Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Relationship, Virulence Factors, Drug Resistance Profile and Biofilm Formation Ability of Vibrio parahaemolyticus Isolated From Mussel

The objective of this study was to investigate the virulence factors, genetic relationship, antibiotic resistance profile and the biofilm formation ability of Vibrio parahaemolyticus isolates on shrimp and mussel surfaces at 30°C. In this study, eight (n = 8) V. parahaemolyticus isolated from mussel were examined. We used the polymerase chain reaction (PCR) to examine the distribution of different genes, and Repetitive Extragenic Palindromic-PCR (REP-PCR) to compare the genetic relationship. Disk diffusion technique was used to assess antibiotic and multiple-antibiotic resistance. The biofilm formation assay, and field emission scanning electron microscopy (FE-SEM) were used to evaluate biofilm formation ability. Transmission Electron Microscope (TEM) was used to observe the morphological structure of bacterial cell. Our results indicated that the biofilm-associated genes, 16S rRNA, toxR, and tdh, were present in all the tested V. parahaemolyticus isolates (n = 8). Approximately, 62.5% (5 isolates among 8 isolates) isolates showed strong multiple-antibiotic resistance index with an average value of 0.56. All isolates (n = 8) showed strong genetic relationship and significant biofilm formation ability on shrimp and mussel surfaces. This study demonstrated that the presence of virulence factors, high multiple antibiotic resistance index (MARI) values, and effective biofilm formation ability of V. parahaemolyticus isolates could be a great threat to human health and economic values in future. It was also suggested that a high resistance rate to antibiotic could be ineffective for treating V. parahaemolyticus infections. The continuous monitoring of V. parahaemolyticus antibiotic, molecular and biofilm characteristics is needed to increase seafood safety.
Subantimicrobial Dose Doxycycline Worsens Chronic Arthritis-Induced Bone Microarchitectural Alterations in a Mouse Model: Role of Matrix Metalloproteinases?

Background: Rheumatoid arthritis (RA) is a chronic inflammatory joint disease hallmarked by irreversible damage of cartilage and bone. Matrix metalloproteinases (MMPs) involved in connective tissue remodeling play an important role in this process. Numerous MMPs have been examined in humans and animals, but their functions are still not fully understood. Therefore, we investigated the role of MMPs in the K/BxN serum-transfer model of RA with the broad-spectrum MMP inhibitor subantimicrobial dose doxycycline (SDD) using complex in vivo and in vitro methodolgy. Methods: Chronic arthritis was induced by repetitive i.p. injections of K/BxN serum in C57BL/6J mice. SDD was administered daily in acidified drinking water (0.5 mg/mL, 80 mg/kg) during the 30 days experimental period. Mechanonociceptive threshold of the paw was evaluated by aesthesiometry, grasping ability by grid test, arthritis severity by scoring, neutrophil myeloperoxidase activity by luminescence, vascular hyperpermeability and MMP activity by fluorescence in vivo imaging and the latter also by gelatin zymography, bone structure by micro-computed tomography (micro-CT). Plasma concentrations of doxycycline were determined by liquid chromatography-mass spectrometry analysis. Results: K/BxN serum induced significant inflammatory signs, mechanical hyperalgesia, joint function impairment, increased myeloperoxidase activity and vascular hyperpermeability. Significant increase of MMP activity was also observed both in vivo and ex vivo with elevation of the 57–60, 75, and 92 kDa gelatinolytic isoforms in the arthritic ankle joints, but neither MMP activity nor any above described functional parameters were influenced by SDD. Most importantly, SDD significantly reduced bone mineral density in the distal tibia and enhanced the Euler number in the ankle. Arthritis-induced microarchitectural alterations demonstrating increased irregularity and cancellous bone remodeling, such as increased Euler number was significantly elevated by SDD in both regions. Conclusion: We showed increase of various MMP activities in the joints by in vivo fluorescence imaging together with ex vivo zymography, and investigated their functional significance using the broad-spectrum MMP inhibitor SDD in the translational RA model. This is the first demonstration that SDD worsens arthritis-induced bone microarchitectural alterations, but it appears to be independent of MMP inhibition.
Zafirlukast Is a Dual Modulator of Human Soluble Epoxide Hydrolase and Peroxisome Proliferator-Activated Receptor γ

Cysteinyl leukotriene receptor 1 antagonists (CysLT1RA) are frequently used as add-on medication for the treatment of asthma. Recently, these compounds have shown protective effects in cardiovascular diseases. This prompted us to investigate their influence on soluble epoxide hydrolase (sEH) and peroxisome proliferator activated receptor (PPAR) activities, two targets known to play an important role in CVD and the metabolic syndrome. Montelukast, pranlukast and zafirlukast inhibited human sEH with IC50 values of 1.9, 14.1, and 0.8 μM, respectively. In contrast, only montelukast and zafirlukast activated PPARγ in the reporter gene assay with EC50 values of 1.17 μM (21.9% max. activation) and 2.49 μM (148% max. activation), respectively. PPARα and δ were not affected by any of the compounds. The activation of PPARγ was further investigated in 3T3-L1 adipocytes. Analysis of lipid accumulation, mRNA and protein expression of target genes as well as PPARγ phosphorylation revealed that montelukast was not able to induce adipocyte differentiation. In contrast, zafirlukast triggered moderate lipid accumulation compared to rosiglitazone and upregulated PPARγ target genes. In addition, we found that montelukast and zafirlukast display antagonistic activities concerning recruitment of the PPARγ cofactor CBP upon ligand binding suggesting that both compounds act as PPARγ modulators. In addition, zafirlukast impaired the TNFα triggered phosphorylation of PPARγ2 on serine 273. Thus, zafirlukast is a novel dual sEH/PPARγ modulator representing an excellent starting point for the further development of this compound class.
The Application of Cell-Free Protein Synthesis in Genetic Code Expansion for Post-translational Modifications

The translation system is a sophisticated machinery that synthesizes proteins from 20 canonical amino acids. Recently, the repertoire of such composition has been expanded by the introduction of non-canonical amino acids (ncAAs) with the genetic code expansion strategy, which provides proteins with designed properties and structures for protein studies and engineering. Although the genetic code expansion strategy has been mostly implemented by using living cells as the host, a number of limits such as poor cellular uptake or solubility of specific ncAA substrates and the toxicity of target proteins have hindered the production of certain ncAA-modified proteins. To overcome those challenges, cell-free protein synthesis (CFPS) has been applied as it allows the precise control of reaction components. Several approaches have been recently developed to increase the purity and efficiency of ncAA incorporation in CFPS. Here, we summarized recent development of CFPS with an emphasis on its applications in generating site-specific protein post-translational modifications by the genetic code expansion strategy.
Interacting stressors matter: diet quality and virus infection in honeybee health

Honeybee population declines have been linked to multiple stressors, including reduced diet diversity and increased exposure to understudied viral pathogens. Despite interest in these factors, few experimental studies have explored the interaction between diet diversity and viral infection in honeybees. Here, we used a mixture of laboratory cage and small semi-field nucleus hive experiments to determine how these factors interact. In laboratory experiments, we found that high-quality diets (polyfloral pollen and high-quality single-source pollen) have the potential to reduce mortality in the face of infection with Israeli acute paralysis virus (IAPV). There was a significant interaction between diet and virus infection on mortality, even in the presence of high virus titres, suggesting that good diets can help bees tolerate virus infection. Further, we found that extreme stress in the form of pollen starvation in conjunction with IAPV infection increase exiting behaviour from small experimental hives. Finally, we showed that higher-quality pollen diets have significantly higher iron and calcium content, suggesting micronutrient deficiencies could be an under-explored area of bee nutrition.
A DNA Vaccine Encoding the VAA Gene of Vibrio anguillarum Induces a Protective Immune Response in Flounder

Vibrio anguillarum is a pathogenic bacterium that infects flounder resulting in significant losses in the aquaculture industry. The VAA protein previously identified in flounder is associated with a role in immune protection within these fish. In the present study, a recombinant DNA plasmid encoding the VAA gene of V. anguillarum was constructed and its potential as a DNA vaccine, to prevent the infection of V. anguillarum in flounder fish, investigated. We verified the expression of the VAA protein both in vitro in cell lines and in vivo in flounder fish. The protective effects of pcDNA3.1-VAA (pVAA) were analyzed by determination of the percentage of sIgM+, CD4-1+, CD4-2+, CD8β+ lymphocytes, and the production of VAA-specific antibodies in flounder following their immunization with the DNA vaccine. Histopathological changes in immune related tissues, bacterial load, and relative percentage survival rates of flounder post-challenge with V. anguillarum, were all investigated to assess the efficacy of the pVAA DNA vaccine candidate. Fish intramuscularly immunized with pVAA showed a significant increase in CD4-1+, CD4-2+, and CD8β+ T lymphocytes at days 9, 11, and 14 post-vaccination, reaching peak T-cell levels at days 11 or 14 post-immunization. The percentage of sIgM+ lymphocytes reached peak levels at weeks 4–5 post-immunization. Specific anti-V. anguillarum or anti-rVAA antibodies were induced in inoculated fish at days 28–35 post-immunization. The liver of vaccinated flounder exhibited only slight histopathological changes compared with a significant pathology observed in control immunized fish. Additionally, a lower bacterial burden in the liver, spleen, and kidney were observed in pVAA protected fish in response to bacterial challenge, compared with pcDNA3.1 vector control injected fish. Moreover, the pVAA vaccine confers a relative percentage survival of 50.00% following V. anguillarum infection. In summary, this is the first study indicating an initial induction of the T lymphocyte response, followed by B lymphocyte induction of specific antibodies as a result of DNA immunization of flounder. This signifies the important potential of pVAA as a DNA vaccine candidate for the control of V. anguillarum infection.
Stream Control Transmission Protocol: Errata and Issues in RFC 4960

This document is a compilation of issues found since the publication of RFC4960 in September 2007 based on experience with implementing, testing, and using SCTP along with the suggested fixes. This document provides deltas to RFC4960 and is organized in a time ordered way. The issues are listed in the order they were brought up. Because some text is changed several times the last delta in the text is the one which should be applied. In addition to the delta a description of the problem and the details of the solution are also provided.
The applications of robust estimation method BaySAC in indoor point cloud processing

Abstract Based on Bayesian theory and RANSAC, this paper applies Bayesian Sampling Consensus (BaySAC) method using convergence evaluation of hypothesis models in indoor point cloud processing. We implement a conditional sampling method, BaySAC, to always select the minimum number of required data with the highest inlier probabilities. Because the primitive parameters calculated by the different inlier sets should be convergent, this paper presents a statistical testing algorithm for a candidate model parameter histogram to compute the prior probability of each data point. Moreover, the probability update is implemented using the simplified Bayes’ formula. The performances of the BaySAC algorithm with the proposed strategies of the prior probability determination and the RANSAC framework are compared using real data-sets. The experimental results indicate that the more outliers contain the data points, the higher computational efficiency of our proposed algorithm gains compared with RANSAC. The results also indicate that the proposed statistical testing strategy can determine sound prior inlier probability free of the change of hypothesis models.
Online motion planning for unexplored underwater environments using autonomous underwater vehicles

We present an approach to endow an autonomous underwater vehicle with the capabilities to move through unexplored environments. To do so, we propose a computational framework for planning feasible and safe paths. The framework allows the vehicle to incrementally build a map of the surroundings, while simultaneously (re)planning a feasible path to a specified goal. To accomplish this, the framework considers motion constraints to plan feasible 3D paths, that is, those that meet the vehicle’s motion capabilities. It also incorporates a risk function to avoid navigating close to nearby obstacles. Furthermore, the framework makes use of two strategies to ensure meeting online computation limitations. The first one is to reuse the last best known solution to eliminate time‐consuming pruning routines. The second one is to opportunistically check the states’ risk of collision. To evaluate the proposed approach, we use the Sparus II performing autonomous missions in different real‐world scenarios. These experiments consist of simulated and in‐water trials for different tasks. The conducted tasks include the exploration of challenging scenarios such as artificial marine structures, natural marine structures, and confined natural environments. All these applications allow us to extensively prove the efficacy of the presented approach, not only for constant‐depth missions (2D), but, more important, for situations in which the vehicle must vary its depth (3D).
Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)

Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.
Effect of an 8-Week Plyometric Training Program with Raised Forefoot Platforms on Agility and Vertical Jump Performance

Some athletes use solid rubber platforms strapped onto the forefoot during plyometric exercises in order to increase their explosive performance including vertical jump height and agility. The purpose of this study was to compare the effects of a plyometric training program realized with these ‘raised forefoot platforms,’ designed to keep the heels off the ground, to the same program conducted with regular shoes. Forty-nine subjects performed 2 sessions of plyometric training for eight weeks, either with raised forefoot platforms (n=20) or regular shoes (n=29). Countermovement jump (CMJ) height and agility test time were evaluated at pre-, mid- and post-training program. Compared to baseline values, four and eight weeks of plyometric training significantly increased CMJ and agility performances in the raised forefoot platforms and regular shoes groups. However, compared to regular shoes, wearing raised forefoot platforms during training induced significantly better performances in CMJ at week 4 (+4.4cm) and week 8 (+7.2cm) and in agility at week 8 (−0.466s). Thus, while an 8-week plyometric training program was effective at improving both CMJ and agility performance for both shoe conditions, the improvements were greater for the group wearing raised forefoot platforms.
Impact of foliar fertilization on apple and pear trees in reconciling productivity and alleviation of environmental concerns under arid conditions

ABSTRACT Drought and heat stress are significant factors limiting fruit crop yield in arid conditions. Foliar fertilization is a common practice of supplying fruit crop production with mineral nutrients, especially under limited soil nutrient availability conditions. To evaluate potential effectiveness of the foliar application of macro-, micronutrient and growth regulators on dynamics of physiological parameters of the pear and apple cultivars under abiotic stresses, three–year experiments were carried out under arid conditions at the Russian Research Institute of Arid Agriculture during the 2015–2017 growing seasons. It has been revealed that foliar nutrition reduces the negative influence of heat stress, stabilizes the functional state of plants, thereby enhancing resistance to drought. During the most severe drought periods of vegetation, under the influence of foliar nutrition, there was a significant increase in the total water content (TWC), relative leaf turgidity (RLT) and water retention capacity (WRC); and also index of leaf water deficiency (LWD) was improved as compared to the non-treated control. All foliar treatments involving the macro-, micronutrient and growth regulators significantly enhanced fruit crop yield of pear and apple varieties over the control, yield enhancement was obtained 2.7–22.0 t ha−1 for the Talgar beauty (pear variety), 2.2–19.3 t ha−1 for the Renet Symirenko (apple variety), and 1.6–10.5 t ha−1 for the Starkrimson (apple variety). The most effective treatments for water consumption coefficient (WCC) were plantafol and speedphol. The results suggest that foliar plantafol and speedfol could be used as part of an efficient, sustainable fertilizer program for apple and pear trees for maintaining or improving fruit quality, productivity, and avoiding negative efficacy of abiotic stresses.
Comparison of tumor-targeting properties of directly and indirectly radioiodinated designed ankyrin repeat protein (DARPin) G3 variants for molecular imaging of HER2

Evaluation of human epidermal growth factor receptor 2 (HER2) expression levels in breast and gastroesophageal cancer is used for the stratification of patients for HER2-targeting therapies. The use of radionuclide molecular imaging may facilitate such evaluation in a non-invasive way. Designed ankyrin repeat proteins (DARPins) are engineered scaffold proteins with high potential as probes for radionuclide molecular imaging. DARPin G3 binds with high affinity to HER2 and may be used to visualize this important therapeutic target. Studies on other engineered scaffold proteins have demonstrated that selection of the optimal labeling approach improves the sensitivity and specificity of radionuclide imaging. The present study compared two methods of labeling G3, direct and indirect radioiodination, to select an approach providing the best imaging contrast. G3-H6 was labeled with iodine-124, iodine-125 and iodine-131 using a direct method. A novel construct bearing a C-terminal cysteine, G3-GGGC, was site-specifically labeled using [125I]I-iodo-[(4-hydroxyphenyl)ethyl]maleimide (HPEM). The two radiolabeled G3 variants preserved binding specificity and high affinity to HER2-expressing cells. The specificity of tumor targeting in vivo was demonstrated. Biodistribution comparison of [131I]I-G3-H6 and [125I]I-HPEM-G3-GGGC in mice, bearing HER2-expressing SKOV3 xenografts, demonstrated an appreciable contribution of hepatobiliary excretion to the clearance of [125I]I-HPEM-G3-GGGC and a decreased tumor uptake compared to [131I]I-G3-H6. The direct label provided higher tumor-to-blood and tumor-to-organ ratios compared with the indirect label at 4 h post-injection. The feasibility of high contrast PET/CT imaging of HER2 expression in SKOV3 xenografts in mice using [124I]I-G3-H6 was demonstrated. In conclusion, direct radioiodination is the preferable approach for labeling DARPin G3 with iodine-123 and iodine-124 for clinical single photon emission computed tomography and positron emission tomography imaging.
Scheduling Data-Intensive Tasks on Heterogeneous Many Cores

Scheduling various data-intensive tasks over the processing units of a server has been a heavily studied but still challenging effort. In order to utilize modern multicore servers well, a good scheduling mechanism has to be conscious of different dimensions of parallelism offered by these servers. This requires being aware of the micro-architectural features of processors, the hardware topology connecting the processing units of a server, and the characteristics of these units as well as the data-intensive tasks. The increasing levels of parallelism and heterogeneity in emerging server hardware amplify these challenges in addition to the increasing variety of data-intensive applications. This article ﬁrst surveys the existing scheduling mechanisms targeting the utilization of a multicore server with uniform processing units. Then, it revisits them in the context of emerging server hardware composed of many diverse cores and identiﬁes the main challenges. Finally, it concludes with the description of a preliminary framework targeting these challenges. Even though this article focuses on data-intensive applications on a single server, many of the challenges and opportunities identiﬁed here are not unique to such a setup, and would be relevant to other complex software systems as well as resource-constrained or large-scale hardware platforms.