Minimal Scales from an Extended Hilbert Space

We consider an extension of the conventional quantum Heisenberg algebra, assuming that coordinates as well as momenta fulfil nontrivial commutation relations. As a consequence, a minimal length and a minimal mass scale are implemented. Our commutators do not depend on positions and momenta and we provide an extension of the coordinate coherent state approach to Noncommutative Geometry. We explore, as toy model, the corresponding quantum field theory in a (2+1)-dimensional spacetime. Then we investigate the more realistic case of a (3+1)-dimensional spacetime, foliated into noncommutative planes. As a result, we obtain propagators, which are finite in the ultraviolet as well as the infrared regime.Comment: 16 pages, version which matches that published on CQ

Spinning Loop Black Holes

In this paper we construct four Kerr-like spacetimes starting from the loop black hole Schwarzschild solutions (LBH) and applying the Newman-Janis transformation. In previous papers the Schwarzschild LBH was obtained replacing the Ashtekar connection with holonomies on a particular graph in a minisuperspace approximation which describes the black hole interior. Starting from this solution, we use a Newman-Janis transformation and we specialize to two different and natural complexifications inspired from the complexifications of the Schwarzschild and Reissner-Nordstrom metrics. We show explicitly that the space-times obtained in this way are singularity free and thus there are no naked singularities. We show that the transformation move, if any, the causality violating regions of the Kerr metric far from r=0. We study the space-time structure with particular attention to the horizons shape. We conclude the paper with a discussion on a regular Reissner-Nordstrom black hole derived from the Schwarzschild LBH and then applying again the Newmann-Janis transformation.Comment: 18 pages, 18 figure

Diagnosing numerical Cherenkov instabilities in relativistic plasma simulations based on general meshes

Numerical Cherenkov radiation (NCR) or instability is a detrimental effect frequently found in electromagnetic particle-in-cell (EM-PIC) simulations involving relativistic plasma beams. NCR is caused by spurious coupling between electromagnetic-field modes and multiple beam resonances. This coupling may result from the slow down of poorly-resolved waves due to numerical (grid) dispersion and from aliasing mechanisms. NCR has been studied in the past for finite-difference-based EM-PIC algorithms on regular (structured) meshes with rectangular elements. In this work, we extend the analysis of NCR to finite-element-based EM-PIC algorithms implemented on unstructured meshes. The influence of different mesh element shapes and mesh layouts on NCR is studied. Analytic predictions are compared against results from finite-element-based EM-PIC simulations of relativistic plasma beams on various mesh types.Comment: 31 pages, 20 figure

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics.Results We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived similar to 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads.Conclusions We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes

Galactic rotation curves inspired by a noncommutative-geometry background

This paper discusses the observed at rotation curves of galaxies in the context of noncommutative geometry. The energy density of such a geometry is diffused throughout a region due to the uncertainty encoded in the coordinate commutator. This intrinsic property appears to be sufficient for producing stable circular orbits, as well as attractive gravity, without the need for dark matter.Comment: 12 pages, 3 figures. Published in Gen.Rel.Grav. 44 (2012) 905-91

Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps

Hox and ParaHox genes (HPHGs) are key developmental genes that pattern regional identity along the anterior–posterior body axis of most animals. Here, we identified HPHGs in tadpole shrimps (Pancrustacea, Branchiopoda, Notostraca), an iconic example of the so-called “living fossils” and performed a comparative genomics analysis of HPHGs and the Hox cluster among major branchiopod lineages. Notostraca possess the entire Hox complement, and the Hox cluster seems to be split into two different subclusters, although we were not able to support this finding with chromosome-level assemblies. However, the genomic structure of Hox genes in Notostraca appears more derived than that of Daphnia spp., which instead retains the plesiomorphic condition of a single compact cluster. Spinicaudata and Artemia franciscana show instead a Hox cluster subdivided across two or more genomic scaffolds with some orthologs either duplicated or missing. Yet, branchiopod HPHGs are similar among the various clades in terms of both intron length and number, as well as in their pattern of molecular evolution. Sequence substitution rates are in fact generally similar for most of the branchiopod Hox genes and the few differences we found cannot be traced back to natural selection, as they are not associated with any signals of diversifying selection or substantial switches in selective modes. Altogether, these findings do not support a significant stasis in the Notostraca Hox cluster and further confirm how morphological evolution is not tightly associated with genome dynamics

Intensive post-operative follow-up of breast cancer patients with tumour markers: CEA, TPA or CA15.3 vs MCA and MCA-CA15.3 vs CEA-TPA-CA15.3 panel in the early detection of distant metastases

BACKGROUND: In breast cancer current guidelines do not recommend the routine use of serum tumour markers. Differently, we observed that CEA-TPA-CA15.3 (carcinoembryonic (CEA) tissue polypeptide (TPA) and cancer associated 115D8/DF3 (CA15.3) antigens) panel permits early detection and treatment for most relapsing patients. As high sensitivity and specificity and different cut-off values have been reported for mucin-like carcinoma associated antigen (MCA), we compared MCA with the above mentioned tumour markers and MCA-CA15.3 with the CEA-TPA-CA15.3 panel. METHODS: In 289 breast cancer patients submitted to an intensive post-operative follow-up with tumour markers, we compared MCA (cut-off values, ≥ 11 and ≥ 15 U/mL) with CEA or CA15.3 or TPA for detection of relapse. In addition, we compared the MCA-CA15.3 and CEA-TPA-CA15.3 tumour marker panels. RESULTS: Distant metastases occurred 19 times in 18 (6.7%) of the 268 patients who were disease-free at the beginning of the study. MCA sensitivity with both cut-off values was higher than that of CEA or TPA or CA15.3 (68% vs 10%, 26%, 32% and 53% vs 16%, 42%, 32% respectively). With cut-off ≥ 11 U/mL, MCA showed the lowest specificity (42%); with cut-off ≥ 15 U/mL, MCA specificity was similar to TPA (73% vs 72%) and lower than that of CEA and CA15.3 (96% and 97% respectively). With ≥ 15 U/mL MCA cut-off, MCA sensitivity increased from 53% to 58% after its association with CA15.3. Sensitivity of CEA-TPA-CA15.3 panel was 74% (14 of 19 recurrences). Eight of the 14 recurrences early detected with CEA-TPA-CA15.3 presented as a single lesion (oligometastatic disease) (5) or were confined to bony skeleton (3) (26% and 16% respectively of the 19 relapses). With ≥ 11 U/mL MCA cut-off, MCA-CA15.3 association showed higher sensitivity but lower specificity, accuracy and positive predictive value than the CEA-TPA-CA15.3 panel. CONCLUSION: At both the evaluated cut-off values serum MCA sensitivity is higher than that of CEA, TPA or CA15.3 but its specificity is similar to or lower than that of TPA. Overall, CEA-TPA-CA15.3 panel is more accurate than MCA-CA15.3 association and can "early" detect a few relapsed patients with limited metastatic disease and more favourable prognosis. These findings further support the need for prospective randomised clinical trial to assess whether an intensive post-operative follow-up with an appropriate use of serum tumour markers can significantly improve clinical outcome of early detected relapsing patients

Clinical use of biomarkers in breast cancer: Updated guidelines from the European Group on Tumor Markers (EGTM)

Abstract Biomarkers play an essential role in the management of patients with invasive breast cancer. For selecting patients likely to respond to endocrine therapy, both oestrogen receptors (ERs) and progesterone receptors (PRs) should be measured on all newly diagnosed invasive breast cancers. On the other hand, for selecting likely response to all forms of anti-HER2 therapy (trastuzumab, pertuzumab, lapatinib or ado-trastuzumab emtansine), determination of HER2 expression or gene copy number is mandatory. Where feasible, measurement of ER, PR and HER2 should be performed on recurrent lesions and the primary invasive tumour. Although methodological problems exist in the determination of Ki67, because of its clearly established clinical value, wide availability and low costs relative to the available multianalyte signatures, Ki67 may be used for determining prognosis, especially if values are low or high. In oestrogen receptor (ER)-positive, HER2-negative, lymph node–negative patients, multianalyte tests such as urokinase plasminogen activator (uPA)-PAI-1, Oncotype DX, MammaPrint, EndoPredict, Breast Cancer Index (BCI) and Prosigna (PAM50) may be used to predict outcome and aid adjunct therapy decision-making. Oncotype DX, MammaPrint, EndoPredict and Prosigna may be similarly used in patients with 1–3 metastatic lymph nodes. All laboratories measuring biomarkers for patient management should use analytically and clinically validated assays, participate in external quality assurance programs, have established assay acceptance and rejection criteria, perform regular audits and be accredited by an appropriate organisation

Sub-Planckian black holes and the Generalized Uncertainty Principle

The Black Hole Uncertainty Principle correspondence suggests that there could exist black holes with mass beneath the Planck scale but radius of order the Compton scale rather than Schwarzschild scale. We present a modified, self-dual Schwarzschild-like metric that reproduces desirable aspects of a variety of disparate models in the sub-Planckian limit, while remaining Schwarzschild in the large mass limit. The self-dual nature of this solution under $M \leftrightarrow M^{-1}$ naturally implies a Generalized Uncertainty Principle with the linear form $\Delta x \sim \frac{1}{\Delta p} + \Delta p$. We also demonstrate a natural dimensional reduction feature, in that the gravitational radius and thermodynamics of sub-Planckian objects resemble that of $(1+1)$-D gravity. The temperature of sub-Planckian black holes scales as $M$ rather than $M^{-1}$ but the evaporation of those smaller than $10^{-36}$g is suppressed by the cosmic background radiation. This suggests that relics of this mass could provide the dark matter.Comment: 12 pages, 9 figures, version published in J. High En. Phy