Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation

Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that Pseudomonas aeruginosa PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in P. aeruginosa PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in P. aeruginosa PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene recA. The OMV production was significantly impaired in the irradiated PAO1 Δlys mutant, suggesting that Lys endolysin is associated with OMV production in P. aeruginosa PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the pqsR, lasR, or rhlR genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of P. aeruginosa was independent of the Pseudomonas quinolone signal (PQS).
Recent Advances of Osterix Transcription Factor in Osteoblast Differentiation and Bone Formation

With increasing life expectations, more and more patients suffer from fractures either induced by intensive sports or other bone-related diseases. The balance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption is the basis for maintaining bone health. Osterix (Osx) has long been known to be an essential transcription factor for the osteoblast differentiation and bone mineralization. Emerging evidence suggests that Osx not only plays an important role in intramembranous bone formation, but also affects endochondral ossification by participating in the terminal cartilage differentiation. Given its essentiality in skeletal development and bone formation, Osx has become a new research hotspot in recent years. In this review, we focus on the progress of Osx’s function and its regulation in osteoblast differentiation and bone mass. And the potential role of Osx in developing new therapeutic strategies for osteolytic diseases was discussed.
Insight Into Nanoliposomes as Smart Nanocarriers for Greening the Twenty-First Century Biomedical Settings

The necessity to develop more efficient, biocompatible, patient compliance, and safer treatments in biomedical settings is receiving special attention using nanotechnology as a potential platform to design new drug delivery systems (DDS). Despite the broad range of nanocarrier systems in drug delivery, lack of biocompatibility, poor penetration, low entrapment efficiency, and toxicity are significant challenges that remain to address. Such practices are even more demanding when bioactive agents are intended to be loaded on a nanocarrier system, especially for topical treatment purposes. For the aforesaid reasons, the search for more efficient nano-vesicular systems, such as nanoliposomes, with a high biocompatibility index and controlled releases has increased considerably in the past few decades. Owing to the stratum corneum layer barrier of the skin, the in-practice conventional/conformist drug delivery methods are inefficient, and the effect of the administered therapeutic cues is limited. The current advancement at the nanoscale has transformed the drug delivery sector. Nanoliposomes, as robust nanocarriers, are becoming popular for biomedical applications because of safety, patient compliance, and quick action. Herein, we reviewed state-of-the-art nanoliposomes as a smart and sophisticated drug delivery approach. Following a brief introduction, the drug delivery mechanism of nanoliposomes is discussed with suitable examples for the treatment of numerous diseases with a brief emphasis on fungal infections. The latter half of the work is focused on the applied perspective and clinical translation of nanoliposomes. Furthermore, a detailed overview of clinical applications and future perspectives has been included in this review.
The Co-existence of ADHD With Autism in Saudi Children: An Analysis Using Next-Generation DNA Sequencing

Attention-deficit/hyperactivity disorder (ADHD) is one of the most common neurodevelopmental disorders. Several studies have confirmed the co-existence of other neuropsychiatric disorders with ADHD. Out of 106 individuals suspected to have ADHD, eight Saudi Arabian pediatric patients were diagnosed with ADHD using a dual assessment procedure based on highly significant scores from the international criteria for diagnosis; (full form DMS) DSM-5. Then, these patients were examined for the co-existence of autism and ADHD using different international diagnostic protocols. Four patients with combined ADHD and autism and four ADHD patients without autism were examined for the presence of genetic variants. Six variants (chr1:98165091, chr6:32029183, chr6:32035603, chr6:32064098, chr8:2909992, chr16:84213434) were identified in 75% of the patients with ADHD and autism, indicating that these genes may have a possible role in causing autism. Five variants (The chr2:116525960, chr15:68624396, chr15:91452595, chr15:92647645, and chr16:82673047) may increase to the severity of ADHD. This study recommends screening these eleven variants in ADHD cases and their relevant controls to confirm the prevalence in the Saudi population. It is recommended that future studies examine the 11 variants in detail.
Salmonella spvC Gene Inhibits Pyroptosis and Intestinal Inflammation to Aggravate Systemic Infection in Mice

Salmonella enterica serovar Typhimurium (S). Typhimurium is a primary foodborne pathogen infecting both humans and animals. Salmonella plasmid virulence C (spvC) gene is closely related to S. Typhimurium dissemination in mice, while the mechanisms remain to be fully elucidated. Pyroptosis, a gasdermin-mediated inflammatory cell death, plays a role in host defense against bacterial infection, whereas the effect of spvC on pyroptosis and its function in inflammatory injury induced by S. Typhimurium are rather limited. In our study, C57BL/6 mice and J774A.1 cells infected with S. Typhimurium wild-type strain SL1344, spvC deletion mutant, spvC K136A site-directed mutant, and complemented strain were used to investigate potential pathogenesis of spvC. We verity that SpvC attenuates intestinal inflammation, suppresses pyroptosis through phosphothreonine lyase activity, and reduces pyroptosis in the ceca. Moreover, the reduction of inflammation via spvC results in systemic infection. These findings demonstrate that spvC inhibits pyroptosis and intestinal inflammation to promote bacterial dissemination, which provide new strategies for controlling systemic infection caused by Salmonella and novel insights for the treatment of other corresponding diseases.
Metabolite Fingerprinting of Kersting's Groundnut [Macrotyloma geocarpum (Harms) Maréchal & Baudet] Seeds Using UPLC-qTOF-MS Reveals the Nutraceutical and Antioxidant Potentials of the Orphan Legume

The identification and subsequent quantification of phenolic compounds in plants is the first step toward harnessing their associated nutritional and health benefits. Due to their diverse phenolic compound compositions, grain legumes are known for their high nutritional and health values. The aim of this study was to assess the inter-variations in chemical composition, phytochemical content, and antioxidant capacity of seed extracts from eight Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] landraces. The chemical profiles were evaluated using UPLC-qTOF-MS. Total phenolics and flavonoids content were determined by the Folin-Ciocalteu and aluminum chloride methods, respectively. The antioxidant capacities in the forms of DPPH and ABTS were evaluated using spectrophotometric methods. Principal component analysis was used to define similarities/differences between the landraces. Based on untargeted metabolomics analysis, 57 metabolites were identified, with phenolics, triterpenes, fatty acids, and sphingolipids being the most predominant. The results showed that the black seeded KG1 (Puffeun) had the highest total phenolic (9.44 mg GAE/g) and flavonoid (3.01 mg QE/g) contents, as well as antioxidant capacity (9.17 μg/mL and 18.44 μg/mL based on DDPH and ABTS assays, respectively). The concentrations of ferulic acid hexoside, procyanidin B2, eryodictyiol-7-rutinoside and quercetin pentoside ranged from 51.78–441.31, 1.86–18.25, 3.26–13.95 to 5.44–63.85 μg/mg, respectively. This study presents a useful report on the phytochemical characterization of Kersting's groundnuts and shows that the grains can be used as a source of nutraceuticals for human consumption.
Analysis of student perceptions of scientific models: validation of a Spanish-adapted version of the Students’ Understanding of Models in Science instrument

ABSTRACT We present the results of a study of Chilean students’ understanding of scientific models, using a Spanish-adapted version of the Students’ Understanding of Models in Science instrument (Treagust, D. F., Chittleborough, G., & Mamiala, T. L. (2002). Students understanding of the role of scientific models in learning science. International Journal of Science Education, 24(4), 357–368. doi:10.1080/09500690110066485). The study covered 290 students in three schools in different parts of Chile. Results showed a Cronbach's alpha of 0.86 and medium correlation between the dimensions of the instrument. A confirmatory factor analysis showed that the five dimensions’ theoretical structure is supported by the data, and one-way ANOVA and a t-test showed a balanced, non-discriminatory instrument that is suited for use in the Spanish language. The instrument also showed that Chilean students most need improvement in two of the dimensions – ‘understanding of scientific models in terms of exact replicas’ and the ‘use of scientific models’. This reflects the original data analysed by Treagust et al. (2002) and suggests that these factors are common issues in the teaching and learning of scientific models. Future research will review the data by year and group to determine how students develop the idea of a scientific model and relate this information to science curricula. It will also investigate the link between students’ understanding of scientific models and Anderson & Krathwohl's (2001) cognitive taxonomy.
Dislocations and their dissociation in SixGe1 - x alloys

Abstract The dissociation of dislocations in undeformed SixGe1 - x crystals grown from the melt with low (x = 0.05) and high (x = 0.5) Si contents was investigated using the weak-beam electron microscopy technique. Dislocations with total Burgers vectors b=½ and of various orientations were found to be dissociated into Shockley partials, separated by an intrinsic stacking fault on a {111} glide plane. Extended dislocation nodes were also observed. For x = 0.05 the dissociation widths of single dislocations ranged from Δ = 3.5 ± 1 nm for screw orientations to Δ = 6.2 ± 1 nm for edge orientations. The corresponding values for x = 0.5 were higher, with separations between Δ = 3.9 ± 1 nm and Δ = 6.9 ± 1 nm. Stacking-fault energies γ = 56 ± 8 mJ m−2 for x = 0.05 and γ = 53 ± 8 mJ m−2 for x = 0.5 were deduced from measurements of the dissociation widths as a function of dislocation orientation, using anisotropic elasticity theory. The results are compared with those of previous investigations on elemental .
Anti-sortilin1 Antibody Up-Regulates Progranulin via Sortilin1 Down-Regulation

Progranulin (PGRN) haploinsufficiency associated with loss-of-function mutations in the granulin gene causes frontotemporal dementia (FTD). This suggests that increasing PGRN levels could have promising therapeutic implications for patients carrying GRN mutations. In this study, we explored the therapeutic potential of sortilin1 (SORT1), a clearance receptor of PGRN, by generating and characterizing monoclonal antibodies against SORT1. Anti-SORT1 monoclonal antibodies were generated by immunizing Sort1 knockout mice with SORT1 protein. The antibodies were classified into 7 epitope bins based on their competitive binding to the SORT1 protein and further defined by epitope bin-dependent characteristics, including SORT1-PGRN blocking, SORT1 down-regulation, and binding to human and mouse SORT1. We identified a positive correlation between PGRN up-regulation and SORT1 down-regulation. Furthermore, we also characterized K1-67 antibody via SORT1 down-regulation and binding to mouse SORT1 in vivo and confirmed that K1-67 significantly up-regulated PGRN levels in plasma and brain interstitial fluid of mice. These data indicate that SORT1 down-regulation is a key mechanism in increasing PGRN levels via anti-SORT1 antibodies and suggest that SORT1 is a potential target to correct PGRN reduction, such as that in patients with FTD caused by GRN mutation.
Effect of Plant Growth Promoting Rhizobacteria (PGPR) and Arbuscular Mycorrhizal Fungi (AMF) on Salt Stress Tolerance of Casuarina obesa (Miq.)

Salinity is one of the main abiotic stresses limiting plant growth and development. However, the use of salt-tolerant plants combined with beneficial soil microorganisms could improve the effectiveness of biological methods for saline soil recovery. The aim of this study is to identify the Casuarina obesa/ Arbuscular Mycorrhizal fungi (AMF)/Plant Growth Promoting Rhizobacteria (PGPR) association that could be used in salt-land rehabilitation programs. Thus, the plants were grown under greenhouse on sandy soil, inoculated either with PGPR (Pantoea agglomerans and Bacillus sp.), or with AMF (Rhizophagus fasciculatus and Rhizophagus aggregatum) or co inoculated with PGPR and AMF and watered with a saline solution (0, 150, and 300 mM). After 4 months of cultivation, the plants were harvested and the results obtained showed that inoculation improves the survival rate, height and biomass of the plants compared to the control plants. The results also showed that inoculation increases the total amount of chlorophyll and the accumulation of plant proline at all levels of salt concentration. However, P. agglomerans and Bacillus sp. strains alone or in combination with R. fasciculatus increased plant growth. This study showed that these strains of PGPR, whether or not associated with AMF, could be biological tools to improve C. obesa performance under saline stress conditions.
Emerald Ash Borer Specific Gene Silencing Has No Effect on Non-target Organisms

The sequence complementarity of the RNA interference (RNAi) pathway allows for targeted suppression of genes essential for insect survival, and enables development of pest management strategies specific to a given species while reducing the likelihood of adversely impacting non-target organisms (NTOs). The feasibility of manipulating the RNAi pathway to cause mortality in the highly invasive emerald ash borer (EAB) has been demonstrated. Here the spectrum of activity of three double stranded RNAs (dsRNAs) targeting the genes hsp, shi, and sn-rnp in EAB was evaluated in model insects representing five functional guilds including herbivore, predator, detritivore, pollinator, parasitoid; the last represented by the classical biological control agents currently deployed for EAB management in North America. All NTOs were exposed to EAB-specific dsRNAs in diet bioassays that measured potential lethal effects. Gene expression and in silico analysis were also assessed on NTOs for which gene sequences were publicly available. Bioassays demonstrated no lethal effects on our model insects, suggesting a narrow spectrum of activity for the three EAB-specific dsRNAs evaluated. The gene expression and in silico analyses suggest potential sublethal effects on our model pollinator; however we found no effects on insect survival. Overall, our results suggest no adverse effects of the RNAi strategy targeting EAB genes on the survival of the selected non-target organisms we evaluated. The results from this study provide guidance for future RNAi risk analyses that will allow this technology to move forward to a deployment stage.
Optical Properties of Liquid Germanium

The reflectivity of liquid germanium is measured in the photon energy range 3.1 to 5.4 eV and approximate values of optical constants are determined by a Kramers-Kronig analysis. It is shown that the dependence of the optical constants on photon energy can be well described by free carrier formulas for energies up to 2.2 eV. At higher energies, evidence for interband transitions has been found. It appears that the first absorption band starts at about 5 eV but its peak lies outside the presently available photon energy range. Das Reflexionsvermogen von flussigem Germanium wird im Photonenergiebereich zwischen 3,1 und 5,4 eV untersucht. Naherungsausdrucke fur die optischen Konstanten werden mit Hilfe der Kramers-Kronig-Analyse erhalten. Es wird gezeigt, das die optischen Konstanten bis zu Photonenenergien von 2,2 eV gut durch freie-Trager-Beziehungen beschrieben werden konnen. Bei hohen Energien werden Band-Band-Ubergange gefunden. Die erste Absorptionsbande beginnt bei etwa 5 eV, ihr Maximum liegt aber auserhalb der verfugbaren Photonenenergien.
Comparative Analysis of Systemic and Tumor Microenvironment Proteomes From Children With B-Cell Acute Lymphocytic Leukemia at Diagnosis and After Induction Treatment

Among the childhood diseases, B-cell acute lymphocytic leukemia (B-ALL) is the most frequent type of cancer. Despite recent advances concerning disease treatment, cytotoxic chemotherapy remains the first line of treatment in several countries, and the modifications induced by such drugs in the organism are still poorly understood. In this context, the present study provided a comparative high-throughput proteomic analysis of the cumulative changes induced by chemotherapeutic drugs used in the induction phase of B-ALL treatment in both peripheral blood (PB) and bone marrow compartment (BM) samples. To reach this goal, PB and BM plasma samples were comparatively analyzed by using label-free proteomics at two endpoints: at diagnosis (D0) and the end of the cumulative induction phase treatment (D28). Proteomic data was available via ProteomeXchange with identifier PXD021584. The resulting differentially expressed proteins were explored by bioinformatics approaches aiming to identify the main gene ontology processes, pathways, and transcription factors altered by chemotherapy, as well as to understand B-ALL biology in each compartment at D0. At D0, PB was characterized as a pro-inflammatory environment, with the involvement of several downregulated coagulation proteins as KNG, plasmin, and plasminogen. D28 was characterized predominantly by immune response-related processes and the super expression of the transcription factor IRF3 and transthyretin. RUNX1 was pointed out as a common transcription factor found in both D0 and D28. We chose to validate the proteins transthyretin and interferon-gamma (IFN-γ) by commercial kits and expressed the results as PB/BM ratios. Transthyretin ratio was augmented after induction chemotherapy, while IFN-γ was reduced at the end of the treatment. Considering that most of these proteins were not yet described in B-ALL literature, these findings added to understanding disease biology at diagnosis and highlighted a possible role for transthyretin and IFN-γ as mechanisms related to disease resolution.
Antimicrobial Resistance as a Hidden Menace Lurking Behind the COVID-19 Outbreak: The Global Impacts of Too Much Hygiene on AMR

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus that was recently discovered in 2019. While the world is working hard to overcome and control the coronavirus disease 2019 (COVID-19) pandemic, it is also crucial to be prepared for the great impacts of this outbreak on the development of antimicrobial resistance (AMR). It is predicted that inappropriate and too much use of antibiotics, biocides, and disinfectants during this pandemic may raise disastrous effects on antibiotic stewardship programs and AMR control all around the world. Furthermore, the use of certain antibiotics alone or in combination with antiviral agents or other medications for the treatment of secondary bacterial infections among COVID-19 patients may be regarded as a major factor that negatively affects host immune response by disrupting mitochondrial function and activity. Herein, we suggest that the current management strategies to control AMR and prioritize antibiotic stewardship schemes should be extremely highlighted in relation to the COVID-19 outbreak. The rising concerns about excessive use of antimicrobials and biocides and taking too much hygiene also need to be addressed during this pandemic due to their impacts on AMR, public health, and the environment.
Global Interconnects in VLSI Complexity Single Flux Quantum Systems

On-chip signal routing has become an issue of growing importance in modern VLSI complexity single flux quantum (SFQ) systems. In this paper, different routing methods for these systems are described. The routing methods include either passive transmission lines (PTLs) or Josephson transmission lines (JTLs) as interconnects. Driving multiple SFQ gates is also a challenging issue in automated layout and clock tree synthesis (CTS) due to the limited fanout of SFQ gates. To support multiple fanout, splitters are used to distribute multiple SFQ pulses. These splitters require significant area, delay, and power. In this paper, several area and power efficient splitters are proposed for large scale SFQ integrated circuits. A primary issue within a long SFQ interconnect is resonance effects due to the imperfect match between the PTLs and Josephson junctions. A repeater insertion methodology for long interconnect to reduce and manage these resonance effects is also described. Summarizing, guidelines and tradeoffs appropriate for automated layout and synthesis are described for driving long and short interconnect in VLSI complexity SFQ systems.
A Novel Predictive Tool for Determining the Risk of Early Death From Stage IV Endometrial Carcinoma: A Large Cohort Study

Background Endometrial carcinoma is a common gynecological malignancy. Stage IV endometrial carcinoma is associated with a high risk of early death; however, there is currently no effective prognostic tool to predict early death in stage IV endometrial cancer. Methods Surveillance, Epidemiology, and End Results (SEER) data from patients with stage IV endometrial cancer registered between 2004 and 2015 were used in this study. Important independent prognostic factors were identified by univariate and multivariate logistic regression analyses. A nomogram of all-cause and cancer-specific early deaths was constructed using relevant risk factors such as tumor size, histological grade, histological classification, and treatment (surgery, radiotherapy, chemotherapy). Results A total of 2,040 patients with stage IV endometrial carcinoma were included in this study. Of these, 299 patients experienced early death (≤3 months) and 282 died from cancer-specific causes. The nomogram of all-cause and cancer-specific early deaths showed good predictive power and clinical practicality with respect to the area under the receiver operating characteristic curve and decision curve analysis. The internal validation of the nomogram revealed a good agreement between predicted early death and actual early death. Conclusions We developed a clinically useful nomogram to predict early mortality from stage IV endometrial carcinoma using data from a large cohort. This tool can help clinicians screen high-risk patients and implement individualized treatment regimens.