Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Next-Generation Sequencing for the Determination of the Bacterial Community in the Gut Contents of Brackish Copepod Species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)

Simple Summary Copepods are important components of marine coastal food chains, supporting fishery resources by providing prey items mainly for fish. Copepods interact with small microorganisms via feeding on phytoplankton. DNA methods can determine the gut contents of copepods and provide important information regarding how copepods interact with phytoplankton and bacteria. In the present study, we designed a method for extracting the gut content DNA from small-sized copepods that are important in coastal and brackish areas. Based on DNA analyses, Rhodobacteraceae, which is common in marine waters and sediments, was most abundant in the gut contents of the three copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus). However, the detailed composition of bacteria was different among species and locations. The results suggested that environmental variables and species-specific feeding behaviour can affect the gut bacterial community. The bacteria play an important role in digestion and in the overall degradation and release of metabolites to the outside water. Further analyses with advanced methods regarding DNA isolation from small microorganisms and identification skills using a DNA library for better understanding of biological interactions and matter cycling in marine food webs are required. Abstract The gut bacterial communities of copepods can affect metabolic processes, and consequently, their activity can be related to the release of organic substances to the environment. Hence, they are important for organic matter cycling in marine coast food webs. However, information regarding the variation in gut bacterial communities based on copepod species and environmental variations is limited. We analysed the differences in gut bacterial communities from dominant copepod species, i.e., Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus, in a brackish reservoir. The core bacteria among the copepod species and locations consisted of the following main operational taxonomic units (OTUs): Novosphingobium capsulatum and the family Rhodobacteraceae belonging to Alphaproteobacteria, which is abundant in seawater and freshwater aquatic ecosystems as a zooplankton-associated bacterial community. The bacterial community composition of each copepod (except the core species) showed high variability. The bacterial community diversity differed depending on the copepod species and the sites’ environmental conditions, especially salinity, e.g., compositional variations in the bacterial community of P. inopinus were high at sites with low salinity. Therefore, the gut bacterial community of each copepod species responds differently to the environment.
Comparative Evaluation of Four Extraction Methods of Antioxidant Compounds from Decatropis bicolor in Aqueous Medium Applying Response Surface Design

The objective of this paper is to compare conventional, ultrasound, microwave, and French press methods for the extraction of antioxidant compounds from Decatropis bicolor in an aqueous medium. This plant is widely used in Mexican traditional medicine for breast cancer treatment. Despite that, there are few studies on D. bicolor. Two response surface designs were applied to establish the best conditions of the liberation of antioxidants from D. bicolor, which were determined by DPPH• and Ferric Reducing Antioxidant Power (FRAP) techniques. The total phenolic content was evaluated by the Folin-Ciocalteu method. The results showed that D. bicolor is a source of antioxidants (669–2128 mg ET/100 g and 553–1920 mg EFe2+/100 g, respectively) and phenolic compounds (2232–9929 mg EGA/100 g). Among the physical factors that were analyzed, the temperature was the determinant factor to liberate the compounds of interest by using low concentrations of the sample and short times of extraction. The French press was the most efficient method, obtaining values of antioxidant activity and phenolic compounds even higher than those reported by using extraction methods with solvents such as methanol.
Ablation of Aquaporin-9 Ameliorates the Systemic Inflammatory Response of LPS-Induced Endotoxic Shock in Mouse

Septic shock is the most severe complication of sepsis, being characterized by a systemic inflammatory response following bacterial infection, leading to multiple organ failure and dramatically high mortality. Aquaporin-9 (AQP9), a membrane channel protein mainly expressed in hepatocytes and leukocytes, has been recently associated with inflammatory and infectious responses, thus triggering strong interest as a potential target for reducing septic shock-dependent mortality. Here, we evaluated whether AQP9 contributes to murine systemic inflammation during endotoxic shock. Wild type (Aqp9+/+; WT) and Aqp9 gene knockout (Aqp9−/−; KO) male mice were submitted to endotoxic shock by i.p. injection of lipopolysaccharide (LPS; 40 mg/kg) and the related survival times were followed during 72 h. The electronic paramagnetic resonance and confocal microscopy were employed to analyze the nitric oxide (NO) and superoxide anion (O2−) production, and the expression of inducible NO-synthase (iNOS) and cyclooxigenase-2 (COX-2), respectively, in the liver, kidney, aorta, heart and lung of the mouse specimens. LPS-treated KO mice survived significantly longer than corresponding WT mice, and 25% of the KO mice fully recovered from the endotoxin treatment. The LPS-injected KO mice showed lower inflammatory NO and O2− productions and reduced iNOS and COX-2 levels through impaired NF-κB p65 activation in the liver, kidney, aorta, and heart as compared to the LPS-treated WT mice. Consistent with these results, the treatment of FaO cells, a rodent hepatoma cell line, with the AQP9 blocker HTS13268 prevented the LPS-induced increase of inflammatory NO and O2−. A role for AQP9 is suggested in the early acute phase of LPS-induced endotoxic shock involving NF-κB signaling. The modulation of AQP9 expression/function may reveal to be useful in developing novel endotoxemia therapeutics.
Identification of the hub gene BUB1B in hepatocellular carcinoma via bioinformatic analysis and in vitro experiments

Background Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers and the fourth leading cause of cancer-related deaths in the world. Although the treatment of HCC has made great progress in recent years, the therapeutic effects on HCC are still unsatisfactory due to difficulty in early diagnosis, chemoresistance and high recurrence rate post-surgery. Methods In this study, we identified differentially expressed genes (DEGs) based on four Gene Expression Omnibus (GEO) datasets (GSE45267, GSE98383, GSE101685 and GSE112790) between HCC and normal hepatic tissues. A protein–protein interaction (PPI) network was established to identify the central nodes associated with HCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the central nodes were conducted to find the hub genes. The expression levels of the hub genes were validated based on the ONCOMINE and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Additionally, the genetic alterations of the hub genes were evaluated by cBioPortal. The role of the hub genes on the overall survival (OS) and relapse survival (RFS) of HCC patients was evaluated by Kaplan-Meier plotter. At last, the mechanistic role of the hub genes was illustrated by in vitro experiments. Results We found the following seven hub genes: BUB1B, CCNB1, CCNB2, CDC20, CDK1, MAD2L1 and RRM2 using integrated bioinformatics analysis. All of the hub genes were significantly upregulated in HCC tissues. And the seven hub genes were associated with the OS and RFS of HCC patients. Finally, in vitro experiments indicated that BUB1B played roles in HCC cell proliferation, migration, invasion, apoptosis and cell cycle by partially affecting mitochondrial functions. Conclusions In summary, we identified seven hub genes that were associated with the expression and prognosis of HCC. The mechanistic oncogenic role of BUB1B in HCC was first illustrated. BUB1B might play an important role in HCC and could be potential therapeutic targets for HCC.
Reg4 and its downstream transcriptional activator CD44ICD in stage II and III colorectal cancer

Reg4 is highly expressed in gastrointestinal malignancies and acts as a mitogenic and pro-invasive factor. Our recent works suggest that Reg4 binds with CD44 and induces its proteolytic cleavage to release intra-cytoplasmic domain of CD44 (CD44ICD). The goal of this study is to demonstrate clinical significance of the Reg4-CD44/CD44ICD pathway in stage II/III colon cancer and its association with clinical parameters of aggression. We constructed a tissue microarray (TMA) of 93 stage II/III matched colon adenocarcinoma patients, 23 with recurrent disease. The TMA was immunohistochemically stained for Reg4, CD44, and CD44ICD proteins and analyzed to identify associations with tumor characteristics, recurrence and overall survival. The TMA data analysis showed a significant correlation between Reg4 and CD44 (r2 = 0.23, P = 0.028), CD44 and CD44ICD (r2 = 0.36, p = 0.0004), and Reg4 and CD44ICD (r2 = 0.45, p ≤ 0.0001). Reg4 expression was associated with larger tumor size (r2 = 0.23, p = 0.026). Although, no association was observed between Reg4, CD44, or CD44ICD expression and disease recurrence, Reg4-positive patients had a median survival of 4 years vs. 7 years for Reg4-negative patients (p = 0.04) in patients who recurred. Inhibition of the Reg4-CD44/CD44ICD pathway may be a future therapeutic target for colon cancer patients.
Fourier Transform Infrared (FTIR) Spectroscopic Analyses of Microbiological Samples and Biogenic Selenium Nanoparticles of Microbial Origin: Sample Preparation Effects

To demonstrate the importance of sample preparation used in Fourier transform infrared (FTIR) spectroscopy of microbiological materials, bacterial biomass samples with and without grinding and after different drying periods (1.5–23 h at 45 °C), as well as biogenic selenium nanoparticles (SeNPs; without washing and after one to three washing steps) were comparatively studied by transmission FTIR spectroscopy. For preparing bacterial biomass samples, Azospirillum brasilense Sp7 and A. baldaniorum Sp245 (earlier known as A. brasilense Sp245) were used. The SeNPs were obtained using A. brasilense Sp7 incubated with selenite. Grinding of the biomass samples was shown to result in slight downshifting of the bands related to cellular poly-3-hydroxybutyrate (PHB) present in the samples in small amounts (under ~10%), reflecting its partial crystallisation. Drying for 23 h was shown to give more reproducible FTIR spectra of bacterial samples. SeNPs were shown to contain capping layers of proteins, polysaccharides and lipids. The as-prepared SeNPs contained significant amounts of carboxylated components in their bioorganic capping, which appeared to be weakly bound and were largely removed after washing. Spectroscopic characteristics and changes induced by various sample preparation steps are discussed with regard to optimising sample treatment procedures for FTIR spectroscopic analyses of microbiological specimens.
Validation of a Three-Dimensional Head and Neck Spheroid Model to Evaluate Cameras for NIR Fluorescence-Guided Cancer Surgery

Near-infrared (NIR) fluorescence-guided surgery is an innovative technique for the real-time visualization of resection margins. The aim of this study was to develop a head and neck multicellular tumor spheroid model and to explore the possibilities offered by it for the evaluation of cameras for NIR fluorescence-guided surgery protocols. FaDu spheroids were incubated with indocyanine green (ICG) and then included in a tissue-like phantom. To assess the capability of Fluobeam® NIR camera to detect ICG in tissues, FaDu spheroids exposed to ICG were embedded in 2, 5 or 8 mm of tissue-like phantom. The fluorescence signal was significantly higher between 2, 5 and 8 mm of depth for spheroids treated with more than 5 µg/mL ICG (p < 0.05). The fluorescence intensity positively correlated with the size of spheroids (p < 0.01), while the correlation with depth in the tissue-like phantom was strongly negative (p < 0.001). This multicellular spheroid model embedded in a tissue-like phantom seems to be a simple and reproducible in vitro tumor model, allowing a comparison of NIR cameras. The ideal configuration seems to be 450 μm FaDu spheroids incubated for 24 h with 0.05 mg/mL of ICG, ensuring the best stability, toxicity, incorporation and signal intensity.
Identification and Detection of Botryosphaeria dothidea from Kiwifruit (Actinidia chinensis) in China

Kiwifruit is very popular among consumers due to its high nutritional value. The increasing expansion in kiwifruit cultivation has led to the spread of rot diseases. To identify the pathogens causing kiwifruit ripe rots in China, 24 isolates were isolated from the diseased fruit and wart in trees. Botryosphaeria dothidea was recognized as the pathogen causing kiwifruit ripe rot and wart in the tree through internal transcribed spacer (ITS) sequencing, pathogenicity testing, morphological and microscopic characteristics. The rapid and accurate detection of this pathogen will lead to better disease monitoring and control efforts. A loop-mediated isothermal amplification (LAMP) method was then developed to rapidly and specifically identify B. dothidea. These results offer value to further research into kiwifruit ripe rot, such as disease prediction, pathogen rapid detection, and effective disease control.
Bronsted acid-surfactant (BAS) catalysed cyclotrimerization of aryl methyl ketone

Article history: Received March 30, 2012 Received in Revised form May 9, 2012 Accepted 21 May 2012 Available online 21 May 2012 A bronsted acid-surfactant catalysed and simple, mild, metal catalyst free and chemo-selective method has been developed for synthesis of 1, 3, 5-triaryl benzenes from aryl methyl ketones. The advantages of this protocol subsume green and sustainable reaction medium, mild reaction conditions, easy product recovery and its good yields. © 2012 Growing Science Ltd. All rights reserved.
Prevalence of Sexual Abuse in Adults with Intellectual Disability: Systematic Review and Meta-Analysis

This study presents the results of a systematic review on the prevalence of sexual abuse experienced in adulthood by individuals with intellectual disability. An electronic and manual search of academic journals was performed on four databases via EBSCO Host: Academic Search Complete, PsycINFO, Medline, CINAHL Full-Text. In addition, PubMed, ProQuest, and Web of Science (core collection) were searched. After an initial selection of 1037 documents, 25 articles remained for quantitative synthesis. The combined prevalence of sexual abuse in adults with intellectual disability was 32.9% (95% CI: 22.7–43.0) and sensitivity analysis revealed that the prevalence was not outweighed by a single study. Overall, the United Kingdom had the highest prevalence (r = 34.1%), and the USA had the lowest (r = 15.2%). The overall prevalence in females was lower (r = 31.8%) than that in males (r = 39.9%). Subgroup analyses revealed that prevalence of sexual abuse was higher in institutionalized individuals. The most prevalent profile of abuser is of a peer with intellectual disability. Prevalence increases from mild to severe levels of intellectual disability and decreases in profound levels. It is also more prevalent when the informant is the individual with intellectual disability than when someone else reports abuse. In sum, one in three adults with intellectual disability suffers sexual abuse in adulthood. Special attention should be paid for early detection and intervention in high risk situations.
Inorganic Nanoparticle-Loaded Exosomes for Biomedical Applications

Exosomes are intrinsic cell-derived membrane vesicles in the size range of 40–100 nm, serving as great biomimetic nanocarriers for biomedical applications. These nanocarriers are known to bypass biological barriers, such as the blood–brain barrier, with great potential in treating brain diseases. Exosomes are also shown to be closely associated with cancer metastasis, making them great candidates for tumor targeting. However, the clinical translation of exosomes are facing certain critical challenges, such as reproducible production and in vivo tracking of their localization, distribution, and ultimate fate. Recently, inorganic nanoparticle-loaded exosomes have been shown great benefits in addressing these issues. In this review article, we will discuss the preparation methods of inorganic nanoparticle-loaded exosomes, and their applications in bioimaging and therapy. In addition, we will briefly discuss their potentials in exosome purification.
Hybrid Polycarbosilane-Siloxane Dendrimers: Synthesis and Properties

A series of carbosilane dendrimers of the 4th, 6th, and 7th generations with a terminal trimethylsilylsiloxane layer was synthesized. Theoretical models of these dendrimers were developed, and equilibrium dendrimer conformations obtained via molecular dynamics simulations were in a good agreement with experimental small-angle X-ray scattering (SAXS) data demonstrating molecule monodispersity and an almost spherical shape. It was confirmed that the glass transition temperature is independent of the dendrimer generation, but is greatly affected by the chemical nature of the dendrimer terminal groups. A sharp increase in the zero-shear viscosity of dendrimer melts was found between the 5th and the 7th dendrimer generations, which was qualitatively identical to that previously reported for polycarbosilane dendrimers with butyl terminal groups. The viscoelastic properties of high-generation dendrimers seem to follow some general trends with an increase in the generation number, which are determined by the regular branching structure of dendrimers.
Discrimination of the Geographical Origin of Soybeans Using NMR-Based Metabolomics

With the increase in soybean trade between countries, the intentional mislabeling of the origin of soybeans has become a serious problem worldwide. In this study, metabolic profiling of soybeans from the Republic of Korea and China was performed by nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical analysis to predict the geographical origin of soybeans. The optimal orthogonal partial least squares-discriminant analysis (OPLS-DA) model was obtained using total area normalization and unit variance (UV) scaling, without applying the variable influences on projection (VIP) cut-off value, resulting in 96.9% sensitivity, 94.4% specificity, and 95.6% accuracy in the leave-one-out cross validation (LOO-CV) test for discriminating between Korean and Chinese soybeans. Soybeans from the northeastern, middle, and southern regions of China were successfully differentiated by standardized area normalization and UV scaling with a VIP cut-off value of 1.0, resulting in 100% sensitivity, 91.7%–100% specificity, and 94.4%–100% accuracy in a LOO-CV test. The methods employed in this study can be used to obtain essential information for the authentication of soybean samples from diverse geographical locations in future studies.
Investigation of Multiparameter Laser Stripping of AlTiN and DLC C Coatings

The lifetime and properties of cutting tools and forming moulds can be prolonged and enhanced by the deposition of hard, thin coatings. After a certain period of usage, the coating will deteriorate. Any remaining coating must be removed prior to successful recoating. Laser stripping is a fast and environmentally friendly coating removal method. In this paper, we present laser removal of two types of coatings deposited on a 1.2379 tool steel substrate, namely, an AlTiN coating with high hardness and a DLC C coating with a small coefficient of friction (COF). A powerful nanosecond laser was employed to remove the coating from the substrate with high efficiency, along with suitable residual surface roughness. Measurements were taken of surface roughness, removed depth, and working time on a stripped area of 1 cm2. The samples were evaluated under a microscope, with a 3D profilometer, and by EDS chemical analysis. Successful removal of the coating was confirmed by optical analysis, but detailed chemical characterisation showed that about 30% of the coating element may remain on the surface. Moreover, a working time of less than 7.5 s per cm2 was obtained in this study. In addition, it was shown that the application of a second low energy, high frequency laser beam pass leads to remelting of the peaks of the material and reduced surface roughness.
Demonstration of Green Solvent Performance on O,S,N-Heterocycles Synthesis: Metal-Free Click Chemistry and Buchwald—Hartwig Coupling

The development of new and greener approaches to organic synthesis has been a trend in recent years. Continuing the latest publications of our team, in this work, we demonstrate the efficiency of three solvents: eucalyptol (1,8-cineole), cyclopentyl methyl ether (CPME), and 2-methyltetrahydrofuran (2-MeTHF) for the synthesis of O,S,N-heterocyclic compounds.
Unexpected Vulnerability to High Temperature in the Mediterranean Alpine Shrub Erysimum scoparium (Brouss. ex Willd.) Wettst

Current understanding of the effects of extreme temperature on alpine evergreens is very limited for ecosystems under Mediterranean climate (characterised by a drought period in summer), despite being exceptionally biodiverse systems and highly vulnerable under a global change scenario. We thus assessed (i) seasonal change and (ii) effect of ontogeny (young vs. mature leaves) on thermal sensitivity of Erysimum scoparium, a keystone evergreen of Teide mountain (Canary Islands). Mature leaves were comparatively much more vulnerable to moderately high leaf-temperature (≥+40 and <+50 °C) than other alpine species. Lowest LT50 occurred in autumn (−9.0 ± 1.6 °C as estimated with Rfd, and −12.9 ± 1.5 °C with Fv/Fm). Remarkably, young leaves showed stronger freezing tolerance than mature leaves in spring (LT50 −10.3 ± 2.1 °C vs. −5.6 ± 0.9 °C in mature leaves, as estimated with Rfd). Our data support the use of Rfd as a sensitive parameter to diagnose temperature-related damage in the leaves of mountain plants. On a global change scenario, E. scoparium appears as a well-prepared species for late-frost events, however rather vulnerable to moderately high temperatures.