Deuterium burning measurement at LUNA and its astrophysical and nuclear implications

The D(p,γ) 3He reaction is responsible for the deuterium destruction during the Big Bang Nucleosynthesis (BBN) and affects the primordial deuterium abundance. This latter is sensitive to fundamental cosmological parameters such as the baryon density and the effective number of relativistic species. In this paper, we describe the most precise direct measurement of the D(p,γ) 3He reaction in the BBN energy range (Ecm = 30–280 keV) at the LUNA (Laboratory for Underground Nuclear Astrophysics) facility in Gran Sasso National Laboratories. Experimental results, cosmological consequences, and future prospects are reported here

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle

ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA

MOTIVATION: The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single nucleotide variants (SNVs) in circulating cell free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. RESULTS: We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. AVAILABILITY: ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus and it is also available at CRAN official R repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Small optic suspensions for Advanced LIGO input optics and other precision optical experiments

We report on the design and performance of small optic suspensions developed to suppress seismic motion of out-of-cavity optics in the Input Optics subsystem of the Advanced LIGO interferometric gravitational wave detector. These compact single stage suspensions provide isolation in all six degrees of freedom of the optic, local sensing and actuation in three of them, and passive damping for the other three

22Ne and 23Na ejecta from intermediate-mass stars: The impact of the new LUNA rate for 22Ne(p,gamma)23Na

We investigate the impact of the new LUNA rate for the nuclear reaction $^{22}$Ne$(p,\gamma)^{23}$Na on the chemical ejecta of intermediate-mass stars, with particular focus on the thermally-pulsing asymptotic giant branch (TP-AGB) stars that experience hot-bottom burning. To this aim we use the PARSEC and COLIBRI codes to compute the complete evolution, from the pre-main sequence up to the termination of the TP-AGB phase, of a set of stellar models with initial masses in the range $3.0\,M_{\odot} - 6.0\,M_{\odot}$, and metallicities $Z_{\rm i}=0.0005$, $Z_{\rm i}=0.006$, and $Z_{\rm i} = 0.014$. We find that the new LUNA measures have much reduced the nuclear uncertainties of the $^{22}$Ne and $^{23}$Na AGB ejecta, which drop from factors of $\simeq 10$ to only a factor of few for the lowest metallicity models. Relying on the most recent estimations for the destruction rate of $^{23}$Na, the uncertainties that still affect the $^{22}$Ne and $^{23}$Na AGB ejecta are mainly dominated by evolutionary aspects (efficiency of mass-loss, third dredge-up, convection). Finally, we discuss how the LUNA results impact on the hypothesis that invokes massive AGB stars as the main agents of the observed O-Na anti-correlation in Galactic globular clusters. We derive quantitative indications on the efficiencies of key physical processes (mass loss, third dredge-up, sodium destruction) in order to simultaneously reproduce both the Na-rich, O-poor extreme of the anti-correlation, and the observational constraints on the CNO abundance. Results for the corresponding chemical ejecta are made publicly available

The genetic heritage of Alpine local cattle breeds using genomic SNP data

Background: Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results: After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions: This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies

HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Background Breast cancer is the most common malignancy in women worldwide. Among the breast cancer subtypes, triple-negative breast cancer (TNBC) is the most aggressive and the most difficult to treat. One of the master regulators in TNBC progression is the architectural transcription factor HMGA1. This study aimed to further explore the HMGA1 molecular network to identify molecular mechanisms involved in TNBC progression. Methods RNA from the MDA-MB-231 cell line, silenced for HMGA1 expression, was sequenced and, with a bioinformatic analysis, molecular partners HMGA1 could cooperate with in regulating common downstream gene networks were identified. Among the putative partners, the FOXM1 transcription factor was selected. The relationship occurring between HMGA1 and FOXM1 was explored by qRT-PCR, co-immunoprecipitation and protein stability assays. Subsequently, the transcriptional activity of HMGA1 and FOXM1 was analysed by luciferase assay on the VEGFA promoter. The impact on angiogenesis was assessed in vitro, evaluating the tube formation ability of endothelial cells exposed to the conditioned medium of MDA-MB-231 cells silenced for HMGA1 and FOXM1 and in vivo injecting MDA-MB-231 cells, silenced for the two factors, in zebrafish larvae. Results Here, we discover FOXM1 as a novel molecular partner of HMGA1 in regulating a gene network implicated in several breast cancer hallmarks. HMGA1 forms a complex with FOXM1 and stabilizes it in the nucleus, increasing its transcriptional activity on common target genes, among them, VEGFA, the main inducer of angiogenesis. Furthermore, we demonstrate that HMGA1 and FOXM1 synergistically drive breast cancer cells to promote tumor angiogenesis both in vitro in endothelial cells and in vivo in a zebrafish xenograft model. Moreover, using a dataset of breast cancer patients we show that the co-expression of HMGA1, FOXM1 and VEGFA is a negative prognostic factor of distant metastasis-free survival and relapse-free survival. Conclusions This study reveals FOXM1 as a crucial interactor of HMGA1 and proves that their cooperative action supports breast cancer aggressiveness, by promoting tumor angiogenesis. Therefore, the possibility to target HMGA1/FOXM1 in combination should represent an attractive therapeutic option to counteract breast cancer angiogenesis

Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were observed among domesticated bovid populations from different geographic areas, except for Bali cattle. Our findings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic differentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene flow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, reflecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived-breeds, in the past experienced a similar non-European influence, with African and indicine introgression

Thermal gradient-induced forces on geodetic reference masses for LISA

The low frequency sensitivity of space-borne gravitational wave observatories will depend critically on the geodetic purity of the trajectories of orbiting test masses. Fluctuations in the temperature difference across the enclosure surrounding the free-falling test mass can produce noisy forces through several processes, including the radiometric effect, radiation pressure, and outgassing. We present here a detailed experimental investigation of thermal gradient-induced forces for the LISA gravitational wave mission and the LISA Pathfinder, employing high resolution torsion pendulum measurements of the torque on a LISA-like test mass suspended inside a prototype of the LISA gravitational reference sensor that will surround the test mass in orbit. The measurement campaign, accompanied by numerical simulations of the radiometric and radiation pressure effects, allows a more accurate and representative characterization of thermal-gradient forces in the specific geometry and environment relevant to LISA free-fall. The pressure dependence of the measured torques allows clear identification of the radiometric effect, in quantitative agreement with the model developed. In the limit of zero gas pressure, the measurements are most likely dominated by outgassing, but at a low level that does not threaten the LISA sensitivity goals.Comment: 21 pages, 16 figures, submitted to Physical Review

Emergence of a non trivial fluctuating phase in the XY model on regular networks

We study an XY-rotor model on regular one dimensional lattices by varying the number of neighbours. The parameter $2\ge\gamma\ge1$ is defined. $\gamma=2$ corresponds to mean field and $\gamma=1$ to nearest neighbours coupling. We find that for $\gamma<1.5$ the system does not exhibit a phase transition, while for $\gamma > 1.5$ the mean field second order transition is recovered. For the critical value $\gamma=\gamma_c=1.5$, the systems can be in a non trivial fluctuating phase for whichthe magnetisation shows important fluctuations in a given temperature range, implying an infinite susceptibility. For all values of $\gamma$ the magnetisation is computed analytically in the low temperatures range and the magnetised versus non-magnetised state which depends on the value of $\gamma$ is recovered, confirming the critical value $\gamma_{c}=1.5$