Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving in vivo human cerebral cortical surface reconstruction using data-driven super-resolution.

Accurate and automated reconstruction of the in vivo human cerebral cortical surface from anatomical magnetic resonance (MR) images facilitates the quantitative analysis of cortical structure. Anatomical MR images with sub-millimeter isotropic spatial resolution improve the accuracy of cortical surface and thickness estimation compared to the standard 1-millimeter isotropic resolution. Nonetheless, sub-millimeter resolution acquisitions require averaging multiple repetitions to achieve sufficient signal-to-noise ratio and are therefore long and potentially vulnerable to subject motion. We address this challenge by synthesizing sub-millimeter resolution images from standard 1-millimeter isotropic resolution images using a data-driven supervised machine learning-based super-resolution approach achieved via a deep convolutional neural network. We systematically characterize our approach using a large-scale simulated dataset and demonstrate its efficacy in empirical data. The super-resolution data provide improved cortical surfaces similar to those obtained from native sub-millimeter resolution data. The whole-brain mean absolute discrepancy in cortical surface positioning and thickness estimation is below 100 μm at the single-subject level and below 50 μm at the group level for the simulated data, and below 200 μm at the single-subject level and below 100 μm at the group level for the empirical data, making the accuracy of cortical surfaces derived from super-resolution sufficient for most applications.
Get Vigorous with Physical Exercise and Improve Your Well-Being at Work!

The aim of this study is to investigate whether people who exercise regularly have higher levels of psychological well-being at work. Doing physical exercise is a habit that not only has consequences for physical and mental health, but it can also have positive consequences for organizations because physical exercise makes it easier for the employee to recover from physical, mental, and emotional effort during the workday, thus showing higher levels of engagement the next day. Through the analysis of structural equation models in a sample of 485 workers from different Spanish and Latin American companies, this study shows that subjects who exercise more have higher levels of vigor in physical exercise, which is positively related to high levels of well-being at work. This means that organizations that promote activities related to physical exercise among their employees are building a process of resource recovery, which, through the vigor of these activities, makes workers feel less stressed and more satisfied, thus experiencing greater well-being at work. Therefore, at a practical level, these results suggest that the practice of physical exercise is a tool for organizations that want to promote their employees’ psychological well-being.
Proteomics identifies EGF‐like domain multiple 7 as a potential therapeutic target for epidermal growth factor receptor‐positive glioma

Glioma, the most frequent primary tumor of the central nervous system, has poor prognosis. The epidermal growth factor receptor (EGFR) pathway and angiogenesis play important roles in glioma growth, invasion, and recurrence. The present study aimed to use proteomic methods to probe into the role of the EGF‐EGFR‐angiogenesis axis in the tumorigenesis of glioma and access the therapeutic efficacy of selumetinib on glioma.
Rationally Attenuated Vaccines for Venezuelan Equine Encephalitis Protect Against Epidemic Strains with a Single Dose

Venezuelan equine encephalitis virus (VEEV) is a re-emerging virus of human, agriculture, and bioweapon threat importance. No FDA-approved treatment is available to combat Venezuelan equine encephalitis in humans, prompting the need to create a vaccine that is safe, efficacious, and cannot be replicated in the mosquito vector. Here we describe the use of a serotype ID VEEV (ZPC-738) vaccine with an internal ribosome entry site (IRES) to alter gene expression patterns. This ZPC/IRES vaccine was genetically engineered in two ways based on the position of the IRES insertion to create a vaccine that is safe and efficacious. After a single dose, both versions of the ZPC/IRES vaccine elicited neutralizing antibody responses in mice and non-human primates after a single dose, with more robust responses produced by version 2. Further, all mice and primates were protected from viremia following VEEV challenge. These vaccines were also safer in neonatal mice than the current investigational new drug vaccine, TC-83. These results show that IRES-based attenuation of alphavirus genomes consistently produce promising vaccine candidates, with VEEV/IRES version 2 showing promise for further development.
Improved Light Conditions at the Fruit Truss Accelerate Harvest Time and Enhance Ascorbic Acid Concentration in a Low-truss, High-density Tomato Production System

Light conditions are poor around the lower trusses of tomato plants in a low truss number, high plant density production system. We determined the effects of leaf rearrangements above the fruit trusses on fruit maturation and quality in tomato plants pinched above the third truss and cultivated under a high-density growing system. Integrated solar radiation at first and second fruit trusses and surface temperature of fruits at second fruit truss were increased in plants treated with leaf rearrangements above the trusses compared with those of the control, and the maturation of fruits at the third truss treated with leaf rearrangement was 4.6 days earlier than that of the control. The concentration of ascorbic acid (AsA) in fruits of plants treated with leaf rearrangement was higher than that of control fruits. However, leaf rearrangement had no effect on yield and Brix of the fruit. These results indicated that higher solar radiation together with leaf rearrangement promoted fruit maturation and increased AsA content in the fruit of lower trusses of tomato plants cultivated under a low truss number, high plant density growing system.
Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.
Landscape-Scale CO 2 , H 2 O Vapour and Energy Flux of Moist-Wet Coastal Tundra Ecosystems over Two Growing Seasons

1 Eddy covariance was used to measure landscape-scale fluxes of C02, H20 vapour and energy in moist-wet sedge tundra ecosystems of coastal arctic Alaska. 2 Net radiation (Rn) was partitioned equally into sensible (H) and latent heat (Le), although a larger proportion of Rn was partitioned into Le during and after the early season snow-melt period, while proportionally more Rn was partitioned into H as the season progressed. Ground heat flux (G) comprised an average of 15% of Rn throughout the growing season. 3 Interannual variation in evapotranspiration (ET) was negligible despite a 30% increase in total precipitation in 1995. On average, seasonal estimates of ET were 120 mm (1 3 mm day-'), which are similar to estimates found in the literature. 4 Net CO2 influx generally peaked during the mid-day period when photosynthetic photon flux density (PPFD) was at a diurnal maximum, while peak net efflux occurred between 23.00 and 02.00 hours when PPFD was at a diurnal minimum. Most of the variation in diurnal net CO2 exchange was explained by diurnal variations in PPFD, with the functional response best described as a rectangular hyperbola. 5 The coastal tundra landscapes were net sources of 0 02-0 05 mol m-2 day-' during the early season snow-melt period. During the mid-season peak in productivity, which occurred as early as 10 July in 1994 and as late as 10 August in 1995, these landscapes were net sinks of on average 0 09 mol m-2 day-'. Sink strength decreased considerably after the mid-season peak in productivity, presumably because of reductions in PPFD, an increase in water table depth, relatively high temperatures, and a decline in leaf area. 6 Over both growing seasons, the coastal tundra landscapes were sinks of 1-7 mol m-2. This is comparable with the 'long-term' estimate of net CO2 exchange calculated from the literature.
Use of photoacoustic imaging for monitoring vascular disrupting cancer treatments

Vascular disrupting agents disrupt tumor vessels, blocking the nutritional and oxygen supply tumors need to thrive. This is achieved by damaging the endothelium lining of blood vessels, resulting in red blood cells (RBCs) entering the tumor parenchyma. RBCs present in the extracellular matrix are exposed to external stressors resulting in biochemical and physiological changes. The detection of these changes can be used to monitor the efficacy of cancer treatments. Spectroscopic photoacoustic (PA) imaging is an ideal candidate for probing RBCs due to their high optical absorption relative to surrounding tissue. The goal of this work is to use PA imaging to monitor the efficacy of the vascular disrupting agent 5,6‐Dimethylxanthenone‐4‐acetic acid (DMXAA) through quantitative analysis. Then, 4T1 breast cancer cells were injected subcutaneously into the left hind leg of eight BALB/c mice. After 10 days, half of the mice were treated with 15 mg/kg of DMXAA and the other half were injected with saline. All mice were imaged using the VevoLAZR X PA system before treatment, 24 and 72 hours after treatment. The imaging was done at six wavelengths and linear spectral unmixing was applied to the PA images to quantify three forms of hemoglobin (oxy, deoxy and met‐hemoglobin). After imaging, tumors were histologically processed and H&E and TUNEL staining were used to detect the tissue damage induced by the DMXAA treatment. The total hemoglobin concentration remained unchanged after treatment for the saline treated mice. For DMXAA treated mice, a 10% increase of deoxyhemoglobin concentration was detected 24 hours after treatment and a 22.6% decrease in total hemoglobin concentration was observed by 72 hours. A decrease in the PA spectral slope parameters was measured 24 hours after treatment. This suggests that DMXAA induces vascular damage, causing red blood cells to extravasate. Furthermore, H&E staining of the tumor showed areas of bleeding with erythrocyte deposition. These observations are further supported by the increase in TUNEL staining in DMXAA treated tumors, revealing increased cell death due to vascular disruption. This study demonstrates the capability of PA imaging to monitor tumor vessel disruption by the vascular disrupting agent DMXAA.
A Missense Variant in ALDH5A1 Associated with Canine Succinic Semialdehyde Dehydrogenase Deficiency (SSADHD) in the Saluki Dog

Dogs provide highly valuable models of human disease due to the similarity in phenotype presentation and the ease of genetic analysis. Seven Saluki puppies were investigated for neurological abnormalities including seizures and altered behavior. Magnetic resonance imaging showed a diffuse, marked reduction in cerebral cortical thickness, and symmetrical T2 hyperintensity in specific brain regions. Cerebral cortical atrophy with vacuolation (status spongiosus) was noted on necropsy. Genome-wide association study of 7 affected and 28 normal Salukis revealed a genome-wide significantly associated region on CFA 35. Whole-genome sequencing of three confirmed cases from three different litters revealed a homozygous missense variant within the aldehyde dehydrogenase 5 family member A1 (ALDH5A1) gene (XM_014110599.2: c.866G>A; XP_013966074.2: p.(Gly288Asp). ALDH5A1 encodes a succinic semialdehyde dehydrogenase (SSADH) enzyme critical in the gamma-aminobutyric acid neurotransmitter (GABA) metabolic pathway. Metabolic screening of affected dogs showed markedly elevated gamma-hydroxybutyric acid in serum, cerebrospinal fluid (CSF) and brain, and elevated succinate semialdehyde in urine, CSF and brain. SSADH activity in the brain of affected dogs was low. Affected Saluki dogs had striking similarities to SSADH deficiency in humans although hydroxybutyric aciduria was absent in affected dogs. ALDH5A1-related SSADH deficiency in Salukis provides a unique translational large animal model for the development of novel therapeutic strategies.
Enzymatic properties of hepatitis C virus NS3 serine protease and bio-engineering of serine protease inhibitors (serpins) against the NS3 protease and elastase

Hepatitis C virus (HCV) has infected millions of people worldwide and emerged as a global health crisis. H C V NS3 serine protease domain (aa:1027-1218) of the H C V polyprotein, is required for the processing and maturation of the H C V viral non-structural (NS) proteins. As an essential protease for viral replication, H C V NS3 protease has been considered as a strategic target for anti-HCV drug development. This thesis investigates the designs and inhibitory properties of novel serine protease inhibitor (serpin) variants against the H C V NS3 protease. First, the substrate specificity of NS3 protease is evaluated for the purpose of generating protein-based inhibitors to target it. Data from kinetic experiments suggested that NS3 protease activity is greatly enhanced with the addition of its NS4A cofactor and that the three key residues in the substrate necessary for efficient recognition and cleavage by NS3 protease are cysteine in PI , serine/alanine in P ' l and aspartic/glutamic acids in P6 position. This information was used to bio-engineer 5 (serpins) variants based on ai-Antitrypsin (ai-AT) scaffold. Variants of a i -AT contained different mutations in the serpin Reactive Site Loop (RSL) involving the PI , P4, P6 & P ' l positions. The biological activities and the newly gained specificities of the a i -AT and its variants were tested mainly by performing SDS-stable complex formation studies and enzyme kinetic experiments directed against NS3 protease and elastase. Results show that NS3 protease was able to form a 72 kDa SDS-stable complex with a i -AT and 4 of its variants. Taken together, the ability of a i -AT and its variants to interact and form SDS-stable complexes with NS3 protease may represent an entry point for a novel class of protein-based H C V NS3 protease inhibitors.
Measuring liquidity in Indian stock market: A dimensional perspective

Market liquidity ensures the marketability of security and is an indispensable feature of stock markets. Previous studies have emphasized the role of stock market liquidity in empirical finance. However, they have inadequately explored its multidimensional nature. This study eliminates the ambiguities related to market liquidity by precisely measuring it by using popular and proven liquidity measures. As such, the present study aims to evaluate market liquidity in terms of depth, breadth, tightness, and immediacy in the Indian equity market and also identifies crucial interdependencies between liquidity dimensions. The study selects 500 stocks constituting the NIFTY 500 index of the National Stock Exchange, India, as of 26th May 2019. The data on trading volume, bid price, ask price, the number of shares outstanding, closing share prices were retrieved for the period from 1st April 2009 to 31st March 2019. The study employs Share Turnover, Amihud Illiquidity Ratio, Relative Quoted Spreads, and Coefficient of Elasticity of Trading for liquidity measurement. The Vector Auto-Regressive (VAR) model is used to establish the simultaneous relationships between liquidity dimensions. The analysis is conducted at the aggregate market level as well as across turnover based stock groups divided based on their rankings in terms of stock specific share turnover. The empirical results evidenced the presence of consistent depth, strong breadth, and immediacy but lower tightness in the Indian equity market. The market depth and tightness appear to be relevant in determining dimensional interdependencies. Also, less frequently traded stocks exhibit higher illiquidity in the wake of lower tightness. The findings of this study will assist the investors to wisely understand the multifaceted nature of market liquidity and base their trading decisions accordingly. Moreover, the regulators of the stock exchange can devise liquidity enhancing policies based on the directional movements among liquidity dimensions.
Repositioning Natural Antioxidants for Therapeutic Applications in Tissue Engineering

Although a large panel of natural antioxidants demonstrate a protective effect in preventing cellular oxidative stress, their low bioavailability limits therapeutic activity at the targeted injury site. The importance to deliver drug or cells into oxidative microenvironments can be realized with the development of biocompatible redox-modulating materials. The incorporation of antioxidant compounds within implanted biomaterials should be able to retain the antioxidant activity, while also allowing graft survival and tissue recovery. This review summarizes the recent literature reporting the combined role of natural antioxidants with biomaterials. Our review highlights how such functionalization is a promising strategy in tissue engineering to improve the engraftment and promote tissue healing or regeneration.
Antimicrobial and Amyloidogenic Activity of Peptides Synthesized on the Basis of the Ribosomal S1 Protein from Thermus Thermophilus

Controlling the aggregation of vital bacterial proteins could be one of the new research directions and form the basis for the search and development of antibacterial drugs with targeted action. Such approach may be considered as an alternative one to antibiotics. Amyloidogenic regions can, like antibacterial peptides, interact with the “parent” protein, for example, ribosomal S1 protein (specific only for bacteria), and interfere with its functioning. The aim of the work was to search for peptides based on the ribosomal S1 protein from T. thermophilus, exhibiting both aggregation and antibacterial properties. The biological system of the response of Gram-negative bacteria T. thermophilus to the action of peptides was characterized. Among the seven studied peptides, designed based on the S1 protein sequence, the R23I (modified by the addition of HIV transcription factor fragment for bacterial cell penetration), R23T (modified), and V10I (unmodified) peptides have biological activity that inhibits the growth of T. thermophilus cells, that is, they have antimicrobial activity. But, only the R23I peptide had the most pronounced activity comparable with the commercial antibiotics. We have compared the proteome of peptide-treated and intact T. thermophilus cells. These important data indicate a decrease in the level of energy metabolism and anabolic processes, including the processes of biosynthesis of proteins and nucleic acids. Under the action of 20 and 50 μg/mL R23I, a decrease in the number of proteins in T. thermophilus cells was observed and S1 ribosomal protein was absent. The obtained results are important for understanding the mechanism of amyloidogenic peptides with antimicrobial activity and can be used to develop new and improved analogues.
Hungarian Roma and musical talent: Minority group members' experiences of an apparently positive stereotype.

Minorities do not always welcome apparently positive stereotypes of their group. At first sight, this may appear churlish. However, we show that minority group members' theorizing on the production and operation of apparently positive stereotypes helps explain such a negative reaction. Reporting interview data (N = 30) gathered with Hungarian Roma, we differentiated several bases for a negative response to the popular stereotype of Roma as possessing a distinctive musical talent. Although participants recognized the stereotype had instrumental value in easing everyday intergroup encounters, they also reported that the stereotype reflected the majority group's power to define Roma identity; constrained recognition of qualities that they themselves valued; limited their abilities to act on terms that were their own; and could facilitate the reproduction of more negative Roma stereotypes. Taken together, these findings imply our participants saw this apparently positive stereotype as speaking volumes about the majority's power to define Roma identity without reference to how they themselves defined their identity. We conclude with a discussion of the analytic value of the concept of 'misrecognition' in explaining negative responses to a positive stereotype. We also discuss the potential for such an apparently positive stereotype to facilitate improvements in intergroup relations.
Quantifying the causal pathways contributing to natural selection

The consequences of natural selection can be understood from a purely statistical perspective. In contrast, an explicitly causal approach is required to understand why trait values covary with fitness. In particular, key evolutionary constructs, such as sexual selection, fecundity selection, and so on, are best understood as selection via particular fitness components. To formalize and operationalize these concepts, we must disentangle the various causal pathways contributing to selection. Such decompositions are currently only known for linear models, where they are sometimes referred to as “Wright's rules. ” Here, we provide a general framework, based on path analysis, for partitioning selection among its contributing causal pathways. We show how the extended selection gradient—which represents selection arising from a trait's causal effects on fitness—can be decomposed into path‐specific selection gradients, which correspond to distinct causal mechanisms of selection. This framework allows for nonlinear effects and nonadditive interactions among variables, which may be estimated using standard statistical methods (e.g., generalized linear [mixed] models or generalized additive models). We thus provide a generalization of Wright's path rules that accommodates the nonlinear and nonadditive mechanisms by which natural selection commonly arises.