Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a Fluorescent Assay to Search New Drugs Using Stable tdTomato-Leishmania, and the Selection of Galangin as a Candidate With Anti-Leishmanial Activity

Antimonials continue to be considered the first-line treatment for leishmaniases, but its use entails a wide range of side effects and serious reactions. The search of new drugs requires the development of methods more sensitive and faster than the conventional ones. We developed and validated a fluorescence assay based in the expression of tdTomato protein by Leishmania, and we applied this method to evaluate the activity in vitro of flavonoids and reference drugs. The pIR1SAT/tdTomato was constructed and integrated into the genome of Leishmania (Leishmania) amazonensis. Parasites were selected with nourseothricin (NTC). The relation of L. amaz/tc3 fluorescence and the number of parasites was determined; then the growth in vitro and infectivity in BALB/c mice was characterized. To validate the fluorescence assay, the efficacy of miltefosine and meglumine antimoniate was compared with the conventional methods. After that, the method was used to assess in vitro the activity of flavonoids; and the mechanism of action of the most active compound was evaluated by transmission electron microscopy and ELISA. A linear correlation was observed between the emission of fluorescence of L. amaz/tc3 and the number of parasites (r2 = 0.98), and the fluorescence was stable in the absence of NTC. No differences were observed in terms of infectivity between L. amaz/tc3 and wild strain. The efficacy of miltefosine and meglumine antimoniate determined by the fluorescence assay and the microscopic test showed no differences, however, in vivo the fluorescence assay was more sensitive than limiting dilution assay. Screening assay revealed that the flavonoid galangin (GAL) was the most active compound with IC50 values of 53.09 µM and 20.59 µM in promastigotes and intracellular amastigotes, respectively. Furthermore, GAL induced mitochondrial swelling, lipid inclusion bodies and vacuolization in promastigotes; and up-modulated the production of IL-12 p70 in infected macrophages. The fluorescence assay is a useful tool to assess the anti-leishmanial activity of new compounds. However, the assay has some limitations in the macrophage-amastigote model that might be related with an interfere of flavanol aglycones with the fluorescence readout of tdTomato. Finally, GAL is a promising candidate for the development of new treatment against the leishmaniasis.
Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
Identification and Characterization of the Amphioxus Lck and Its Associated Tyrosine Phosphorylation-Dependent Inhibitory LRR Receptor

Amphioxus (e.g., Branchiostoma belcheri, Bb) has recently emerged as a new model for studying the origin and evolution of vertebrate immunity. Mammalian lymphocyte-specific tyrosine kinase (Lck) plays crucial roles in T cell activation, differentiation and homeostasis, and is reported to phosphorylate both the ITIM and ITSM of PD-1 to induce the recruitment of phosphatases and thus the inhibitory function of PD-1. Here, we identified and cloned the amphioxus homolog of human Lck. By generating and using an antibody against BbLck, we found that BbLck is expressed in the amphioxus gut and gill. Through overexpression of BbLck in Jurkat T cells, we found that upon TCR stimulation, BbLck was subjected to tyrosine phosphorylation and could partially rescue Lck-dependent tyrosine phosphorylation in Lck-knockdown T cells. Mass spectrometric analysis of BbLck immunoprecipitates from immunostimulants-treated amphioxus, revealed a BbLck-associated membrane-bound receptor LRR (BbLcLRR). By overexpressing BbLcLRR in Jurkat T cells, we demonstrated that BbLcLRR was tyrosine phosphorylated upon TCR stimulation, which was inhibited by Lck knockdown and was rescued by overexpression of BbLck. By mutating single tyrosine to phenylalanine (Y-F), we identified three tyrosine residues (Y539, Y655, and Y690) (3Y) of BbLcLRR as the major Lck phosphorylation sites. Reporter gene assays showed that overexpression of BbLcLRR but not the BbLcLRR-3YF mutant inhibited TCR-induced NF-κB activation. In Lck-knockdown T cells, the decline of TCR-induced IL-2 production was reversed by overexpression of BbLck, and this reversion was inhibited by co-expression of BbLcLRR but not the BbLcLRR-3YF mutant. Sequence analysis showed that the three tyrosine-containing sequences were conserved with the tyrosine-based inhibition motifs (ITIMs) or ITIM-like motifs. And TCR stimulation induced the association of BbLcLRR with tyrosine phosphatases SHIP1 and to a lesser extent with SHP1/2. Moreover, overexpression of wild-type BbLcLRR but not its 3YF mutant inhibited TCR-induced tyrosine phosphorylation of multiple signaling proteins probably via recruiting SHIP1. Thus, we identified a novel immunoreceptor BbLcLRR, which is phosphorylated by Lck and then exerts a phosphorylation-dependent inhibitory role in TCR-mediated T-cell activation, implying a mechanism for the maintenance of self-tolerance and homeostasis of amphioxus immune system and the evolutionary conservatism of Lck-regulated inhibitory receptor pathway.
Visualization of Respiratory Commensal Bacteria in Context of Their Natural Host Environment

Commensal microbes are an integral component of mammalian physiology. 16S rRNA gene-specific next generation sequencing from DNA of total organs, swabs or lavages has revolutionized the characterization of bacterial communities in virtually every ecological niche of the body. Culturomics, next allowed the isolation and characterization of commensal bacteria in the lab and the establishment of artificial communities of bacteria, which were eventually reintroduced in model organisms. Spatial organization of microbiota within a given host environment is critical to the physiological or pathological phenotypes provoked by commensal microbiota. In situ hybridization (ISH) is a complementary technique to sequencing and culturing to visualize the presence of individual bacterial operational taxonomic unit (OTUs) in context of the colonized organ. We recently applied highly sensitive in situ RNA hybridization to detection of commensal bacteria in low abundance respiratory tract samples of mice housed under specific pathogen free conditions. This technique allows species-specific detection of living bacteria using RNAScopeTM technology, while preserving the natural environment of the organ. We here provide a detailed step-by-step protocol describing the detection of commensal lung bacteria in respiratory tissue.
Freely Generated Word Responses Analyzed With Artificial Intelligence Predict Self-Reported Symptoms of Depression, Anxiety, and Worry

Background Question-based computational language assessments (QCLA) of mental health, based on self-reported and freely generated word responses and analyzed with artificial intelligence, is a potential complement to rating scales for identifying mental health issues. This study aimed to examine to what extent this method captures items related to the primary and secondary symptoms associated with Major Depressive Disorder (MDD) and Generalized Anxiety Disorder (GAD) described in the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). We investigated whether the word responses that participants generated contained information of all, or some, of the criteria that define MDD and GAD using symptom-based rating scales that are commonly used in clinical research and practices. Method Participants (N = 411) described their mental health with freely generated words and rating scales relating to depression and worry/anxiety. Word responses were quantified and analyzed using natural language processing and machine learning. Results The QCLA correlated significantly with the individual items connected to the DSM-5 diagnostic criteria of MDD (PHQ-9; Pearson’s r = 0.30–0.60, p < 0.001) and GAD (GAD-7; Pearson’s r = 0.41–0.52, p < 0.001; PSWQ-8; Spearman’s r = 0.52–0.63, p < 0.001) for respective rating scales. Items measuring primary criteria (cognitive and emotional aspects) yielded higher predictability than secondary criteria (behavioral aspects). Conclusion Together these results suggest that QCLA may be able to complement rating scales in measuring mental health in clinical settings. The approach carries the potential to personalize assessments and contributes to the ongoing discussion regarding the diagnostic heterogeneity of depression.
Surgical Diagnosis and Treatment of Primary Retroperitoneal Liposarcoma

Background: Primary retroperitoneal liposarcoma (PRPLS) is the most common soft tissue sarcoma of the retroperitoneum with high recurrence rate and short overall survival (OS). Methods: A retrospective review of 51 patients with PRPLS, treated between September 1, 2009 and November 30, 2020, was conducted to evaluate clinical outcomes of PRPLS resection. Patient demographics, histopathologic subtypes, overall survival (OS), progression-free survival (PFS), disease recurrence rate, and tumor stage were reviewed and analyzed. Univariate analysis was done to identify factors potentially affecting OS and PFS of PRPLS patients. Multivariate Cox proportional hazards analysis was used to evaluate the impact of various clinicopathological factors on OS and PFS of PRPLS patients. Results: Fifty-one PRPLS patients (28 Males, 23 Females; mean age 56.25 years) were evaluated. There was no significant effect of age, gender, contiguous organ resection, degree of differentiation and tumor size on the OS and PFS of the patients. Univariate analysis showed that negative surgical margin and early tumor stage significantly correlated with OS and PFS (all P < 0.001). Multivariate analysis showed that tumor stage [hazard ratio (HR) = 1.177, P = 0.001] was an independent predictors of poor progression-free survival, and surgical margins [HR = 4.0674 P = 0.038] and tumor stage [HR = 1.167 P = 0.001] were identified as independent predictors of poor overall survival. Conclusion: Negative surgical margin is a prognostic factor of OS, and can prolong the postoperative survival time of PRPLS patients. Tumor stage is a prognostic factor for OS and PFS, and can influence the survival of PRPLS patients. Earlier tumor stages of PRPLS are associated with significantly better outcomes.
Organ Growth and Intestinal Functions of Preterm Pigs Fed Low and High Protein Formulas With or Without Supplemental Leucine or Hydroxymethylbutyrate as Growth Promoters

The goal of enteral nutritional support for infants born preterm or small for gestational age (SGA) is to achieve normal growth and development. Yet, this is difficult to achieve because of intestinal immaturity. Our objective was to determine if birth weight, protein intake, and the growth promoters leucine (10 g/L) or calcium-ß-hydroxy-ß-methylbutryate (HMB; 1.1 g/L) would affect trajectories of intestinal growth and functions and weights of other organs. Preterm pigs were delivered at gestational day 105 (91% of term) and fed for 6 or 7 days isocaloric formulas that differed in protein content (50 g or 100 g protein/L), with and without the growth promoters leucine or HMB. For comparative purposes organ weights were measured within 12 h after delivery for six term pigs of low and six of average birth weights. The responses of intestinal growth and total intestinal brush border membrane carbohydrases to protein level and supplemental leucine were of greater magnitude for preterm pigs of lower birth weight. Forskolin stimulated chloride secretion in the proximal small intestine was lower for pigs fed the low protein milk replacers. Capacities of the entire small intestine to transport glucose (mmol/kg-day) were not responsive to protein level, leucine, or HMB, and did not differ between small and large pigs. Relative organ weights of the small and average weight term pigs were similar, but some differed from those of the preterm pigs suggesting preterm birth and the standards of care used for this study altered the trajectories of development for the intestine and other organs. Although leucine is an effective generalized growth promoter that enhances gut development of small preterm pigs, it does not mitigate compromised neurodevelopment. Our findings using preterm pigs as a relevant preclinical model indicate nutrition support strategies can influence development of some gastrointestinal tract characteristics and the growth of other organs.
Retinal Axon Interplay for Binocular Mapping

In most mammals, retinal ganglion cell axons from each retina project to both sides of the brain. The segregation of ipsi and contralateral projections into eye-specific territories in their main brain targets—the dorsolateral geniculate nucleus and the superior colliculus—is critical for the processing of visual information. The investigation of the developmental mechanisms contributing to the wiring of this binocular map in mammals identified competitive mechanisms between axons from each retina while interactions between axons from the same eye were challenging to explore. Studies in vertebrates lacking ipsilateral retinal projections demonstrated that competitive mechanisms also exist between axons from the same eye. The development of a genetic approach enabling the differential manipulation and labeling of neighboring retinal ganglion cells in a single mouse retina revealed that binocular map development does not only rely on axon competition but also involves a cooperative interplay between axons to stabilize their terminal branches. These recent insights into the developmental mechanisms shaping retinal axon connectivity in the brain will be discussed here.
Miscanthus Grass as a Novel Functional Fiber Source in Extruded Feline Diets

Although dietary fiber is not considered an essential nutrient in a complete and balanced diet for felines, it provides a substrate for fermentation by gut microbiota, thus promoting gastrointestinal health through the production of fermentative metabolites, as well as improving laxation. The aim of this research was to evaluate the novel fiber source, Miscanthus grass (Miscanthus giganteus), in comparison with traditional fiber sources and their effects on fecal quality, apparent total tract digestibility (ATTD), fecal fermentative end products, and microbiota of healthy adult cats. Four dietary treatments were evaluated, differing in dietary fiber source. The diets were formulated to meet or exceed the AAFCO (2018) nutritional profile for adult cats and contained either cellulose (CO), Miscanthus grass fiber (MF), a blend of Miscanthus fiber and tomato pomace (MF + TP), or beet pulp (BP). The study was conducted using a completely randomized design with 28 neutered adult, domesticated shorthair cats (19 females and 9 males, mean age 2.2 ± 0.03 years; mean body weight 4.6 ± 0.7 kg, mean body condition score 5.6 ± 0.6). The experimental period comprised 21 days, and a fresh fecal and a total fecal collection were performed during the last 4 days of the trial period. Daily food intake (DM basis) was similar across all groups (P > 0.05). Additionally, treatment did not affect fecal output (as-is or DM basis), fecal score, or fecal pH (P > 0.05). Cats fed BP had significantly higher total dietary fiber ATTD than all the other treatments (P < 0.05) and the highest concentrations of total short-chain fatty acid, acetate, and propionate (P < 0.05), while butyrate concentrations were similar for all treatments (P > 0.05). Inclusion of dietary fibers was effective in modulating gut microbiota. Cats fed diets containing Miscanthus grass had greater α-diversity than cats fed BP. As no adverse effects on health, fecal quality, or ATTD of macronutrients were observed with the inclusion of 9% Miscanthus grass fiber or fiber blend, the data suggest that Miscanthus grass fiber and fiber blends are viable alternatives to the traditional dietary fiber sources used in commercial extruded feline diets, being most comparable to cellulose.
Myofibre Hypertrophy in the Absence of Changes to Satellite Cell Content Following Concurrent Exercise Training in Young Healthy Men

Concurrent exercise training has been suggested to create an ‘interference effect,’ attenuating resistance training-based skeletal muscle adaptations, including myofibre hypertrophy. Satellite cells support myofibre hypertrophy and are influenced by exercise mode. To determine whether satellite cells contribute to the ‘interference effect’ changes in satellite cell and myonuclear content were assessed following a period of training in 32 recreationally active males (age: 25 ± 5 year; body mass index: 24 ± 3 kg⋅m–2; mean ± SD) who undertook 12-week of either isolated (3 d⋅w–1) resistance (RES; n = 10), endurance (END; n = 10), or alternate day (6 d⋅w–1) concurrent (CET, n = 12) training. Skeletal muscle biopsies were obtained pre-intervention and after 2, 8, and 12 weeks of training to determine fibre type-specific cross-sectional area (CSA), satellite cell content (Pax7+DAPI+), and myonuclei (DAPI+) using immunofluorescence microscopy. After 12 weeks, myofibre CSA increased in all training conditions in type II (P = 0.0149) and mixed fibres (P = 0.0102), with no difference between conditions. Satellite cell content remained unchanged after training in both type I and type II fibres. Significant correlations were observed between increases in fibre type-specific myonuclear content and CSA of Type I (r = 0.63, P < 0.0001), Type II (r = 0.69, P < 0.0001), and mixed fibres (r = 0.72, P < 0.0001). Resistance, endurance, and concurrent training induce similar myofibre hypertrophy in the absence of satellite cell and myonuclear pool expansion. These findings suggest that myonuclear accretion via satellite cell fusion is positively correlated with hypertrophy after 12 weeks of concurrent training, and that individuals with more myonuclear content displayed greater myofibre hypertrophy.
Growth Differentiation Factor 15 Predicts Cancer Death in Patients With Cardiovascular Risk Factors: The J-HOP Study

Background: Disease-related anorexia-cachexia is associated with poor prognosis of patients with cardiovascular disease (CVD) or cancer. Growth differentiation factor-15 (GDF-15) has emerged as a central regulator of appetite and body weight. However, the exact role of GDF-15 in lean patients has not been elucidated. Aim: Our aim is to evaluate whether the association of GDF-15 with mortality, including cancer death, differs according to body mass index (BMI) level. Methods and Results: We collected blood samples from 4,061 patients with CV risk factors who were enrolled in the nationwide practice-based J-HOP (Japan Morning Surge-Home Blood Pressure) study. Serum GDF-15 levels were determined by immunoassay analysis. During a mean follow-up period of 6.6 years, we observed 174 (6.7/1000 person-year) all-cause deaths, 68 (2.6/1000 person-year) cancer deaths, and 56 (2.2/1000 person-year) CV deaths. Patients were stratified according to the cut-points of GDF-15 at 1,200 ng/L and BMI at 22.5 and 25.0 kg/m2. The association between the GDF-15/BMI based study groups and each outcome was evaluated by Cox-proportional hazard models with adjustment for established risk factors. The multivariate Cox regression model showed that patients with elevated GDF-15 (≥1,200 ng/L) and low BMI (<22.5 kg/m2) were significantly associated with increased risk of all outcomes [all-cause death, hazard ratio (HR) 3.15, 95% confidence interval (CI) 1.85–5.34, p < 0.001; cancer death, HR 3.52, 95%CI 1.64–7.57, p = 0.001; CV death, HR 2.88, 95%CI 1.20–6.92, p = 0.018, respectively] compared to a reference group with non-elevated GDF-15 and normal BMI (22.5–25.0 kg/m2). In analyses of a subgroup with low BMI (<22.5 kg/m2), patients with elevated GDF-15 had 4.79-fold increased risk of cancer death and 11-fold greater risk of CV death when compared with patients with non-elevated GDF-15 (<1,200 ng/L) after adjustment for established risk factors. Conclusion: In patients with CV risk factors, GDF-15 was associated with all-cause, cancer, and CV death. This relationship was especially remarkable in patients with low BMI. The serum GDF-15 levels in patients with low BMI might be a useful marker to identify the potential for anorexia-cachexia associated with CVD and cancer.
Decision Support System Applications for Scheduling in Professional Team Sport. The Team's Perspective

Background: Periodization implies the systematic planning of training and competition with the goal of reaching the best possible performance in the most important competition. In team sports, this consists of finding a flight-and-practice schedule that maximizes the opportunities to perform the periodized contents (e.g., trips, practices, games, and days off). This process is conducted whilst considering known constraints (e.g., competitive schedule, roster availability, weather, especial events, holidays, or emotional effect of days away). The way a scheduling decision support system (DSS) leads users to make a decision should allow for flexibility, whilst minimizing users' confusion and facilitating the understanding of the recommendation given by the scheduling decision support system. Traditional approaches to solving scheduling problems use either simulation models, analytical models, heuristic approaches or a combination of these methods. When it comes to evaluate how the scheduling DSS is performing, three overarching aspects need to be reviewed: context satisfaction, process efficiency, and output quality. Appropriate training periodization and scheduling of trips and training sessions are critical for teams to optimize training and recovery processes in order to maximize health and performance. This article presents a methodological framework for designing decision-support systems for scheduling in professional team sports.