Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Potential of High-Voltage Electric Field Cold Plasma (HVCP) Using a Dielectric Barrier Discharge (DBD) as a Plasma Source on the Quality Parameters of Carrot Juice

The main aim of the current investigation was to contemplate the impact of high-voltage electric field cold plasma (HVCP) on different quality characteristics (enzymes, microbial activities, coloring pigments, ascorbic acid, polyphenolic compounds, °Brix, acidity, and color index) of carrot juice in correlation with thermal processing. A carrot juice (250 mL) sample sealed in pre-sterilized food-grade bottles, which placed between two dielectric quartz plates for HVCP treatment. The gap between the plates was 30 mm, and a stable and uniform plasma dielectric barrier discharge (DBD) generated for 3 and 4 min at 60, 70, and 80 kV. Air was used as a working gas during the DBD-based plasma treatment. The observed rise in temperature was 2–5 °C during the HVCP treatment. A water bath was used to carry out thermal treatment (100 °C for 5 min). The maximum inactivation of enzymes and microorganisms was achieved with thermal treatment and then with HVCP treatment at 70 kV for 4 min. However, maximum retention of coloring compounds, ascorbic acid, total phenols, flavonoids, and tannins was found following HVCP (70 kV for 4 min) treatment compared to thermal treatment. The °Brix, pH, and acidity remained unchanged irrespective of treatments. These findings suggest that HVCP treatment at 70 kV for 4 min may be a good alternative to thermal treatment, and it may successfully be applied in carrot juice production, resulting in reduced enzymes, lower microbial activity, and improved bioactive compounds. The prospects of overcoming the existing conventional physical and chemical methods for sterilization make it a novel and more economical technique to maintain food’s natural nourishment, composition, appearance, structure, and freshness.
The Berezinskii-Kosterlitz-Thouless transition of mobile Hamiltonian polar particles

The phase of matter is the state of a system in a region on a macroscopic scale. At this macroscopic scale, in equilibrium, physical properties of the system are homogeneous. Statistical physics tries to explain the homogeneity and the associated properties from microscopic interactions and by laws of nature. On a macroscopic scale, the systems to investigate are many-body systems like gases, liquids or solids. They are characterized by thermodynamic functions like the free energy. Order parameters, like for example the magnetization in magnetic systems, play a special role here. Most of the time they are associated with a breaking of symmetry when transitioning from one phase to another. This however is not a universal observation. One example for which this is not the case is the Berezinskii-Kosterlitz-Thouless phase transition (KT-transition). This particular transition can be studied in two-dimensional XY-models, where there is a phase transition without the breaking of continuous symmetries. First theoretical descriptions trace back to the works of Berezinskii [Ber71], as well as Kosterlitz and Thouless [Kos73, Kos74, Kos16]. They initially investigated a system of classical spins fixed on the nodes of a square lattice. Consequently, only the rotational degree of freedom remains. In this work we start with the model of [LB16] who introduces a coupling of spins to velocities of mobile particles. After a numerical analysis of different integration methods for the equations of motion and investigations of this system, we remove the coupling. By that, we mimic an XYmodel with additional translational degrees of freedom. For this system we examine the system with respect to the occurrence of the KT-transition by computer simulations. We apply several general tools for the analysis of magnetic systems. Subsequently we look into topological defects in the system, namely vortices and anti-vortices. For temperatures lower than the transition temperature T < TKT , defects are closely bound together, while for temperatures T > TKT they can proliferate in the system and can be treated like a gas of unbound defects. Moreover, we investigate spatial and temporal spin-correlations to estimate the critical exponent in the system, as well as the critical temperature. For a reference we first simulate an XY-model on a trigonal lattice as a comparison for our results in the mobile model. In both systems we do find the KT-transition by the occurrence of unbound topological defects and from the critical exponents we calculate from the spin-correlation functions.
Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling

Stimulation of PC-12 cells with epidermal (EGF) versus nerve (NGF) growth factors (GFs) biases the distribution between transient and sustained single-cell ERK activity states, and between proliferation and differentiation fates within a cell population. We report that fibroblast GF (FGF2) evokes a distinct behavior that consists of a gradually changing population distribution of transient/sustained ERK signaling states in response to increasing inputs in a dose response. Temporally-controlled GF perturbations of MAPK signaling dynamics applied using microfluidics reveals that this wider mix of ERK states emerges through the combination of an intracellular feedback, and competition of FGF2 binding to FGF receptors (FGFR) and heparan-sulfate proteoglycans (HSPGs) co-receptors. We show that the latter experimental modality is instructive for model selection using a Bayesian parameter inference. Our results provide novel insights into how different receptor tyrosine kinase (RTK) systems differentially wire the MAPK network to fine tune fate decisions at the cell population-level. Microfluidics, Erk Signaling Dynamics, Mechanistic Modelling, Parameter Estimation, Cell Fate Determination
Tractable calculation of the Green’s tensor for shear wave propagation in an incompressible, transversely isotropic material

Assessing material properties from observations of shear wave propagation following an acoustic radiation force impulse (ARFI) excitation is difficult in anisotropic materials because of the complex relations among the propagation direction, shear wave polarizations, and material symmetries. In this paper, we describe a method to calculate shear wave signals using Green’s tensor methods in an incompressible, transversely isotropic (TI) material characterized by three material parameters. The Green’s tensor is written as the sum of an analytic expression for the SH propagation mode, and an integral expression for the SV propagation mode that can be evaluated by interpolation within precomputed integral functions with an efficiency comparable to the evaluation of a closed-form expression. By using parametrized integral functions, the number of required numerical integrations is reduced by a factor of 102–109 depending on the specific problem under consideration. Results are presented for the case of a point source positioned at the origin and a tall Gaussian source similar to an ARFI excitation. For an experimental configuration with a tilted material symmetry axis, results show that shear wave signals exhibit structures that are sufficiently complex to allow measurement of all three material parameters that characterize an incompressible, TI material.
Enzymatic O-glycosylation of etoposide aglycone by exploration of the substrate promiscuity for glycosyltransferases.

The 4-O-β-D-glucopyranoside of DMEP ((-)-4-desmethylepipodophyllotoxin) (GDMEP), a natural product from Podophyllum hexandrum, is the direct precursor to the topoisomerase inhibitor etoposide, used in dozens of chemotherapy regimens for various malignancies. The biosynthesis pathway for DMEP has been completed, while the enzyme for biosynthesizing GDMEP is still unclear. Here, we report the enzymatic O-glycosylation of DMEP with 53% conversion by exploring the substrate promiscuity and entrances of glycosyltransferases. Notably, we found 6 essential amino acid residues surrounding the putative substrate entrances exposed to the protein surface in UGT78D2, CsUGT78D2 and CsUGT78D2-like, and these residues may determine substrate specificity and high O-glycosylation activity towards DMEP. Our results provide an effective route for one-step synthesis of GDMEP. Identification of the key residues and entrances of glycosyltransferases will promote precise identification of glycosyltransferase biocatalysts for novel substrates and provide a rational basis for glycosyltransferase engineering.
School engagement of children in early grades: Psychometric, and gender comparisons

School engagement reflects the degree to which students are invested, motivated and willing to participate in learning at their school and this relates to future academic and professional success. Although school engagement is a primary factor predicting educational dropout or successful school completion in Europe and North America, little is known about school engagement factors in non-English speaking countries. We adapted a 15-item school engagement scale and assessed validity and reliability of the Russian translation on a sample of Russian school-aged children (N = 537, 6–12 years, 46% females) who attended at public schools in Moscow. Results of the final factorial structure that included emotional, cognitive and behavioral components were selected based on its excellent fit indices and principles of parsimony. Component results show that the emotional component has the highest internal consistency and the behavioral component has the lowest. Although, all components are significantly interrelated, we observed no gender differences and no significant correlation with age. Theoretically, our data agree with the notion that children’s emotional engagement in schools sets the foundation for learning, participating and succeeding in school activities. Practically, the proposed scale in Russian can be used in educational and clinical settings with Russian speaking children.
A Folding Paper-Based Aptasensor Platform Coated with Novel nanoassemblies for Instant and Highly Sensitive Detection of 17β-Estradiol.

Owing to its critical role in the development of female reproductive tissues and as a clinical biomarker, there is an urgent need to develop a rapid and cost-effective method to sensitively detect 17β-estradiol (E2). In this work, a folding aptasensor platform with microfluidic channels for the label-free electrochemical detection of E2 is described. The platform, designed with a delicate folding structure, integrates filter holes, microfluidic channels, reaction chambers, and a three-electrode system, and is extremely easy to use. To increase the detection sensitivity and immobilize the aptamer, we synthesized a novel nanoassembly consisting of amine-functionalized single-walled carbon nanotubes (NH2-SWCNTs)/new methylene blue (NMB)/gold nanoparticles (AuNPs) and modified the working electrode with this nanoassembly. The calibration curve obtained from the experimental results exhibited a linear range between 10 pg mL-1 and 500 ng mL-1(R2=0.993), and a detection limit of 5 pg mL-1 was achieved (S/N=3). Furthermore, experiments to detect E2 in clinical serum were conducted, and the results were highly similar to those obtained using a large electrochemical luminescence apparatus. By integrating multiple functional components, adopting novel nanoassemblies, and using a folding structure, this paper-based platform not only has great potential as a simple and convenient integrated device for point-of-care testing (POCT) of E2, but also as a portable, low-cost, and highly sensitive aptasensor platform capable of detecting many diagnostic biomarkers with the appropriate aptamers.
Alarm communication networks as a driver of community structure in African savannah herbivores

Abstract Social information networks have the potential to shape the spatial structure of ecological communities by promoting the formation of mixed‐species groups. However, what actually drives social affinity between species in the wild will depend on the characteristics of the species available to group. Here we first present an agent‐based model that predicts trait‐related survival benefits from mixed‐species group formation in a multi‐species community and we then test the model predictions in a community‐wide field study of African savannah herbivores using multi‐layered network analysis. We reveal benefits from information transfer about predators as a key determinant of mixed‐species group formation, and that dilution benefits alone are not enough to explain patterns in interspecific sociality. The findings highlight the limitations of classical ecological approaches focusing only on direct trophic interactions when analysing community structure and suggest that declines in species occupying central social network positions, such as key informants, can have significant repercussions throughout communities.
Pancreatic cancer: An update on diagnosis and management.

BACKGROUND Pancreatic cancer has the highest mortality rate among all main cancer types and is the fourth leading cause of cancer death in Australia. OBJECTIVE This review focuses on the 95% of pancreatic cancers that arise as pancreatic ductal adenocarcinoma, with the aim to summarise current recommendations for diagnosis and treatment. DISCUSSION No cardinal symptoms for pancreatic cancer exist. Weight loss combined with abdominal symptoms or back pain in individuals aged ≥60 years prompts urgent computed tomography of the abdomen, while individuals aged ≥40 years with jaundice require direct specialist referral. Pancreatic cancer is categorised as resectable, borderline resectable, locally advanced or metastatic. Resectable disease is treated with surgical resection and adjuvant chemotherapy. Borderline resectable and locally advanced disease are treated with neoadjuvant therapy, followed by surgical exploration if the disease is non-progressive. Metastatic and unresectable disease is treated with chemotherapy or best supportive care. Nutritional support is required for most patients.
Analysis of virulence potential of Escherichia coli O145 isolated from cattle feces and hide samples based on whole genome sequencing

Escherichia coli O145 serogroup is one of the big six non-O157 Shiga toxin producing E. coli (STEC) that causes foodborne illnesses in the United States and other countries. Cattle are a major reservoir of STEC, which harbor them in their hindgut and shed in the feces. Cattle feces is the main source of hide and subsequent carcass contaminations during harvest leading to foodborne illnesses in humans. The objective of our study was to determine the virulence potential of STEC O145 strains isolated from cattle feces and hide samples. A total of 71 STEC O145 strains isolated from cattle feces (n = 16), hide (n = 53), and human clinical samples (n = 2) were used in the study. The strains were subjected to whole genome sequencing using Illumina MiSeq platform. The average draft genome size of the fecal, hide, and human clinical strains were 5.41, 5.28, and 5.29 Mb, respectively. The average number of genes associated with mobile genetic elements was 260, 238, and 259, in cattle fecal, hide, and human clinical strains, respectively. All strains belonged to O145:H28 serotype and carried eae subtype γ. Shiga toxin 1a was the most common Shiga toxin gene subtype among the strains, followed by stx2a and stx2c. The strains also carried genes encoding type III secretory system proteins, nle, and plasmid-encoded virulence genes. Phylogenetic analysis revealed clustering of cattle fecal strains separately from hide strains, and the human clinical strains were more closely related to the hide strains. All the strains belonged to sequence type (ST)-32. The virulence gene profile of STEC O145 strains isolated from cattle sources was similar to that of human clinical strains and were phylogenetically closely related to human clinical strains. The genetic analysis suggests the potential of cattle STEC O145 strains to cause human illnesses. Inclusion of more strains from cattle and their environment in the analysis will help in further elucidation of the genetic diversity and virulence potential of cattle O145 strains.
Levels of Human Immunodeficiency Virus DNA Are Determined Before ART Initiation and Linked to CD8 T-Cell Activation and Memory Expansion

Abstract Initiation of antiretroviral therapy (ART) in early compared with chronic human immunodeficiency virus (HIV) infection is associated with a smaller HIV reservoir. This longitudinal analysis of 60 individuals who began ART during primary HIV infection (PHI) investigates which pre- and posttherapy factors best predict HIV DNA levels (a correlate of reservoir size) after treatment initiation during PHI. The best predictor of HIV DNA at 1 year was pre-ART HIV DNA, which was in turn significantly associated with CD8 memory T-cell differentiation (effector memory, naive, and T-bet−Eomes− subsets), CD8 T-cell activation (CD38 expression) and T-cell immunoglobulin and mucin-domain containing-3 (Tim-3) expression on memory T cells. No associations were found for any immunological variables after 1 year of ART. Levels of HIV DNA are determined around the time of ART initiation in individuals treated during PHI. CD8 T-cell activation and memory expansion are linked to HIV DNA levels, suggesting the importance of the initial host-viral interplay in eventual reservoir size.
Coupling environment and physiology to predict effects of climate change on the taxonomic and functional diversity of fish assemblages in the Murray-Darling Basin, Australia

This study uses species distribution modeling and physiological and functional traits to predict the impacts of climate change on native freshwater fish in the Murray-Darling Basin, Australia. We modelled future changes in taxonomic and functional diversity in 2050 and 2080 for two scenarios of carbon emissions, identifying areas of great interest for conservation. Climatic-environmental variables were used to model the range of 23 species of native fish under each scenario. The consensus model, followed by the physiological filter of lethal temperature was retained for interpretation. Our study predicts a severe negative impact of climate change on both taxonomic and functional components of ichthyofauna of the Murray-Darling Basin. There was a predicted marked contraction of species ranges under both scenarios. The predictions showed loss of climatically suitable areas, species and functional characters. There was a decrease in areas with high values of functional richness, dispersion and uniqueness. Some traits are predicted to be extirpated, especially in the most pessimistic scenario. The climatic refuges for fish fauna are predicted to be in the southern portion of the basin, in the upper Murray catchment. Incorporating future predictions about the distribution of ichthyofauna in conservation management planning will enhance resilience to climate change.
Clarke Error Grid Analysis on Graph Paper and Microsoft Excel

Clarke Error Grid Analysis (CEGA) is an essential tool for checking the clinical accuracy of self-monitoring of blood glucose (SMBG) monitors. Currently, there is no freeware (software) that can be used to generate the error grid. If we think about statistical analysis of data, the first thing comes to our mind is—which software to use—SPSS, GraphPad, R, or any other? The machine has now taken all the burden of our complex statistical analysis. However, in many resource-limited settings, the costly statistical software package is still not available. Recently, we faced difficulty in the conduct of a CEGA. We were searching about it on the internet; however, we could not find a solution which we can adopt. Then, we decided to do it manually. First, we took a graph paper and marked it according to the original CEGA plot. Then, we plotted the glucose levels (X-axis for reference method and Y-axis for SMBG) on the graph paper and tabulated the numbers according to different zones (viz., A, B, C, D, and E). We faced the second challenge while making a digital image of the graph. Simply taking a picture with a smartphone was not of sufficient quality. Furthermore, scanning a large graph paper was not feasible in our setting. Hence, we used Microsoft Excel. We entered the data (reference method in the first column and SMBG in the second column) and inserted a scatter plot. We formatted the Xand Y-axis from 0 to 450. Then, we manually inserted lines to make the grid. Later, we converted it to a portable document format (PDF) and generated a JPG image from the PDF. Figure 1 shows an example of the graph with grid lines with some random data as red dots. Anyone facing a similar problem in any resource-limited settings can carry out CEGA manually on graph paper and can generate a manuscript-ready digital image with the help of spreadsheet software. Furthermore, Parkes Error Grid analysis, another method of reporting accuracy of SMBG monitors, can also be conducted with the similar method.
BBX4, a phyB-interacting and modulated regulator, directly interacts with PIF3 to fine tune red light-mediated photomorphogenesis

Significance Phytochrome B (phyB) is the predominant red light photoreceptor that transduces red light signals to downstream signaling. On red light exposure, photoactivated phyB interacts with a transcription factor termed PHYTOCHROME INTERACTING FACTOR 3 (PIF3), a repressor of red light signaling, triggering its rapid phosphorylation and subsequent degradation. Thus, phyB-PIF3 defines a critical regulatory hub for red light-mediated seedling development. In this study, we show that B-BOX CONTAINING PROTEIN 4 (BBX4) is a key component involved in the phyB-PIF3 regulatory module. phyB directly interacts with BBX4 and positively controls the abundance of BBX4 in red light. Accumulated BBX4 directly interacts with PIF3 to inhibit its transcriptional activation activity toward target genes, thereby promoting photomorphogenesis. Phytochrome B (phyB) absorbs red light signals and subsequently initiates a set of molecular events in plant cells to promote photomorphogenesis. Here we show that phyB directly interacts with B-BOX CONTAINING PROTEIN 4 (BBX4), a positive regulator of red light signaling, and positively controls its abundance in red light. BBX4 associates with PHYTOCHROME INTERACTING FACTOR 3 (PIF3) and represses PIF3 transcriptional activation activity and PIF3-controlled gene expression. The degradation of BBX4 in darkness is dependent on CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and the 26S proteasome system. Collectively, BBX4 acts as a key component of the phyB-PIF3–mediated signaling module and fine tunes the red light action. phyB promotes the accumulation of BBX4, which in turn serves to repress PIF3 action through direct physical interaction to promote photomorphogenic development in red light.