Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of SMAP soil moisture for the SMAPVEX15 field campaign using a hyper‐resolution model

Accurate global mapping of soil moisture is the goal of the Soil Moisture Active Passive (SMAP) mission, which is expected to improve the estimation of water, energy, and carbon exchanges between the land and the atmosphere. Like other satellite products, the SMAP soil moisture retrievals need to be validated, with the validation relying heavily on in situ measurements. However, a one‐to‐one comparison is ill advised due to the spatial mismatch of the large SMAP footprint (∼40 km) and the point scale in situ measurements. This study uses a recently developed hyper‐resolution land surface model—HydroBlocks—as a tool to upscale in situ soil moisture measurements for the SMAPVEX15 (SMAP Validation Experiment 2015) field campaign during 2–18 August 2015. Calibrated against in situ observation, HydroBlocks shows a satisfactory Kling‐Gupta efficiency (KGE) of 0.817 and RMSE of 0.019 m3/m3 for the calibration period. These results indicate that HydroBlocks can be used to upscale in situ measurements for this site. Different from previous studies, here in situ measurements are upscaled using a land surface model without bias correction. The upscaled soil moisture is then used to evaluate SMAP (passive) soil moisture products. The comparison of the upscaled network to SMAP shows that the retrievals are generally able to capture the areal‐averaged soil moisture temporal variations. However, SMAP appears to be oversensitive to summer precipitation. We expect these findings can be used to improve the SMAP soil moisture product and thus facilitate its usage in studying the water, energy, and carbon cycles.
Identification and validation of an H2AZ1-based index model: a novel prognostic tool for hepatocellular carcinoma

The H2A.Z variant histone 1 (H2AZ1) is aberrantly expressed in various tumors, correlating with an unfavorable prognosis. However, its role in hepatocellular carcinoma (HCC) remains unclear. We aimed to elucidate the pathways affected by H2AZ1 and identify promising therapeutic targets for HCC. Following bioinformatic analysis of gene expression and clinical data from The Cancer Genome Atlas and Gene Expression Omnibus database, we found 6,344 dysregulated genes related to H2AZ1 overexpression in HCC tissues (P < 0.05). We performed weighted gene co-expression network analysis to identify the gene module most related to H2AZ1. The H2AZ1-based index was further developed using Cox regression analysis, which revealed that the poor prognosis in the high H2AZ1-based index group could be attributed to elevated tumor stemness (P < 0.05). Moreover, the clinical model showed good prognostic potential (AUC > 0.7). We found that H2AZ1 knockdown led to reduced superoxide dismutase (SOD) activity, elevated malondialdehyde (MDA) levels, and increased apoptosis rate in tumor cells (P < 0.001). Thus, we developed an H2AZ1-based index model with the potential to predict the prognosis of patients with HCC. Our findings provide initial evidence that H2AZ1 overexpression plays a pivotal role in HCC initiation and progression.
Identification of the Bioavailable Peptidome of Chia Protein Hydrolysate and the In Silico Evaluation of Its Antioxidant and ACE Inhibitory Potential

The incorporation of novel, functional, and sustainable foods in human diets is increasing because of their beneficial effects and environmental-friendly nature. Chia (Salvia hispanica L.) has proved to be a suitable source of bioactive peptides via enzymatic hydrolysis. These peptides could be responsible for modulating several physiological processes if able to reach the target organ. The bioavailable peptides contained in a hydrolysate obtained with Alcalase, as functional foods, were identified using a transwell system with Caco-2 cell culture as the absorption model. Furthermore, 20 unique peptides with a molecular weight lower than 1000 Da and the higher statistical significance of the peptide-precursor spectrum match (−10 log P) were assessed by in silico tools to suggest which peptides could be those exerting the demonstrated bioactivity. From the characterized peptides, considering the molecular features and the results obtained, the peptides AGDAHWTY, VDAHPIKAM, PNYHPNPR, and ALPPGAVHW are anticipated to be contributing to the antioxidant and/or ACE inhibitor activity of the chia protein hydrolysates.
Design and implementation of an integrative system for configurable exergames targeting the senior population

Exergames have been proposed as a solution for the promotion of physical activity in the senior population. The diversity of needs and limitations of the target users demand that the exergaming systems allow the configuration and adjustment of game parameters according to each user profile. Such systems are ideal to use in nursing homes, senior gymnasiums, or even rehabilitation centers. Health and sports professionals are then the main interacting users with the interface of such exergaming systems. Configuration can be difficult and time-consuming when considering complex systems with a significant amount of parameter choices. Since professionals working on such places already have time constraints, if they face long-time configuration of these systems they might give up of using them. Therefore, there is an evident need for systems that assist professionals in two ways. First, providing management support for training sessions and plans with exergames. Second, providing automatic decision-making processes that assist in game selection and parameters configuration to fit the user needs. The acceptance and effectiveness of such systems can only be achieved if the main prospective interactors with the system are involved in the development process so that the system can fulfill the users’ needs and expectations. This thesis reports on the design, implementation, and usability evaluation of an integrative system using some of the most-known human-centric techniques, such as interviews, card sorting, and paper prototyping. Results of a usability study of the UI and the main functionalities of the system showed a considerable acceptance and interest by the professionals. The usability study revealed to be a great resource to find aspects of the system that should be further considered for improvement in future iterations. Furthermore, the high results of the USE (Usefulness, Satisfaction, and Ease of use) questionnaire confirm that this system is a promising tool that sports professionals may be willing to use in their daily practice.
Systematic pulmonary embolism follow-up increases diagnostic rates of chronic thromboembolic pulmonary hypertension and identifies less severe disease: results from the ASPIRE Registry

Background Diagnostic rates and risk factors for the subsequent development of chronic thromboembolic pulmonary hypertension (CTEPH) following pulmonary embolism (PE) are not well defined. Methods Over a 10-year period (2010-2020), consecutive patients attending a PE follow-up clinic in Sheffield (population 554,600) and all patients diagnosed with CTEPH, at a PH referral centre in Sheffield (referral population estimated 15-20 million) were included. Results Of 1956 patients attending the Sheffield PE clinic 3 months following a diagnosis of acute PE, 41 were diagnosed with CTEPH with a cumulative incidence of 2.10%, with 1.89% diagnosed within 2 years. Of 809 patients presenting with pulmonary hypertension and diagnosed with CTEPH, 32 were Sheffield residents and 777 non-Sheffield residents. Patients diagnosed with CTEPH at the PE follow-up clinic had shorter symptom duration (p<0.01), better exercise capacity (p<0.05) and less severe pulmonary haemodynamics (p<0.01), compared to patients referred with suspected pulmonary hypertension. Patients with no major transient risk factors present at the time of acute PE had a significantly higher risk of CTEPH compared to patients with major transient risk factors, OR of 3.6 (95% CI 1.11 to 11.91, p=0.03), The presence of 3 CT features of pulmonary hypertension in combination with ≥2 of 4 features of chronic thromboembolic pulmonary disease (CTEPD) at the index PE was present in 19% of patients who developed CTEPH and in 0% of patients who did not. Diagnostic rates and pulmonary endarterectomy rates were higher at 13.2/million/year and 3.6/million/year for Sheffield residents compared to 3.9–5.2/million/year and 1.7–2.3/million/year for non-Sheffield residents, respectively. Conclusions In the real world setting a dedicated PE follow-up pathway identifies patients with less severe CTEPH and increases population-based CTEPH diagnostic and pulmonary endarterectomy rates. At the time of acute PE diagnosis the absence of major transient risk factors, CT features of pulmonary hypertension and chronic thromboembolism are risk factors for a subsequent diagnosis of CTEPH.
Flame characteristics for fires in southern fuels

-Equations describing flow in buoyant turbulent jets have been applied to the derivation of characteristics for forest fire flames. Approximate solutions are used to develop relationships for flame lengths, angles, heights, and tip velocities for fires heading with the wind and burning in calm air as functions of Byram's fire intensity, I (Btu/ft-sec). Flame length and velocity relationships are tested with data taken during controlled burns in southern fuels and with data from the literature. Backfire data are described by the equations for calm-air conditions. Both theoretical and experimental results show that flame lengths for backfires and headfires vary as I~ and I l! z. respectively; flame tip velocities vary as I v. , and I \12 .
Major lower extremity amputations – risk of re-amputation, time to re-amputation, and risk factors: a nationwide cohort study from Denmark

Background and purpose Re-amputation after lower extremity amputation is frequent. The primary aim of our study was to investigate cumulative re-amputation risk after transtibial amputation (TTA), knee disarticulation (KD), and transfemoral amputation (TFA) and secondarily to investigate time to re-amputation, and risk factors. Methods This observational cohort study was based on data from the Danish Nationwide Health registers. The population included first-time major lower extremity amputations (MLEA) performed in patients ≥ 50 years between 2010 and 2021. Both left and right sided MLEA from the same patient were included as index procedures. Results 11,743 index MLEAs on 10,052 patients were included. The overall cumulative risks for re-amputation were 29% (95% confidence interval [CI] 27–30), 30% (CI 26–35), and 11% (CI 10–12) for TTA, KD, and TFA, respectively. 58% of re-amputations were performed within 30 days after index MLEA. Risk factors for re-amputation within 30 days were dyslipidemia (hazard ratio [HR] 1.2, CI 1.0–1.3), renal insufficiency (HR 1.2, CI 1.1–1.4), and prior vascular surgery (HR 1.3, CI 1.2–1.5). Conclusion The risk of re-amputation was more than twice as high after TTA (29%) and KD (30%) compared with TFA (11%). Most re-amputations were conducted within 30 days of the index MLEA. Dyslipidemia, renal insufficiency, and prior vascular surgery were associated with higher risk of re-amputation.
WOCE AMS Radiocarbon I: Pacific Ocean Results (P6, P16 and P17)

AMS radiocarbon results from the World Ocean Circulation Experiment in the Pacific Ocean show dramatic changes in the inventory and distribution of bomb-produced 14C since the time of the GEOSECS survey (8/73–6/74). Near-surface Δ14C values for the eastern portion of both the northern and southern subtropical gyres decreased by 25–50‰, with the change being greater in the north. Equatorial near-surface values have increased by ca. 25‰. Changes in the 250–750-m depth range are dramatically different between the northern and southern basins. The intermediate and mode waters of the southern basin have increased by as much as 75‰ since GEOSECS. Waters of similar density in the northern hemisphere are not exposed to the Southern Ocean circulation regime and are significantly less ventilated, showing maximum changes of ca. 50‰.
Mitochondrial DNA analysis in ayu (Plecoglossus altivelis) raises a urgent conservation need for its southernmost population

The central-marginal hypothesis predicts that genetic diversity decreases and genetic differentiation increases toward the species distribution margin. We analyzed the mitochondrial DNA control region of ayu (Plecoglossus altivelis) collected from different localities, including central and marginal populations, to test the hypothesis. The results show that the ayu populations at southern marginal habitats (Tien Yen River in Vietnam and Yakugachi River in Amami-oshima Island) displayed low genetic diversity (Haplotype diversity, H = 0.52 and 0.67; Nucleotide diversity, Pi = 0.01 and 0.006, respectively) and significantly differed from the central populations (p < 0.001), consistent with the central-marginal hypothesis. However, ayu populations at the center of their distribution range (Shinano River in Honsyu and Hamoji River in Sado Island) and the northern marginal habitats (Yoichi River in Hokkaido and Aonae River in Okushiri Island) exhibited high genetic diversity (H = 1 for all rivers; Pi = 0.024–0.029). The genetic differences between the populations at the center and the northern marginal habitats were insignificant (p > 0.05). This study showed that in ayu, the central-marginal hypothesis is valid in the southern direction but not in the northern direction. Urgent conservation is needed for the genetically distinct population in the degraded southern habitat with severely low genetic diversity.
Lysosomal degradation of ACVR1-Activin complexes negatively regulates signaling of Activins and Bone Morphogenetic Proteins

BMP/TGFß family ligands have mainly been studied as factors that initiate Smad signaling. Activin A stands out as it initiates Smad2/3 signaling through ACVR1B, whereas it generates non-signaling complexes (NSCs) with ACVR1 which can inhibit ACVR1-mediated BMP signaling. In the genetic disorder fibrodysplasia ossificans progressiva (FOP), which is caused by missense mutations in ACVR1 (ACVR1.FOP), Activin•ACVR1.FOP•type II receptor complexes activate Smad1/5 signaling, mimicking those formed with BMPs. As the NSCs that Activin A forms with ACVR1 are stoichiometrically identical with the signaling complexes formed with ACVR1.FOP, we explored how NSCs differ from their signaling counterparts. We demonstrate that NSCs rapidly traffic to the lysosome and are degraded, thereby reducing Activin A levels, in addition to removing ACVR1 and associated type II receptors. Hence, Activin-ACVR1 NSCs negatively regulate both the availability of Activin A and the level of BMP signaling mediated by ACVR1. Hence, lysosomal trafficking and degradation of NSC is a novel regulatory mechanism of BMP/TGFß signaling whose physiological roles remain largely unexplored.
Casein kinase 1 controls components of a TORC2 signaling network in budding yeast

Tor kinases play diverse and essential roles in control of nutrient signaling and cell growth. Tor kinases are assembled into two large multiprotein complexes referred to as Tor Complex 1 and Tor Complex 2 (TORC1 and TORC2). In budding yeast, TORC2 controls a signaling network that relays signals regarding carbon source that strongly influence growth rate and cell size. However, the mechanisms that control TORC2 signaling are poorly understood. Activation of TORC2 requires Mss4, a phosphoinositol kinase that initiates assembly of a multi-protein complex at the plasma membrane that recruits and activates downstream targets of TORC2. Localization of Mss4 to the plasma membrane is controlled by phosphorylation and previous work suggested that yeast homologs of casein kinase 1γ, referred to as Yck1 and Yck2, control phosphorylation of Mss4. Here, we generated a new analog-sensitive allele of YCK2 and used it to test whether Yck1/2 influence signaling in the TORC2 network. We found that multiple components of the TORC2 network are strongly influenced by Yck1/2 signaling.
The evolutionary origins of the lysosome-related organelle sorting machinery reveal fundamental homology in post-endosome trafficking pathways

The major organelles and pathways of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (∼1.5 billion years ago) and their acquisition were defining milestones during the process of eukaryogenesis itself. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct inter-organelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of new cellular compartments, infer ancestral states pre-dating LECA, and can even provide insight into the process of eukaryogenesis itself. Here we undertake a molecular evolutionary analysis, including providing a transcriptome of the jakobid flagellate Reclinomonas americana, exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles, the so-called Biogenesis of Lysosome-related Organelle Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery, and by inference the corresponding sorting pathway, was likely in place prior to the divergence of eukaryotes and is found in a much more diverse array of eukaryotes than is currently assumed. As such, this sorting pathway is likely an underappreciated facet of broader eukaryotic cellular function. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1/MON1, and a newly identified relationship with HOPS/CORVET) offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LRO biogenesis machinery from prokaryotic origins to current eukaryotic diversity, Asgard archaea to animals, integrating it into the larger mechanistic framework describing endomembrane evolution.
Assessing the effects of acute temperature changes of sea water temperature due to climate change on Scottish farmed Atlantic salmon and investigating genetic mitigation

Changes in growth, survival, maturation and health in Atlantic salmon post-smolts were observed under moderate and more extreme heat-wave conditions for the west coast of Scotland. A Scottish Atlantic salmon breeding programme population of 518 salmon of age 13-14 months, was observed for 4 weeks in summer, in tanks with ambient water temperature or ∼ 4 degrees and ∼ 8 degrees above ambient temperature. Data were recorded for the fish before and after the challenge. All fish were genotyped using a custom SNP (single nucleotide polymorphism) array (8,978 SNP genotypes after quality control). Temperature-dependant genotype-by-environment interactions and the potential for selective breeding to improve resilience were investigated. Statistical analyses revealed significant differences between thermal environments for body weight, average daily weight gain, and survival, while higher temperature induced earlier maturation, and an increase of gill health scores. QPCR (quantitative polymerase chain reaction) analyses revealed the presence of Aeromonas hydrophila, a pathogen typically more prevalent in warmer climates. Using genomic relationships and animal mixed models, body weight and average daily weight gain provided moderate heritabilities, while between-tank genetic correlations were close to 1, indicating no significant re-ranking of genotypes between the different thermal environments. These findings suggest that even short-term exposure to heat stress may be sufficient to negatively impact survival and gill health, and induce earlier maturation. However, observations took place within a commercial farm where having replicates for each thermal environment was not possible, hence further experiments with larger populations, exposed to more prolonged heat stress are needed.
West Nile virus is transmitted within mosquito populations through infectious mosquito excreta

Understanding transmission routes of arboviruses is key to control their epidemiology and global health burden. Using West Nile virus and Culex mosquitoes, we tested whether arboviruses are transmitted through mosquito excreta. First, we determined the presence of infectious virions in excreta and quantified a high concentration of infectious units per excreta. Second, we showed that virion excretion starts early after oral infection and remains constant for a long period, regardless of mosquito infection level. These results highlight the infectiousness of excreta from infected mosquitoes. Third, we found that both larvae and pupae were susceptible to infection, although pupae were highly permissive. Forth, we established the proof-of-concept that immature mosqui-toes can be infected by infectious excreta, demonstrating a new excreta-mediated mode of transmission. Finally, by mathematically modelling excreta-mediated transmission in the field, we demonstrated its potential impact on arbovirus epidemiology. Our study uncovers a new route of transmission for arboviruses, unveiling mechanisms of viral maintenance in mosquito reservoirs and of vector species shift that contribute to zoonotic emergence.
Localization of S1P1 Receptor Signaling in the rat, mouse and human Central Nervous System

Some specific lipid molecules present in the brain are signaling molecules at the intracellular compartments or behaving as neurotransmitters or neuromodulators of other systems, binding to specific G protein-coupled receptors (GPCR) for neurolipids. One of these receptors is the sphingosine 1-phosphate receptor subtype 1, coupled to Gαi/o-proteins and involved in cell proliferation, growth or neuroprotection. Thus, an interesting target for neurodegenerative diseases, such as Alzheimer’s. The present study compares the human cerebral distribution of the activity mediated by S1P1 receptor with the that in the brain of rodent experimental models, rat and mice by functional autoradiography, measuring the [35S]GTPγS binding stimulated by the S1P1 receptor selective agonist CYM-5442 to get the anatomy of the S1P1 receptor activity. The S1P1 receptor-mediated activity is, together with that of the CB1 cannabinoid receptor, one of the highest recorded for any GPCR in most of the grey matter areas of the brain, reaching up to 50%-500% over basal, depending on the agonist and brain area. The S1P1 receptor signaling is very relevant in those areas that regulate learning and memory processes, such as the basal forebrain, but also in others involved in control of motor processes or nociception e.g. basal ganglia. The results also reveal that the rat would be a preferable experimental model to extrapolate for the S1P1 receptor-mediated responses in human brain.