Miracle-dz/UniFAR-FTUs huggingface dataset:
Antioxidant Activity and Chemical Characteristics of Supercritical CO2 and Water Extracts from Willow and Poplar

Renewable feedstock from perennial industrial crops, including those cultivated on marginal land in a short-rotation coppice system, could be an important contribution to the bioeconomy. The majority of data available on the topic are limited to the production of bioenergy from this type of biomass. According to the concept of bioeconomy, biomass-based bioproducts have priority over energy production. This paper characterizes the chemical composition and antioxidant activity of extracts from bark (b), wood (w) or a mixture of bark and wood (b + w) from Salix purpurea, Salix viminalis and Populus nigra obtained using supercritical carbon dioxide (scCO2), scCO2 and water (1%, w/w) or only water. Generally, a high concentration of polyphenols was obtained after extraction with scCO2 and water, while the lowest concentration was found in extracts obtained with scCO2. The highest concentration of polyphenols (p < 0.05) was obtained in an extract from P. nigra (b) (502.62 ± 9.86 mg GAE/g dry matter (d.m.)) after extraction with scCO2 and water, whereas the lowest polyphenol concentration was observed in an scCO2 extract from S. purpurea (b) (6.02 ± 0.13 mg GAE/g d.m.). The flavonoids were effectively separated by extraction with scCO2 (0.88–18.37 mg QE/g d.m.). A positive linear relationship between the antioxidant activity determined by DPPH and ABTS assays and the concentration of polyphenols was demonstrated, R2 = 0.8377 and R2 = 0.9568, respectively. It is most probable that the concentration of flavonoids, rather than the concentration of polyphenols, determines the chelating activity of Fe2+. The Fe2+-chelating activity of scCO2 extracts ranged from 75.11% (EC50 = 5.41 mg/cm3, S. purpurea, b + w) to 99.43% (EC50 = 0.85 mg/cm3, P. nigra, b + w). The lowest chelating activity was demonstrated by the extracts obtained with scCO2 and water (maximum 26.36%, S. purpurea, b + w). In extracts obtained with scCO2 and water, p-hydroxybenzoic acid (210–428 µg/g), p-coumaric acid (56–281 µg/g), saligenin (142–300 µg/g) and salicortin (16–164 µg/g) were the dominant polyphenols. All of these chemical compounds occurred mainly in the free form. The S. purpurea, S. viminalis and P. nigra biomass proved to be an attractive source of biologically active compounds for various possible applications in food, drugs or cosmetics. These compounds could be extracted using an environmentally friendly method with scCO2 and water as a co-solvent.
Estimating detailed soil water profile records from point measurements

Temporal and spatial patterns of soil water content affect many soil processes including evaporation, infiltration, ground water recharge, erosion and vegetation distribution. This paper describes the analysis of a soil moisture dataset comprising a combination of continuous time series of measurements at a few depths and locations, and occasional roving measurements at a large number of depths and locations. The objectives of the paper are: (i) to develop a technique for combining continuous measurements of soil water contents at a limited number of depths within a soil profile with occasional measurements at a large number of depths, to enable accurate estimation of the soil moisture vertical pattern and the integrated profile water content; and (ii) to estimate time series of soil moisture content at locations where there are just occasional soil water measurements available and some continuous records from nearby locations.
Surgical Site Infection Following Primary Definitive Fusion for Pediatric Spinal Deformity

The overall surgical site infection (SSI) rate was low (1.4%) in patients with pediatric spinal deformity. The most common causative bacteria were methicillin-resistant followed by gram-negative rods. Independent risk factors for SSI in pediatric patients undergoing spinal deformity surgery were scoliosis etiology, American Society of Anesthesiologists class 3, and administration of antibiotic therapy twice daily. Study Design. A retrospective multicenter study. Objective. To determine the surgical site infection (SSI) rate, associated risk factors, and causative pathogens in pediatric patients with spinal deformity. Summary of Background Data. There have been no extensive investigations of the risk factors for SSI in Japan. Methods. Demographic data, radiographic findings, and the incidence of SSI were retrospectively analyzed in 1449 pediatric patients who underwent primary definitive fusion surgery for spinal deformity at any of 15 institutions from 2015 to 2017. SSI was defined according to the US Centers for Disease Control and Prevention guideline. Results. The incidence of all SSIs was 1.4% and that of deep SSIs was 0.76%. The most common pathogenic microbes were methicillin-resistant staphylococci (n = 5) followed by gram-negative rods (n = 4), methicillin-sensitive staphylococci (n = 1), and others (n = 10). In univariate analysis, younger age, male sex, a diagnosis of kyphosis, type of scoliosis, American Society of Anesthesiologists (ASA) class ≥3, mental retardation urinary incontinence, combined anterior-posterior fusion, greater magnitude of kyphosis, three-column osteotomy, use of blood transfusion, and number of antibiotic administration were associated with the likelihood of SSI (all P < 0.05). Multivariate logistic regression analysis identified the following independent risk factors for SSI: syndromic scoliosis etiology (vs. idiopathic scoliosis; adjusted odds ratio [OR] 16.106; 95% confidence interval [CI] 2.225–116.602), neuromuscular scoliosis etiology (vs. idiopathic scoliosis; adjusted OR 11.814; 95% CI 1.109–125.805), ASA class 3 (vs. class 2; adjusted OR 15.231; 95% CI 1.201–193.178), and administration of antibiotic therapy twice daily (vs. three times daily; adjusted OR 6.121; 95% CI 1.261–29.718). Conclusion. The overall infection rate was low. The most common causative bacteria were methicillin-resistant followed by gram-negative rods. Independent risk factors for SSI in pediatric patients undergoing spinal deformity surgery were scoliosis etiology, ASA class 3, and administration of antibiotic therapy twice daily. Level of Evidence: 3
Carbon nanocapsules and single‐layered nanotubes produced with platinum‐group metals (Ru, Rh, Pd, Os, Ir, Pt) by arc discharge

Encapsulation of platinum‐group metals (Ru, Rh, Pd, Os, Ir, Pt) within carbon nanocapsules and synthesis of single‐layered (SL) carbon nanotubes by arc evaporation of metal/carbon composites have been studied. Transmission electron microscopy revealed that all the platinum‐group metals, forming small particles (10–200 nm in diameter), were encapsulated within multilayered graphitic cages. Particles trapped in the cages were single‐domain crystallites in normal metallic phases. Rh, Pd, and Pt showed catalytic activity for growing SL carbon tubes, but the other metals did not. Bundles of dense SL tubes with diameter 1.3–1.7 nm were extruding radially from metal particles for Rh and Pd; the sizes of core particles were 20–30 nm for Rh, and 50–200 nm for Pd. In the case of Pt, one or a few SL tubes (typically 1.3–2.0 nm in diameter and sometimes ∼3 nm) grew from a tiny particle (∼10 nm).
Correlation between vancomycin clearance and cystatin C‐based glomerular filtration rate in paediatric patients

Because of limitations with the serum creatinine‐based glomerular filtration rate (GFRcr), estimates of the serum cystatin C‐based glomerular filtration rate (GFRcys) are getting attention to predict vancomycin clearance (CLvan). We evaluated the correlations between (i) CLvan and GFRcr, and (ii) CLvan and GFRcys in paediatric patients.
Nitroxide Radicals@US‐Tubes: New Spin Labels for Biomedical Applications

The encapsulation of nitroxide radicals within ultrashort (ca. 50 nm) single‐walled carbon nanotubes (US‐tubes) is achieved. Tempo‐ and Iodo‐Tempo@US‐tubes are characterized by thermogravimetric analysis (TGA), X‐ray photoelectron spectroscopy (XPS), and Raman spectroscopy. Electron paramagnetic resonance (EPR) spectra display characteristic signals due to the detection of the spin probes within the US‐tubes. Longitudinal proton relaxivities (r1) of both nitroxide@US‐tubes samples are 7 to 13 times greater than the free nitroxide radicals in solution, giving relaxivities comparable to the clinical contrast agent (CA) Magnevist. In addition, transverse proton relaxivities (r2) show unprecedented proton relaxation enhancement in comparison to any other reported nitroxide radical‐based system or the clinically approved T2 CA, Resovist, under the same conditions. T2‐weighted magnetic resonance imaging (MRI) phantom images show that the encapsulation of nitroxide radicals within the US‐tubes produces good contrast enhancement due to their high r2 relaxivities. The nitroxide radicals@US‐tube agents are a new promising class of spin probes for MRI and electronic paramagnetic resonance imaging (EPRI) labeling, tracking, and diagnosis.
Calcium Signaling and Mitochondrial Function in Presenilin 2 Knock-Out Mice: Looking for Any Loss-of-Function Phenotype Related to Alzheimer’s Disease

Alzheimer′s disease (AD) is the most common age-related neurodegenerative disorder in which learning, memory and cognitive functions decline progressively. Familial forms of AD (FAD) are caused by mutations in amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) genes. Presenilin 1 (PS1) and its homologue, presenilin 2 (PS2), represent, alternatively, the catalytic core of the γ-secretase complex that, by cleaving APP, produces neurotoxic amyloid beta (Aβ) peptides responsible for one of the histopathological hallmarks in AD brains, the amyloid plaques. Recently, PSEN1 FAD mutations have been associated with a loss-of-function phenotype. To investigate whether this finding can also be extended to PSEN2 FAD mutations, we studied two processes known to be modulated by PS2 and altered by FAD mutations: Ca2+ signaling and mitochondrial function. By exploiting neurons derived from a PSEN2 knock-out (PS2–/–) mouse model, we found that, upon IP3-generating stimulation, cytosolic Ca2+ handling is not altered, compared to wild-type cells, while mitochondrial Ca2+ uptake is strongly compromised. Accordingly, PS2–/– neurons show a marked reduction in endoplasmic reticulum–mitochondria apposition and a slight alteration in mitochondrial respiration, whereas mitochondrial membrane potential, and organelle morphology and number appear unchanged. Thus, although some alterations in mitochondrial function appear to be shared between PS2–/– and FAD-PS2-expressing neurons, the mechanisms leading to these defects are quite distinct between the two models. Taken together, our data appear to be difficult to reconcile with the proposal that FAD-PS2 mutants are loss-of-function, whereas the concept that PS2 plays a key role in sustaining mitochondrial function is here confirmed.
Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Antibodies are becoming a frontline therapy for SARS-CoV-2, but the risk of viral evolutionary escape remains unclear. Here we map how all mutations to SARS-CoV-2’s receptor-binding domain (RBD) affect binding by the antibodies in Regeneron’s REGN-COV2 cocktail and Eli Lilly’s LY-CoV016. These complete maps uncover a single amino-acid mutation that fully escapes the REGN-COV2 cocktail, which consists of two antibodies targeting distinct structural epitopes. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2, as well as in lab viral escape selections. Finally, the maps reveal that mutations escaping each individual antibody are already present in circulating SARS-CoV-2 strains. Overall, these complete escape maps enable immediate interpretation of the consequences of mutations observed during viral surveillance.
Avian Malaria and Related Parasites from Resident and Migratory Birds in the Brazilian Atlantic Forest, with Description of a New Haemoproteus Species

Determining the prevalence and local transmission dynamics of parasitic organisms are necessary to understand the ability of parasites to persist in host populations and disperse across regions, yet local transmission dynamics, diversity, and distribution of haemosporidian parasites remain poorly understood. We studied the prevalence, diversity, and distributions of avian haemosporidian parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon among resident and migratory birds in Serra do Mar, Brazil. Using 399 blood samples from 66 Atlantic Forest bird species, we determined the prevalence and molecular diversity of these pathogens across avian host species and described a new species of Haemoproteus. Our molecular and morphological study also revealed that migratory species were infected more than residents. However, vector infective stages (gametocytes) of Leucocytozoon spp. , the most prevalent parasites found in the most abundant migrating host species in Serra do Mar (Elaenia albiceps), were not seen in blood films of local birds suggesting that this long-distance Austral migrant can disperse Leucocytozoon parasite lineages from Patagonia to the Atlantic Forest, but lineage sharing among resident species and local transmission cannot occur in this part of Brazil. Our study demonstrates that migratory species may harbor a higher diversity and prevalence of parasites than resident species, but transportation of some parasites by migratory hosts may not always affect local transmission.
[Systematic review and screening of basic Chinese herbs for traditional Chinese medicine compounds combined with levodopa medicine in treatment of Parkinson's disease].

To systematically evaluate the efficacy of traditional Chinese medicine(TCM) compounds combined with levodopa medicine in the treatment of Parkinson's disease(PD), and screen basic herbs to provide certain evidence-based medical proof and program for better guidance on clinical drug use. Six databases were searched to screen out the randomized controlled trial on the TCM compounds combined with levodopa medicine in the treatment of PD. Literature quality of the included studies was evaluated by improved Jadad rating scale, and the Meta-analysis was performed by RevMan 5.3 software. After the data of the basic TCM compounds involved were sorted out, the strong association rules were found by using Apriori algorithm of SPSS Modeler 18.0 software, and then the basic herbs for the treatment of PD could be picked out. A total of 20 studies were eventually included, involving 1 784 patients. Ten studies were of high-quality literature, Jadad score≥4 points. Meta-analysis showed that efficacy of TCM combined with levodopa medicine was better than levodopa medicine alone in lowering Unified Parkinson's Disease Rating Scale(UPDRS) score: UPDRS Ⅰ(MD=-0.43, 95%CI[-0.62,-0.24], P<0.000 1), UPDRS Ⅱ(MD=-2.72, 95%CI[-3.24,-2.21], P<0.000 01), UPDRS Ⅲ(MD =-1.97, 95%CI[-2.69,-1.25], P<0.000 01), UPDRS Ⅳ(MD=-0.28, 95%CI[-0.46,-0.11], P=0.002). And the improvement in UPDRS score reduction rate of TCM combined with levodopa medicine was better than that in levodopa medicine alone: effective rate(OR=4.81, 95%CI[3.50, 6.62], P<0.000 01). Data mining results showed that the basic prescription for treating PD consisted of Paeoniae Radix Alba-Rehmanniae Radix Praeparata-Gastrodiae Rhizoma in general. According to each part of UPDRS, the basic prescription for treating mentation, behavior and mood(UPDRS Ⅰ) consists of Paeoniae Radix Alba-Rehmanniae Radix Praeparata-Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle, Among which Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle might have unique efficacy. The basic prescriptions for treating UPDRS Ⅱ and UPDRS Ⅲ consisted of Paeoniae Radix Alba-Rehmanniae Radix Praeparata, or Chuanxiong Rhizoma-Angelicae Sinensis Radix(two drug combinations). However, in the treatment of UPDRS Ⅳ, the drugs were scattered. But due to the limitations in the quantity and quality of clinical studies, the results obtained still need further research and clinical confirmation of its efficacy.
Nanopore-mediated protein delivery enabling three-color single-molecule tracking in living cells

Significance Multichannel single-molecule tracking is a powerful tool to probe molecular interactions with high spatial-temporal resolution. Current methods have at least two major limitations: the lack of high-performance intracellular single-molecule fluorescence probes and the difficulty of multispecies single-molecule labelling. Here, we employ a nanopore-electroporation technique to deliver organic dye-labelled proteins into living cells to achieve multi-color single molecule tracking. These organic dyes have better optical and chemical properties than the probes currently used. Therefore, we significantly expand the selection of intracellular single-molecule probes to widely available dyes. We demonstrate the application of this technique by revealing detailed spatial resolution and dynamics of membrane EGFR signaling transductions, which will shed light on the understanding of its fundamental mechanism. Multicolor single-molecule tracking (SMT) provides a powerful tool to mechanistically probe molecular interactions in living cells. However, because of the limitations in the optical and chemical properties of currently available fluorophores and the multiprotein labeling strategies, intracellular multicolor SMT remains challenging for general research studies. Here, we introduce a practical method employing a nanopore-electroporation (NanoEP) technique to deliver multiple organic dye-labeled proteins into living cells for imaging. It can be easily expanded to three channels in commercial microscopes or be combined with other in situ labeling methods. Utilizing NanoEP, we demonstrate three-color SMT for both cytosolic and membrane proteins. Specifically, we simultaneously monitored single-molecule events downstream of EGFR signaling pathways in living cells. The results provide detailed resolution of the spatial localization and dynamics of Grb2 and SOS recruitment to activated EGFR along with the resultant Ras activation.
State and Location of Water Adsorbed on Clay Minerals: Consequences of the Hydration and Swelling-Shrinkage Phenomena

The application of the Frenkel-Halsey-Hill (FHH) formalism to the water desorption isotherms obtained for the whole range of the activity of water with the pressure membrane device (0.98 < aw < 1) and with the desiccator (0 < aw < 0.98) gives information concerning the nature and the relative importance of the 2 mechanisms involved in the dehydration—hydration processes: adsorption and capillary condensation. The state and location of water are described in each domain. An equation that gives the thickness t of the film of water adsorbed on the walls of pores versus the activity of water is developed. This t-curve is used to get, from the desorption isotherm, the pore size distribution curve of the studied hydrated materials. Then concepts of surface and fabric of clay pastes are discussed as a function of hydration and a mechanism is proposed to explain swelling and shrinkage of finely divided materials. Three kinds of surfaces, related to the aggregate fabric, are defined as a function of their capacity to adsorb water. Each kind of surface is determined by a specific technique: the total surface area (St) by ethylene glycol adsorption, the external surface area of particles (Ss) by nitrogen adsorption and the external surface area of aggregates (Se) by hydraulic conductivity measurements. As a consequence it is only with completely dispersed clays that swelling is a function of St. With unwell-dispersed clays, water adsorption, which induces swelling, successively occurs on St, Ss and Se surfaces.
Genome-Wide Identification and Characterization of Calcium-Dependent Protein Kinase (CDPK) and CDPK-Related Kinase (CRK) Gene Families in Medicago truncatula

Calcium-dependent protein kinase (CDPK or CPK) and CDPK-related kinase (CRK) play an important role in plant growth, development, and adaptation to environmental stresses. However, their gene families had been yet inadequately investigated in Medicago truncatula. In this study, six MtCRK genes were computationally identified, they were classified into five groups with MtCDPKs based on phylogenetic relationships. Six pairs of segmental duplications were observed in MtCDPK and MtCRK genes and the Ka/Ks ratio, an indicator of selection pressure, was below 0.310, indicating that these gene pairs underwent strong purifying selection. Cis-acting elements of morphogenesis, multiple hormone responses, and abiotic stresses were predicted in the promoter region. The spatial expression of MtCDPKs and MtCRKs displays diversity. The expression of MtCDPKs and MtCRKs could be regulated by various stresses. MtCDPK4, 14, 16, 22, and MtCRK6 harbor both N-myristoylation site and palmitoylation site and were anchored on plasma membrane, while MtCDPK7, 9, and 15 contain no or only one N-acylation site and were distributed in cytosol and nucleus, suggesting that the N-terminal acylation sites play a key role in subcellular localization of MtCDPKs and MtCRKs. In summary, comprehensive characterization of MtCDPKs and MtCRKs provide a subset of candidate genes for further functional analysis and genetic improvement against drought, cold, salt and biotic stress.
Obesogenic Programming Effects during Lactation: A Narrative Review and Conceptual Model Focusing on Underlying Mechanisms and Promising Future Research Avenues

Animal studies have consistently demonstrated that maternal obesity and a high-fat diet during lactation enhances obesity risk in the offspring. However, less is known about these potential obesogenic programming effects in obese humans. We propose three important pathways that may explain obesogenic programming effects of human breastmilk. First, human milk components and hormones may directly affect child eating and satiety characteristics. Second, human milk constituents can affect child microbiota that, in turn, may influence child eating and weight outcomes. Third, human milk composition may affect child eating and weight outcomes through flavor exposure. We reviewed a few very recent findings from well-powered longitudinal or experimental human research with regard to these three pathways. Moreover, we provide a research agenda for future intervention research with the overarching aim to prevent excessive pediatric weight gain during lactation and beyond. The ideas presented in this paper may represent important “black box” constructs that explain obesogenic programming effects during lactation. It should be noted, however, that given the scarcity of studies, findings should be seen as working hypotheses to further test in future research.
assessment of coronary microleakage marker capacity of three dyes

Objective: The aim of this study was to assess the marker capacity of 2% methylene blue, 2% Rhodamine B and 5% nickel sulfate. Methods: After biomechanical canal preparation in 84 single-root pre-molar teeth extracted from human beings, the access cavities were sealed with Coltosol ® and the specimens were made impermeable, except for 1 mm adjacent to the temporary sealing. The samples were immersed in the staining solutions and kept in an oven at 37 oC for 3 and 7 days, and were submitted to thermal cycling. During this period, 300 cycles (5 oC and 55 °C) of 30 seconds each were performed in a specific appliance with a digital programmer for temperature, time and number of cycles. Longitudinal sections of the specimens were obtained and observed under stereomicroscopic lens. Results: The statistical results by the Analysis of Variance showed a significant difference (p<0.05) among the groups and between the two time intervals assessed. Conclusion: There was greater leakage in the 7 day interval in all groups, and the Rhodamine B dye exhibited the higher mean leakage depth values in the two time intervals, followed by methylene blue and nickel sulfate.