Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrix plasticity in SiC/Ti-15-3 composite

An experimental method is described which allows for the observation of slip bands due to matrix plasticity in the SiC/Ti-15-3 composite system. A post-test heat treatment and subsequent chemical etch is employed to reveal slip bands in the titanium matrix. Composite specimens of various laminates were examined after tensile testing at room temperature. This method definitively shows that matrix plasticity has occurred in all the laminates investigated and at load/strain levels which were insufficient to cause fiber breakage.
Proteomic profiling of extracellular vesicles released from vascular smooth muscle cells during initiation of phosphate-induced mineralization

ABSTRACT Purpose/Aim: Elevated serum phosphate is one of the major factors contributing to vascular calcification. Studies suggested that extracellular vesicles released from vascular smooth muscle cells significantly contribute to the initiation and progression of this pathology. Recently, we have demonstrated that elevated phosphate stimulates release of extracellular vesicles from osteogenic cells at the initiation of the mineralization process. Here, we used MOVAS cell line as an in vitro model of vascular calcification to examine whether vascular smooth muscle cells respond to high phosphate levels in a similar way and increase formation of extracellular vesicles. Materials and Methods: Vesicles residing in extracellular matrix as well as vesicles released to culture medium were evaluated by nanoparticle tracking analyses. In addition, using mass spectrometry and protein profiling, protein composition of extracellular vesicles released by MOVAS cells under standard growth conditions and upon exposure to high phosphate was compared. Results: Significant increase of the number of extracellular vesicles was detected after 72 h of exposure of cells to high phosphate. Elevated phosphate levels also affected protein composition of extracellular vesicles released from MOVAS cells. Finally, the comparative analyses of proteins in extracellular vesicles isolated from extracellular matrix and from conditioned medium identified significant differences in protein composition in these two groups of extracellular vesicles. Conclusions: Results of this study demonstrate that exposure of MOVAS cells to high phosphate levels stimulates the release of extracellular vesicles and changes their protein composition.
Improved recommendations via (more) collaboration

We consider in this paper a popular class of recommender systems that are based on Collaborative Filtering (CF for short). CF is the process of predicting customer ratings to items based on previous ratings of (similar) users to (similar) items, and is typically used by a single organization, using its own customer ratings. We argue here that a multi-organization collaboration, even for organizations operating in different subject domains, can greatly improve the quality of the recommendations that the individual organizations provide to their users. To substantiate this claim, we present C2F (Collaborative CF), a recommender system that retains the simplicity and efficiency of classical CF, while allowing distinct organizations to collaborate and boost their recommendations. C2F employs CF in a distributed fashion that improves the quality of the generated recommendations, while minimizing the amount of data exchanged between the collaborating parties. Key ingredient of the solution are succinct signatures that can be computed locally for items (users) in a given organization and suffice for identifying similar items (users) in the collaborating organizations. We show that the use of such compact signatures not only reduces data exchange but also allows to speed up, by over 50%, the recommendations computation time.
Topical review of firms' annual reports on mergers and acquisitions using latent dirichlet allocation

In this paper, we present discernible trends in the annual report announcements made by publicly traded firms from India that are engaged in Mergers and Acquisitions (M&A) over the period 2010-2016. We use Latent Dirichlet Allocation (LDA) to observe the underlying topics in the reports and to find the latent factors that hint at a firm's prospective M&A decision. The findings link firm's annual report with future M&A action by illuminating on the textual features. This enables investors to diligently arrive at their investment plans.
Deficient Surveillance and Phagocytic Activity of Myeloid Cells Within Demyelinated Lesions in Aging Mice Visualized by Ex Vivo Live Multiphoton Imaging

Aging impairs regenerative processes including remyelination, the synthesis of a new myelin sheath. Microglia and other infiltrating myeloid cells such as macrophages are essential for remyelination through mechanisms that include the clearance of inhibitory molecules within the lesion. Prior studies have shown that the quantity of myeloid cells and the clearance of inhibitory myelin debris are deficient in aging, contributing to the decline in remyelination efficiency with senescence. It is unknown, however, whether the impaired clearance of debris is simply the result of the reduced number of phagocytes or if the dynamic activity of myeloid cells within the demyelinating plaque also declines with aging and this question is relevant to the proper design of therapeutics to mobilize myeloid cells for repair. Herein, we describe a high-resolution multiphoton ex vivo live imaging protocol that visualizes individual myelinated/demyelinated axons and lipid-containing myeloid cells to investigate the demyelinated lesion of aging female mice. We found that aging lesions have fewer myeloid cells and that these have reduced phagocytosis of myelin. Although the myeloid cells are actively migratory within the lesion of young mice and have protrusions that seem to survey the environment, this motility and surveillance is significantly reduced in aging mice. Our results emphasize the necessity of not only increasing the number of phagocytes, but also enhancing their activity once they are within demyelinated lesions. The high-resolution live imaging of demyelinated lesions can serve as a platform with which to discover pharmacological agents that rejuvenate intralesional remodeling that promotes the repair of plaques. SIGNIFICANCE STATEMENT The repair of myelin after injury depends on myeloid cells that clear debris and release growth factors. As organisms age, remyelination becomes less efficient correspondent with fewer myeloid cells that populate the lesions. It is unknown whether the dynamic activity of cells within lesions is also altered with age. Herein, using high-resolution multiphoton ex vivo live imaging with several novel features, we report that myeloid cells within demyelinated lesions of aging mice have reduced motility, surveillance, and phagocytic activity, suggesting an intralesional impairment that may contribute to the age-related decline in remyelination efficiency. Medications to stimulate deficient aging myeloid cells should not only increase their representation, but also enter into lesions to stimulate their activity.
Fringe removal for continuous-wave terahertz imaging based on cartoon-texture decomposition

Continuous-wave (CW) terahertz (THz) imaging system has advantages of high power, compact structure and low cost, thus having been investigated for widespread applications. In typical reflection mode of CW imaging, the obtained image is usually degraded by repeated fringes, which is caused by interference phenomenon. The undesired interference signal originates from the reflection of surfaces of samples and lenses. When the samples are titled placed or their surfaces are uneven, the detected signal intensity is fluctuant even if the same sample lies in different positions. Therefore, small-sized or weekly absorbing objects are hard to be distinguished. Based on cartoon-texture decomposition, we propose a practical method to restore CW THz reflection images. After decomposition, the fringes and the objects are separated. In order to preserve edges, sharpening and fusion steps are employed respectively. The object in the final image is obvious with little loss of information.
Incidence and Prevalence of Spinal Cord Injury in Canada: A National Perspective

Background: Despite decades of research, there are no national estimates of the incidence or prevalence of spinal cord injury (SCI) in Canada. Our objective was to utilize the best available data to estimate the incidence and prevalence of traumatic SCI (TSCI) and non-traumatic SCI (NTSCI) in Canada for 2010. Methods: Initial incidence (number of TSCIs at injury scene) and discharge incidence (number discharged into the community) were calculated using published TSCI rates from Alberta and NTSCI rates from Australia. Prevalence was estimated by applying TSCI and NTSCI discharge incidence rates to historical Canadian population demographics using a cohort survival model and age-specific mortality rates for tetraplegia and paraplegia. Results: The estimated 2010 initial incidence of TSCI is 1,785 cases per year, and the discharge incidence is 1,389 (41 per million). The estimated discharge incidence for NTSCI is 2,286 cases (68 per million). The prevalence of SCI in Canada is estimated to be 85,556 persons (51% TSCI and 49% NTSCI). Conclusions: This study provides the first estimates of the incidence and prevalence of SCI in Canada. More population-based studies are needed, particularly for NTSCI, as an increasing number of Canadians are expected to be affected by SCI.
The Role of NOD Mice in Type 1 Diabetes Research: Lessons from the Past and Recommendations for the Future

For more than 35 years, the NOD mouse has been the primary animal model for studying autoimmune diabetes. During this time, striking similarities to the human disease have been uncovered. In both species, unusual polymorphisms in a major histocompatibility complex (MHC) class II molecule confer the most disease risk, disease is caused by perturbations by the same genes or different genes in the same biological pathways and that diabetes onset is preceded by the presence of circulating autoreactive T cells and autoantibodies that recognize many of the same islet antigens. However, the relevance of the NOD model is frequently challenged due to past failures translating therapies from NOD mice to humans and because the appearance of insulitis in mice and some patients is different. Nevertheless, the NOD mouse remains a pillar of autoimmune diabetes research for its usefulness as a preclinical model and because it provides access to invasive procedures as well as tissues that are rarely procured from patients or controls. The current article is focused on approaches to improve the NOD mouse by addressing reasons why immune therapies have failed to translate from mice to humans. We also propose new strategies for mixing and editing the NOD genome to improve the model in ways that will better advance our understanding of human diabetes. As proof of concept, we report that diabetes is completely suppressed in a knock-in NOD strain with a serine to aspartic acid substitution at position 57 in the MHC class II Aβ. This supports that similar non-aspartic acid substitutions at residue 57 of variants of the human class II HLA-DQβ homolog confer diabetes risk.
Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele–climate association analyses to reveal two Eucalyptus EST‐SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS‐like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene‐homologous EST‐SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.
Analysis of plastic flow in an amorphous soap bubble raft by the use of an inter-bubble potential

Abstract The changes in potential energy, free volume, and internal shear strain in clusters undergoing shear transformations during the shearing of amorphous soap bubble rafts have been analysed by means of a generalized inter-bubble potential initially developed by Nicolson and by Lomer. A unique inverse correlation was found between the activation free energy barriers of transformations and the initial state of free volume of the transforming sites. Two separate branches of correlation, one for concentrated shear transformations and the other for diffuse shear transformations have been identified. When proper scaling between the inter-bubble potential and the appropriate close-packed metal potential is applied to the results, the distribution of activation free energies found from the soap bubble model gives remarkably good agreement with the experimentally measured distributions in metallic glasses obtained by Argon and Kuo earlier. The inverse correlation, found between activation free energy and fre.
Behavioral repertoire learning in robotics

Learning in robotics typically involves choosing a simple goal (e.g. walking) and assessing the performance of each controller with regard to this task (e.g. walking speed). However, learning advanced, input-driven controllers (e.g. walking in each direction) requires testing each controller on a large sample of the possible input signals. This costly process makes difficult to learn useful low-level controllers in robotics. Here we introduce BR-Evolution, a new evolutionary learning technique that generates a behavioral repertoire by taking advantage of the candidate solutions that are usually discarded. Instead of evolving a single, general controller, BR-evolution thus evolves a collection of simple controllers, one for each variant of the target behavior; to distinguish similar controllers, it uses a performance objective that allows it to produce a collection of diverse but high-performing behaviors. We evaluated this new technique by evolving gait controllers for a simulated hexapod robot. Results show that a single run of the EA quickly finds a collection of controllers that allows the robot to reach each point of the reachable space. Overall, BR-Evolution opens a new kind of learning algorithm that simultaneously optimizes all the achievable behaviors of a robot.
Modeling gene‐wise dependencies improves the identification of drug response biomarkers in cancer studies

Motivation: In recent years, vast advances in biomedical technologies and comprehensive sequencing have revealed the genomic landscape of common forms of human cancer in unprecedented detail. The broad heterogeneity of the disease calls for rapid development of personalized therapies. Translating the readily available genomic data into useful knowledge that can be applied in the clinic remains a challenge. Computational methods are needed to aid these efforts by robustly analyzing genome‐scale data from distinct experimental platforms for prioritization of targets and treatments. Results: We propose a novel, biologically motivated, Bayesian multitask approach, which explicitly models gene‐centric dependencies across multiple and distinct genomic platforms. We introduce a gene‐wise prior and present a fully Bayesian formulation of a group factor analysis model. In supervised prediction applications, our multitask approach leverages similarities in response profiles of groups of drugs that are more likely to be related to true biological signal, which leads to more robust performance and improved generalization ability. We evaluate the performance of our method on molecularly characterized collections of cell lines profiled against two compound panels, namely the Cancer Cell Line Encyclopedia and the Cancer Therapeutics Response Portal. We demonstrate that accounting for the gene‐centric dependencies enables leveraging information from multi‐omic input data and improves prediction and feature selection performance. We further demonstrate the applicability of our method in an unsupervised dimensionality reduction application by inferring genes essential to tumorigenesis in the pancreatic ductal adenocarcinoma and lung adenocarcinoma patient cohorts from The Cancer Genome Atlas. Availability and Implementation : The code for this work is available at https://github.com/olganikolova/gbgfa Contact :nikolova@ohsu.edu or margolin@ohsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Reproducibility of MRI Dixon-Based Attenuation Correction in Combined PET/MR with Applications for Lean Body Mass Estimation

The aim of this study was to assess the reproducibility of standard, Dixon-based attenuation correction (MR-AC) in PET/MR imaging. A further aim was to estimate a patient-specific lean body mass (LBM) from these MR-AC data. Methods: Ten subjects were positioned in a fully integrated PET/MR system, and 3 consecutive multibed acquisitions of the standard MR-AC image data were acquired. For each subject and MR-AC map, the following compartmental volumes were calculated: total body, soft tissue (ST), fat, lung, and intermediate tissue (IT). Intrasubject differences in the total body and subcompartmental volumes (ST, fat, lung, and IT) were assessed by means of coefficients of variation (CVs) calculated across the 3 consecutive measurements and, again, across these measurements but excluding those affected by major artifacts. All subjects underwent a body composition measurement using air displacement plethysmography (ADP) that was used to calculate a reference LBMADP. A second LBM estimate was derived from available MR-AC data using a formula incorporating the respective tissue volumes and densities as well as the subject-specific body weights. A third LBM estimate was obtained from a sex-specific formula (LBMFormula). Pearson correlation was calculated for LBMADP, LBMMR-AC, and LBMFormula. Further, linear regression analysis was performed on LBMMR-AC and LBMADP. Results: The mean CV for all 30 scans was 2.1 ± 1.9% (TB). When missing tissue artifacts were excluded, the CV was reduced to 0.3 ± 0.2%. The mean CVs for the subcompartments before and after exclusion of artifacts were 0.9 ± 1.1% and 0.7 ± 0.7% for the ST, 2.9 ± 4.1% and 1.3 ± 1.0% for fat, and 3.6 ± 3.9% and 1.3 ± 0.7% for the IT, respectively. Correlation was highest for LBMMR-AC and LBMADP (r = 0.99). Linear regression of data excluding artifacts resulted in a scaling factor of 1.06 for LBMMR-AC. Conclusion: LBMMR-AC is shown to correlate well with standard LBM measurements and thus offers routine LBM-based SUV quantification in PET/MR. However, MR-AC images must be controlled for systematic artifacts, including missing tissue and tissue swaps. Efforts to minimize these artifacts could help improve the reproducibility of MR-AC.
Compiling a text re-use detection corpus from scientific papers with semi-real cases of plagiarism

Automatic plagiarism detection deals with retrieval of reused fragment of texts in a document and finding source documents. Due to development of various methods for plagiarism detection, large scale plagiarism corpora are needed to evaluate these methods. Despite of their importance, few plagiarism detection corpora developed in recent years, especially in low resource languages. Because of legal issues, releasing a collection of real cases of plagiarism for evaluation purposes is not ethical. Due to these limitations, simulation and artificial based methods are the two main approaches to compile a plagiarism corpus. These approaches try to simulate real cases of plagiarism, from different point of views. However, there are still fundamental differences between simulated corpora and real cases of plagiarism. In this paper a semi-real approach is proposed to create a collection of plagiarism cases as a corpus. This approach is based on eliminating correct references from scientific papers to make them as plagiarized passages. Unlike methods based on simulated and artificial approaches, the proposed corpus can correctly simulate real cases of text re-use. The evaluation result shows high accuracy of proposed corpus with respect to n-gram similarity for different ranges of N.
Optimal Allocation of Monitoring Trails for Fast SRLG Failure Localization in All-Optical Networks

We study SRLG (Shared Risk Link Group) failure monitoring and localization in all-optical WDM (Wavelength Division Multiplexing) networks. All links in each SRLG are logically grouped as a whole, and they fail at the same time when the SRLG failure event occurs. To achieve fast SRLG failure localization, monitoring is carried out at the optical layer using the recently proposed monitoring trail (m-trail) structure. By formulating an ILP (Integer Linear Program), we optimally solve the m-trail allocation problem to achieve unambiguous SRLG failure localization with the minimum monitoring cost. We claim that our work provides the first study in optimally allocating free-routed m-trails for achieving fast and unambiguous SRLG failure localization, with flexible tradeoff between the monitor cost and the bandwidth cost (i.e., supervisory wavelength-links).
Host MicroRNA-217 Promotes White Spot Syndrome Virus Infection by Targeting Tube in the Chinese Mitten Crab (Eriocheir sinensis)

MicroRNAs (miRNAs), a group of small molecule non-encoding RNAs, are key post-transcriptional regulators of gene expression that are implicated in many biological processes. In the current study, miR-217 from Eriocheir sinensis was selected for studying its roles during host–virus interaction. Overexpression or silencing of miR-217 led to considerable effects on white spot syndrome virus (WSSV) replication, implying that miR-217 played a positive role in WSSV infection. In insect High Five cells, miR-217 significantly inhibited Tube gene expression by binding to the 3′-untranslated region of the Tube. Overexpression of miR-217 in crab led to downregulation of tube expression. Knockdown of Tube in vivo led to significant enhancement of WSSV infection and inhibited the expression of five antimicrobial peptide (AMP) genes (Anti-lipopolysaccharide factor ALF1, ALF2, ALF3; Crustin Crus1, Crus2) in WSSV-challenged crabs. Overexpression of miR-217 also led to downregulation of these AMP genes in WSSV-challenged crabs. Our results showed that host miRNA played positive roles in virus infection by regulation of host tube gene, which is the key component of Toll signaling pathway.