Miracle-dz/UniFAR-FTUs huggingface dataset:
GRAPES: a Generic Environment for P2P Streaming

Practical implementation of new P2P streaming systems requires a lot of coding and is often tedious and costly, slowing down the technology transfer from the research community to real users. GRAPES aims at relieving this burden, and speed-up application development, by providing a set of open-source components conceived as basic build- ing blocks for building new P2P streaming applications. GRAPES is designed to be usable in different environments and situations, to have a minimal set of pre-requisites and dependencies, and not to impose any particular constraints on applications using it. The development of streamers in the Napa-Wine project [1] has shown that using GRAPES P2P streaming applications with different characteristics can be developed by only writing a small amount of glue code that connects the desired functionalities and dictates the architecture of the streamer.
The Apical Complex Provides a Regulated Gateway for Secretion of Invasion Factors in Toxoplasma

The apical complex is the definitive cell structure of phylum Apicomplexa, and is the focus of the events of host cell penetration and the establishment of intracellular parasitism. Despite the importance of this structure, its molecular composition is relatively poorly known and few studies have experimentally tested its functions. We have characterized a novel Toxoplasma gondii protein, RNG2, that is located at the apical polar ring—the common structural element of apical complexes. During cell division, RNG2 is first recruited to centrosomes immediately after their duplication, confirming that assembly of the new apical complex commences as one of the earliest events of cell replication. RNG2 subsequently forms a ring, with the carboxy- and amino-termini anchored to the apical polar ring and mobile conoid, respectively, linking these two structures. Super-resolution microscopy resolves these two termini, and reveals that RNG2 orientation flips during invasion when the conoid is extruded. Inducible knockdown of RNG2 strongly inhibits host cell invasion. Consistent with this, secretion of micronemes is prevented in the absence of RNG2. This block, however, can be fully or partially overcome by exogenous stimulation of calcium or cGMP signaling pathways, respectively, implicating the apical complex directly in these signaling events. RNG2 demonstrates for the first time a role for the apical complex in controlling secretion of invasion factors in this important group of parasites.
Demand for Slant: How Abstention Shapes Voters' Choice of News Media

Political commentators warn that the fragmentation of the modern media landscape induces voters to withdraw into ? information cocoons? and segregate along ideological lines. We show that the option to abstain breaks ideological segregation and generates ? cross-over? in news consumption: voters with considerable leanings toward a candidate demand information that is less biased toward that candidate than voters who are more centrist. This non-monotonicity in the demand for slant makes voters? ideologies non-recoverable from their choice of news media and generates disproportionate demand for media outlets that are centrist or only moderately biased. It also implies that polarization of the electorate may lead to ideological moderation in news consumption. Thus, our results cast doubt on the oft-prophesied, imminent demise of mainstream media and may help to explain recent empirical findings showing less ideological segregation in news consumption than predicted by extant theories.
Tailoring Infrastructure Software Product Lines by Static Application Analysis

Besides ordinary applications, also infrastructure software such as operating systems or database management systems is being developed as a software product line. With proper tool support these systems can be configured easily by selecting features in a feature model. However, in the future multi-level architectures of layered product lines will be common practice. For humans the feature-based configuration will become increasingly complex, as the number of configurable features will be tremendous. Our goal is to reduce this complexity. The approach is based on the observation that many configuration decisions could be automated by statically analyzing the code of layers on top of an infrastructure product line. Motivated by use cases the paper presents the concepts behind our analysis tool, which is able to automate the configuration in many cases. First results in the context of a feature-oriented version of the Berkeley DB illustrate the potential of this novel approach.
Phosphorylation of Marburg virus VP30 at serines 40 and 42 is critical for its interaction with NP inclusions.

The Marburg virus (MBGV) nucleocapsid complex is composed of four viral proteins (NP, L, VP35, and VP30) and the negative-strand nonsegmented genomic RNA. NP, L, and VP35 are functionally conserved among the order Mononegavirales, whereas VP30, a phosphoprotein, represents a filovirus-specific nucleocapsid protein. In the present paper, we have characterized the localization and function of VP30 phosphorylation. The main phosphorylation sites are represented by seven serine residues in the region of amino acid 40 to 51 of VP30. Additionally, trace amounts of phosphothreonine were detected. Substitution of serine residues 40 and 42 by alanine abolished the interaction of VP30 with NP-induced inclusion bodies, which contain nucleocapsid-like structures formed by NP. Substitution of the other phosphoserine residues had little effect on this interaction. Replacement of the introduced alanine residues 40 and 42 by aspartate restored the interaction between VP30 and the NP inclusions pointing to the importance of negative charges at these particular positions.
Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers

Significance Although transfer RNAs (tRNAs) are best known as adapter molecules essential for translation, recent biochemical and computational evidence has led to a previously unexpected conceptual consensus that tRNAs are not always end products but can further serve as a source of small functional RNAs. Here we report that a novel type of tRNA-derived small RNA, termed SHOT-RNAs, are specifically and abundantly expressed in sex hormone-dependent breast and prostate cancers. SHOT-RNAs are produced from aminoacylated mature tRNAs by angiogenin-mediated cleavage of the anticodon loop, which is promoted by sex hormones and their receptors. We identified the complete repertoire of SHOT-RNAs, and also found their functional significance in cell proliferation. These results have unveiled a novel tRNA-engaged pathway in tumorigenesis. Sex hormones and their receptors play critical roles in the development and progression of the breast and prostate cancers. Here we report that a novel type of transfer RNA (tRNA)-derived small RNA, termed Sex HOrmone-dependent TRNA-derived RNAs (SHOT-RNAs), are specifically and abundantly expressed in estrogen receptor (ER)-positive breast cancer and androgen receptor (AR)-positive prostate cancer cell lines. SHOT-RNAs are not abundantly present in ER− breast cancer, AR− prostate cancer, or other examined cancer cell lines from other tissues. ER-dependent accumulation of SHOT-RNAs is not limited to a cell culture system, but it also occurs in luminal-type breast cancer patient tissues. SHOT-RNAs are produced from aminoacylated mature tRNAs by angiogenin-mediated anticodon cleavage, which is promoted by sex hormones and their receptors. Resultant 5′- and 3′-SHOT-RNAs, corresponding to 5′- and 3′-tRNA halves, bear a cyclic phosphate (cP) and an amino acid at the 3′-end, respectively. By devising a “cP-RNA-seq” method that is able to exclusively amplify and sequence cP-containing RNAs, we identified the complete repertoire of 5′-SHOT-RNAs. Furthermore, 5′-SHOT-RNA, but not 3′-SHOT-RNA, has significant functional involvement in cell proliferation. These results have unveiled a novel tRNA-engaged pathway in tumorigenesis of hormone-dependent cancers and implicate SHOT-RNAs as potential candidates for biomarkers and therapeutic targets.
Quantitative or semi-quantitative PCR: reality versus myth.

A l t h o u g h PCR is beginning to come of age, it is still quite common to read in the literature such statements as "PCR is not really a quantitative method" or "PCR has been shown at best to be a semi-quantitative procedure. " Why is that in 1992 many people are still reluctant to associate PCR and quantitation of nucleic acids? I believe this misconception is the unfortunate result of a constant questioning of the credibility of PCR as being incapable of quantitative analysis. Initially, PCR was not viewed as having great quantitative power, an opinion exemplified by the fact that the first two books on PCR technology had no mention of quantitation. ~ Indeed, it should come as no surprise that the factor that makes PCR so powerful, i.e., its ability to amplify small amounts of nucleic acids, exponentially (3.4) is also the factor that makes the technique so challenging as a quantitative method. Anything that is capable of interfering with the exponential amplification might ruin the intrinsic quantitative ability of PCR. (s) Therefore, the art of quantitative PCR is devoted to minimizing the amount of interference with the actual doubling of the target amplicon at each cycle and compensating for the inescapable, even if minimized, interference with the very doubling.
Atmospheric Chemistry and Physics Discussions Interactive comment on “ Oxidative capacity of the Mexico City atmosphere – Part 1 : A radical source perspective

C1) P5369 et seq. The paper suffers from its selectivity in the presentation of measurement methods. Details are given for those techniques used directly by the authors, but there is not even a reference in section 2.1 to the methods used for OH, HO2 and RO2. It would be useful to be able to see those data presumably via a referenced paper. Similarly there is little information on concentrations of NOx,hydrocarbons etc. It is difficult to interpret the data, as a result, and one is left very much in the hands of the authors. Some information should be contained in this paper (e.g. campaign diurnal averages, or some other concise method of presentation.) References to the sources
Delaunay Deformable Models: Topology-Adaptive Meshes Based on the Restricted Delaunay Triangulation

In this paper, we propose a robust and efficient Lagrangian approach, which we call Delaunay deformable models, for modeling moving surfaces undergoing large deformations and topology changes. Our work uses the concept of restricted Delaunay triangulation, borrowed from computational geometry. In our approach, the interface is represented by a triangular mesh embedded in the Delaunay tetrahedralization of interface points. The mesh is iteratively updated by computing the restricted Delaunay triangulation of the deformed objects. Our method has many advantages over popular Eulerian techniques such as the level set method and over hybrid Eulerian-Lagrangian techniques such as the particle level set method: localization accuracy, adaptive resolution, ability to track properties associated to the interface, seamless handling of triple junctions. Our work brings a rigorous and efficient alternative to existing topology-adaptive mesh techniques such as T-snakes.
Secure Time Synchronization in Sensor Networks

Time synchronization is critical in sensor networks at many layers of their design. It enables better duty-cycling of the radio, accurate and secure localization, beamforming, and other collaborative signal processing tasks. These benefits make time-synchronization protocols a prime target of malicious adversaries who want to disrupt the normal operation of a sensor network. In this article, we analyze attacks on existing time synchronization protocols for wireless sensor networks and we propose a secure time synchronization toolbox to counter these attacks. This toolbox includes protocols for secure pairwise and group synchronization of nodes that either lie in the neighborhood of each other or are separated by multiple hops. We provide an in-depth analysis of the security and the energy overhead of the proposed protocols. The efficiency of these protocols has been tested through an experimental study on Mica2 motes.
Structural analysis of the role of TPX2 in branching microtubule nucleation

The mitotic spindle consists of microtubules (MTs), which are nucleated by the &ggr;-tubulin ring complex (&ggr;-TuRC). How the &ggr;-TuRC gets activated at the right time and location remains elusive. Recently, it was uncovered that MTs nucleate from preexisting MTs within the mitotic spindle, which requires the protein TPX2, but the mechanism basis for TPX2 action is unknown. Here, we investigate the role of TPX2 in branching MT nucleation. We establish the domain organization of Xenopus laevis TPX2 and define the minimal TPX2 version that stimulates branching MT nucleation, which we find is unrelated to TPX2’s ability to nucleate MTs in vitro. Several domains of TPX2 contribute to its MT-binding and bundling activities. However, the property necessary for TPX2 to induce branching MT nucleation is contained within newly identified &ggr;-TuRC nucleation activator motifs. Separation-of-function mutations leave the binding of TPX2 to &ggr;-TuRC intact, whereas branching MT nucleation is abolished, suggesting that TPX2 may activate &ggr;-TuRC to promote branching MT nucleation.
A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF.

BACKGROUND & AIMS Crohn's disease (CD) has the highest prevalence in Ashkenazi Jewish populations. We sought to identify rare, CD-associated frameshift variants of high functional and statistical effects. METHODS We performed exome sequencing and array-based genotype analyses of 1477 Ashkenazi Jewish individuals with CD and 2614 Ashkenazi Jewish individuals without CD (controls). To validate our findings, we performed genotype analyses of an additional 1515 CD cases and 7052 controls for frameshift mutations in the colony-stimulating factor 2-receptor β common subunit gene (CSF2RB). Intestinal tissues and blood samples were collected from patients with CD; lamina propria leukocytes were isolated and expression of CSF2RB and granulocyte-macrophage colony-stimulating factor-responsive cells were defined by adenomatous polyposis coli (APC) time-of-flight mass cytometry (CyTOF analysis). Variants of CSF2RB were transfected into HEK293 cells and the expression and functions of gene products were compared. RESULTS In the discovery cohort, we associated CD with a frameshift mutation in CSF2RB (P = 8.52 × 10(-4)); the finding was validated in the replication cohort (combined P = 3.42 × 10(-6)). Incubation of intestinal lamina propria leukocytes with granulocyte-macrophage colony-stimulating factor resulted in high levels of phosphorylation of signal transducer and activator of transcription (STAT5) and lesser increases in phosphorylation of extracellular signal-regulated kinase and AK straining transforming (AKT). Cells co-transfected with full-length and mutant forms of CSF2RB had reduced pSTAT5 after stimulation with granulocyte-macrophage colony-stimulating factor, compared with cells transfected with control CSF2RB, indicating a dominant-negative effect of the mutant gene. Monocytes from patients with CD who were heterozygous for the frameshift mutation (6% of CD cases analyzed) had reduced responses to granulocyte-macrophage colony-stimulating factor and markedly decreased activity of aldehyde dehydrogenase; activity of this enzyme has been associated with immune tolerance. CONCLUSIONS In a genetic analysis of Ashkenazi Jewish individuals, we associated CD with a frameshift mutation in CSF2RB. Intestinal monocytes from carriers of this mutation had reduced responses to granulocyte-macrophage colony-stimulating factor, providing an additional mechanism for alterations to the innate immune response in individuals with CD.
Immunohistochemistry of chromogranin A and B, and secretogranin II in the canine endocrine pancreas.

The chromogranins are large acidic proteins contained in secretion granules of adrenal medullary cells. These proteins are also presumed to be regular constituents of other endocrine cells, e.g., pancreatic endocrine cells. In our previous immunohistochemical studies performed in the endocrine pancreas of 10 mammalian species, only canine endocrine cells lacked any immunoreactivity for chromogranin A. Therefore, this problem was reinvestigated in the present study. Antisera against bovine and rat chromogranin A, B, and C (= secretogranin II) were applied under various conditions of the immunohistochemical protocol. Upon meeting certain requirements, chromogranin-immunoreactivities were found also in canine pancreatic B- (insulin), PP- (pancreatic polypeptide), and EC- (enterochromaffin) cells. The immunohistochemical data suggest that canine chromogranins partially differ structurally or immunologically from bovine chromogranins and completely from rat chromogranins. In addition, the present findings confirm our previous findings about both interspecies differences in the cellular localization of chromogranins in the endocrine pancreas and the peculiar localization of secretogranin II to pancreatic PP-cells. Finally, the present methodological studies have shown that even the buffer used in the immunohistochemical protocol may be decisive for a false-positive or false-negative immunostaining.
Multi-class cosegmentation

Bottom-up, fully unsupervised segmentation remains a daunting challenge for computer vision. In the cosegmentation context, on the other hand, the availability of multiple images assumed to contain instances of the same object classes provides a weak form of supervision that can be exploited by discriminative approaches. Unfortunately, most existing algorithms are limited to a very small number of images and/or object classes (typically two of each). This paper proposes a novel energy-minimization approach to cosegmentation that can handle multiple classes and a significantly larger number of images. The proposed cost function combines spectral- and discriminative-clustering terms, and it admits a probabilistic interpretation. It is optimized using an efficient EM method, initialized using a convex quadratic approximation of the energy. Comparative experiments show that the proposed approach matches or improves the state of the art on several standard datasets.
Sterol regulatory element-binding proteins induce an entire pathway of cholesterol synthesis.

To evaluate the effects of sterol regulatory element-binding proteins (SREBPs) on the expression of the individual enzymes in the cholesterol synthetic pathway, we examined expression of these genes in the livers from wild-type and transgenic mice overexpressing nuclear SREBP-1a or -2. As estimated by a Northern blot analysis, overexpression of nuclear SREBP-1a or -2 caused marked increases in mRNA levels of the whole battery of cholesterogenic genes. This SREBP activation covers not only rate-limiting enzymes such as HMG CoA synthase and reductase that have been well established as SREBP targets, but also all the enzyme genes in the cholesterol synthetic pathway tested here. The activated genes include mevalonate kinase, mevalonate pyrophosphate decarboxylase, isopentenyl phosphate isomerase, geranylgeranyl pyrophosphate synthase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, lanosterol synthase, lanosterol demethylase, and 7-dehydro-cholesterol reductase. These results demonstrate that SREBPs activate every step of cholesterol synthetic pathway, contributing to an efficient cholesterol synthesis.
A Study of Hogbomite in the V-Ti-Fe Deposits of Karnataka

Hogbomite is of widespread occurrence as an accessory and minor mineral in the V-Ti-Fe ore deposits of Ubrani, Tavarekere, Masanikere, Magyatahalli and Devaranarsipur in Shimoga district and Mulemane in Uttar Kannada district. Both primary and secondary hogbomite are found. The mineral shows considerable variation in chemistry. The analytical data indicate that hogbomite structure is relatively more open than that of coexisting magnetite/ilmenite and can admit a variety of substitutions.
Immune Cells and Molecular Networks in Experimentally Induced Pulpitis

Dental pulp is a dynamic tissue able to resist external irritation during tooth decay by using immunocompetent cells involved in innate and adaptive responses. To better understand the immune response of pulp toward gram-negative bacteria, we analyzed biological mediators and immunocompetent cells in rat incisor pulp experimentally inflamed by either lipopolysaccharide (LPS) or saline solution (phosphate-buffered saline [PBS]). Untreated teeth were used as control. Expression of pro- and anti-inflammatory cytokines, chemokine ligands, growth factors, and enzymes were evaluated at the transcript level, and the recruitment of the different leukocytes in pulp was measured by fluorescence-activated cell-sorting analysis after 3 h, 9 h, and 3 d post-PBS or post-LPS treatment. After 3 d, injured rat incisors showed pulp wound healing and production of reparative dentin in both LPS and PBS conditions, testifying to the reversible pulpitis status of this model. IL6, IL1-β, TNF-α, CCL2, CXCL1, CXCL2, MMP9, and iNOS gene expression were significantly upregulated after 3 h of LPS stimulation as compared with PBS. The immunoregulatory cytokine IL10 was also upregulated after 3 h, suggesting that LPS stimulates not only inflammation but also immunoregulation. Fluorescence-activated cell-sorting analysis revealed a significant, rapid, and transient increase in leukocyte levels 9 h after PBS and LPS stimulation. The quantity of dendritic cells was significantly upregulated with LPS versus PBS. Interestingly, we identified a myeloid-derived suppressor cell–enriched cell population in noninjured rodent incisor dental pulp. The percentage of this population, known to regulate immune response, was higher 9 h after inflammation triggered with PBS and LPS as compared with the control. Taken together, these data offer a better understanding of the mechanisms involved in the regulation of dental pulp immunity that may be elicited by gram-negative bacteria.