Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Community Diversity and Screening of Growth-Affecting Bacteria From Isochrysis galbana Following Antibiotic Treatment

Algal cultures are generally co-cultures of algae and bacteria, especially when considering outdoor cultivation. However, the effects of associated bacteria on algal growth remain largely unexplored, particularly in the context of Isochrysis galbana. In the present study, we investigated the effects of antibiotic on the growth of I. galbana and its associated bacterial community. We found advantageous responses of I. galbana to antibiotic exposure, evidenced by the increased growth, and the maximal photochemical efficiency of PSII (Fv/Fm). Since antibiotics can cause major disturbances within bacterial community, we further conducted 16S rDNA amplicon sequencing to determine the changes of bacterial community diversity following antibiotic treatment. We found that antibiotic treatment considerably and negatively affected the abundance and diversity of bacterial community, and 17 significantly decreased bacterial species in the antibiotic-treated medium, including Pseudomonas stutzeri, were identified. Further co-culture experiments revealed that P. stutzeri inhibited the growth of I. galbana, and the inhibitory activity was retained in the cell-free bacterial filtrate. These results indicated that the negative effect of bacteria was not exclusively transmitted through contact with I. galbana but could be also mediated via secretory compounds. Taken together, our findings not only fully characterized the bacterial community associated with I. galbana and how the bacterial community changed in response to antibiotic perturbations, but also provided a valuable information about the interactions between I. galbana and its associated bacteria, which might help improve the yield, and quality of I. galbana during its cultivation processes.
Latent Variable Models for Semantic Orientations of Phrases

We propose models for semantic orientations of phrases as well as classification methods based on the models. Although each phrase consists of multiple words, the semantic orientation of the phrase is not a mere sum of the orientations of the component words. Some words can invert the orientation. In order to capture the property of such phrases, we introduce latent variables into the models. Through experiments, we show that the proposed latent variable models work well in the classification of semantic orientations of phrases and achieved nearly 82% classification accuracy.
The Methodology of Numerical Simulations of Separation Process in SPR-Separator

The article describes the methodology of hydrocyclone SPR separator numerical simulation, which is used for oil lubricant and liquid impurities separation on technological lines of circulation lubrication of metallurgical machines. The methodology of hydrocyclone SPR separator numerical simulation was developed with taking into account up-to-date articles about the study of hydrocyclone equipment. It was done for determining the relation between the main structural dimensions of the device and the flow parameters, as well as the separation efficiency of the heterogeneous inlet mixture. Numerical simulations were performed by using ANSYS namely its module Fluent Flow. The methodology of the finite volume computational grid building was described. This methodology takes into account the geometry features of the model, such as the presence of surfaces curvature and small gaps compared to other linear dimensions. Settings of the Fluent module was described with design features of the SPR-separator and its working parameters. Eulerian multiphase flow model, k-ε RNG turbulence model with Swirl Dominated Flow settings was chosen. According to the results of the numerical simulation was determined the main hydrodynamic characteristics of the flow which presented as isolines in the middle section of the separator and value of the separation efficiency of the heterogeneous mixture. New design of a spiral nozzle was proposed for expansion of the range of effective work.
A novel server selection technique for improving the response time of a replicated service

Server replication is an approach often used to improve the ability of a service to handle a large number of clients. One of the important factors in the efficient utilization of replicated servers is the ability to direct client requests to the best server, according to some optimality criteria. In this paper we target an environment in which servers are distributed across the Internet, and clients identify servers using our application-layer any-casting service. Our goal is to allocate servers to clients in a way that minimizes a client's response time. To that end, we develop an approach for estimating the performance that a client would experience when accessing particular servers. Such information is maintained in a resolver that clients can query to obtain the identity of the server with the best response time. Our performance collection technique combines server push with client probes to estimate the expected response time. A set of experiments is used to demonstrate the properties of our performance determination approach and to show its advantages when used within the application-layer anycasting architecture.
Innate Lymphoid Cells in Mucosal Immunity

Innate lymphoid cells (ILCs) are innate counterparts of T cells that contribute to immune responses by secreting effector cytokines and regulating the functions of other innate and adaptive immune cells. ILCs carry out some unique functions but share some tasks with T cells. ILCs are present in lymphoid and non-lymphoid organs and are particularly abundant at the mucosal barriers, where they are exposed to allergens, commensal microbes, and pathogens. The impact of ILCs in mucosal immune responses has been extensively investigated in the gastrointestinal and respiratory tracts, as well as in the oral cavity. Here we review the state-of-the-art knowledge of ILC functions in infections, allergy and autoimmune disorders of the mucosal barriers.
Field-Based High-Throughput Phenotyping for Maize Plant Using 3D LiDAR Point Cloud Generated With a “Phenomobile”

With the rapid rising of global population, the demand for improving breeding techniques to greatly increase the worldwide crop production has become more and more urgent. Most researchers believe that the key to new breeding techniques lies in genetic improvement of crops, which leads to a large quantity of phenotyping spots. Unfortunately, current phenotyping solutions are not powerful enough to handle so many spots with satisfying speed and accuracy. As a result, high-throughput phenotyping is drawing more and more attention. In this paper, we propose a new field-based sensing solution to high-throughput phenotyping. We mount a LiDAR (Velodyne HDL64-S3) on a mobile robot, making the robot a “phenomobile. ” We develop software for data collection and analysis under Robotic Operating System using open source components and algorithm libraries. Different from conducting phenotyping observations with an in-row and one-by-one manner, our new solution allows the robot to move around the parcel to collect data. Thus, the 3D and 360° view laser scanner can collect phenotyping data for a large plant group at the same time, instead of one by one. Furthermore, no touching interference from the robot would be imposed onto the crops. We conduct experiments for maize plant on two parcels. We implement point cloud merging with landmarks and Iterative Closest Points to cut down the time consumption. We then recognize and compute the morphological phenotyping parameters (row spacing and plant height) of maize plant using depth-band histograms and horizontal point density. We analyze the cloud registration and merging performances, the row spacing detection accuracy, and the single plant height computation accuracy. Experimental results verify the feasibility of the proposed solution.
Exploring Self-Consciousness From Self- and Other-Image Recognition in the Mirror: Concepts and Evaluation

A historical review of the concepts of self-consciousness is presented, highlighting the important role of the body (particularly, body perception but also body action), and the social other in the construction of self-consciousness. More precisely, body perception, especially intermodal sensory perception including kinesthetic perception, is involved in the construction of a sense of self allowing self-other differentiation. Furthermore, the social other, through very early social and emotional interactions, provides meaning to the infant’s perception and contributes to the development of his/her symbolization capacities. This is a necessary condition for body image representation and awareness of a permanent self in a time-space continuum (invariant over time and space). Self-image recognition impairments in the mirror are also discussed regarding a comprehensive developmental theory of self-consciousness. Then, a neuropsychological and neurophysiological approach to self-consciousness reviews the role of complex brain activation/integration pathways and the mirror neuron system in self-consciousness. Finally, this article offers new perspectives on self-consciousness evaluation using a double mirror paradigm to study self- and other- image and body recognition.
Mechanical Analysis Challenges in MicroElectronic Packaging

Electrical and thermal performance enhancing features in modern integrated circuits have increased demands on the electronic package. This paper reviews two solder joint failure mechanisms; thermal cycle fatigue under compressive load and solders joint cracking in shock. Two modeling techniques are employed to study these mechanisms, response surface modeling and modal analysis. Response surface modeling is shown to be an effective means of determining the impact of multiple design variables. Modal analysis is used to calibrate a complex system model, prior to simulating shock events.
The Relations between Prosocial Behaviors and Self-Regulation: Evidences from the Validation of the PTM-R for Portuguese Early Adolescents

Abstract The main goal of this study is to understand the relationship between different types of prosocial behaviors and different forms of self-regulation, as part of the adaptation and validation of the Portuguese version of the Prosocial Tendencies Measure-Revised (PTM-R). A total of 403 early adolescents (M = 11.81; SD = .92; 52.91% girls) completed self-reported measures. The evaluation of psychometric properties of the PTM-R involved a confirmatory factorial analysis, followed by the examination of factorial internal consistency and factorial invariance analyses across gender groups and school retention groups (retention vs. no-retention). The results support the premise that a 6-factor model similar to the original measure is the most appropriate factorial solution for the PTM-R Portuguese version (χ2(174) = 1.725, p < . 001, CFI = . 95, RMSEA = . 030, SRMR = . 08). The levels of internal consistency for the different subscales ranged from . 67 to . 78. Further convergent and divergent validity tests reveal that different forms of prosocial behavior are more often related to girls’ cognitive, affective and behavioral regulation and that students who failed at least one school year and thus had to repeat it denote poorer relations between prosocial behaviors and self-regulation dimensions, as opposed to more successful students. In conclusion, the Portuguese version of the PTM-R has adequate psychometric properties and its use for research purposes in the field of social development may be appropriate. The discussion focuses on the implications of these findings for future research on prosociality.
Two-Stage Method for Adaptive Binarization of Raster Engineering Drawings

The paper describes the proposed original model and the developed two-stage method for adaptive binarization of raster engineering drawings. The method allows binarization of images whose brightness histograms are not bimodal. At the same time, thin contour lines on resulting images are saved. The method is adaptive to brightness of image background. Comparative analysis of testing results of the developed method and some well-known methods for binarization raster images confirms that the proposed solutions are effective. The method was tested on a representative set of 40 different quality raster engineering drawings.
Lipid Mediators From Timothy Grass Pollen Contribute to the Effector Phase of Allergy and Prime Dendritic Cells for Glycolipid Presentation

Plant pollen are an important source of antigens that evoke allergic responses. Protein antigens have been the focus of studies aiming to elucidate the mechanisms responsible for allergic reactions to pollen. However, proteins are not the sole active agent present in pollen. It is known that pollen grains contain lipids essential for its reproduction and bioactive lipid mediators. These small molecular compounds are co-delivered with the allergens and hence have the potential to modulate the immune response of subjects by activating their innate immune cells. Previous reports showed that pollen associated lipid mediators exhibited neutrophil- and eosinophil-chemotactic activity and induced polarization of dendritic cells (DCs) toward a Th2-inducing phenotype. In our study we performed chemical analyses of the pollen associated lipids, that are rapidly released upon hydration. As main components we have identified different types of phytoprostanes (PhytoPs), and for the first time phytofurans (PhytoFs), with predominating 16-F1t-PhytoPs (PPF1-I), 9-F1t-PhytoPs (PPF1-II), 16-E1t-PhytoPs (PPE1-I) and 9-D1t-PhytoPs (PPE1-II), and 16(RS)-9-epi-ST-Δ14-10-PhytoFs. Interestingly 16-E1t-PhytoP and 9-D1t-PhytoPs were found to be bound to glycerol. Lipid-containing samples (aqueous pollen extract, APE) induced murine mast cell chemotaxis and IL-6 release, and enhanced their IgE-dependent degranulation, demonstrating a role for these lipids in the immediate effector phase of allergic inflammation. Noteworthy, mast cell degranulation seems to be dependent on glycerol-bound, but not free phytoprostanes. On murine dendritic cells, APE selectively induced the upregulation of CD1d, likely preparing lipid-antigen presentation to iNKT cells. Our report contributes to the understanding of the activity of lipid mediators in the immediate effector phase of allergic reactions but identifies a yet undescribed pathway for the recognition of pollen-derived glycolipids by iNKT cells.
Altered Resting-State Functional Activity in Medication-Naive Patients With First-Episode Major Depression Disorder vs. Healthy Control: A Quantitative Meta-Analysis

Background: There is an urgent need for a meta-analysis that characterizes the brain states of major depression disorder (MDD) patients and potentially provides reliable biomarkers, because heterogeneity in the results of resting-state functional neuroimaging has been observed between studies, with some patients not showing the consistent changes, or even opposite patterns. Thus, we evaluated consistent regional brain activity alterations in medication-naive patients with first-episode unipolar MDD and compared the results with those in healthy controls (HCs). Methods: A systematic database search was conducted (in PubMed, Ovid, and Web of Knowledge) between January 1984 and July 2016 to select resting-state functional activity studies with a voxel-wise analysis in MDD. We used anisotropic effect size-signed differential mapping to perform a whole-brain meta-analysis, comparing functional alterations between first-episode medication-naive unipolar MDD patients and HCs by integrating the studies. In addition, subgroup meta-analysis was conducted to control for the MRI analysis method. Moreover, the meta-regression analyses were performed to examine the potential effects of mean age, education duration, illness duration, and severity of depressive symptoms. Results: A total of 12 studies were included, comparing 313 MDD patients with 283 HCs. The pooled and subgroup meta-analysis found that the MDD patients showed hyperactivity in the left parahippocampal gyrus, left supplementary motor area, left amygdala, left hippocampus, and left middle frontal gyrus (MFG; orbital part), and hypoactivity in the left lingual gyrus, left middle occipital gyrus, right cuneus cortex, right MFG (orbital part), and left cerebellum. In the meta-regression analyses, the mean illness duration was positively associated with hyper-activation in the left parahippocampal gyrus and hypoactivation in the hemispheric lobule IV/V of the left cerebellum. Conclusions: This meta-analysis indicated that MDD patients had significant and robust resting-state brain activity alteration in amygdala, left hippocampus and other regions, which implicated this finding in the pathophysiology of cognitive and emotional impairment in MDD patients.
Combined MEK Inhibition and BMP2 Treatment Promotes Osteoblast Differentiation and Bone Healing in Nf1Osx−/− Mice

Neurofibromatosis type I (NF1) is an autosomal dominant disease with an incidence of 1/3000, caused by mutations in the NF1 gene, which encodes the RAS/GTPase‐activating protein neurofibromin. Non‐bone union after fracture (pseudarthrosis) in children with NF1 remains a challenging orthopedic condition to treat. Recent progress in understanding the biology of neurofibromin suggested that NF1 pseudarthrosis stems primarily from defects in the bone mesenchymal lineage and hypersensitivity of hematopoietic cells to TGFβ. However, clinically relevant pharmacological approaches to augment bone union in these patients remain limited. In this study, we report the generation of a novel conditional mutant mouse line used to model NF1 pseudoarthrosis, in which Nf1 can be ablated in an inducible fashion in osteoprogenitors of postnatal mice, thus circumventing the dwarfism associated with previous mouse models where Nf1 is ablated in embryonic mesenchymal cell lineages. An ex vivo–based cell culture approach based on the use of Nf1flox/flox bone marrow stromal cells showed that loss of Nf1 impairs osteoprogenitor cell differentiation in a cell‐autonomous manner, independent of developmental growth plate–derived or paracrine/hormonal influences. In addition, in vitro gene expression and differentiation assays indicated that chronic ERK activation in Nf1‐deficient osteoprogenitors blunts the pro‐osteogenic property of BMP2, based on the observation that only combination treatment with BMP2 and MEK inhibition promoted the differentiation of Nf1‐deficient osteoprogenitors. The in vivo preclinical relevance of these findings was confirmed by the improved bone healing and callus strength observed in Nf1osx−/− mice receiving Trametinib (a MEK inhibitor) and BMP2 released locally at the fracture site via a novel nanoparticle and polyglycidol‐based delivery method. Collectively, these results provide novel evidence for a cell‐autonomous role of neurofibromin in osteoprogenitor cells and insights about a novel targeted approach for the treatment of NF1 pseudoarthrosis. © 2014 American Society for Bone and Mineral Research.
Detection of Social Network Toxic Comments with Usage of Syntactic Dependencies in the Sentences

Social networks sometimes become a medium for threats, insults and other components of cyberbullying. A huge number of people are involved in online social networks. Hence, a protection of network users from anti-social behavior is an important activity. One of the major tasks of such activity is automated detecting the toxic comments with threats, insults, obscene etc. The bag of words statistics and bag of symbols statistics are typical features for the toxic comments detection. The effect of syntactic dependencies in sentences on the quality of detection of the social network toxic comments is studied in the article for the first time. Syntactic dependences are relationships with proper nouns, personal pronouns, possessive pronouns, etc. Twenty syntactic features of sentences have been verified in the total. The paper shows that 3 additional specific features significantly improve the quality of toxic comments detection. These three features are: the number of dependences with proper nouns in the singular, the number of dependences that contain bad words, and the number of dependences between personal pronouns and bad words. The experiments are based on data from kaggle competition "Toxic Comment Classification Challenge". For our experiments, the original dataset with 159751 comments was reduced to 106590 comments due to problems with human-free extraction of the syntactic features. We use mean of the error rates for each types of misclassification as the metric of quality due to unbalanced dataset. A decision tree is used as a classifier. The decision trees were synthesized for two splitting rules: Gini index and deviance criterion.
Community Structure and Functional Gene Profile of Bacteria on Healthy and Diseased Thalli of the Red Seaweed Delisea pulchra

Disease is increasingly viewed as a major factor in the ecology of marine communities and its impact appears to be increasing with environmental change, such as global warming. The temperate macroalga Delisea pulchra bleaches in Southeast Australia during warm summer periods, a phenomenon which previous studies have indicated is caused by a temperature induced bacterial disease. In order to better understand the ecology of this disease, the bacterial communities associated with threes type of samples was investigated using 16S rRNA gene and environmental shotgun sequencing: 1) unbleached (healthy) D. pulchra 2) bleached parts of D. pulchra and 3) apparently healthy tissue adjacent to bleached regions. Phylogenetic differences between healthy and bleached communities mainly reflected relative changes in the taxa Colwelliaceae, Rhodobacteraceae, Thalassomonas and Parvularcula. Comparative metagenomics showed clear difference in the communities of healthy and diseased D. pulchra as reflected by changes in functions associated with transcriptional regulation, cation/multidrug efflux and non-ribosomal peptide synthesis. Importantly, the phylogenetic and functional composition of apparently healthy tissue adjacent to bleached sections of the thalli indicated that changes in the microbial communities already occur in the absence of visible tissue damage. This shift in unbleached sections might be due to the decrease in furanones, algal metabolites which are antagonists of bacterial quorum sensing. This study reveals the complex shift in the community composition associated with bleaching of Delisea pulchra and together with previous studies is consistent with a model in which elevated temperatures reduce levels of chemical defenses in stressed thalli, leading to colonization or proliferation by opportunistic pathogens or scavengers.