Miracle-dz/UniFAR-FTUs huggingface dataset:
Silica-Lipid Hybrid Microparticles as Efficient Vehicles  for Enhanced Stability and Bioaccessibility of Curcumin

SUMMARY Curcumin is an active ingredient with multiple functions, but its application is often restricted due to its poor water solubility, weak stability, and consequently low bioaccessibility. Based on this, the aim of this work is to develop a new vehicle to overcome these restrictions. Here we developed a curcumin-loaded nanoemulsion and then curcumin-loaded silica-lipid hybrid microparticles through emulsification and vacuum drying, respectively. The loading of curcumin in the nanoemulsion and microparticles was (0.30±0.02) and (0.67±0.02) %, respectively. FTIR and XRD analyses of microparticles revealed that curcumin was encapsulated in porous, amorphous silica. In vitro antioxidant activities showed that the encapsulation would not affect the antioxidant activity of curcumin. In vitro simulated digestion indicated that nanoemulsion and microparticles had higher curcumin bioaccessibility than the control group. The storage stability of microparticles remained the same during 6 weeks in the dark at 4, 25 and 40 °C. Moreover, the microparticles had a better chemical stability than nanoemulsion under the light. The cell viability was over 80% when the concentration of nanocarriers was less than 45 μg/mL. Hence, the microparticles could be a promising means to load curcumin and improve its solubility, light stability and bioaccessibility.
Microfluidic Approaches for Investigating Aggregated Forms of Disease-Related Proteins

The self-assembly of soluble proteins is a common phenomenon observed in nature. It ranges from the formation of functional biomaterials, such as actin filaments and tubulin microtubules that form the cytoeskeleton, to the abnormal deposition of aberrant aggregates that lead to disease. There are nearly 50 diseases currently associated with protein misfolding and amyloid formation, among them several neurodegenerative disorders such as Alzheimer’s, Parkinson’s and prion diseases. Recent evidence indicates that the most toxic species are the low molecular weight oligomers formed during the onset of the aggregation process. These oligomeric species are commonly difficult to analyse due to their low abundance, transient nature and heterogeneity in their structure. In fact, prions, known to be associated with transmissible spongiform encephalopathies, have not yet been fully characterised as parts of the prion composition seem to lose infectivity through various in vitro purification and isolation procedures. In nature, non-homogeneous solution conditions and molecular crowding are key factors as there might be multiple species associated with the disease. However, traditional biophysical techniques allow the study of biomolecules under ideal conditions, such as high concentrations and monodisperse size distribution. Furthermore, among the limitations of the traditional methods are the sensitivity as well as the sample preparation, which in some cases may require to chemically modify the molecule. In this thesis, I describe the development of a sensitive label-free method to enable the study of protein complexes and proteins under biologically relevant environment, such as brain homogenates, by combining immunochemistry with microfluidic strategies. In this thesis I describe the development of Immuno Diffusional Sizing (IDS), a method that combines diffusional sizing with the sensitivity and specificity of immunoassay detection. In Chapter 3, I explain the optimisation of the devices developed to size a range of particle sizes in heterogeneous mixtures, from small protein monomers to large aggregates. IDS is a label-free method capable of sizing proteins down to the nanoand picomolar concentrations, in complex solutions. The applications of this method to monomeric and aggregated forms of disease-related proteins are described in Chapter 4.
DNA Methylation and Its Role in the Development of Leukemia

Epigenetic changes play an essential role in cancer pathogenesis. It has been established by next-generation sequencing that more than 50% of the human cancers carry mutations in mechanisms involved in the organization of the chromatin and epigenetic regulations. DNA methylation is among the most common epigenetic changes in leukemia. In contrast to DNA mutations which are passively inherited from DNA replication, epimutations, for example, the hypermethylation and epigenetic silencing of tumor suppressor genes, must be actively maintained because of being reversible. Actually, the reversibility of epimutations by small-molecule inhibitors provides the basis for the use of such inhibitors in new cancer therapy strategies. However, DNA methylation mechanism and its role in leukemia are not fully understood; there are some serious concerns about the use of these drugs. In this study, we will review the mechanisms of DNA methylation and the genes that are methylated in leukemia. Moreover, new interesting findings of the epigenetic changes causeed by adult T-cell leukemia/lymphoma have been fully discussed.
Three haplotypes found in populations of the red imported fire ant invading China.

The red imported fire ant, Solenopsis invicta, is an invasive species of economic concern （primarily an agricultural and ecosystem pest）. Such ant was found in some areas of Guangdong and Hong Kong at the end of 2004. By examining genetic variation of the mitochondrial cytochrome oxidase Ⅰ （CO Ⅰ） gene, we analyzed the colony introduction of 13 populations of such ant. A 904 bp fragment of the COⅠ gene was sequenced for 56 individuals from 28 nests. Three haplotypes were obtained. Using the uncorrected pairwise sequence divergence, we found that the divergence between haplotype Ⅱ and haplotype Ⅲ was smallest. All three haplotypes were observed in the Hong Kong population, while only one or two haplotypes were observed in the other populations. Such data of the highest genetic diversity in Hong Kong population suggested that Hong Kong may be the original place of the ant invading other areas in China. All of the three haplotypes observed in Hong Kong population were reported in Argentina, and it is so inferred that the Chinese fire ant may come from Argentina or South America.
Reproductive frequency and size-dependence of fecundity in the Giant Gartersnake (Thamnophis gigas)

—How reproductive output changes with age or size is a key life-history trait that can affect which demographic rates most influence population growth. Although many studies have investigated the reproductive ecology of gartersnakes, we know little about reproduction in the threatened Giant Gartersnake, Thamnophis gigas. We used X-radiography to determine reproductive status and estimated fecundity for 73 female T. gigas collected from several regions within the range of this species in the Sacramento Valley of California, USA, and synthesize these data with data from litters born in captivity to improve our understanding of reproduction in this species. Average total litter size determined from X-rays (15.9) and captive-born litters (15.5) are within the ranges reported from other gartersnakes, but captive-born litters had high rates of stillbirth. Only 154 of 202 neonates from captive snakes were born alive, and seven of 13 litters contained at least one stillborn neonate. We found that fecundity was positively related to maternal snout-vent length, and some evidence that larger litters contained smaller neonates. The proportion of X-rayed females that were gravid was 0.50 in 2014, 0.47 in and 2015, and 0.64 in 2016. Central California experienced an exceptional drought from 2012–2015, which may have affected the reproductive output and frequency of T. gigas. Our estimates of reproductive frequency and size-dependent fecundity in T. gigas provide valuable information that can be used in demographic models of this threatened species. Our results demonstrate that X-radiography is a useful, minimally invasive means to study fecundity in wild populations of snakes.
Availability of Logging Residues and Likelihood of Their Utilization for Electricity Production in the US South

This study estimated quantities of logging residues that can physically be recovered from harvest sites and utilized for electricity production in the US South. Because of a small number of mills utilizing logging residues, this study determined their willingness to utilize additional logging residues to produce electricity as a function of woody residue utilization characteristics of a mill and mill management’s attitudes toward factors limiting utilization of this feedstock. Approximately 98 percent of logging residues occur within a 35-mile hauling distance from mills. Although almost all physically available logging residues could be recovered with a relatively short hauling distance, a mail survey indicated that only 4 percent of mills utilized this feedstock. Willingness to utilize additional logging residues to produce electricity by mill management was positively associated with the quantity of woody residues already used and anticipated equipment upgrades to facilitate electricity production, whereas it was negatively related with the quantity of generated mill residues. Mill management that considered a lack of storage space an important limitation was less likely to utilize additional logging residues. Increased utilization of logging residues for electricity production will be contingent on the implementation of bioenergy favorable policies and availability of technical and financial assistance to mills.
How Much Forest Persists Through Fire? High-Resolution Mapping of Tree Cover to Characterize the Abundance and Spatial Pattern of Fire Refugia Across Mosaics of Burn Severity

Wildfires in forest ecosystems produce landscape mosaics that include relatively unaffected areas, termed fire refugia. These patches of persistent forest cover can support fire-sensitive species and the biotic legacies important for post-fire forest recovery, yet little is known about their abundance and distribution within fire perimeters. Readily accessible 30-m resolution satellite imagery and derived burn severity products are commonly employed to characterize post-fire landscapes; however, coarse image resolution, generalized burn severity thresholds, and other limitations can constrain accurate representation of fire refugia. This study quantifies the abundance and pattern of fire refugia within 10 fires occurring in ponderosa pine and dry mixed-conifer forests between 2000 and 2003. We developed high-resolution maps of post-fire landscapes using semi-automated, object-based classification of 1-m aerial imagery, conducted imagery- and field-based accuracy assessments, and contrasted these with Landsat-derived burn severity metrics. Fire refugia area within burn perimeters ranged from 20% to 57%. Refugia proportion generally decreased with increasing Landsat-derived burn severity, but still accounted for 3–12% of areas classified as high severity. Patch size ranged from 1-m2 isolated trees to nearly 8000 ha, and median patch size was 0.01 ha—substantially smaller than a 30-m Landsat pixel. Patch size was negatively related to burn severity; distance to fire refugia from open areas was positively related to burn severity. Finally, optimized thresholds of 30-m post-fire normalized burn ratio (NBR) and relative differenced normalized burn ratio (RdNBR) delineated fire refugia with an accuracy of 77% when validated against the 1-m resolution maps. Estimations of fire refugia abundance based on Landsat-derived burn severity metrics are unlikely to detect small, isolated fire refugia patches. Finer-resolution maps can improve understanding of the distribution of forest legacies and inform post-fire management activities including reforestation and treatments.
Candidate genes in coffee (Coffea arabica L.) leaves associated with rust (Hemileia vastatrix Berk. & Br) stress

Background. Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. & Br, is one of the most threatening diseases for Coffea arabica L. It is hypothesized that host tolerance to CLR relies on non-race-specific resistance genes. Methods. This study evaluated gene expression in leaves of two susceptible coffee cultivars (one inbred and one F1 hybrid) under different stress conditions: rust control (fungicide and untreated) and fruit thinning (thinned and un-thinned) treatments. RNA-seq analysis focused on the association of differentially expressed genes (DEGs) with CLR and associated the effect of the most significant genes into the phenotype, using regression and prediction statistical models. Results. Gene expression and gene ontology (GO) analysis allowed identification of 100 genes associated with quantitative traits. From these, 88 were correlated with rust incidence, rust severity, and rust sporulation. The expression of genes coding for pathogenesis-related proteins increased positively with rust incidence in the inbred, while genes involved in homoeostasis and broader cell wall structuring processes were upregulated in the F1 hybrid. The enriched gene functions and associations revealed that a possible hypersensitive response (HR) in the inbred and a systemic acquired resistance (SAR) in the F1 hybrid were involved in the tolerance mechanisms to CLR stress. This is the first study to demonstrate the specific interactions between CLR and host at a molecular level, useful for identifying control targets for breeding perennial species.
In-field whole plant maize architecture characterized by Latent Space Phenotyping

Collecting useful, interpretable, and biologically relevant phenotypes in a resource-efficient manner is a bottleneck to plant breeding, genetic mapping, and genomic prediction. Autonomous and affordable sub-canopy rovers are an efficient and scalable way to generate sensor-based datasets of in-field crop plants. Rovers equipped with light detection and ranging (LiDar) can produce three-dimensional reconstructions of entire hybrid maize fields. In this study, we collected 2,103 LiDar scans of hybrid maize field plots and extracted phenotypic data from them by Latent Space Phenotyping (LSP). We performed LSP by two methods, principal component analysis (PCA) and a convolutional autoencoder, to extract meaningful, quantitative Latent Space Phenotypes (LSPs) describing whole-plant architecture and biomass distribution. The LSPs had heritabilities of up to 0.44, similar to some manually measured traits, indicating they can be selected on or genetically mapped. Manually measured traits can be successfully predicted by using LSPs as explanatory variables in partial least squares regression, indicating the LSPs contain biologically relevant information about plant architecture. These techniques can be used to assess crop architecture at a reduced cost and in an automated fashion for breeding, research, or extension purposes, as well as to create or inform crop growth models.
Consolidation of reward memory during sleep does not require dopaminergic activation

Sleep enhances memories, especially, if they are related to future rewards. Although dopamine has been shown to be a key determinant during reward learning, the role of dopaminergic neurotransmission for amplifying reward-related memories during sleep remains unclear. In the present study, we scrutinize the idea that dopamine is needed for the preferential consolidation of rewarded information. We blocked dopaminergic neurotransmission, thereby aiming to wipe out preferential sleep-dependent consolidation of high over low rewarded memories during sleep. Following a double-blind, balanced, crossover design 20 young healthy men received the dopamine d2-like receptor blocker Sulpiride (800 mg) or placebo, after learning a Motivated Learning Task. The task required participants to memorize 80 highly and 80 lowly rewarded pictures. Half of them were presented for a short (750 ms) and a long duration (1500 ms), respectively, which enabled to dissociate effects of reward on sleep-associated consolidation from those of mere encoding depth. Retrieval was tested after a retention interval of 20 h that included 8 h of nocturnal sleep. As expected, at retrieval, highly rewarded memories were remembered better than lowly rewarded memories, under placebo. However, there was no evidence for an effect of blocking dopaminergic neurotransmission with Sulpiride during sleep on this differential retention of rewarded information. This result indicates that dopaminergic activation is not required for the preferential consolidation of reward-associated memory. Rather it appears that dopaminergic activation only tags such memories at encoding for intensified reprocessing during sleep.
Stimulus-Specific Information Flow Across the Canonical Cortical Microcircuit

The vast majority of mammalian neocortex consists of a stereotypical microcircuit, the canonical cortical microcircuit (CCM), consisting of a granular input layer, positioned between superficial and deep layers. Due to this uniform layout, neuronal activation tends to follow a similar laminar sequence, with unique information extracted at each step. For example, the primate primary visual cortex (V1) combines the two eyes’ signals, extracts stimulus orientation and modulates its activity depending on stimulus history. Several theories have been proposed on when and where these processes happen within the CCM’s laminar activation sequence, but it has been methodologically challenging to test these hypotheses. Here, we use time-resolved multivariate pattern analysis (MVPA) to decode information regarding the eye-of-origin, stimulus orientation and stimulus repetition from simultaneously measured spiking responses across V1’s laminar microcircuit. We find that eye-of-origin information was decodable for the entire duration of stimulus presentation, but diminished in the deepest layers of V1, consistent with the notion that two eyes’ signals are combined within the upper layers. Conversely, orientation information was transient and equally pronounced across the microcircuit, in line with the idea that this information is relayed to other areas for further processing. Moreover, when stimuli were repeated, information regarding orientation was enhanced at the expense of eye-of origin information, suggesting that V1 modulates information flow to optimize specific stimulus dimensions. Taken together, these findings provide empirical evidence that adjudicates between long-standing hypotheses and reveals how information transfer within the CCM supports unique cortical functions. Significance Statement Despite the brain’s daunting complexity, there are common organizing principles across brain areas. For example, neocortical activation follows a stereotypical pattern that spreads from input layers towards layers above and below. While this activation pattern is well known, it has been challenging to ascertain how unique types of information are extracted within this common sequence in different brain areas. Here we use machine learning to track the flow of stimulus-specific information across the layers of visual cortex. We found that information regarding several separate stimulus dimensions was routed uniquely within the common activation sequence in a manner that confirmed prior model predictions. This finding demonstrates how differences in information flow within the stereotypical neocortical activation sequence shape area-specific functions.
Analysis of new retrogenes provides insight into dog adaptive evolution

Abstract The origin and subsequent evolution of new genes have been considered as an important source of genetic and phenotypic diversity in organisms. Dog breeds show great phenotypic diversity for morphological, physiological, and behavioral traits. However, the contributions of newly originated retrogenes, which provide important genetic bases for dog species differentiation and adaptive traits, are largely unknown. Here, we analyzed the dog genome to identify new RNA‐based duplications and comprehensively investigated their origin, evolution, functions in adaptive traits, and gene movement processes. First, we totally identified 3,025 retrocopies including 476 intact retrogenes, 2,518 retropseudogenes, and 31 chimerical retrogenes. Second, selective pressure along with ESTs expression analysis showed that most of the intact retrogenes were significantly under stronger purifying selection and subjected to more functional constraints when compared to retropseudogenes. Furthermore, a large number of retrocopies and chimerical retrogenes that occurred approximately 22 million years ago implied a burst of retrotransposition in the dog genome after the divergence time between dog and its closely related species red fox. Interestingly, GO and pathway analyses showed that new retrogenes had expanded in glutathione biosynthetic/metabolic process which likely provided important genetic basis for dogs' adaptation to scavenge human waste dumps. Finally, consistent with the results in human and mouse, a significant excess of functional retrogenes movement on and off the X chromosome in the dog confirmed a general pattern of gene movement process in mammals which was likely driven by natural selection or sexual antagonism. Together, these results increase our understanding that new retrogenes can reshape the dog genome and provide further exploration of the molecular mechanisms underlying the dogs' adaptive evolution.
Effect of medium-chain TAG and exercise on satiety, energy intake and energy balance

Abstract The present study examined whether the combination of medium-chain TAG (MCT) along with exercise suppresses energy intake to a greater extent compared with either intervention alone. Twelve participants consumed a porridge breakfast containing 692·9 kJ of either vegetable or MCT oil on two separate occasions: one followed by rest for 240 min and another followed by rest broken up with 1 h of cycling at 65 % $\dot V$ O2peak starting at 120 min. At 240 min, participants consumed a buffet lunch to satiation and recorded their food intake for the rest of the day. Expired air samples (for calculation of energy expenditure (EE)) and subjective ratings of appetite on visual analogue scales were taken every 30 min, and gastric emptying (GE) breath samples were taken every 15 min. No effect of either breakfast or exercise condition was observed on energy intake at any time point (P > 0·05) or no effect was observed on subjective appetite ratings (P > 0·05). Exercise trials resulted in significantly higher EE compared with resting trials (2960·6 kJ, 95 % CI 2528·9, 3392·2; P < 0·001), and MCT increased resting EE over 4 h compared with long-chain TAG (LCT) (124·8 kJ, 95 % CI 13·5, 236·0; P = 0·031). GE was accelerated by exercise, regardless of the breakfast consumed, but delayed by MCT in both resting and exercise trials. The results show that exercise causes energy deficits via increased EE without promoting dietary compensation. MCT has no effect on energy intake or satiety but increases EE under resting conditions. There is no additive effect of MCT and exercise on EE, intake or appetite ratings.
Climatic Response of Cedrela fissilis Radial Growth in the Ombrophilous Mixed Forest, Paraná, Brazil

We examined the climatic response of Cedrela fissilis radial growth based on precipitation, air relative humidity, temperature and monthly thermal amplitude. It was intended to assess how the secondary growth of C. fissilis is influenced by the climatic variables and which one are the best growth predictors in Ombrophilous Mixed Forest, southern Brazil. Wood cores were processed using classical dendrochronology methodology. Principal Components Analysis, Generalized Linear Models and correlation were used to explore the relationship between radial growth and climate. Our results indicated that the best radial growth predictor is the temperature: the seasonal behavior, under well-watered conditions, seems to have a dominant effect on growth responses. Changes in tree growth corresponding to an increase in temperatures suggest a sensitivity of the species to climate changes. These results are important to help understand how the global warming may influence long-lived pioneer tree growth.