Miracle-dz/UniFAR-FTUs huggingface dataset:
The Crystal Structure of Bacillus cereus HblL1

The Hbl toxin is a three-component haemolytic complex produced by Bacillus cereus sensu lato strains and implicated as a cause of diarrhoea in B. cereus food poisoning. While the structure of the HblB component of this toxin is known, the structures of the other components are unresolved. Here, we describe the expression of the recombinant HblL1 component and the elucidation of its structure to 1.36 Å. Like HblB, it is a member of the alpha-helical pore-forming toxin family. In comparison to other members of this group, it has an extended hydrophobic beta tongue region that may be involved in pore formation. Molecular docking was used to predict possible interactions between HblL1 and HblB, and suggests a head to tail dimer might form, burying the HblL1 beta tongue region.
A novel polythiophene derivative as a sensitive colorimetric and fluorescent sensor for the detection of ATP

A novel cationic water-soluble polythiophene derivative, the poly[N,N,N-trimethyl-3-(thiophen-3-yl)propenaminium chloride] (PTPA-Cl) was chosen as a sensitive colorimetric and fluorescent probe to differentiate adenosine triphosphate (ATP), the present work shows for the first time the difference between ATP and coenzyme A (CoA). ATP has much stronger colorimetric and fluorescent than CoA. When bound to different charged analytes, the polythiophene derivative probe emitted light with different colors due to the unique spectral properties of the conformation sensitive probe, and the sensing interaction can be apparently observed by naked eyes. Moreover, the cationic water-soluble polythiophene shows selectivity to ATP in the presence of other charged analytes and as well a high sensitivity with the detection limit at 10−8 M by using fluorometry at aqueous solution.
New compounds based on anthracene as a good candidate for organic dye-sensitized solar cells: Theoretical investigations

The specific properties of organic-conjugated molecules and polymers are of great importance since they have become the most promising materials for the optoelectronic device technology such as solar cells. The use of low band gap materials is a viable method for better harvesting of the solar spectrum and increasing its efficiency. The control of the parameter of these materials is a research issue of ongoing interest. In this work, quantum chemical investigation was performed to explore the optical and electronic properties of a series of different compounds based on anthracene. Different electron side groups were introduced to investigate their effects on the electronic structure. The theoretical knowledge of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of the components is basic in studying organic solar cells; so the HOMO, LUMO, Gap energy and open circuit voltage (Voc) of the studied compounds have been calculated and reported. These properties suggest these materials as good candidate for organic dye-sensitized solar cells.
Eco-Environmental Aspects of COVID-19 Pandemic and Potential Control Strategies

A new coronavirus-strain from a zoonotic reservoir (probably bat)—termed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—has recently claimed more than two million deaths worldwide. Consequently, a burst of scientific reports on epidemiology, symptoms, and diagnosis came out. However, a comprehensive understanding of eco-environmental aspects that may contribute to coronavirus disease 2019 (COVID-19) spread is still missing, and we therefore aim to focus here on these aspects. In addition to human–human direct SARS-CoV-2 transmission, eco-environmental sources, such as air aerosols, different public use objects, hospital wastes, livestock/pet animals, municipal wastes, ventilation facilities, soil and groundwater potentially contribute to SARS-CoV-2 transmission. Further, high temperature and humidity were found to limit the spread of COVID-19. Although the COVID-19 pandemic led to decrease air and noise pollution during the period of lockdown, increased use of masks and gloves is threatening the environment by water and soil pollutions. COVID-19 badly impacted all the socio-economic groups in different capacities, where women, slum dwellers, and the people lacking social protections are the most vulnerable. Finally, sustainable strategies, waste management, biodiversity reclaim, eco-friendly lifestyle, improved health infrastructure and public awareness, were proposed to minimize the COVID-19 impact on our society and environment. These strategies will seemingly be equally effective against any future outbreak.
FOXO regulates the expression of antimicrobial peptides and promotes phagocytosis of hemocytes in shrimp antibacterial immunity

Invertebrates rely on innate immunity, including humoral and cellular immunity, to resist pathogenic infection. Previous studies showed that forkhead box transcription factor O (FOXO) participates in mucosal immune responses of mammals and the gut humoral immune regulation of invertebrates. However, whether FOXO is involved in systemic and cellular immunity regulation in invertebrates remains unknown. In the present study, we identified a FOXO from shrimp (Marsupenaeus japonicus) and found that it was expressed at relatively basal levels in normal shrimp, but was upregulated significantly in shrimp challenged by Vibrio anguillarum. FOXO played a critical role in maintaining hemolymph and intestinal microbiota homeostasis by promoting the expression of Relish, the transcription factor of the immune deficiency (IMD) pathway for expression of antimicrobial peptides (AMPs) in shrimp. We also found that pathogen infection activated FOXO and induced its nuclear translocation by reducing serine/threonine kinase AKT activity. In the nucleus, activated FOXO directly regulated the expression of its target Amp and Relish genes against bacterial infection. Furthermore, FOXO was identified as being involved in cellular immunity by promoting the phagocytosis of hemocytes through upregulating the expression of the phagocytotic receptor scavenger receptor C (Src), and two small GTPases, Rab5 and Rab7, which are related to phagosome trafficking to the lysosome in the cytoplasm. Taken together, our results indicated that FOXO exerts its effects on homeostasis of hemolymph and the enteric microbiota by activating the IMD pathway in normal shrimp, and directly or indirectly promoting AMP expression and enhancing phagocytosis of hemocytes against pathogens in bacteria-infected shrimp. This study revealed the different functions of FOXO in the mucosal (local) and systemic antibacterial immunity of invertebrates.
Proteome of Stored RBC Membrane and Vesicles from Heterozygous Beta Thalassemia Donors

Genetic characteristics of blood donors may impact the storability of blood products. Despite higher basal stress, red blood cells (RBCs) from eligible donors that are heterozygous for beta-thalassemia traits (βThal+) possess a differential nitrogen-related metabolism, and cope better with storage stress compared to the control. Nevertheless, not much is known about how storage impacts the proteome of membrane and extracellular vesicles (EVs) in βThal+. For this purpose, RBC units from twelve βThal+ donors were studied through proteomics, immunoblotting, electron microscopy, and functional ELISA assays, versus units from sex- and aged-matched controls. βThal+ RBCs exhibited less irreversible shape modifications. Their membrane proteome was characterized by different levels of structural, lipid raft, transport, chaperoning, redox, and enzyme components. The most prominent findings include the upregulation of myosin proteoforms, arginase-1, heat shock proteins, and protein kinases, but the downregulation of nitrogen-related transporters. The unique membrane proteome was also mirrored, in part, to that of βThal+ EVs. Network analysis revealed interesting connections of membrane vesiculation with storage and stress hemolysis, along with proteome control modulators of the RBC membrane. Our findings, which are in line with the mild but consistent oxidative stress these cells experience in vivo, provide insight into the physiology and aging of stored βThal+ RBCs.
Feature Preserving Autofocus Algorithm for Phase Error Correction of SAR Images

Autofocus is an essential technique for airborne synthetic aperture radar (SAR) imaging to correct phase errors mainly due to unexpected motion error. There are several well-known conventional autofocus methods such as phase gradient autofocus (PGA) and minimum entropy (ME). Although these methods are still widely used for various SAR applications, each method has drawbacks such as limited bandwidth of estimation, low convergence rate, huge computation burden, etc. In this paper, feature preserving autofocus (FPA) algorithm is newly proposed. The algorithm is based on the minimization of the cost function containing a regularization term. The algorithm is designed for postprocessing purpose, which is different from the existing regularization-based algorithms such as sparsity-driven autofocus (SDA). This difference makes the proposed method far more straightforward and efficient than those existing algorithms. The experimental results show that the proposed algorithm achieves better performance, convergence, and robustness than the existing postprocessing autofocus algorithms.
Crystallinity and β Phase Fraction of PVDF in Biaxially Stretched PVDF/PMMA Films

Polyvinylidene fluoride (PVDF) and poly(methyl methacrylate) (PMMA) blend films were prepared using biaxial stretching. The effects of PMMA content and stretching ratio on the crystallinity and β phase fraction of PVDF in blend films were investigated. The distributions of crystallinity and β phase fraction on variable locations were also studied. The results of FTIR and XRD showed that β phase appeared in PVDF/PMMA blends after extrusion and casting procedures. Although β phase fraction decreased after preheating, there was still an increasing trend during following biaxial stretching. More importantly, the increase in PMMA content improved β phase fraction, and the highest β phase fraction of 93% was achieved at PMMA content of 30 wt% and stretching ratio of 2×2. Besides, the reduction in PMMA content and the increase in stretching ratio improved the crystallinity of PVDF. The mechanical properties of the stretched films were significantly improved by increasing the stretching ratio as well. The uniform stress distribution on different regions of biaxial stretching films contributed to the uniform distribution of β phase fraction and crystallinity of PVDF with the aid of simulation. This work confirmed that biaxial stretching can be a candidate method to prepare PVDF/PMMA blend films with uniform distributions of comparable β phase and crystallinity of PVDF.
Hydrothermal synthesis of Fe3O4 particles with various shapes

Magnetite (Fe3O4) particles with various shapes have been synthesized through a simple hydrothermal reaction. The experimental results reveal that the control of the morphology and size of magnetite particles could be realized by adjusting reaction parameters. The diamond-like and prism-shuttle-like magnetite particles with micro-size are obtained by using Fe3O(OCOCH3)6NO3 and FeCl2·4H2O as iron sources. The rod-like and spherical magnetite particles with nano-size are obtained by using Fe3O(OCOCH3)6NO3 and FeSO4·7H2O as iron sources. Ethylenediamine and hydrazine are used as organic bases. The particle size changed from micro-size to nano-size when FeSO4·7H2O was used as the starting material instead of FeCl2·4H2O. The growth mechanism of magnetite particles also is discussed. The magnetic properties of all magnetite particles exhibit ferromagnetic behavior according to the magnetic hysteresis curve measured at 5 K.
Pathogenic Hydrogel? A Novel-Entrapment Neuropathy Model Induced by Ultrasound-Guided Perineural Injections

Entrapment neuropathy (EN) is a prevalent and debilitative condition caused by a complex pathogenesis that involves a chronic compression–edema–ischemia cascade and perineural adhesion that results in excessive shear stress during motion. Despite decades of research, an easily accessible and surgery-free animal model mimicking the mixed etiology is currently lacking, thus limiting our understanding of the disease and the development of effective therapies. In this proof-of-concept study, we used ultrasound-guided perineural injection of a methoxy poly(ethylene glycol)-b-Poly(lactide-co-glycoilide) carboxylic acid (mPEG-PLGA-BOX) hydrogel near the rat’s sciatic nerve to induce EN, as confirmed sonographically, electrophysiologically, and histologically. The nerve that was injected with hydrogel appeared unevenly contoured and swollen proximally with slowed nerve conduction velocities across the injected segments, thus showing the compressive features of EN. Histology showed perineural cellular infiltration, deposition of irregular collagen fibers, and a possible early demyelination process, thus indicating the existence of adhesions. The novel method provides a surgery-free and cost-effective way to establish a small-animal model of EN that has mixed compression and adhesion features, thus facilitating the additional elucidation of the pathophysiology of EN and the search for promising treatments.
Assessment of Gastrointestinal Autonomic Dysfunction: Present and Future Perspectives

The autonomic nervous system delicately regulates the function of several target organs, including the gastrointestinal tract. Thus, nerve lesions or other nerve pathologies may cause autonomic dysfunction (AD). Some of the most common causes of AD are diabetes mellitus and α-synucleinopathies such as Parkinson’s disease. Widespread dysmotility throughout the gastrointestinal tract is a common finding in AD, but no commercially available method exists for direct verification of enteric dysfunction. Thus, assessing segmental enteric physiological function is recommended to aid diagnostics and guide treatment. Several established assessment methods exist, but disadvantages such as lack of standardization, exposure to radiation, advanced data interpretation, or high cost, limit their utility. Emerging methods, including high-resolution colonic manometry, 3D-transit, advanced imaging methods, analysis of gut biopsies, and microbiota, may all assist in the evaluation of gastroenteropathy related to AD. This review provides an overview of established and emerging assessment methods of physiological function within the gut and assessment methods of autonomic neuropathy outside the gut, especially in regards to clinical performance, strengths, and limitations for each method.
Monitoring Master Swimmers’ Performance and Active Drag Evolution along a Training Mesocycle

This study aimed to analyze the effects of a swimming training mesocycle in master swimmers’ performance and active drag. Twenty-two 39.87 ± 6.10 year-old master swimmers performed a 25 m front crawl at maximal intensity before and after a typical four-week training mesocycle. Maximum, mean and minimum speeds, speed decrease and hip horizontal intra-cyclic velocity variation were assessed using an electromechanical speedometer, and the active drag and power to overcome drag were determined using the measuring active drag system. Maximum, mean and minimum front crawl speeds improved from pre- to post-training (mean ± 95% CI: 3.1 ± 2.8%, p = 0.04; 2.9 ± 1.6%, p = 0.01; and 4.6 ± 3.1%, p = 0.01; respectively) and the speed decrease along the 25 m test lowered after the training period (82.5 ± 76.3%, p = 0.01). The training mesocycle caused a reduction in the active drag at speeds corresponding to 70% (5.0 ± 3.9%), 80% (5.6 ± 4.0%), and 90% (5.9 ± 4.0%), but not at 100% (5.9 ± 6.7%), of the swimmers’ maximal exertions in the 25 m test. These results showed that four weeks of predominantly aerobic training could improve master swimmers’ performance and reduce their hydrodynamic drag while swimming mainly at submaximal speeds.
Doxycycline-Doped Polymeric Membranes Induced Growth, Differentiation and Expression of Antigenic Phenotype Markers of Osteoblasts

Polymeric membranes are employed in guided bone regeneration (GBR) as physical barriers to facilitate bone in-growth. A bioactive and biomimetic membrane with the ability to participate in the healing and regeneration of the bone is necessary. The aim of the present study was to analyze how novel silicon dioxide composite membranes functionalized with zinc or doxycycline can modulate the osteoblasts’ proliferation, differentiation, and expression of selected antigenic markers related to immunomodulation. Nanostructured acrylate-based membranes were developed, blended with silica, and functionalized with zinc or doxycycline. They were subjected to MG63 osteoblast-like cells culturing. Proliferation was assessed by MTT-assay, differentiation by evaluating the alkaline phosphatase activity by a spectrophotometric method and antigenic phenotype was assessed by flow cytometry for selected markers. Mean comparisons were conducted by one-way ANOVA and Tukey tests (p < 0.05). The blending of silica nanoparticles in the tested non-resorbable polymeric scaffold improved the proliferation and differentiation of osteoblasts, but doxycycline doped scaffolds attained the best results. Osteoblasts cultured on doxycycline functionalized membranes presented higher expression of CD54, CD80, CD86, and HLA-DR, indicating a beneficial immunomodulation activity. Doxycycline doped membranes may be a potential candidate for use in GBR procedures in several challenging pathologies, including periodontal disease.
Internalization, Cytotoxicity, Apoptosis, and Tumor Necrosis Factor-α Expression in Rat Alveolar Macrophages Exposed to Various Dusts Occurring in the Ceramics Industry

In 1997 The International Agency for Research on Cancer classified some exposures to crystalline silica as carcinogenic to humans. Such exposures were acknowledged to be very variable, and even in the same monograph it was admitted that coal dust, containing as much as 20% quartz, could not be classified. Clearly there is a need to develop methods for assessing any risks posed by various silica containing dusts in different workplaces. A European collective research project, SILICERAM, was launched with the aim of assessing the toxicity of various dusts in the ceramics industry and improving worker protection. This study examined the effect of particles, namely, DQ12 quartz, China clay, feldspar, and a sample resembling a typical mixture used in the ceramic industry (a “contrived sample” or CS), on NR8383, a rat alveolar macrophage (AM) cell line. Titanium dioxide and aluminum oxide were also used as negative controls. Confocal microscopy observations showed internalization of DQ12 and CS in NR8383. Cell viability decreased dramatically after a 2-h incubation exposure period with DQ12 (−71%). CS was less toxic than DQ12 at 2 h. China clay and feldspar were slightly cytotoxic to NR8383 cells. DQ12 induced apoptosis, with a smaller effect of CS and China clay. TNFα gene expression was analyzed by RT-PCR. DQ12, at a noncytotoxic dose of 10 μ g/cm2, induced a significant expression of TNFα (+2 times increase). In contrast, similar doses of CS and China clay did not produce a significant increase, while TiO2 and Al2O3 displayed no effect. Co-treatment with 10 μ M aluminum lactate significantly reduced the effects of silica-containing particles on cytoxicity, apoptosis, and TNFα expression.
Towards Human Motion Tracking Enhanced by Semi-Continuous Ultrasonic Time-of-Flight Measurements

Human motion analysis is a valuable tool for assessing disease progression in persons with conditions such as multiple sclerosis or Parkinson’s disease. Human motion tracking is also used extensively for sporting technique and performance analysis as well as for work life ergonomics evaluations. Wearable inertial sensors (e.g., accelerometers, gyroscopes and/or magnetometers) are frequently employed because they are easy to mount and can be used in real life, out-of-the-lab-settings, as opposed to video-based lab setups. These distributed sensors cannot, however, measure relative distances between sensors, and are also cumbersome when it comes to calibration and drift compensation. In this study, we tested an ultrasonic time-of-flight sensor for measuring relative limb-to-limb distance, and we developed a combined inertial sensor and ultrasonic time-of-flight wearable measurement system. The aim was to investigate if ultrasonic time-of-flight sensors can supplement inertial sensor-based motion tracking by providing relative distances between inertial sensor modules. We found that the ultrasonic time-of-flight measurements reflected expected walking motion patterns. The stride length estimates derived from ultrasonic time-of-flight measurements corresponded well with estimates from validated inertial sensors, indicating that the inclusion of ultrasonic time-of-flight measurements could be a feasible approach for improving inertial sensor-only systems. Our prototype was able to measure both inertial and time-of-flight measurements simultaneously and continuously, but more work is necessary to merge the complementary approaches to provide more accurate and more detailed human motion tracking.
Low-Toxic, Earth-Abundant Nanostructured Materials for Thermoelectric Applications

This article presents recent research directions in the study of Earth-abundant, cost-effective, and low-toxic advanced nanostructured materials for thermoelectric generator (TEG) applications. This study’s critical aspect is to systematically evaluate the development of high-performance nanostructured thermoelectric (TE) materials from sustainable sources, which are expected to have a meaningful and enduring impact in developing a cost-effective TE system. We review both the performance and limitation aspects of these materials at multiple temperatures from experimental and theoretical viewpoints. Recent developments in these materials towards enhancing the dimensionless figure of merit, Seebeck coefficient, reduction of the thermal conductivity, and improvement of electrical conductivity have also been discussed in detail. Finally, the future direction and the prospects of these nanostructured materials have been proposed.
SERS Biosensor Based on Engineered 2D-Aperiodic Nanostructure for In-Situ Detection of Viable Brucella Bacterium in Complex Matrix

Brucella is a foodborne pathogen globally affecting both the economy and healthcare. Surface Enhanced Raman Spectroscopy (SERS) nano-biosensing can be a promising strategy for its detection. We combined high-performance quasi-crystal patterned nanocavities for Raman enhancement with the use of covalently immobilized Tbilisi bacteriophages as high-performing bio-receptors. We coupled our efficient SERS nano-biosensor to a Raman system to develop an on-field phage-based bio-sensing platform capable of monitoring the target bacteria. The developed biosensor allowed us to identify Brucella abortus in milk by our portable SERS device. Upon bacterial capture from samples (104 cells), a signal related to the pathogen recognition was observed, proving the concrete applicability of our system for on-site and in-food detection.