Miracle-dz/UniFAR-FTUs huggingface dataset:
Basal epidermis collective migration and local Sonic hedgehog signaling promote skeletal branching morphogenesis in zebrafish fins

Adult zebrafish fins develop and robustly regenerate an elaborately branched bony ray skeleton. During caudal fin regeneration, basal epidermal-expressed Sonic hedgehog (Shh) locally promotes ray branching by partitioning pools of adjacent progenitor osteoblasts (pObs). We investigated if and how Shh signaling similarly functions during developmental ray branching. As during regeneration, shha is uniquely expressed by basal epidermal cells (bEps) overlying pOb pools at the distal aspect of outgrowing juvenile fins. Lateral splitting of each shha-expressing epidermal domain followed by the pOb pools precedes overt ray branching. We use ptch2:Kaede fish and Kaede photoconversion to identify short stretches of shha+ bEps and tightly juxtaposed pObs as the active zone of Hh/Smoothened (Smo) signaling. Basal epidermal distal collective cell migration continuously replenishes each shha+ domain with individual cells transiently expressing and responding to Shh. In contrast, pObs maintain Hh/Smo activity until differentiating. Hh/Smo inhibition using the small molecule BMS-833923 (BMS) prevents branching in all fins, paired and unpaired, with minimal effects on fin outgrowth or skeletal differentiation. Staggered addition of BMS indicates Hh/Smo signaling acts throughout the branching process. We use live time-lapse imaging and cell tracking to find Hh/Smo signaling restrains the distal movement of bEps by apparent ‘tethering’ to pObs. We conclude short-range Shh/Smo signaling enables ray branching by re-positioning pObs during both fin development and regeneration. We propose instructive basal epidermal collective migration and Shh/Smo-promoted heterotypic cell adhesion between bEps and pObs underlies this unique branching morphogenesis.
Personalization of mathematical models of human atrial action potential

Atrial cardiomyocytes demonstrate a wide spectrum of patient-specific, tissue-specific, and pathology-specific action potential (AP) phenotypes due to differences in protein expression and posttranslational modifications. Accurate simulation of the AP excitation and propagation in healthy or diseased atria requires a mathematical model capable of reproducing all the differences by parameter rescaling. In the present study, we have benchmarked two widely used electrophysiological models of the human atrium: the Maleckar and the Grandi models. In particular, patch-clamp AP recordings from human atrial myocytes were fitted by the genetic algorithm (GA) to test the models' versatility. We have shown that the Maleckar model results in a more accurate fitting of heart rate dependence of action potential duration (APD) and resting potential (RP). On the other hand, both models demonstrate the poor fitting of the plateau phase and spike-and-dome morphologies. We propose that modifications to L-type calcium current-voltage relationships are required to improve atrial models' fidelity.
Caspase-3 Activation Correlates With the Initial Mitochondrial Membrane Depolarization in Neonatal Cerebellar Granule Neurons

In this study we evaluated the effect of the reduction in the endoplasmic reticulum calcium concentration ([Ca2+]ER), changes in the cytoplasmic calcium concentration ([Ca2+]i), alteration of the mitochondrial membrane potential, and the ER stress in the activation of caspase-3 in neonatal cerebellar granule cells (CGN). The cells were loaded with Fura-2 to detect changes in the [Ca2+]i and with Mag-fluo-4 to measure variations in the [Ca2+]ER or with TMRE to follow modifications in the mitochondrial membrane potential in response to five different inducers of CGN cell death. These inducers were staurosporine, thapsigargin, tunicamycin, nifedipine and plasma membrane repolarization by switching culture medium from 25 mM KCl (K25) to 5 mM KCl (K5). Additionally, different markers of ER stress were determined and all these parameters were correlated with the activation of caspase-3. The different inducers of cell death in CGN resulted in three different levels of activation of caspase-3. The highest caspase-3 activity occurred in response to K5. At the same time, staurosporine, nifedipine, and tunicamycin elicited an intermediate activation of caspase-3. Importantly, thapsigargin did not activate caspase-3 at any time. Both K5 and nifedipine rapidly decreased the [Ca2+]i, but only K5 immediately reduced the [Ca2+]ER and the mitochondrial membrane potential. Staurosporine and tunicamycin increased the [Ca2+]i and they decreased both the [Ca2+]ER and mitochondrial membrane potential, but at a much lower rate than K5. Thapsigargin strongly increased the [Ca2+]i, but it took 10 min to observe any decrease in the mitochondrial membrane potential. Three cell death inducers -K5, staurosporine, and thapsigargin- elicited ER stress, but they took 30 min to have any effect. Thapsigargin, as expected, displayed the highest efficacy activating PERK. Moreover, a specific PERK inhibitor did not have any impact on cell death triggered by these cell death inducers. Our data suggest that voltage-gated Ca2+ channels, that are not dihydropyridine-sensitive, load the ER with Ca2+ and this Ca2+ flux plays a critical role in keeping the mitochondrial membrane potential polarized. A rapid decrease in the [Ca2+]ER resulted in rapid mitochondrial membrane depolarization and strong activation of caspase-3 without the intervention of the ER stress in CGN.
Performance in even a simple perceptual task depends on mouse secondary visual areas

Primary visual cortex (V1) in the mouse projects to numerous brain areas, including several secondary visual areas, frontal cortex, and basal ganglia. While it has been demonstrated that optogenetic silencing of V1 strongly impairs visually-guided behavior, it is not known which downstream areas are required for visual behaviors. Here we trained mice to perform a contrast-increment change detection task, for which substantial stimulus information is present in V1. Optogenetic silencing of visual responses in secondary visual areas revealed that their activity is required for even this simple visual task. In vivo electrophysiology showed that, although inhibiting secondary visual areas could produce some feedback effects in V1, the principal effect was profound suppression at the location of the optogenetic light. The results show that pathways through secondary visual areas are necessary for even simple visual behaviors.
Risk Prediction for Non-alcoholic Fatty Liver Disease Based on Biochemical and Dietary Variables in a Chinese Han Population

Nonalcoholic fatty liver disease (NAFLD) is a common liver disease globally, but there are no optimal methods for its prediction or diagnosis. The present cross-sectional study proposes a non-invasive tool for NAFLD screening. The study included 2,446 individuals, of whom 574 were NAFLD patients. Multivariable logistic regression analysis was used to identify risk factors for NAFLD and incorporate them in a risk prediction nomogram model; the variables included both clinical and lifestyle-related variables. Following stepwise regression, BMI, waist circumference, serum triglyceride, high-density lipoprotein cholesterol, alanine aminotransferase, presence of diabetes and hyperuricemia, tuber and fried food consumption were identified as significant risk factors and used in the model. The final nomogram was found to have good discrimination ability (area under the receiver operating characteristic curve = 0.843 [95% CI: 0.819-0.867]), and reasonable accuracy for the prediction of NAFLD risk. A cut-off score of <180 for the nomogram was found to have high sensitivity and predictivity for the exclusion of individuals from screening. The model can be used as a non-invasive tool for mass screening.
OASL as a Diagnostic Marker for Influenza Infection Revealed by Integrative Bioinformatics Analysis With XGBoost

Host response biomarkers offer a promising alternative diagnostic solution for identifying acute respiratory infection (ARI) cases involving influenza infection. However, most of the published panels involve multiple genes, which is problematic in clinical settings because polymerase chain reaction (PCR)-based technology is the most widely used genomic technology in these settings, and it can only be used to measure a small number of targets. This study aimed to identify a single-gene biomarker with a high diagnostic accuracy by using integrated bioinformatics analysis with XGBoost. The gene expression profiles in dataset GSE68310 were used to construct a co-expression network using weighted correlation network analysis (WGCNA). Fourteen hub genes related to influenza infection (blue module) that were common to both the co-expression network and the protein–protein interaction network were identified. Thereafter, a single hub gene was selected using XGBoost, with feature selection conducted using recursive feature elimination with cross-validation (RFECV). The identified biomarker was oligoadenylate synthetases-like (OASL). The robustness of this biomarker was further examined using three external datasets. OASL expression profiling triggered by various infections was different enough to discriminate between influenza and non-influenza ARI infections. Thus, this study presented a workflow to identify a single-gene classifier across multiple datasets. Moreover, OASL was revealed as a biomarker that could identify influenza patients from among those with flu-like ARI. OASL has great potential for improving influenza diagnosis accuracy in ARI patients in the clinical setting.
A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species

Unprecedented quantities of sequence data have been generated from the newly emergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of COVID-19. We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function.
High Diagnostic Accuracy of Visible 5‐ALA Fluorescence in Meningioma Surgery According to Histopathological Analysis of Tumor Bulk and Peritumoral Tissue

Complete neurosurgical resection of intracranial meningiomas is essential to avoid residual tumor tissue and thus minimize the risk of tumor recurrence. However, local recurrence of meningiomas is not uncommon mainly due to insufficient intraoperative detection of residual tumor tissue within the tumor bulk or peritumoral tissue such as bone and satellite lesions. Although 5‐aminolevulinic acid (5‐ALA) induced fluorescence was found to visualize the majority of meningiomas, no comprehensive histopathological assessment of fluorescing samples from the tumor bulk and peritumoral tissue is available. The aim of our study was thus to histopathologically analyze a large series of tissue samples derived from meningioma surgery to assess the positive predictive value (PPV) of visible 5‐ALA fluorescence.
Epidemiology of Dermatophytoses in Switzerland According to a Survey of Dermatophytes Isolated in Lausanne between 2001 and 2018

Dermatophytes are the most common pathogenic agents of superficial mycoses in humans and animals. Knowledge of their epidemiology can facilitate the prevention of dermatophytosis and improve prophylactic measures. We sought to determine the incidence of the different dermatophyte species diagnosed in Lausanne (Switzerland) from 2001 to 2018. In total, 10,958 dermatophytes were isolated from patients and 459 from pets. Overall, 99% of tinea unguium and tinea pedis were caused by Trichophyton rubrum and Trichophyton interdigitale with a prevalence ratio of 3:1. Trichophyton violaceum and Trichophyton soudanense were mainly found in tinea capitis in patients of African and Mediterranean origin. Interestingly, while Epidermophyton floccosum and Trichophyton verrucosum were prevalent 50 years ago in an epidemiological analysis carried out in the same laboratory from 1967 to 1970, these two species were rarely detected from 2001 to 2018. Trichophyton mentagrophytes, Trichophyton benhamiae and Microsporum canis were the prevalent zoophilic pathogenic species in children and young adults. Our investigation of animal samples revealed the main reservoirs of these zoophilic species to be cats and dogs for T. mentagrophytes and M. canis, and Guinea pigs for T. benhamiae. This study provides an epidemiological overview of dermatophytoses in Switzerland to improve their surveillance.
Degradation of Sargassum crassifolium Fucoidan by Ascorbic Acid and Hydrogen Peroxide, and Compositional, Structural, and In Vitro Anti-Lung Cancer Analyses of the Degradation Products

Fucoidans possess multiple biological functions including anti-cancer activity. Moreover, low-molecular-weight fucoidans are reported to possess more bioactivities than native fucoidans. In the present study, a native fucoidan (SC) was extracted from Sargassum crassifolium pretreated by single-screw extrusion, and three degraded fucoidans, namely, SCA (degradation of SC by ascorbic acid), SCH (degradation of SC by hydrogen peroxide), and SCAH (degradation of SC by ascorbic acid + hydrogen peroxide), were produced. The extrusion pretreatment can increase the extraction yield of fucoidan by approximately 4.2-fold as compared to the non-extruded sample. Among SC, SCA, SCH, and SCAH, the chemical compositions varied but structural features were similar. SC, SCA, SCH, and SCAH showed apoptotic effects on human lung carcinoma A-549 cells, as illustrated by loss of mitochondrial membrane potential (MMP), decreased B-cell leukemia-2 (Bcl-2) expression, increased cytochrome c release, increased active caspase-9 and -3, and increased late apoptosis of A-549 cells. In general, SCA was found to exhibit high cytotoxicity to A-549 cells and a strong ability to suppress Bcl-2 expression. SCA also showed high efficacy to induce cytochrome c release, activate caspase-9 and -3, and promote late apoptosis of A-549 cells. Therefore, our data suggest that SCA could have an adjuvant therapeutic potential in the treatment of lung cancer. Additionally, we explored that the Akt/mammalian target of rapamycin (mTOR) signaling pathway is involved in SC-, SCA-, SCH-, and SCAH-induced apoptosis of A-549 cells.
Vitamin D3 Supplementation in Drinking Water Prior to Slaughter Improves Oxidative Status, Physiological Stress, and Quality of Pork

The aims of this study were to investigate the effect of vitamin D3 administration in drinking water during lairage time prior to slaughter on physiological stress, oxidative status, and pork quality characteristics. Two experiments were carried out. The first one was performed to examine the effect of vitamin D3 supplementation in drinking water, and the second one to check the effect of supplementation dose (500,000 IU/L vs. 700,000 IU/L). Serum calcium concentration was greater in pigs receiving vitamin D3 in water when compared to the control group. In experiment 1, a 40% α-tocopherol increase in meat from the group supplemented with vitamin D3 (500,000 IU/animal) was observed, that resulted in a tendency of decreased meat malondialdehyde (MDA) values at days 5 and 8 after refrigerated storage. In experiment 2, since water intake was higher (800,000 IU and 1,120,000 IU/animal of vitamin D3 consumption) effects on oxidative status were more profound and vitamin D3 supplementation increased serum α-tocopherol and decreased cortisol and serum TBARS. These effects were also observed in meat; TBARS levels were decreased after 3 days of refrigerated storage. In both experiments meat from pigs that received vitamin D3 in drinking water had a lower proportion of total free-polyunsaturated fatty acids (mainly n-6) when compared to the unsupplemented pigs, and these were positively correlated with TBARS production at day 5 of refrigerated storage (r = 0.53 and 0.38 for experiments 1 and 2, respectively). Meat from pigs receiving vitamin D3 in water showed reduced cohesiveness, gumminess, and chewiness values compared to the control group. The magnetic resonance imaging study of muscle confirmed the effects on water retention with lesser transverse relaxation time in pigs supplemented with vitamin D3. No vitamin D3 dose effect was observed, apart from muscle α-tocopherol concentration that was higher in pigs supplemented with 700,000 compared to those supplemented with 500,000 UI/L.
Effects of stoichiometry and temperature perturbations on beech leaf litter decomposition, enzyme activities and protein expression

Abstract. Microbes are major players in leaf litter decomposition and therefore advances in the understanding of their control on element cycling are of paramount importance. Our aim was to investigate the influence of leaf litter stoichiometry in terms of carbon (C) : nitrogen (N) : phosphorus (P) ratios on the decomposition processes and to track changes in microbial community structures and functions in response to temperature stress treatments. To elucidate how the stoichiometry of beech leaf litter (Fagus sylvatica L.) and stress treatments interactively affect the microbial decomposition processes, a terrestrial microcosm experiment was conducted. Beech litter from different Austrian sites covering C:N ratios from 39 to 61 and C:P ratios from 666 to 1729 were incubated at 15 °C and 60% moisture for six months. Part of the microcosms were then subjected to severe changes in temperature (+30 °C and −15 °C) to monitor the influence of temperature stress. Extracellular enzyme activities were assayed and respiratory activities measured. A semi-quantitative metaproteomics approach (1D-SDS PAGE combined with liquid chromatography and tandem mass spectrometry; unique spectral counting) was employed to investigate the impact of the applied stress treatments in dependency of litter stoichiometry on structure and function of the decomposing community. In litter with narrow C:nutrient (C:N, C:P) ratios, microbial decomposers were most abundant. Cellulase, chitinase, phosphatase and protease activity decreased after heat and freezing treatments. Decomposer communities and specific functions varied with site, i.e. stoichiometry. The applied stress combined with the respective time of sampling evoked changes of enzyme activities and litter pH. Freezing treatments resulted in a decline in residual plant litter material and increased fungal abundance, indicating slightly accelerated decomposition. Overall, a strong effect of litter stoichiometry on microbial community structures and functions was detected, but decomposition was mainly driven by a combination of the investigated factors. Temperature perturbations resulted in short- to medium-term alterations of microbial functions; especially high temperature treatments blocked decomposing enzymes.
Spatiotemporal dynamics in a seasonal metacommunity structure is predictable: the case of floodplain‐fish communities

The metacommunity framework has greatly advanced our understanding about the importance of local and regional processes structuring ecological communities. However, information on how metacommunity structure and the relative strengths of their underlying mechanisms change through time is largely lacking. Dynamic systems that undergo environmental temporal changes and disturbances, such as floodplains, serve as natural laboratories to explore how their metacommunity structure change in time. Here we applied the Elements of Metacommunity Structure framework and variation partitioning analysis to assess how temporal changes in the local environmental factors and regional dispersal processes in the rain season influence a seasonal floodplain-fish metacommunity. Across four months, relevant environmental factors were measured across 21 patches where over 3500 individual fish were sampled. Connectivity was measured using landscape resistance-based metrics and additional spatial variation in metacommunity structure was assessed via spatial autocorrelation functions. The metacommunity structure changed from nestedness, at the beginning of the flood season, to a quasi-Clementsian gradient at the end. Our analyses show that connectivity is only important in the beginning of the flood season whereas environment is only important at the end. These results suggest that this metacommunity is structured by changes between dispersal limitation and environmental filtering through time.
Rotational flywheel training in youth female team sport athletes: could inter-repetition movement variability be beneficial?

BACKGROUND The aim of this study was to analyse the effects of an inter-repetition variable rotational flywheel training program (Variable) over standard rotational flywheel training (Standard). METHODS Twenty-four youth female team-sports players were randomly assigned to both training groups (Variable, n = 12; Standard, n = 12), which consisted of 1 set of 3 rotational flywheel exercises x 10-12 repetitions, biweekly for a period of 6-weeks. The participants included in Variable group were instructed to perform the movement randomly in one of the three directions (0o, 45o right, and 45o left). Measurements included reactive strength, jumping, change of direction, and sprinting tests; patellar tendon condition was also assessed. RESULTS Substantial improvements were found in vertical jump with left leg (16.9%), lateral jump with right leg (13.6%), and patellar condition in left leg (4.1%) for Standard group, but also in reactive strength index in right leg landing (33.9%), vertical jump with right (10.1%) and left leg (12.0%) for Variable group. A significant interaction effect (group x time) wasobserved on patellar condition in right leg (F = 10.02, p < 0.01, η 2 = 0.37), favoring Variable group. CONCLUSIONS Rotational flywheel training programs were beneficial for youth-female team-sports athletes, although the movement variability may play a key role to develop different and specific physical adaptations.
A shift in distribution of humpback whales, Megaptera novaeangliae, in response to prey in the southern Gulf of Maine

From the mid-1970's to the mid-80's, Stellwagen Bank was an important humpba<:k whale feeding area with sand lance (Ammodytesspp.) as the major prey. Between 1988 and 1994. however, the number of hump­ back whales we identified each year on Stellwagen declined from a high of258 (1990) to 7 (1994), and the mean num­ ber of whales identified per day fell from 17.7 (1988) to 0.9 (1994). Adult whales decreased steadily after 1988; juveniles decreased rapidly after 1991. Echo-sounder data from Stellwagen showed that prey trace levels declined from 19.1% ofthe vertical water column in 1990 to 2.8% in 1992 (no readings were taken in 1988-89,or 1993-94). Si­ multaneously, the number of whales identified on Jeffreys Ledge, north of Stellwagen Bank, increased dramati­ cally beginning in 1992. Sixty-four per­ centofthe whales identified on Jeffreys in 1992-94 were seen on Stellwagen Bankin 1988 and 1989. We hypothesize that humpback whales shift their dis­ tribution in order to prey upon recov­ ering herring populations, their pri­ mary source offood.
On modeling the common mode inductor

The role of leakage inductance in filter performance and current handling is discussed. It is demonstrated that leakage inductance is desirable. The underlying physics for the common mode (CM) inductor are reviewed. A model which enables the designer to predict the leakage inductance of the CM choke is presented. Experimental data and practical applications are presented. A core selection methodology which incorporates leakage inductance criteria has been defined. Example predictions are demonstrated. <<ETX>>