bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opportunities and challenges of alpha-synuclein as a potential biomarker for Parkinson’s disease and other synucleinopathies
Authors: Magalhães Pedro , Lashuel Hilal A. 
Published: July 2022

AbstractParkinson’s disease (PD), the second most common progressive neurodegenerative disease, develops and progresses for 10–15 years before the clinical diagnostic symptoms of the disease are manifested. Furthermore, several aspects of PD pathology overlap with other neurodegenerative diseases (NDDs) linked to alpha-synuclein (aSyn) aggregation, also called synucleinopathies. Therefore, there is an urgent need to discover and validate early diagnostic and prognostic markers that reflect disease pathophysiology, progression, severity, and potential differences in disease mechanisms between PD and other NDDs. The close association between aSyn and the development of pathology in synucleinopathies, along with the identification of aSyn species in biological fluids, has led to increasing interest in aSyn species as potential biomarkers for early diagnosis of PD and differentiate it from other synucleinopathies. In this review, we (1) provide an overview of the progress toward mapping the distribution of aSyn species in the brain, peripheral tissues, and biological fluids; (2) present comparative and critical analysis of previous studies that measured total aSyn as well as other species such as modified and aggregated forms of aSyn in different biological fluids; and (3) highlight conceptual and technical gaps and challenges that could hinder the development and validation of reliable aSyn biomarkers; and (4) outline a series of recommendations to address these challenges. Finally, we propose a combined biomarker approach based on integrating biochemical, aggregation and structure features of aSyn, in addition to other biomarkers of neurodegeneration. We believe that capturing the diversity of aSyn species is essential to develop robust assays and diagnostics for early detection, patient stratification, monitoring of disease progression, and differentiation between synucleinopathies. This could transform clinical trial design and implementation, accelerate the development of new therapies, and improve clinical decisions and treatment strategies.
Experimental and numerical study of steady state stability in a toluene biodegrading biofilter
Authors: Süß Michael , De Visscher Alex 
Published: July 2022

AbstractDifferent steady states in a toluene biodegrading biofilter were explored experimentally and numerically. Experimental results showed that a gradual increase of the toluene inlet concentration over several weeks leads to a consistently low exit concentration, with a drastic increase at an inlet concentration change from 7.7 to 8.5 g m−3, indicating an alteration in steady state. A significant and sudden drop in the removal efficiency from 88 to 46% was observed. A model that includes nitrogen and biomass dynamics predicted results matching the experimental biofilter performance well, but the timing of the concentration jump was not reproduced exactly. A model that assumes a gradual increase of toluene inlet concentration of 0.272 g m−3 per day, accurately reproduced the experimental relationship between inlet and outlet concentration. Although there was variation between experimental and simulated results, a clear confirmation of the jump from one steady state to another was found.
A global equation-of-state model from mathematical interpolation between low- and high-density limits
Authors: Xue Ti-Wei , Guo Zeng-Yuan 
Published: July 2022

AbstractThe ideal gas equation of state (EOS) model is a well-known low-density limiting model. Recently, an ideal dense matter EOS model for the high-density limit symmetric to the ideal gas model has been developed. Here, by mathematically interpolating between the ideal gas and ideal dense matter limiting models, we establish a global model containing two EOS in the form of P-V-T and P-S-T for arbitrary ranges of densities. Different from empirical or semi-empirical EOS, the coefficients in the global EOS have a clear physical meaning and can be determined from a priori knowledge. The proposed global model is thermodynamically consistent and continuous. It reduces to the ideal gas model when approaching the low-density limit and to the ideal dense matter model when approaching the high-density limit. Verifications for 4He show that the global model reproduces the large-range behavior of matter well, along with providing important insight into the nature of the large-range behavior. Compared to the third-order virial EOS and the Benedict–Webb–Rubin EOS, the global P-V-T EOS has higher descriptive accuracy with fewer coefficients over a wide range of data for N2. The global model is shown to work well in extreme applied sciences. It predicts a linear, inverse relationship between entropy and volume when the temperature-to-pressure ratio is constant, which can explain the entropy-production behavior in shock-Hugoniots.
Standardization and quantitative analysis of Araucaria Heterophylla extract via an UPLC-MS/MS method and its formulation as an antibacterial phytonanoemulsion gel
Authors: Younis Nermin A. , Hemdan A. , Zafer Mai M. , Abd-Elsalam Wessam H. , Abouelatta Samar M. 
Published: July 2022

AbstractSkin infections are among the bacterial infections that present significant therapeutic challenges due to antibiotic resistance. Recently, herbal products clutched a significant attention as safe replacements for other medications but their low aqueous solubility and poor bioavailability are considered major challenges which could be circumvented via formulation. As a species of genera Araucaria, Araucaria Heterophylla possesses pharmacological activities such as antioxidant and antibacterial actions, and this study aimed to standardize the extract of the plant against 4ʹʹʹmethoxyamentoflavone (as a main component of the extract) through a validated UPLC-MS/MS method and evaluate its antibacterial activity, which was followed by loading the standardized extract into a nanoemulsion to form a phytonanoemulsion (PNE), where the design analysis and optimization were performed through a simplex lattice design. The optimized PNE (PNE 3) was then loaded into HPMC/Pluronic F-127 gel (in ratio 1:4) to sustain the release of the active constituent. The heightened penetrability of PNE 3 gel was visualized via confocal laser scanning microscopy, and its prolonged effect was proved thru an in vivo study conducted on male Wistar rats. A histopathological study revealed the safety of the formulation when applied topically. Thus, PNE gel could be a potentially broad-spectrum antibacterial drug delivery system.
Evaluation of foliar application of selenium and flowering stages on selected properties of Iranian Borage as a medicinal plant
Authors: Hosseinzadeh Rostam Kalaei Mazaher , Abdossi Vahid , Danaee Elham 
Published: July 2022

AbstractMany of the active constituents of drug or medicines were originally derived from medicinal plants. Iranian Borage are still being used in regular basis. Selenium (Se) is an essential mineral nutrient for animal and human growth. The aim of this research was to determine the effect of (2, 4, 8 and 16 mg L−1) of as sodium selenate (Na2SeO4) and as sodium selenite (Na2SeO3) on some important properties of Iranian Borage in factorial based on Randomized Complete Block Design via four steps: 2 true leaves stage, ten leaves, 2 weeks and 1 week before flowering. The traits were evaluated during flowering period. Results showed that the highest shoot fresh and dry weight and shoot length, total alkaloid, essential oil percentage were obtained by 4 mg L−1 sodium selenate at the end of flowering. In addition, 4 mg L−1 sodium selenate concentration significantly improved flower yield (diameter, number, weight). The plants were treated with 8 mg L−1 sodium selenate, the higher total phenols and flavonoids, antioxidant activity, soluble sugars, root and fresh weight was seen at end of flowering. When the plants were sprayed with 4 mg L−1 sodium selenite higher total chlorophyll was observed at full of flowering. 16 mg L−1 sodium selenite released the maximum Se acclimation in the petals. 20 composites were discovered containing ɑ-Pinene (23.61%) with sodium selenate in 4 mg L−1. Generally, selenium sources significantly improved morpho-physiological and phytochemical.
Minimising multi-centre radiomics variability through image normalisation: a pilot study
Authors: Campello Víctor M. , Martín-Isla Carlos , Izquierdo Cristian , Guala Andrea , Palomares José F. Rodríguez , Viladés David , Descalzo Martín L. , Karakas Mahir , Çavuş Ersin , Raisi-Estabragh Zahra , Petersen Steffen E. , Escalera Sergio , Seguí Santi , Lekadir Karim 
Published: July 2022

AbstractRadiomics is an emerging technique for the quantification of imaging data that has recently shown great promise for deeper phenotyping of cardiovascular disease. Thus far, the technique has been mostly applied in single-centre studies. However, one of the main difficulties in multi-centre imaging studies is the inherent variability of image characteristics due to centre differences. In this paper, a comprehensive analysis of radiomics variability under several image- and feature-based normalisation techniques was conducted using a multi-centre cardiovascular magnetic resonance dataset. 218 subjects divided into healthy (n = 112) and hypertrophic cardiomyopathy (n = 106, HCM) groups from five different centres were considered. First and second order texture radiomic features were extracted from three regions of interest, namely the left and right ventricular cavities and the left ventricular myocardium. Two methods were used to assess features’ variability. First, feature distributions were compared across centres to obtain a distribution similarity index. Second, two classification tasks were proposed to assess: (1) the amount of centre-related information encoded in normalised features (centre identification) and (2) the generalisation ability for a classification model when trained on these features (healthy versus HCM classification). The results showed that the feature-based harmonisation technique ComBat is able to remove the variability introduced by centre information from radiomic features, at the expense of slightly degrading classification performance. Piecewise linear histogram matching normalisation gave features with greater generalisation ability for classification ( balanced accuracy in between 0.78 ± 0.08 and 0.79 ± 0.09). Models trained with features from images without normalisation showed the worst performance overall ( balanced accuracy in between 0.45 ± 0.28 and 0.60 ± 0.22). In conclusion, centre-related information removal did not imply good generalisation ability for classification.
Root exudate composition reflects drought severity gradient in blue grama (Bouteloua gracilis)
Authors: Ulrich Danielle E. M. , Clendinen Chaevien S. , Alongi Franklin , Mueller Rebecca C. , Chu Rosalie K. , Toyoda Jason , Gallegos-Graves La Verne , Goemann Hannah M. , Peyton Brent , Sevanto Sanna , Dunbar John 
Published: July 2022

AbstractPlant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (Bouteloua gracilisKunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.
Glutathione improves low temperature stress tolerance in pusa sheetal cultivar of Solanum lycopersicum
Authors: Gul Nadia , Ahmad Parvaiz , Wani Tanveer A. , Tyagi Anshika , Aslam Saima 
Published: July 2022

AbstractTo investigate the impact of Glutathione (GSH) in mitigating low-temperature stress in Pusa Sheetal cv. of Solanum lycopersicum and imparting low-temperature tolerance by evaluating the different physiological responses. The plant under research was also being studied for its growth and stress tolerance. Low temperatures (LT) stress was applied to seedlings with or without GSH application 12 h before LT stress (prophylactic dose), after 12 h-LT (preemptive dose), and post 12-h recovery (curative dose). Different concentrations of GSH [0, G1 (0.5 mM), G2 (1 mM) and G3 (2 mM)] against LT stress were used. Antioxidant activities, photosynthesis, growth, and stress tolerance indices were quantified. LT stress caused an oxidative burst in S. lycopersicum seedlings of the Pusa Sheetal cv. as indicated by increased peroxidation of lipids and H2O2 concentration. Glutathione reductase (GR), superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) activities were enhanced. The best concentration was G2 (1 mM), which resulted in a rise in antioxidant activity. Moreover, a decline in lipid peroxidation and H2O2 levels was also seen. The purpose of this study is to identify the role of GSH in reducing LT stress and to find the best dose concentration. This is the first report to assess the GSH-mediated LT stress tolerance in S. lycopersicum (Pusa Sheetal cv.). Therefore, exogenous GSH application of optimal concentration of GSH to LT stressed S. lycopersicum can be an effective approach for augmenting the plant detoxification system and promoting its growth and development.
Thermodynamic basis for the demarcation of Arctic and alpine treelines
Authors: Martin Meredith Richardson , Kumar Praveen , Sonnentag Oliver , Marsh Philip 
Published: July 2022

AbstractAt the edge of alpine and Arctic ecosystems all over the world, a transition zone exists beyond which it is either infeasible or unfavorable for trees to exist, colloquially identified as the treeline. We explore the possibility of a thermodynamic basis behind this demarcation in vegetation by considering ecosystems as open systems driven by thermodynamic advantage—defined by vegetation’s ability to dissipate heat from the earth’s surface to the air above the canopy. To deduce whether forests would be more thermodynamically advantageous than existing ecosystems beyond treelines, we construct and examine counterfactual scenarios in which trees exist beyond a treeline instead of the existing alpine meadow or Arctic tundra. Meteorological data from the Italian Alps, United States Rocky Mountains, and Western Canadian Taiga-Tundra are used as forcing for model computation of ecosystem work and temperature gradients at sites on both sides of each treeline with and without trees. Model results indicate that the alpine sites do not support trees beyond the treeline, as their presence would result in excessive CO$$_2$$

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loss and extended periods of snowpack due to temperature inversions (i.e., positive temperature gradient from the earth surface to the atmosphere). Further, both Arctic and alpine sites exhibit negative work resulting in positive feedback between vegetation heat dissipation and temperature gradient, thereby extending the duration of temperature inversions. These conditions demonstrate thermodynamic infeasibility associated with the counterfactual scenario of trees existing beyond a treeline. Thus, we conclude that, in addition to resource constraints, a treeline is an outcome of an ecosystem’s ability to self-organize towards the most advantageous vegetation structure facilitated by thermodynamic feasibility.
Structure-based prediction of BRAF mutation classes using machine-learning approaches
Authors: Krebs Fanny S. , Britschgi Christian , Pradervand Sylvain , Achermann Rita , Tsantoulis Petros , Haefliger Simon , Wicki Andreas , Michielin Olivier , Zoete Vincent 
Published: July 2022

AbstractThe BRAF kinase is attracting a lot of attention in oncology as alterations of its amino acid sequence can constitutively activate the MAP kinase signaling pathway, potentially contributing to the malignant transformation of the cell but at the same time rendering it sensitive to targeted therapy. Several pathologic BRAF variants were grouped in three different classes (I, II and III) based on their effects on the protein activity and pathway. Discerning the class of a BRAF mutation permits to adapt the treatment proposed to the patient. However, this information is lacking new and experimentally uncharacterized BRAF mutations detected in a patient biopsy. To overcome this issue, we developed a new in silico tool based on machine learning approaches to predict the potential class of a BRAF missense variant. As class I only involves missense mutations of Val600, we focused on the mutations of classes II and III, which are more diverse and challenging to predict. Using a logistic regression model and features including structural information, we were able to predict the classes of known mutations with an accuracy of 90%. This new and fast predictive tool will help oncologists to tackle potential pathogenic BRAF mutations and to propose the most appropriate treatment for their patients.
Detection of NO3− introduced in plasma-irradiated dry lettuce seeds using liquid chromatography-electrospray ionization quantum mass spectrometry (LC-ESI QMS)
Authors: Okumura Takamasa , Attri Pankaj , Kamataki Kunihiro , Yamashita Naoto , Tsukada Yuichi , Itagaki Naho , Shiratani Masaharu , Ishibashi Yushi , Kuchitsu Kazuyuki , Koga Kazunori 
Published: July 2022

AbstractDischarge plasma irradiates seeds with reactive oxygen and nitrogen species (RONS). However, RONS introduced in seeds by plasma irradiation have not been successfully detected thus far. This study provides experimental evidence that nitrate ion NO3− is introduced in lettuce seeds as RONS upon irradiation with atmospheric-pressure air dielectric barrier discharge plasma. Plasma irradiation for 5 min promotes seed germination. The components of the plasma-irradiated seeds were examined using electrospray ionization quantum mass spectrometry (ESI QMS), which revealed that the plasma irradiation introduced an ion with a mass of 62 m/z in detectable amounts. This ion was identified as NO3− by liquid chromatography (LC), multiple wavelength detector (MWD), and LC-ESI QMS. A one-dimensional simulation at electron temperature Te = 1 eV, electron density Ne = 1013/m3, and gas temperature Tg = 300 K indicated the introduction of NO3−, involving nitric oxide NO. NO3− is one of the most important ions that trigger signal transduction for germination when introduced in seeds. The scanning electron microscopy (SEM) images revealed that there was no change on the surface of the seeds after plasma irradiation. Plasma irradiation is an effective method of introducing NO3− in seeds in a dry process without causing damage.
Coronamoeba villafranca gen. nov. sp. nov. (Amoebozoa, Dermamoebida) challenges the correlation of morphology and phylogeny in Amoebozoa
Authors: Kudryavtsev Alexander , Voytinsky Fyodor , Volkova Ekaterina 
Published: July 2022

AbstractCoronamoeba villafranca gen. nov. sp. nov. is a small amoeba isolated from the surface planktonic biotope in the Bay of Villefranche (Mediterranean Sea). It has a confusing set of morphological and molecular characters. Its locomotive form is subcylindrical and monopodial with monoaxial cytoplasmic flow and occasional hyaline bulging at the anterior edge (a monotactic morphotype). Based on this set of characters, this amoeba is most similar to members of the genus Nolandella (Tubulinea, Euamoebida). However, molecular phylogenetic analysis based on only the small subunit ribosomal RNA (SSU rRNA) gene and on two concatenated markers (SSU rRNA gene and actin) robustly places this species in the Discosea, specifically, in a clade with Dermamoeba and Paradermamoeba (Dermamoebida) as the closest described relatives, and several SSU rRNA clones from environmental DNA. A unique glycocalyx of the studied amoeba consisting of complex separate units with pentameric symmetry may be considered a unifying character of this species with other dermamoebids. The monotactic morphotype demonstrated by these amoebae primarily occurs in Tubulinea but was recently confirmed in other clades of Amoebozoa (e.g. Dactylopodida and Variosea). This morphotype may be the plesiomorphic mode of cell organization in Amoebozoa that might have evolved in the last amoebozoan common ancestor (LACA) and conserved in several lineages of this group. It may reflect basic characteristics of the cytoskeletal structure and functions in Amoebozoa.
Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes
Authors: Schroeder Lauren , Elton Sarah , Ackermann Rebecca Rogers 
Published: July 2022

AbstractAfro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.