Miracle-dz/UniFAR-FTUs huggingface dataset:
Host–Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis

Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.
Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs

The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods—DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)—are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers—e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on π-electron delocalization are also documented.
Near-Infrared Radiation-Based Mild Photohyperthermia Therapy of Non-Melanoma Skin Cancer with PEGylated Reduced Nanographene Oxide

Using a one-step thermal reduction and non-covalent chemical functionalization process, PEGylated reduced nanographene oxide (rGOn-PEG) was produced from nanographene oxide (GOn) and characterized in terms of particle size, dispersion stability, chemistry, and photothermal properties, in view of its use for photothermal therapy (PTT) of non-melanoma skin cancer. GOn infrared spectrum presented more intense bands assigned to oxygen containing functional groups than observed for rGOn-PEG. GOn C/O ratio decreased more than 50% comparing with rGOn-PEG and nitrogen was present in the latter (N at % = 20.6) due to introduction of PEG-NH2. Thermogravimetric analysis allowed estimating the amount of PEG in rGOn-PEG to be of about 56.1%. Simultaneous reduction and PEGylation increased the lateral dimensions from 287 ± 139 nm to 521 ± 397 nm, as observed by transmission electron microscopy and dynamic light scattering. rGOn-PEG exhibited ≈13-fold higher absorbance in the near-infrared radiation (NIR) region, as compared to unmodified GOn. Low power (150 mW cm−2) NIR irradiation using LEDs resulted in rGOn-PEG heating up to 47 °C, which is within the mild PTT temperature range. PEGylation strongly enhanced the dispersibility of rGOn in physiological media (phosphate buffered saline, fetal bovine serum, and cell culture medium) and also improved the biocompatibility of rGOn-PEG, in comparison to GOn (25–250 μg mL−1). After a single NIR LED irradiation treatment of 30 min, a decrease of ≈38% in A-431 cells viability was observed for rGOn-PEG (250 μg mL−1). Together, our results demonstrate the potential of irradiating rGOn-PEG using lower energy, cheaper, smaller, and safer LEDs, as alternative to high power lasers, for NIR mild hyperthermia therapy of cancer, namely non-melanoma skin cancer.
Programmed Death 1 Ligand Expression in the Monocytes of Patients with Hepatocellular Carcinoma Depends on Tumor Progression

Monocytes (CD14+ cells) from advanced-stage hepatocellular carcinoma (HCC) patients express programmed death 1 ligand (PD-L)/PD-1 and suppress the host antitumor immune response. However, it is unclear whether cancer progression is associated with CD14+ cells. We compared CD14+ cell properties before and after cancer progression in the same HCC patients and examined their role in antitumor immunity. CD14+ cells were isolated from 15 naïve early-stage HCC patients before treatment initiation and after cancer progression to advanced stages. Although CD14+ cells from patients at early HCC stages exhibited antitumor activity in humanized murine chimera, CD14+ cells from the same patients after progression to advanced stages lacked this activity. Moreover, CD14+ cells from early HCC stages scantly expressed PD-L1 and PD-L2 and produced few cytokines, while CD14+ cells from advanced stages showed increased PD-L expression and produced IL-10 and CCL1. CD14+ cells were also isolated from five naïve advanced-stage HCC patients before treatment as well as after treatment-induced tumor regression. The CD14+ cells from patients with advanced-stage HCC expressed PD-L expressions, produced IL-10 and CCL1, and exhibited minimal tumoricidal activity. After treatment-induced tumor regression, CD14+ cells from the same patients did not express PD-Ls, failed to produce cytokines, and recovered tumoricidal activity. These results indicate that PD-L expression as well as CD14+ cell phenotype depend on the tumor stage in HCC patients. PD-L expressions of monocytes may be used as a new marker in the classification of cancer progression in HCC.
Evaluation of Gross Motor Coordination and Physical Fitness in Children: Comparison between Soccer and Multisport Activities

The early detection and continuous monitoring of children’s motor competence levels and physical fitness is very important. The purpose of this study was to determine the differences in motor coordination of children enrolled in soccer and multisport activities. The participants of this study included 147 boys and girls (mean age 7.60 ± 0.85 years). The total sample of subjects was composed of two subgroups: children who were enrolled in organized exercise programs—multisports (n = 77), and children who were engaged in soccer training (n = 70). Motor coordination was evaluated with the Kiphard–Schilling body coordination test (KTK). Physical fitness was assessed with a 20 m shuttle run test, 4 × 10 m shuttle run test, standing long jump, and handgrip strength. The ANCOVA showed significant differences (p < 0.05) with large effect size between groups for tests hopping for height (d = 0.93), total motor quotient (d = 1.31), jumping sideways (d = 1.32), and moving sideways (d = 1.59), after adjusting for age and gender. There were no significant differences between groups in the physical fitness tests. It can be concluded that children enrolled in multisport activities have higher levels of motor coordination than children who are enrolled only in soccer. Therefore, multiple sport training programs should be considered and encouraged by parents, educators, and other training professionals.
The CMOS Highly Linear Current Amplifier with Current Controlled Gain for Sensor Measurement Applications

This paper introduces a new current-controlled current-amplifier suitable for precise measurement applications. This amplifier was developed with strong emphasis on linearity leading to low total harmonic distortion (THD) of the output signal, and on linearity of the gain control. The presented circuit is characterized by low input and high output impedances. Current consumption is significantly smaller than with conventional quadratic current multipliers and is comparable in order to the maximum processed input current, which is ±200 µA. This circuit is supposed to be used in many sensor applications, as well as a precise current multiplier for general analog current signal processing. The presented amplifier (current multiplier) was designed by an uncommon topology based on linear sub-blocks using MOS transistors working in their linear region. The described circuit was designed and fabricated in a C035 I3T25 0.35-µm ON Semiconductor process because of the demand of the intended application for higher supply voltage. Nevertheless, the topology is suitable also for modern smaller CMOS technologies and lower supply voltages. The performance of the circuit was verified by laboratory measurement with parameters comparable to the Cadence simulation results and presented here.
DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment

Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens.
A Semi-Dissolving Microneedle Patch Incorporating TEMPO-Oxidized Bacterial Cellulose Nanofibers for Enhanced Transdermal Delivery

Although dissolving microneedles have garnered considerable attention as transdermal delivery tools, insufficient drug loading remains a challenge owing to their small dimension. Herein, we report a one-step process of synthesizing semi-dissolving microneedle (SDMN) patches that enable effective transdermal drug delivery without loading drugs themselves by introducing TEMPO-oxidized bacterial cellulose nanofibers (TOBCNs), which are well dispersed, while retaining their unique properties in the aqueous phase. The SDMN patch fabricated by the micro-molding of a TOBCN/hydrophilic biopolymer mixture had a two-layer structure comprising a water-soluble needle layer and a TOBCN-containing insoluble backing layer. Moreover, the SDMN patch, which had a hole in the backing layer where TOBCNs are distributed uniformly, could offer novel advantages for the delivery of large quantities of active ingredients. In vitro permeation analysis confirmed that TOBCNs with high water absorption capacity could serve as drug reservoirs. Upon SDMN insertion and the application of drug aqueous solution through the drug inlet hole, the TOBCNs rapidly absorbed the solution and supplied it to the needle layer. Simultaneously, the needle layer dissolved in body fluids and the drug solution to form micro-channels, which enabled the delivery of larger quantities of drugs to the skin compared to that enabled by solution application alone.
VEGFA and NFE2L2 Gene Expression and Regulation by MicroRNAs in Thyroid Papillary Cancer and Colloid Goiter

Deregulation of VEGFA (Vascular Endothelial Growth Factor A) and NFE2L2 (Nuclear Factor (Erythroid-derived 2)-Like 2), involved in angiogenesis and oxidative stress, can lead to thyroid cancer progression. MiR-17-5p and miR-612 are possible regulators of these genes and may promote thyroid disorders. In order to evaluate the involvement of VEGFA, NFE2L2, hsa-miR-17-5p, and hsa-miR-612 in thyroid pathology, we examined tissue samples from colloid goiter, papillary thyroid cancer (PTC), and a normal thyroid. We found higher levels of VEGFA and NFE2L2 transcripts and the VEGFA protein in goiter and PTC samples than in normal tissue. In the goiter, miR-612 and miR-17-5p levels were lower than those in PTC. Tumors, despite showing lower VEGFA mRNA expression, presented higher VEGFA protein levels compared to goiter tissue. In addition, NRF2 (Nuclear Related Transcription Factor 2) protein levels in tumors were higher than those in goiter and normal tissues. Inhibition of miR-17-5p resulted in reduced NFE2L2 expression. Overall, both transcript and protein levels of NFE2L2 and VEGFA were elevated in PTC and colloid goiter. Hsa-miR-612 showed differential expression in PTC and colloid goiter, while hsa-miR-17-5p showed differential expression only in colloid goiter, suggesting that hsa-miR-17-5p may be a positive regulator of NFE2L2 expression in PTC.
Coupling Ultrafiltration-Based Processes to Concentrate Phenolic Compounds from Aqueous Goji Berry Extracts

In this work, a membrane-based process for the purification and concentration of antioxidant compounds from aqueous Goji (Lycium barbarum L.) berry extracts was investigated. The aqueous extract was previously clarified with hollow fiber ultrafiltration (UF) membranes in order to remove suspended solids and β-carotene and to produce a clarified extract enriched in phenolic compounds. Then, three UF flat sheet polyamide membranes with a molecular weight cut-off (MWCO) in the range 1000–3500 Da were tested to purify and concentrate phenolic compounds from the clarified extract. The effect of MWCO and transmembrane pressure (TMP) on the performance of selected membranes in terms of productivity and selectivity towards total dissolved solids (TDS), total phenolic compounds (TPC), total carbohydrates (TC) and total antioxidant activity (TAA) was evaluated. Experimental results indicated that the 2500 Da membrane exhibited a lower fouling index, higher cleaning efficiency, lower rejection towards carbohydrates (lower than 30%) and higher rejection towards phenolic compounds (higher than 50%) in comparison to the other investigated membranes. The inclusion of a diafiltration process in the treatment of the clarified extract with this membrane in a spiral-wound configuration improved the concentration of sugar compounds in the permeate stream and increased the purification of phenolic compounds in the retentate fraction.
Breeding and Development of the Columbian Ground Squirrel

It has long been well known that it is difficult to induce wild animals to breed in captivity. This difficulty seems general and has been referred to by Darwin, in his "Origin of Species by Natural Selection. " chapter 1, page 10: "Many facts clearly show how eminently susceptible the reproductive system is to very slight changes in surrounding conditions. Nothing is more easy than to tame an animal, and few things more difficult than to get it to breed freely under confinement. " In the extensive and long-continued investigations recorded in this paper only four Columbian ground squirrels (Citellus columbianus) were successfully bred, and the data accompanying the rearing of their broods secured. The equipment necessary for the securing of such data must of necessity be of such nature as to give the animals under observation the utmost freedom. In securing the data here recorded very ample yards were enclosed and in them were the original dens of the wild squirrels to be studied. So ample and free-ranging were these yards, that the animals were practically at liberty to come and go as they desired; yet at all times they were under the absolute control of the investigator. Into these yards squirrels which were carefully branded, weighed, and recorded were turned, segregated according to sex; and here they lived a life of comparative freedom. In fact, they were so nearly under normal conditions that they never became very tame, but always darted into the holes as wild squirrels do when approached. Shortly after coming from hibernation they showed signs of a desire to breed, thus enabling us to take the first steps in determining the gestation period. Branding system. The convenience of a branding system was at once apparent. It became necessary to recognize with the binoculars, instantly, definitely, and without disturbance, from the quiet of the cabins, any squirrel running at liberty in the yards. This necessity led to the development of a double system of brands known as temporary and permanent. The temporary brand was made by singeing
Structural Property Study for GeSn Thin Films

The structural properties of GeSn thin films with different Sn concentrations and thicknesses grown on Ge (001) by molecular beam epitaxy (MBE) and on Ge-buffered Si (001) wafers by chemical vapor deposition (CVD) were analyzed through high resolution X-ray diffraction and cross-sectional transmission electron microscopy. Two-dimensional reciprocal space maps around the asymmetric (224) reflection were collected by X-ray diffraction for both the whole structures and the GeSn epilayers. The broadenings of the features of the GeSn epilayers with different relaxations in the ω direction, along the ω-2θ direction and parallel to the surface were investigated. The dislocations were identified by transmission electron microscopy. Threading dislocations were found in MBE grown GeSn layers, but not in the CVD grown ones. The point defects and dislocations were two possible reasons for the poor optical properties in the GeSn alloys grown by MBE.
The Involvement of Exosomes in Glioblastoma Development, Diagnosis, Prognosis, and Treatment

Brain tumours are a serious concern among both physicians and patients. The most feared brain tumour is glioblastoma (GBM) due to its heterogeneous histology, substantial invasive capacity, and rapid postsurgical recurrence. Even in cases of early management consisting of surgery, chemo-, and radiotherapy, the prognosis is still poor, with an extremely short survival period. Consequently, researchers are trying to better understand the underlying pathways involved in GBM development in order to establish a more personalised approach. The latest focus is on molecular characterisation of the tumour, including analysis of extracellular vesicles (EVs), nanostructures derived from both normal and pathological cells that have an important role in intercellular communication due to the various molecules they carry. There are two types of EV based on their biogenesis, but exosomes are of particular interest in GBM. Recent studies have demonstrated that GBM cells release numerous exosomes whose cargo provides them the capacity to facilitate tumour cell invasion and migration, to stimulate malignant transformation of previously normal cells, to increase immune tolerance towards the tumour, to induce resistance to chemotherapy, and to enhance the GBM vascular supply. As exosomes are specific to their parental cells, their isolation would allow a deeper perspective on GBM pathogenesis. A new era of molecular manipulation has emerged, and exosomes are rapidly proving their value not only as diagnostic and prognostic markers, but also as tools in therapies specifically targeting GBM cells. Nonetheless, further research will be required before exosomes could be used in clinical practice. This review aims to describe the structural and functional characteristics of exosomes and their involvement in GBM development, diagnosis, prognosis and treatment.
Optimized CorT Total to Compare Scheimpflug vs Dual Scheimpflug/Placido Imaging Devices.

PURPOSE To compare the manufacturer-provided measures of total corneal power (TCP) generated by Scheimpflug and dual Scheimpflug/Placido imaging as compared to corneal topographic astigmatism calculated on the basis of measured TCP data (CorT Total). SETTING Emory University, Atlanta, Georgia, USA. DESIGN Retrospective case series. METHODS TCP values were exported from virgin eyes that underwent imaging with both the Scheimpflug (Pentacam HR) and dual Scheimpflug-Placido (Galilei G4) imaging devices to compute an optimized CorT total. The standard deviation of the ocular residual astigmatism (ORAsd), which serves as a value describing the vectoral difference between the corneal astigmatism measure and manifest refractive cylinder at the corneal plane, was evaluated for all eyes to compare manufacturer-provided measurements vs the optimized CorT Total. RESULTS The Scheimpflug CorT Total had the lowest ORAsd (0.306 diopter [D], spherical equivalent [SE] 0.018) of all the parameters evaluated, although the difference was not statistically significant (p=0.22) from the dual Scheimpflug/Placido CorT Total (0.32 2D; SE 0.017). For the Scheimpflug device, the CorT Total had a statistically significant lower (p<0.05) ORAsd in comparison to the best measure on the device (total corneal refractive power Apex zone 2 mm - 0.324 D; SE 0.021). For dual Scheimpflug/Placido measurements, the CorT Total had the lowest ORAsd (0.322 D; SE 0.017) but the difference was not statistically significant (p=0.43) from the lowest manufacturer-provided measure (TCP 2). CONCLUSIONS CorT Total generated with the Scheimpflug device corresponded better with the manifest refractive cylinder than all measures of total corneal astigmatism calculated by the software from both the Scheimpflug and the Dual Scheimpflug/Placido devices.
Anaerobic bacteria as indicators of faecal pollution

In several well-authenticated instances intestinal pathogens, including Salmonella species, have been isolated from water in the absence of bacteria, such as Escherichia coli, commonly used to detect faecal pollution. The present study examines certain anaerobic, non-sporing commensals of the intestinal tract as alternative ‘indicator’ bacteria. The numbers of bifidobacteria and Bacteroides fragilis recovered from faecal specimens were between 109 and 1010 per gram while the Gram-positive, anaerobic cocci numbered only about 10 6 per gram. In sewage, this numerical difference was eliminated by a rapid loss of viability of bifidobacteria and B. fragilis so that the counts of all three types of bacteria approximated to those of E. coli. Storage tests with aerated and non-aerated sewage established that further loss of viability of bifidobacteria and B. fragilis occurred only fairly slowly. In samples of water from the Dighty Water and River Tay Estuary, shown to be faecally polluted, the three anaerobic types of bacteria were recovered in numbers roughly equal to those of E. coli and their persistence in the surface of the bed of the Dighty Water was also at least equal to that of E. coli. These results demonstrated that, in spite of their strictly anaerobic growth requirements, Bifidobacteria, B. fragilis and the Gram-positive, anaerobic cocci persist in aerobic, aqueous environments. If their habitat can be shown to be reasonably restricted to the intestinal tract they are likely, under special circumstances, to be useful indicators of faecal pollution.