Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms Underlying the Protective Effect of the Peroxiredoxin-6 Are Mediated via the Protection of Astrocytes during Ischemia/Reoxygenation

Ischemia-like conditions reflect almost the entire spectrum of events that occur during cerebral ischemia, including the induction of oxidative stress, Ca2+ overload, glutamate excitotoxicity, and activation of necrosis and apoptosis in brain cells. Mechanisms for the protective effects of the antioxidant enzyme peroxiredoxin-6 (Prx-6) on hippocampal cells during oxygen-glucose deprivation/reoxygenation (OGD/R) were investigated. Using the methods of fluorescence microscopy, inhibitory analysis, vitality tests and PCR, it was shown that 24-h incubation of mixed hippocampal cell cultures with Prx-6 does not affect the generation of a reversible phase of a OGD-induced rise in Ca2+ ions in cytosol ([Ca2+]i), but inhibits a global increase in [Ca2+]i in astrocytes completely and in neurons by 70%. In addition, after 40 min of OGD, cell necrosis is suppressed, especially in the astrocyte population. This effect is associated with the complex action of Prx-6 on neuroglial networks. As an antioxidant, Prx-6 has a more pronounced and astrocyte-directed effect, compared to the exogenous antioxidant vitamin E (Vit E). Prx-6 inhibits ROS production in mitochondria by increasing the antioxidant capacity of cells and altering the expression of genes encoding redox status proteins. Due to the close bond between [Ca2+]i and intracellular ROS, this effect of Prx-6 is one of its protective mechanisms. Moreover, Prx-6 effectively suppresses not only necrosis, but also apoptosis during OGD and reoxygenation. Incubation with Prx-6 leads to activation of the basic expression of genes encoding protective kinases—PI3K, CaMKII, PKC, anti-apoptotic proteins—Stat3 and Bcl-2, while inhibiting the expression of signaling kinases and factors involved in apoptosis activation—Ikk, Src, NF-κb, Caspase-3, p53, Fas, etc. This effect on the basic expression of the genome leads to the cell preconditions, which is expressed in the inhibition of caspase-3 during OGD/reoxygenation. A significant effect of Prx-6 is directed on suppression of the level of pro-inflammatory cytokine IL-1β and factor TNFα, as well as genes encoding NMDA- and kainate receptor subunits, which was established for the first time for this antioxidant enzyme. The protective effect of Prx-6 is due to its antioxidant properties, since mutant Prx-6 (mutPrx-6, Prx6-C47S) leads to polar opposite effects, contributing to oxidative stress, activation of apoptosis and cell death through receptor action on TLR4.
Masticatory muscle architectural correlates of dietary diversity in Canidae, Ursidae, and across the order Carnivora

Carnivorans represent extreme ecomorphological diversity, encompassing remarkable variation in form, habitat, and diet. The relationship between the masticatory musculature and dietary ecology has been explored in a number of carnivoran lineages, including felids and the superfamily Musteloidea. In this study, we present novel architectural data on two additional carnivoran families—Ursidae and Canidae—and supplement these previous studies with additional felid, musteloid, herpestid, hyaenid, and viverrid taxa (a total of 53 species across 10 families). Gross dissection data were collected following a standardized protocol—sharp dissection followed by chemical digestion. Summed jaw adductor forces were also transformed into bite force estimates (BF) using osteologically calculated leverages. All data were linearized, log‐transformed, and size‐adjusted using two proxies for each taxon—body mass (BM) and cranial geometric mean—to assess relative scaling trends. These architectural data were then analyzed in the context of dietary ecology to examine the impact of dietary size (DS) and dietary mechanical properties (DMP). Muscle mass, physiological cross‐sectional area, and BF scaled with isometry or positive allometry in all cases, whereas fascicle lengths (FLs) scaled with isometry or negative allometry. With respect to diet, BM‐adjusted FLs were strongly correlated with DS in musteloids, but not in any other lineage. The relationship between size‐adjusted BF and DMP was also significant within musteloids, and across the sample as a whole, but not within other individual lineages. This interfamilial trend may reflect the increased morphological and dietary diversity of musteloids relative to other carnivoran groups.
Functional Genomic Insights into Probiotic Bacillus siamensis Strain B28 from Traditional Korean Fermented Kimchi

Bacillus siamensis strain B28 was previously isolated from traditional Korean fermented kimchi and inhibited expression of the microphthalmia-associated transcription factor and β-catenin in human embryonic kidney 293 cells. Here, we determined the complete genome sequence of strain B28 and compared it with other strains to elucidate its potential probiotic properties. Strain B28 does not contain antibiotic resistance-, hemolysin- or enterotoxin-encoding genes. The genome includes genes related to survival in extreme conditions, adhesion in the gut, and synthesis of the bacteriocin. Considering the potential for enhancement of human health, the strain B28 genome encodes genes related to production of eight essential amino acids, γ-aminobutyric acid, branched-chain fatty acids, γ-glutamyltransferase, and subtilisin. There are genes for the synthesis of uracil, lipoteichoic acid, glutathione, and several reactive oxygen species-scavenging enzymes. Experimentally, strain B28 exhibited sensitivity to eight antibiotics and antibacterial activity against seven foodborne pathogens. B. siamensis B28 is a safe strain with potential for development as a probiotic.
Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins

Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.
Tailoring Morphology and Vertical Yield of Self-Catalyzed GaP Nanowires on Template-Free Si Substrates

Tailorable synthesis of III-V semiconductor heterostructures in nanowires (NWs) enables new approaches with respect to designing photonic and electronic devices at the nanoscale. We present a comprehensive study of highly controllable self-catalyzed growth of gallium phosphide (GaP) NWs on template-free silicon (111) substrates by molecular beam epitaxy. We report the approach to form the silicon oxide layer, which reproducibly provides a high yield of vertical GaP NWs and control over the NW surface density without a pre-patterned growth mask. Above that, we present the strategy for controlling both GaP NW length and diameter independently in single- or two-staged self-catalyzed growth. The proposed approach can be extended to other III-V NWs.
Stem Cells: Innovative Therapeutic Options for Neurodegenerative Diseases?

Neurodegenerative diseases are characterized by the progressive loss of structure and/or function of both neurons and glial cells, leading to different degrees of pathology and loss of cognition. The hypothesis of circuit reconstruction in the damaged brain via direct cell replacement has been pursued extensively so far. In this context, stem cells represent a useful option since they provide tissue restoration through the substitution of damaged neuronal cells with exogenous stem cells and create a neuro-protective environment through the release of bioactive molecules for healthy neurons, as well. These peculiar properties of stem cells are opening to potential therapeutic strategies for the treatment of severe neurodegenerative disorders, for which the absence of effective treatment options leads to an increasingly socio-economic burden. Currently, the introduction of new technologies in the field of stem cells and the implementation of alternative cell tissues sources are pointing to exciting frontiers in this area of research. Here, we provide an update of the current knowledge about source and administration routes of stem cells, and review light and shadows of cells replacement therapy for the treatment of the three main neurodegenerative disorders (Amyotrophic lateral sclerosis, Parkinson’s, and Alzheimer’s disease).
Skeletal Effects of Bone-Targeted TGFbeta Inhibition in a Mouse Model of Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is a severe progressive muscle disease that is frequently associated with secondary osteoporosis. Previous studies have shown that TGFbeta inactivating antibody improves the muscle phenotype in mdx mice, a model of DMD. In the present study, we assessed the skeletal effects of treatment with a bone-targeted TGFbeta antibody (PCT-011) in mdx mice. Micro-computed tomography showed that 8 weeks of intraperitoneal administration of PCT-011 (10 mg per kg body mass, 3 times per week) was associated with more than twofold higher trabecular bone volume at the distal femur, which was explained by a higher trabecular number. At the femoral midshaft, PCT-011 exposure increased cortical thickness but did not significantly affect the results of three-point bending tests. Histomorphometric analyses of the lumbar vertebra 4 showed that PCT-011 treatment led to a lower bone formation rate. In conclusion, treatment with the TGFbeta antibody PCT-011 had a positive effect on bone development in mdx mice. Inhibiting TGFbeta activity thus appears to be a promising approach to treat bone fragility in the context of DMD.
Differentiation Behaviour of Adipose-Derived Stromal Cells (ASCs) Seeded on Polyurethane-Fibrin Scaffolds In Vitro and In Vivo

Adipose-derived stromal cells (ASCs) are a promising cell source for tissue engineering and regenerative medicine approaches for cartilage replacement. For chondrogenic differentiation, human (h)ASCs were seeded on three-dimensional polyurethane (PU) fibrin composites and induced with a chondrogenic differentiation medium containing TGF-ß3, BMP-6, and IGF-1 in various combinations. In addition, in vitro predifferentiated cell-seeded constructs were implanted into auricular cartilage defects of New Zealand White Rabbits for 4 and 12 weeks. Histological, immunohistochemical, and RT-PCR analyses were performed on the constructs maintained in vitro to determine extracellular matrix (ECM) deposition and expression of specific cartilage markers. Chondrogenic differentiated constructs showed a uniform distribution of cells and ECM proteins. RT-PCR showed increased gene expression of collagen II, collagen X, and aggrecan and nearly stable expression of SOX-9 and collagen I. Rabbit (r)ASC-seeded PU-fibrin composites implanted in ear cartilage defects of New Zealand White Rabbits showed deposition of ECM with structures resembling cartilage lacunae by Alcian blue staining. However, extracellular calcium deposition became detectable over the course of 12 weeks. RT-PCR showed evidence of endochondral ossification during the time course with the expression of specific marker genes (collagen X and RUNX-2). In conclusion, hASCs show chondrogenic differentiation capacity in vitro with the expression of specific marker genes and deposition of cartilage-specific ECM proteins. After implantation of predifferentiated rASC-seeded PU-fibrin scaffolds into a cartilage defect, the constructs undergo the route of endochondral ossification.
Dynamic Information Flow Tracking: Taxonomy, Challenges, and Opportunities

Dynamic information flow tracking (DIFT) has been proven an effective technique to track data usage; prevent control data attacks and non-control data attacks at runtime; and analyze program performance. Therefore, a series of DIFT techniques have been developed recently. In this paper, we summarize the current DIFT solutions and analyze the features and limitations of these solutions. Based on the analysis, we classify the existing solutions into three categories, i.e., software, hardware, software and hardware co-design. We discuss the DIFT design from the perspective of whole system and point out the limitations of current DIFT frameworks. Potential enhancements to these solutions are also presented. Furthermore, we present suggestions about the possible future direction of DIFT solutions so that DIFT can help improve security levels.
Implementation of Deep Ultraviolet Raman Spectroscopy

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Development and Validation of the Mood Instability Questionnaire-Trait (MIQ-T)

Background and objectives: Mood instability (MI) is a stable trait associated with psychiatric disorders, yet there is a lack of tools to measure MI. The purpose of this study was to develop and validate the Mood Instability Questionnaire-Trait (MIQ-T) to evaluate MI in mood disorder patients. Material and methods: Items were taken from various established questionnaires to create an initial list of MIQ-T questions. Data from 309 psychiatric patients (n = 309; 62 major depressive disorder, 58 bipolar I disorder, and 189 bipolar II disorder) were gathered from their medical records and were utilized in an exploratory factor analysis to clarify the underlying components of MI. Then, anonymous survey data from 288 individuals from the general population were included in the analysis as a comparison group. Associations between MIQ-T and other previously validated clinical instruments for mood disorders were examined to test external validity. Results: The exploratory factor analysis demonstrated that the five-factor structure (Lability, Upward Tendency, Downward Tendency, Childhood Instability, and Seasonality) of 59 items was the most appropriate with clear, cohesive features. MIQ-T exhibited high internal consistency (α = 0.96) and moderate to strong correlations with other previously validated clinical instruments, which were consistent with theoretical predictions, providing evidence of criterion validity. Short forms were also created to address the high internal consistency value, which can indicate redundancy, and to increase the approachability of the measure. We found that the patients with bipolar II disorder had higher MIQ-T scores than the patients with bipolar I disorder or major depressive disorder and the comparison group. Conclusion: Together, these findings validate the newly developed MIQ-T as an instrument of mood instability. MIQ-T can be a potential research tool for mood disorder.
Patient-Specific Guided Osteotomy to Correct a Symptomatic Malunion of the Left Forearm

We present a case report of a 12-year old female with a midshaft forearm fracture. Initial conservative treatment with a cast failed, resulting in a malunion. The malunion resulted in functional impairment for which surgery was indicated. A corrective osteotomy was planned using 3D analyses of the preoperative CT-scan. Subsequently, patient-specific guides were printed and used during the procedure to precisely correct the malunion. Three months after surgery, the radiographs showed full consolidation and the patient was pain-free with full range of motion and comparable strength in both forearms. The current case report shows that a corrective osteotomy with patient-specific guides based on preoperative 3D analyses can help surgeons to plan and precisely correct complex malunions resulting in improved functional outcomes.
Integrating Geometric Data into Topology Optimization via Neural Style Transfer

This research proposes a novel topology optimization method using neural style transfer to simultaneously optimize both structural performance for a given loading condition and geometric similarity for a reference design. For the neural style transfer, the convolutional layers of a pre-trained neural network extract and quantify characteristic features from the reference and input designs for optimization. The optimization analysis is evaluated as a single weighted objective function with the ability for the user to control the influence of the neural style transfer with the structural performance. As seen in architecture and consumer-facing products, the visual appeal of a design contributes to its overall value along with mechanical performance metrics. Using this method, a designer allows the tool to find the ideal compromise of these metrics. Three case studies are included to demonstrate the capabilities of this method with various loading conditions and reference designs. The structural performances of the novel designs are within 10% of the baseline without geometric reference, and the designs incorporate features in the given reference such as member size or meshed features. The performance of the proposed optimizer is compared against other optimizers without the geometric similarity constraint.
New Insights on the Vibrational Dynamics of 2-Methoxy-, 4-Methoxy- and 4-Ethoxy-Benzaldehyde from INS Spectra and Periodic DFT Calculations

The dynamics of 2-methoxybenzaldehyde, 4-methoxybenzaldehyde, and 4-ethoxybenzaldehyde in the solid state are assessed through INS spectroscopy combined with periodic DFT calculations. In the absence of experimental data for 4-ethoxybenzaldehyde, a tentative crystal structure, based on its similarity with 4-methoxybenzaldehyde, is considered and evaluated. The excellent agreement between calculated and experimental spectra allows a confident assignment of the vibrational modes. Several spectral features in the INS spectra are unambiguously assigned and torsional potential barriers for the methyl groups are derived from experimental frequencies. The intramolecular nature of the potential energy barrier for methyl rotation about O–CH3 bonds compares with the one reported for torsion about saturated C–CH3 bonds. On the other hand, the intermolecular contribution to the potential energy barrier may represent 1/3 of the barrier height in these systems.
Changes in the Gut Bacteria Composition of Healthy Men with the Same Nutritional Profile Undergoing 10-Week Aerobic Exercise Training: A Randomized Controlled Trial

Nutrient consumption and body mass index (BMI) are closely related to the gut microbiota, and exercise effects on gut bacteria composition may be related to those variables. Thus, we aimed to investigate the effect of 10-week moderate aerobic exercise on the cardiorespiratory fitness and gut bacteria composition of non-obese men with the same nutritional profile. Twenty-four previously sedentary men (age 25.18 [SD 4.66] years, BMI 24.5 [SD 3.72] kg/m2) were randomly assigned into Control (CG; n = 12) or Exercise Groups (EG; n = 12). Body composition, cardiorespiratory parameters, blood markers, dietary habits and gut bacteria composition were evaluated. EG performed 150 min per week of supervised moderate (60–65% of VO2peak) aerobic exercise, while CG maintained their daily routine. The V4 16S rRNA gene was sequenced and treated using QIIME software. Only EG demonstrated marked improvements in cardiorespiratory fitness (VO2peak, p < 0.05; Effect Size = 0.971) without changes in other gut bacteria-affecting variables. Exercise did not promote clustering based on diversity indices (p > 0.05), although significant variations in an unclassified genus from Clostridiales order and in Streptococcus genus were observed (p < 0.05). Moreover, α-diversity was correlated with VO2peak (Pearson’s R: 0.47; R2 0.23: 95%CI: 0.09 to 0.74, p = 0.02) and BMI (Pearson’s R: −0.50; R2 0.25: 95%CI: −0.75 to −0.12, p = 0.01). Roseburia, Sutterella and Odoribacter genera were associated with VO2peak, while Desulfovibrio and Faecalibacterium genera were associated with body composition (p < 0.05). Our study indicates that aerobic exercise at moderate intensity improved VO2peak and affected gut bacteria composition of non-obese men who maintained a balanced consumption of nutrients.
Comprehensive Use of Routine Clinical Parameters to Identify Patients at Risk of New-Onset Atrial Fibrillation in Acute Myocardial Infarction

(1) Background: New-onset atrial fibrillation (NOAF) is a significant complication of acute myocardial infarction (AMI). Our study aimed to investigate whether routinely checked clinical parameters aid in NOAF identification in modernly treated AMI patients. (2) Patients and methods: Patients admitted consecutively within 2017 and 2018 to the University Clinical Centre in Gdańsk (Poland) with AMI diagnosis (necrosis evidence in a clinical setting consistent with acute myocardial ischemia) were enrolled. Medical history and clinical parameters were checked during NOAF prediction. (3) Results: NOAF was diagnosed in 106 (11%) of 954 patients and was significantly associated with in-hospital mortality (OR 4.54, 95% CI 2.50–8.33, p < 0.001). Age, B-type natriuretic peptide (BNP), C-reactive protein (CRP), high-sensitivity troponin I, total cholesterol, low-density lipoprotein cholesterol, potassium, hemoglobin, leucocytes, neutrophil/lymphocyte ratio, left atrium size, and left ventricular ejection fraction (LVEF) were associated with NOAF in the univariate logistic analysis, whereas age ≥ 66 yo, BNP ≥ 340 pg/mL, CRP ≥ 7.7 mg/L, and LVEF ≤ 44% were associated with NOAF in the multivariate analysis. (4) Conclusions: NOAF is a multifactorial, significant complication of AMI, leading to a worse prognosis. Simple, routinely checked clinical parameters could be helpful indices of this arrhythmia in current invasively treated patients with AMI.