Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying i-bridge Across Online Social Networks

Users recently are joining multiple online social networks simultaneously. The different accounts owned by the same user in multiple social networks are most of time isolated from each other. Identifying the same users, so called i-bridge, across networks is an important task for many interesting inter-network based applications such as viral marketing, presidential campaigns, product announcement, etc. In this paper, we tackle the problem of me edge identification across online social networks. Indeed, for each user in the source network, we extract the set of similar accounts in the target network and then a set of friends for each similar account in the target network will be extracted. A suitable comparison will be performed using similarity functions between the two sets of friends in the source and target networks to identify bridge users. Experiments are performed through the extraction of users from the two most popular social networks, Facebook and Twitter, and then extract the list of friends for these users. Then, the me edge link identification is built through the exploitation of the friends sets assigned to user accounts in different social networks. Experiments on two real-world social networks Facebook and Twitter provide a high identification rate of me edge links.
Volvox barberi flocks, forming near-optimal, two-dimensional, polydisperse lattice packings

Volvox barberi is a multicellular green alga forming spherical colonies of 10000-50000 differentiated somatic and germ cells. Here, I show that these colonies actively self-organize over minutes into “flocks” that can contain more than 100 colonies moving and rotating collectively for hours. The colonies in flocks form two-dimensional, irregular, “active crystals”, with lattice angles and colony diameters both following log-normal distributions. Comparison with a dynamical simulation of soft spheres with diameters matched to the Volvox samples, and a weak long-range attractive force, show that the Volvox flocks achieve optimal random close-packing. A dye tracer in the Volvox medium revealed large hydrodynamic vortices generated by colony and flock rotations, providing a likely source of the forces leading to flocking and optimal packing.
[Report of a case with 14q12 triplication and literature review for FOXG1 related diseases].

OBJECTIVE To report on the first case with chromosome 14q12 triplication involving the FOXG1 gene. METHODS The clinical, radiological and array-based comparative genomic hybridization (aCGH) data of a patient was analyzed, in addition with a literature review. RESULTS The 9-year-old girl has suffered from severe psychomotor delay, infantile spasms, severe mental retardation, absent language, autistic spectrum disorders, impaired ambulation, poor functional hand use and microcephaly, which were considered as manifestation of FOXG1 related diseases. Magnetic resonance imaging has documented heterotopic gray matter changes. aCGH showed a 1.9 Mb triplication in the 14q12 region, which involved the FOXG1 and a predicted gene 14orf23. CONCLUSION For patients with early-onset severe psychomotor retardation, epilepsy, microcephaly, severe cognitive impairment and encephalodysplasia, analysis of copy number variations and mutations of the FOXG1 gene is crucial for the diagnosis.
Needs and preferences of patients with head and neck cancer in integrated care

Incorporation of patients’ perspectives in daily practice is necessary to adapt care to users’ needs. However, information on patients’ needs and preferences for integrated care is lacking. The aim was to explore these needs and preferences, taking patients with head and neck cancer (HNC) as example, to adapt current integrated care to be more patient‐centred.
Branched-Chain Amino Acids : Metabolism , Physiological Function , and Application Branched-Chain Amino Acids : Enzyme and Substrate Regulation 1 – 3

The three branched-chain amino acids (BCAAs) are the most hydrophobic of the amino acids and play crucial roles in determining the structures of globular proteins as well as the interaction of the transmembrane domains of membranous proteins with phospholipid bilayers. However, the three BCAAs do not behave identically. In terms of protein secondary structure, valine and isoleucine exhibit a definite preference for the b-structure, whereas leucine has a higher preference for the a-helix. Although mutation of one BCAA to another is commonly regarded as conservative, there are well-documented examples of such substitutions that have a significant effect on protein function. The occurrence of BCAA in nature is, therefore, attributable to their primary role in protein structure, not to their secondary metabolic roles. These functions are important for almost all proteins; therefore, BCAA commonly account for ;20–25% of most dietary proteins. Dietary BCAA largely escape first-pass splanchnic metabolism. The first steps in their catabolism are common to all three, involving the BCAA aminotransferase (BCAT) and branchedchain a-keto acid dehydrogenase (BCKD). Their further metabolism employs distinct pathways to different endproducts (glucose and/or ketone bodies). However, the fact that the flux-generating step for the catabolism of the three BCAAs occurs at one of the common steps indicates that the production of these downstream products are not individually regulated and, hence, may not play important individual roles. The catabolism of the BCAAs is highly regulated by both allosteric and covalent mechanisms. BCKD is inhibited by phosphorylation and activated by dephosphorylation. Allosteric inhibition of the kinase by the branched-chain keto acids (BCKA) (particularly by a-ketoisocaproate) serves both as a mechanism for promoting the catabolism of excess quantities of these amino acids as well as for conserving low concentrations of these dietary essential amino acids. Cytosolic and mitochondrial isoenzymes of BCAT have been identified. They are thought to play an important role in brain neurotransmitter metabolism. J. Nutr. 136: 207S–211S, 2006.
Haplotype Analysis Improved Evidence for Candidate Genes for Intramuscular Fat Percentage from a Genome Wide Association Study of Cattle

In genome wide association studies (GWAS), haplotype analyses of SNP data are neglected in favour of single point analysis of associations. In a recent GWAS, we found that none of the known candidate genes for intramuscular fat (IMF) had been identified. In this study, data from the GWAS for these candidate genes were re-analysed as haplotypes. First, we confirmed that the methodology would find evidence for association between haplotypes in candidate genes of the calpain-calpastatin complex and musculus longissimus lumborum peak force (LLPF), because these genes had been confirmed through single point analysis in the GWAS. Then, for intramuscular fat percent (IMF), we found significant partial haplotype substitution effects for the genes ADIPOQ and CXCR4, as well as suggestive associations to the genes CEBPA, FASN, and CAPN1. Haplotypes for these genes explained 80% more of the phenotypic variance compared to the best single SNP. For some genes the analyses suggested that there was more than one causative mutation in some genes, or confirmed that some causative mutations are limited to particular subgroups of a species. Fitting the SNPs and their interactions simultaneously explained a similar amount of the phenotypic variance compared to haplotype analyses. Haplotype analysis is a neglected part of the suite of tools used to analyse GWAS data, would be a useful method to extract more information from these data sets, and may contribute to reducing the missing heritability problem.
MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit. ie/courtney/MATtrack.zip.
Conditional and Reversible Activation of Class A and B G Protein-Coupled Receptors Using Tethered Pharmacology

Understanding the activation and internalization of G protein-coupled receptors (GPCRs) using conditional approaches is paramount to developing new therapeutic strategies. Here, we describe the design, synthesis, and testing of ExONatide, a benzylguanine-linked peptide agonist of the glucagon-like peptide-1 receptor (GLP-1R), a class B GPCR required for maintenance of glucose levels in humans. ExONatide covalently binds to SNAP-tagged GLP-1R-expressing cells, leading to prolonged cAMP generation, Ca2+ rises, and intracellular retention of the receptor. These effects were readily switched OFF following cleavage of the introduced disulfide bridge using the cell-permeable reducing agent beta-mercaptoethanol (BME). A similar approach could be extended to a class A GPCR using GhrelON, a benzylguanine-linked peptide agonist of the growth hormone secretagogue receptor 1a (GHS-R1a), which is involved in food intake and growth. Thus, ExONatide and GhrelON allow SNAP-tag-directed activation of class A and B GPCRs involved in gut hormone signaling in a reversible manner. This tactic, termed reductively cleavable agONist (RECON), may be useful for understanding GLP-1R and GHS-R1a function both in vitro and in vivo, with applicability across GPCRs.
SCREW-BASED RELATIVE JACOBIAN FOR MANIPULATORS COOPERATING IN A TASK

A current trend in Robotics is the analysis and the design of cooperative manipulation system, i.e. systems composed of multiple manipulator units interacting one another in a coordinated way. A cooperative system is characterized by higher manipulability and load capacity with respect to single-manipulator systems. The concept of the relative Jacobian is used to generate trajectories in the joint space, for two robots in cooperation executing a specified task. This paper proposes an alternative method to derive the relative Jacobian, here designated screw-based relative Jacobian, that relates the velocities of a tool (attached to one manipulator), relative to a blank (attached to another manipulator) as a function of the manipulators joint velocities, using the screw representation of differential kinematics, and the method of successive screw displacements. It is presented a systematic method to calculate the relative Jacobian in a compact, direct and simple form. The presented method is specially suitable when the geometry of manipulators becomes more general and for systems with spatial manipulators. A Cartesian-space tool path, defined relative to the blank, is resolved in the joint space.
A Novel Preparation Method For PLGA Microspheres Using Non Toxic Solvent Emulsified In Supercritical CO 2

Email: mykien.tran@etud.univ-angers.fr ABSTRACT Purpose. To generate biodegradable poly(lactic-co-glycolic a id) (PLGA) microparticles without using volatile organic solvent for a sustai ned protein release. Methods. The formulation of microparticles is based on the formation of an emulsion of polymer solution in CO2 medium. Polymer solution was prepared in injectabl e non-volatile solvent such as glycofurol or isosorbide dimethyl e ther. Moreover, encapsulation experiments were carried out using lysozyme as model protein. A n experimental design was built-up to go further in the understanding of the system and to b e ter predict the encapsulation yield. Results. Spherical microparticles were successfully generat ed. Encapsulation yield of lysozyme can reach up to about 85% within our chose n ranges of parameters. Conclusion. This method with the use of non-toxic solvents is uitable for the preparation of PLGA microspheres. Further characterization step wi ll be performed to confirm its utility in controlled release of therapeutic protein.
Coordinated Regulation of Cap-Dependent Translation and MicroRNA Function by Convergent Signaling Pathways

ABSTRACT Cell growth and proliferation require the coordinated activation of many cellular processes, including cap-dependent mRNA translation. MicroRNAs oppose cap-dependent translation and set thresholds for expression of target proteins. Emerging data suggest that microRNA function is enhanced by cellular activation due in part to induction of the RNA-induced silencing complex (RISC) scaffold protein GW182. In the current study, we demonstrate that increased expression of GW182 in activated or transformed immune cells results from effects of phosphoinositol 3-kinase–Akt–mechanistic target of rapamycin (PI3K-Akt-mTOR) and Jak-Stat-Pim signaling on the translation of GW182 mRNA. Both signaling pathways enhanced polysome occupancy and eukaryotic initiation factor 4E (eIF4E) binding to the 5′ 7mG cap of GW182 mRNA. The effect of Jak-Stat-Pim signaling on polysome occupancy and expression of GW182 protein was greater than that of PI3K-Akt-mTOR signaling, likely resulting from enhanced eIF4A-dependent unwinding of G-quadruplexes in the 5′ untranslated region of GW182 mRNA. Consistent with this, GW182 expression and microRNA function were reduced by inhibition of mTOR or Pim kinases, translation initiation complex assembly, or eIF4A function. Taken together, these data provide a mechanistic link between microRNA function and cap-dependent translation that allows activated immune cells to maintain microRNA-mediated repression of targets despite enhanced rates of protein synthesis.
Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana, USA

We used high throughput pyrosequencing to characterize stomach and gut content microbiomes of Crassostrea virginica, the Easter oyster, obtained from two sites, one in Barataria Bay (Hackberry Bay) and the other in Terrebonne Bay (Lake Caillou), Louisiana, USA. Stomach microbiomes in oysters from Hackberry Bay were overwhelmingly dominated by Mollicutes most closely related to Mycoplasma; a more rich community dominated by Planctomyctes occurred in Lake Caillou oyster stomachs. Gut communities for oysters from both sites differed from stomach communities, and harbored a relatively diverse assemblage of phylotypes. Phylotypes most closely related to Shewanella and a Chloroflexi strain dominated the Lake Caillou and Hackberry Bay gut microbiota, respectively. While many members of the stomach and gut microbiomes appeared to be transients or opportunists, a putative core microbiome was identified based on phylotypes that occurred in all stomach or gut samples only. The putative core stomach microbiome comprised 5 OTUs in 3 phyla, while the putative core gut microbiome contained 44 OTUs in 12 phyla. These results collectively revealed novel microbial communities within the oyster digestive system, the functions of the oyster microbiome are largely unknown. A comparison of microbiomes from Louisiana oysters with bacterial communities reported for other marine invertebrates and fish indicated that molluscan microbiomes were more similar to each other than to microbiomes of polychaetes, decapods and fish.
Knockdown of Ki-67 by Dicer-Substrate Small Interfering RNA Sensitizes Bladder Cancer Cells to Curcumin-Induced Tumor Inhibition

Transitional cell carcinoma (TCC) of the urinary bladder is the most common cancer of the urinary tract. Most of the TCC cases are of the superficial type and are treated with transurethral resection (TUR). However, the recurrence rate is high and the current treatments have the drawback of inducing strong systemic toxicity or cause painful cystitis. Therefore, it would be of therapeutic value to develop novel concepts and identify novel drugs for the treatment of bladder cancer. Ki-67 is a large nucleolar phosphoprotein whose expression is tightly linked to cell proliferation, and curcumin, a phytochemical derived from the rhizome Curcuma longa, has been shown to possess powerful anticancer properties. In this study, we evaluated the combined efficacy of curcumin and a siRNA against Ki-67 mRNA (Ki-67-7) in rat (AY-27) and human (T-24) bladder cancer cells. The anticancer effects were assessed by the determination of cell viability, apoptosis and cell cycle analysis. Ki-67-7 (10 nM) and curcumin (10 µM), when treated independently, were moderately effective. However, in their combined presence, proliferation of bladder cancer cells was profoundly (>85%) inhibited; the rate of apoptosis in the combined presence of curcumin and Ki-67-7 (36%) was greater than that due to Ki-67-7 (14%) or curcumin (13%) alone. A similar synergy between curcumin and Ki-67-7 in inducing cell cycle arrest was also observed. Western blot analysis suggested that pretreatment with Ki-67-7 sensitized bladder cancer cells to curcumin-mediated apoptosis and cell cycle arrest by p53- and p21-independent mechanisms. These data suggest that a combination of anti-Ki-67 siRNA and curcumin could be a viable treatment against the proliferation of bladder cancer cells.
Blood Pressure Variability in Acute Ischemic Stroke: Influence of Infarct Location in the Insular Cortex

Background: The aim of this study was to elucidate the influence of insular infarction on blood pressure (BP) variability and outcomes according to the region of the insular cortex affected. Methods: A total of 90 patients diagnosed with acute unilateral ischemic stroke were registered. The BP variability was calculated over 24 h after admission (hyperacute) and for 2–3 days after admission (acute). Patients were classified into groups of right and left, and then right anterior, right posterior, left anterior, and left posterior insular infarction. Results: Patients with insular infarction showed a significantly larger infarct volume, higher modified Rankin scale scores, and lower SD and coefficient of variation (CV) of systolic BP in the hyperacute phase than shown by patients without insular infarction (p < 0.01, p < 0.01, p = 0.02, and p = 0.03, respectively). The SD and CV of systolic BP in the hyperacute phase showed significant differences among the 3 groups with right insular infarction, with left insular infarction, and without insular infarction (p < 0.05 and p < 0.05, respectively). There was a tendency for the systolic BP variability to be lower in patients with right anterior insular infarction than in patients with infarcts in other areas. Conclusion: The right insular cortex, especially the anterior part, might be a hub for autonomic nervous regulation.
Sugar Transporter STP7 Specificity for l-Arabinose and d-Xylose Contrasts with the Typical Hexose Transporters STP8 and STP12

The hexose transporters STP8 and STP12 may contribute to the nutrition of reproductive tissues, whereas the pentose-specific STP7 might be involved in cell wall sugar recycling in Arabidopsis. The controlled distribution of sugars between assimilate-exporting source tissues and sugar-consuming sink tissues is a key element for plant growth and development. Monosaccharide transporters of the SUGAR TRANSPORT PROTEIN (STP) family contribute to the uptake of sugars into sink cells. Here, we report on the characterization of STP7, STP8, and STP12, three previously uncharacterized members of this family in Arabidopsis (Arabidopsis thaliana). Heterologous expression in yeast (Saccharomyces cerevisiae) revealed that STP8 and STP12 catalyze the high-affinity proton-dependent uptake of glucose and also accept galactose and mannose. STP12 additionally transports xylose. STP8 and STP12 are highly expressed in reproductive organs, where their protein products might contribute to sugar uptake into the pollen tube and the embryo sac. stp8.1 and stp12.1 T-DNA insertion lines developed normally, which may point toward functional redundancy with other STPs. In contrast to all other STPs, STP7 does not transport hexoses but is specific for the pentoses l-arabinose and d-xylose. STP7-promoter-reporter gene plants showed an expression of STP7 especially in tissues with high cell wall turnover, indicating that STP7 might contribute to the uptake and recycling of cell wall sugars. Uptake analyses with radioactive l-arabinose revealed that 11 other STPs are able to transport l-arabinose with high affinity. Hence, functional redundancy might explain the missing-mutant phenotype of two stp7 T-DNA insertion lines. Together, these data complete the characterization of the STP family and present the STPs as new l-arabinose transporters for potential biotechnological applications.
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for the rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the widely-used Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples and uses nanograms of genomic DNA. Many hundreds of samples can then be pooled on the same HiSeq lane via custom barcodes. Our method is especially useful for re-sequencing of large numbers of full microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples.