 sleep restriction protocol, whereas subsequent homeostatic sleep and temperature responses to brief sleep deprivation are not affected.
Executive Function and Psychosocial Adjustment in Adolescent Survivors of Pediatric Brain Tumor

ABSTRACT Adolescent survivors of pediatric brain tumor (PBT) are a sparsely studied subset of childhood cancer survivors. Sustaining a PBT may complicate the development of executive functions (EFs), which play a vital role in long-term psychosocial adjustment. In this study, 48 adolescent survivors and their parents completed questionnaires assessing EF, psychological symptoms, fatigue, and adaptive functioning, and 26 survivors underwent neuropsychological assessment. Survivors reported significantly more problems with adaptive functioning than a healthy control group, and this was most strongly associated to executive dysfunction, compared to psychological symptoms and fatigue. The findings have important implications for long-term follow-ups.
miRNAs targeting CYP6ER1 and CarE1 are involved in nitenpyram resistance in Nilaparvata lugens

The evolution of nitenpyram resistance has been confirmed to be related to overexpression of two key metabolic enzyme genes, CYP6ER1 and CarE1, in Nilaparvata lugens, a highly destructive rice pest that causes substantial economic losses and has developed insecticide resistance. As microRNAs (miRNAs) are important post‐transcriptional regulators of gene expression, whether they are involved in nitenpyram resistance is poorly understood in N. lugens. In this study, knockdown of key genes in the miRNA biogenesis pathway (Dicer1, Drosha, and Argonaute1) changed CYP6ER1 and CarE1 abundance, which confirmed the importance of miRNAs in nitenpyram resistance. Furthermore, global screening of miRNAs associated with nitenpyram resistance in N. lugens was performed, and a total of 42 known and 178 novel miRNAs were identified; of these, 57 were differentially expressed between the susceptible and resistant strains, and two (novel_85 and novel_191) were predicted to target CYP6ER1 and CarE1, respectively. Luciferase reporter assays demonstrated that novel_85 and novel_191 bind to the CYP6ER1 and CarE1 coding regions, respectively, and downregulate their expression. Moreover, modulating novel_85 and novel_191 expression by injection of miRNA inhibitors and mimics significantly altered N. lugens nitenpyram susceptibility. This is the first study to systematically screen and identify miRNAs associated with N. lugens nitenpyram resistance, and provides important information that can be used to develop new miRNA‐based targets in insecticide resistance management.
Hysteresis During Sol-Gel and Gel-Sol Phase Transitions of k-Carrageenan: A Photon Transmission Study

Photon transmission techniques were used to study sol-gel and gel-sol transitions in k-carrageenan-water systems with various carrageenan contents. The photon transmission intensity, I tr was monitored against temperature to determine critical phase transition temperatures and transition rates. It was observed that the sol-gel transition temperatures, T sg, were found much lower than the gel-sol, T gs, transition temperatures based on the hysteresis of the phase transition loops. Sol-gel and gel-sol activation energies were determined and it was found that a carrageenan-water system required less energy for the gel-sol transition than for the sol-gel transition.
A novel approach to prepare polymer mixed-brushes via single crystal surface patterning

Polymer mixed-brushes with predetermined morphologies as well as with uniform chain length and chain length distribution of various brushes were prepared on a substrate via single crystal surface patterning with a self-seeding procedure from a dilute solution. The required materials including poly(ethylene glycol)-b-polystyrene (PEG-b-PS) and poly(ethylene glycol)-b-poly(methyl methacrylate) (PEG-b-PMMA) with the same crystalline block molecular weight and different amorphous block molecular weights were synthesized via atom transfer radical polymerization (ATRP). Based on various qualities of the employed solvent and various interactions of the substrate with amorphous blocks, the matrix (PS)-dispersed (PMMA) morphologies were obtained on PEG single crystals. The matrix and dispersed phase regions were detectable by atomic force microscopy (AFM) due to differences in height and stiffness. The domain size of dispersed phase decreased with an increase in the molecular weights of PS and PMMA blocks because hindrance against the presence of PEG-b-PMMA chains increased. Despite the domain size of the dispersed phase ranging from 286 to 351 nm, the crystallization temperature did not have a significant effect on the domain size. By increasing the crystallization temperature, the thickness enhancement, and consequently the tethering density enhancement, was more considerable for PS regions, which can be attributed to the lower osmotic pressure of PS chains. Finally, we grew epitaxial structures consisting of PEG-b-PS, PEG-b-PMMA, and homo-PEG layers to verify the determined thicknesses from mixed-brush systems through the conjunction thickness of the corresponding copolymer and homopolymer crystals.
A coupled human–natural system analysis of freshwater security under climate and population change

Significance Jordan is facing an unfolding water crisis, exacerbated by climate change and conflict-induced refugee influxes. We present a freshwater security analysis for the country, enabled by an integrated systems model that combines simulation of Jordan’s natural and built water environment with thousands of representative human agents determining water allocation and use decisions. Our analysis points to severe, potentially destabilizing, declines in Jordan’s freshwater security. Without intervening measures, over 90% of Jordan’s low-income population will be experiencing critical water insecurity by the end of the century. To gain a foothold on its water future, Jordan must enact an ambitious portfolio of interventions that span supply- and demand-side measures, including large-scale desalinization and comprehensive water-sector reform. Limited water availability, population growth, and climate change have resulted in freshwater crises in many countries. Jordan’s situation is emblematic, compounded by conflict-induced population shocks. Integrating knowledge across hydrology, climatology, agriculture, political science, geography, and economics, we present the Jordan Water Model, a nationwide coupled human–natural-engineered systems model that is used to evaluate Jordan’s freshwater security under climate and socioeconomic changes. The complex systems model simulates the trajectory of Jordan’s water system, representing dynamic interactions between a hierarchy of actors and the natural and engineered water environment. A multiagent modeling approach enables the quantification of impacts at the level of thousands of representative agents across sectors, allowing for the evaluation of both systemwide and distributional outcomes translated into a suite of water-security metrics (vulnerability, equity, shortage duration, and economic well-being). Model results indicate severe, potentially destabilizing, declines in freshwater security. Per capita water availability decreases by approximately 50% by the end of the century. Without intervening measures, >90% of the low-income household population experiences critical insecurity by the end of the century, receiving <40 L per capita per day. Widening disparity in freshwater use, lengthening shortage durations, and declining economic welfare are prevalent across narratives. To gain a foothold on its freshwater future, Jordan must enact a sweeping portfolio of ambitious interventions that include large-scale desalinization and comprehensive water sector reform, with model results revealing exponential improvements in water security through the coordination of supply- and demand-side measures.
Hydraulic Properties in Tissue-cultured Soybean Roots are Affected by Salt, Sugar and Heavy Metals

This work was undertaken to estimate the hydraulic properties of roots of tissue-cultured soybean ( Glycine max [L.] Merr.) subject to stress gradients from varying concentrations of nutrient salts, sugar, and heavy metals (Zn, Cu, Mn, Hg) in the culture solution. Using the paper wick method, we varied the water potential of the culture media from (cid:5) 0.04 to (cid:5) 1.45 MPa. Growth was inhibited as increasing concentration of salt or sucrose, and zinc, copper, manganese and mercury in the culture solution, and the root growth was associated with the magnitude of the growth-induced water potential and hydraulic conductance, although the degree of inhibition at a given concentration differed among individual heavy metal ions. In the zone of elongation, turgor was kept larger than 0.3 MPa under all stress conditions, and thus, the cell volume was kept almost unchanged, indicating that osmotic adjustment was occurring according to rates of water inflow associated with cell expansion.
Increasing Effectiveness of Genetically Modifying Mosquito Populations: Risk Assessment of Releasing Blood-Fed Females

ABSTRACT Releasing mosquito refractory to pathogens has been proposed as a means of controlling mosquito-borne diseases. A recent modeling study demonstrated that instead of the conventional male-only releases, adding blood-fed females to the release population could significantly increase the program’s efficiency, hastening the decrease in disease transmission competence of the target mosquito population and reducing the duration and costs of the release program. However, releasing female mosquitoes presents a short-term risk of increased disease transmission. To quantify this risk, we constructed a Ross–MacDonald model and an individual-based stochastic model to estimate the increase in disease transmission contributed by the released blood-fed females, using the mosquito Aedes aegypti and the dengue virus as a model system. Under baseline parameter values informed by empirical data, our stochastic models predicted a 1.1–5.5% increase in dengue transmission during the initial release, depending on the resistance level of released mosquitoes and release size. The basic reproductive number (R0) increased by 0.45–3.62%. The stochastic simulations were then extended to 10 releases to evaluate the long-term effect. The overall reduction of disease transmission was much greater than the number of potential infections directly contributed by the released females. Releasing blood-fed females with males could also outperform conventional male-only releases when the release strain is sufficiently resistant, and the release size is relatively small. Overall, these results suggested that the long-term benefit of releasing blood-fed females often outweighs the short-term risk.