Miracle-dz/UniFAR-FTUs huggingface dataset:
Imaging FCS delineates subtle heterogeneity in plasma membranes of resting mast cells

A myriad of transient, nanoscopic lipid- and protein-based interactions confer a steady-state organization of plasma membrane in resting cells that is poised to orchestrate assembly of key signaling components upon reception of an extracellular stimulus. Although difficult to observe directly in live cells, these subtle interactions can be discerned by their impact on the diffusion of membrane constituents. Herein, we quantified the diffusion properties of a panel of structurally distinct lipid-anchored and transmembrane (TM) probes in RBL mast cells by multiplexed Imaging Fluorescence Correlation Spectroscopy. We developed a statistical analysis of data combined from many pixels over multiple cells to characterize differences as small as 10% in diffusion coefficients, which reflect differences in underlying interactions. We found that the distinctive diffusion properties of lipid-anchored probes can be explained by their dynamic partitioning into ordered proteo-lipid nanodomains, which encompass a major fraction of the membrane and whose physical properties are influenced by actin polymerization. Effects on diffusion by functional protein modules in both lipid-anchored and TM probes reflect additional complexity in steady-state membrane organization. The contrast we observe between different probes diffusing through the same membrane milieu represent the dynamic resting steady-state, which serves as a baseline for monitoring plasma membrane remodeling that occurs upon stimulation.
Differential protein metabolism and regeneration in hypertrophic diaphragm and atrophic gastrocnemius muscles in hibernating Daurian ground squirrels

Whether differences in regulation of protein metabolism and regeneration are involved in the different phenotypic adaptation mechanisms of muscle hypertrophy and atrophy in hibernators? Two fast-type muscles (diaphragm and gastrocnemius) in summer active and hibernating Daurian ground squirrels were selected to detect changes in cross-sectional area (CSA), fiber type distribution, and protein expression indicative of protein synthesis metabolism (protein expression of P-Akt, P-mTORC1, P-S6K1, and P-4E-BP1), protein degradation metabolism (MuRF1, atrogin-1, calpain-1, calpain-2, calpastatin, desmin, troponin T, Beclin1, and LC3-II), and muscle regeneration (MyoD, myogenin, and myostatin). Results showed the CSA of the diaphragm muscle increased significantly by 26.1%, whereas the CSA of the gastrocnemius muscle decreased significantly by 20.4% in the hibernation group compared with the summer active group. Both muscles displayed a significant fast-to-slow fiber-type transition in hibernation. Our study further indicated that increased protein synthesis, decreased protein degradation, and increased muscle regeneration potential contributed to diaphragm muscle hypertrophy, whereas decreased protein synthesis, increased protein degradation, and decreased muscle regeneration potential contributed to gastrocnemius muscle atrophy. In conclusion, the differences in muscle regeneration and regulatory pattern of protein metabolism may contribute to the different adaptive changes observed in the diaphragm and gastrocnemius muscles of ground squirrels.
The conserved DNMT1 dependent methylation regions in human cells are vulnerable to environmental rotenone

Allele-specific DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin-dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The significance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-traditional ASMs are sensitive to exposures in association with human disease. We first explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal development and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24h. Indeed,14 genes adjacent to our identified regions were differentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes, HCN2 and NEFM, with potential to increase the risk of neurodegeneration. Both regions were significantly hypomethylated in response to rotenone. Our data indicate that non-germline ASMs seem conserved between mouse and human genomes, overlap important regulatory factor binding motifs, and regulate the expression of genes vital to neuronal function. These results support the notion that ASMs are sensitive to environmental factors and may alter the risk of neurological disease later in life by disrupting neuronal development.
The first complete mitochondrial genome of Melongenidae from Hemifusus tuba (Neogastropoda: Buccinoidea)

Abstract Hemifusus tuba is an ecologically and economically important species of Buccinoidea, which comprises an ecologically diverse group of carnivorous marine gastropods. However, the taxonomic classification and phylogenetic studies have so far been limited. In this study, we report the first complete mitochondrial genome of Melongenidae from H. tuba. The mitogenome has 15,483 bp (68.2% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a control region. This study was the first to provide complete mitogenome of Melongenidae and will provide useful genetic information for future phylogenetic and taxonomic classification of Buccinoidea.
Blood parameters of Angus and Nellore young bulls fed diets with or without forage.

ABSTRACT We evaluated blood parameters of Angus and Nellore bulls fed diets with and without forage. Forty animals with initial body weight (BW) of 380±16.2 kg were housed in individual stalls. Eight bulls of each breed were fed a whole shelled corn (WSC) diet [850 g kg−1 of WCS and 150 g kg−1 of a pellet based on soybean meal, dry mater (DM) basis] or a ground corn with silage (GC) diet (300 g kg−1 of silage and 700 g [. ]
From a deep learning model back to the brain - inferring morphological markers and their relation to aging

We present a Deep Learning framework for the prediction of chronological age from structural MRI scans. Previous findings associate an overestimation of brain age with neurodegenerative diseases and higher mortality rates. However, the importance of brain age prediction goes beyond serving as biomarkers for neurological disorders. Specifically, utilizing convolutional neural network (CNN) analysis to identify brain regions contributing to the prediction can shed light on the complex multivariate process of brain aging. Previous work examined methods to attribute pixel/voxel-wise contributions to the prediction in a single image, resulting in ‘explanation maps’ that were found noisy and unreliable. To address this problem, we developed an inference framework for combining these maps across subjects, thus creating a population-based rather than a subject-specific map. We applied this method to a CNN ensemble trained on predicting subjects’ age from raw T1 brain images of 10,176 subjects. Evaluating the model on an untouched test set resulted in mean absolute error of 3.07 years and a correlation between chronological and predicted age of r=0.98. Using the inference method, we revealed that cavities containing CSF, previously found as general atrophy markers, had the highest contribution for age prediction. Comparing maps derived from different models within the ensemble allowed to assess differences and similarities in brain regions utilized by the model. We showed that this method substantially increased the replicability of explanation maps, converged with results from voxel-based morphometry age studies and highlighted brain regions whose volumetric variability contributed the most to the prediction. Highlights CNNs ensemble is shown to estimate “brain age” from sMRI with an MAE of ∼3.1 years A novel framework enables to highlight brain regions contributing to the prediction This framework results in explanation maps showing consistency with the literature As sample size increases, these maps show higher inter-sample replicability CSF cavities reflecting general atrophy were found as a prominent aging biomarker
A Data-Driven Model to Identify Fatigue Level Based on the Motion Data from a Smartphone

The fatigue due to repetitive and physically challenging jobs may result in workers’ poor performance and Work-related Musculoskeletal Disorder (WMSD). Thus, it is imperative to frequently monitor fatigue and take necessary recovery actions. Our purpose was to develop a methodology to objectively classify subjects’ fatigue level in the workplace utilizing the motion sensors embedded in the smartphones. An experiment consisting of twenty-four participants (12 M, 12 F) with a smartphone attached to their right shank was conducted using a fatiguing exercise (squatting), targeted mainly the lower extremity musculature. After each set of an exercise (2-min squatting), participants were asked about their ratings of perceived exertion (RPE), then a reference gait data were collected during a straight walk of 20-32 steps. This process was continued until they reported strong fatigue (≥17). Using the RPE to label the gait data, we have developed machine learning algorithms (i.e., binary and multi-class SVM models) to classify the individuals’ gait into two (no-vs. strong-fatigue) and four levels (no-, low-, medium-, and strong-fatigue). The models reached the accuracies of 91% and 61% for two and four-level classification, respectively. The outcomes of this study may facilitate the implementation of a proactive approach in continuous monitoring of operators’ fatigue level, which may subsequently increase the workers’ performance and reduce the risk of WMSDs.
A systematic review to determine the evidence to support the use of flexion distraction chiropractic technique

Flexion distraction chiropractic technique (FDCT) is a commonly used manual therapy technique which is purported to address various clinical pain syndromes. However, it lacks the credibility of appropriate evidence-based guidelines. An analysis of the literature would be able to inform the development of guidelines. Objectives: The aim of this systematic review was to determine the evidence to support the use of FDCT in clinical practice. Data sources: A systematic review of PubMed and Summons was conducted, using the following search terms: chiropractic, flexion distraction, protocol and / or technique. Study selection: All electronic or paper, English articles, which possessed the required key indexing terms and represented randomised and non-randomised controlled study designs were included. Data extraction: Blinded review of the articles was conducted by three independent reviewers utilising the PEDro (for randomised controlled trials) and NOS for (non-randomised controlled trials). This allowed the methodological rigour of the article to be ranked. This ranking was compared to a critical appraisal of the article in order to achieve an overall decision with regards to the contribution of the article to the level of evidence for FDCT. Data synthesis: 18 review outcomes were aggregated around four clinical categories; two articles each on neck pain, chronic pelvic pain, and physiological outcomes and the remaining twelve on low back pain. There was agreement that the evidence for pelvic pain and physiological function was limited to no evidence and limited respectively. Conflicting evidence existed for neck and low back pain (single and multimodal treatment) with limited and moderate evidence respectively. Conclusion: FDCT is clinically advocated for many conditions. The evidence provided in this review indicates that practitioners should be guarded in their use of FDCT, as the evidence to its widespread use is limited to only those conditions noted in this review. Therefore, further high quality and rigorous studies are required to develop appropriate treatment guidelines for use by practitioners to adequately provide evidence based care in clinical practice.
Assembleias de Ephemeroptera (Insecta) em riachos de cabeceirano bioma Cerrado

Diferentes usos antropicos do solo ameacam a biodiversidade em rios e riachos, especialmente daqueles localizados em paises tropicais em desenvolvimento, em virtude de suas maiores taxas de modificacoes de usos do solo. Para o monitoramento dos efeitos dessas conversoes, tem sido usado organismos sensiveis a disturbios nos sistemas aquaticos. Os mais utilizados sao macroinvertebrados bentonicos, sendo observada diminuicao de organismos sensiveis e predominância daqueles tolerantes em riachos sob pressao de disturbios antropicos. Os objetivos desta dissertacao foram inventariar a fauna de Ephemeroptera em riachos no cerrado, e avaliar o efeito de disturbios antropicos em riachos de cabeceira sobre a estrutura de assembleias de Ephemeroptera (riqueza, abundância e composicao taxonomica), testando ainda sua viabilidade como bioindicador. A hipotese testada foi de que riachos expostos a multiplas perturbacoes antropicas afetam negativamente a estrutura de assembleias de Ephemeroptera. Foram amostrados 80 trechos de riachos nas bacias hidrograficas dos altos rios Araguari e Sao Francisco, sendo mensurada a exposicao a disturbios antropicos em escalas local (leito e vegetacao riparia) e de bacia de drenagem (% de usos do solo). Foi utilizado um Indice de Disturbio Integrado para diferenciar grupos de riachos em condicoes menos e mais perturbadas. Os riachos da bacia do alto rio Araguari apresentaram condicoes menos e mais perturbadas se comparados aos riachos da bacia do alto rio Sao Francisco classificados nas mesmas categorias. A riqueza e abundância de ninfas de Ephemeroptera foram significativamente maiores nos riachos do alto rio Sao Francisco [35 generos (11,38 ± 5,42) e 12.533 ninfas (313,33 ± 356,71)] se comparadas as do alto rio Araguari [30 generos (6,73 ± 8,84) e 3.291 ninfas (82,28 ± 130,64)]. A exposicao a disturbios antropicos em escala de bacia de drenagem influenciou negativamente a riqueza apenas na bacia do alto rio Araguari, onde foi observada maior porcentagem de usos do solo, como areas de agricultura e pastagens. Somente nesta bacia foram encontrados generos indicadores de riachos menos perturbados [Aturbina, Cloeodes (Baetidae) Farrodes, Miroculis, Ulmeritoides (Leptophlebiidae)]. A composicao das assembleias diferiu significativamente tanto em riqueza como em abundância entre as condicoes menos e mais perturbadas apenas nos riachos da bacia do alto rio Araguari. Os resultados sugerem que os Ephemeroptera sao indicadores de riachos em boas condicoes ambientais, sendo mais sensiveis a disturbios em escala de bacia de drenagem, e que bacias com alto grau de exposicao a disturbios antropicos apresentam assembleias diferentes tanto em composicao quanto em abundância de organismos sensiveis.
Spatial scale affects novel and disappeared climate change projections in Alaska

Abstract The formation of novel and disappeared climates between the last glacial maximum (LGM) and the present is important to consider to understand the expansion and contraction of species niches and distributions, as well as the formation and loss of communities and ecological interactions over time. Our choice in climate data resolution has the potential to complicate predictions of the ecological impacts of climate change, since climate varies from local to global scales and this spatial variation is reflected in climate data. To address this issue, we downscaled LGM and modern (1975–2005) 30‐year averaged climate data to 60‐m resolution for the entire state of Alaska for 10 different climate variables, and then upsampled each variable to coarser resolutions (60 m to 12 km). We modeled the distributions of novel and disappeared climates to evaluate the locations and fractional area of novel and disappeared climates for each of our climate variables and resolutions. Generally, novel and disappeared climates were located in southern Alaska, although there were cases where some disappeared climates existed within coastal and interior Alaska. Climate resolution affected the fractional area of novel and disappeared climates in three patterns: As the spatial resolution of climate became coarser, the fractional area of novel and disappeared climates (a) increased, (b) decreased, or (c) had no explainable relationship. Overall, we found the use of coarser climate data increased the fractional area of novel and disappeared climates due to decreased environmental variability and removal of climate extremes. Our results reinforce the importance of downscaling coarse climate data and suggest that studies analyzing the effects of climate change on ecosystems may overestimate or underestimate their conclusions when utilizing coarse climate data.
Predicting Minimal Residual Disease in Acute Myeloid Leukemia through Stochastic Modeling of Clonality

Event-free and overall survival remains poor for acute myeloid leukemia (AML). Chemo-resistant clones contributing to relapse of the disease arise from minimal residual disease (MRD) rather than resulting from newly acquired mutations during or after chemotherapy. MRD is the presence of measurable leukemic cells using non-morphologic assays. It is considered a strong predictor of relapse. The dynamics of clones comprising MRD is poorly understood and is considered influenced by a form of Darwinian selection. We propose a stochastic model based on a multitype (multi-clone) age-dependent Markov branching process to study how random events in MRD contribute to the heterogeneity in response to treatment in a cohort of six patients from The Cancer Genome Atlas database with whole genome sequencing data at two time points. Our model offers a more accurate understanding of how relapse arises and which properties allow a leukemic clone to thrive in the Darwinian competition among leukemic and normal hematopoietic clones. The model suggests a quantitative relationship between MRD and time to relapse and therefore may aid clinicians in determining when and how to implement treatment changes to postpone or prevent the time to relapse. Author summary Relapse affects about 50% of AML patients who achieved remission after treatment, and the prognosis of relapsed AML is poor. Current evidence has shown that in many patients, mutations giving rise to relapse are already present at diagnosis and remain in small numbers in remission, defined as the minimal residual disease (MRD). We propose a mathematical model to analyze how MRD develops into relapse, and how random events in MRD may affect the patient’s fate. This work may aid clinicians in predicting the range of outcomes of chemotherapy, given mutational data at diagnosis. This can help in choosing treatment strategies that reduce the risk of relapse.
Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River

Abstract Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin using 4,434 nuclear loci, and tested the history of freshwater invasion of C. nasus. We found that both C. brachygnathus and C. nasus were valid species, but the resident C. nasus taihuensis and the anadromous C. nasus were not different genetically based on Bayes factor species delimitation (BFD*). Maximum likelihood tree, Network, PCA and STRUCTURE analyses all corroborated the results of BFD*. Two independent freshwater invasion events of C. nasus were supported, with the first event occurring around 4.07 Ma and the second happened around 3.2 Ka. The time of the two freshwater invasions is consistent with different paleogeographic events. Estimation showed that gene flow was higher within ecotypes than between different ecotypes. F‐DIST analyses identified 120 disruptive outliers by comparing C. brachygnathus to anadromous C. nasus, and 21 disruptive outliers by comparing resident C. nasus to anadromous C. nasus. Nine outliers were found to be common between the two comparisons, indicating that independent freshwater invasion of C. nasus might involve similar molecular pathways. The results of this study suggest that adaptation to landlocked freshwater environment of migratory fish can evolve multiple times independently, and morphology of landlocked ecotypes may cause confusion in their taxonomy.
Assessement of features influencing the voting for opinions' helpfulness about services in Portuguese

This paper presents the application of a methodology for evaluation of usefulness of opinions with the aim of identifying which characteristics have more influence on the amount of votes: basic utility (e.g. ratings about the product and/or service, date of publication), textual (e.g. size of words, paragraphs) and semantics (e.g., the meaning of the words of the text). The evaluation was performed in a database extracted from TripAdvisor with opinions about hotels written in Portuguese. Results show that users give more attention to recent opinions with higher scores for value and location of the hotel and with lowest scores for cleanliness and quality of rooms. Texts with small values for intelligibility (more difficult) receive more votes than texts with large values of intelligibility.
Physical fitness in community‐dwelling older adults is linked to dietary intake, gut microbiota, and metabolomic signatures

When humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM) and host metabolome in relation to physical fitness of 207 community dwelling subjects aged +65 years. Stratification on anthropometric/body-composition/physical-performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary-fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e. enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.