Beach morphodynamics and types of foredune erosion generated by storms along the Emilia-Romagna coastline, Italy

The objectives of this study are to examine the response of a dune and beach system on the Adriatic coastline in northern Italy to the arrival of storms, compare it with seasonal (months) and medium-term (3-year) morphodynamic change, and evaluate results predicted by the numerical model XBeach. The studied coastline stretches 4 km from the Bevano River mouth to the north of the site to the township of Lido di Classe to the south, where the beach is protected by coastal structures. Fieldwork consisted of topographic profile surveys using RTK-DGPS technology (7 times over an approx. 3-year period). 103 samples of surface sediment were collected along 20 of the cross-shore profiles at 6 distinct cross-shore positions, selected on the basis of morphological beach characteristics. Data analyses of dune and beach slopes enabled the study area to be divided into 6 separate morphological zones using the spatial (longshore and cross-shore) variation of morphologies located on the backshore and intertidal beach observed in a preliminary survey of the area. Other criteria were a spatial consistency in beach slopes and/or presence/absence of intertidal morphologies identified in the aerial photographs and Lidar data. The swash zone slope did not show any significant variability for the entire area. A weak seasonal trend in the variability of the mean foredune slope was observed, with steeper slopes typically during winter and flatter slopes during summer. Analysis of grain size revealed that the beach sediment is well-sorted fine sand tending to medium, with a decreasing trend in size from the Bevano River mouth southwards towards Lido di Classe. According to the Masselink and Short (1993) classification, the natural part of the study site has an Intermediate Barred Beach (IBB) and following the Short (1999) classification, results in a modally LBT (longshore bar-trough) or LTT (low tide terrace) with a small section being TBR (transverse bar and rip). Storms are considered the main factor controlling changes in the beach and dune slope. The most significant storm was recorded in March 2010 with a peak significant wave height of 3.91 m. Contrary to the seasonal dune trend, several foredune slopes were observed to flatten following this event, which can be attributed to the action of dune slumping from the already weakened dune state. Modelling of foredune erosion, using a process-based model (XBeach), reproduced the erosion of the upper beach and dune toe reasonably well, but is currently limited by the acceptable slope value for dune stability, which does not account for biotic factors (e.g. plant roots). The comparison between the storm impact categories of Sallenger (2000) and the DSF (Dune Stability Factor) of Armaroli et al. (2012) shows a very good correspondence between the effects of the winter 2008–2009 storms and the vulnerability of the dune system predicted using both classifications

Environmental signal shredding on sandy coastlines

How storm events contribute to long-term shoreline change over decades to centuries remains an open question in coastal research. Sand and gravel coasts exhibit remarkable resilience to event-driven disturbances, and, in settings where sea level is rising, shorelines retain almost no detailed information about their own past positions. Here, we use a high-frequency, multi-decadal observational record of shoreline position to demonstrate quantitative indications of morphodynamic turbulence – “signal shredding” – in a sandy beach system. We find that, much as in other dynamic sedimentary systems, processes of sediment transport that affect shoreline position at relatively short timescales may obscure or erase evidence of external forcing. This suggests that the physical effects of annual (or intra-annual) forcing events, including major storms, may convey less about the dynamics of long-term shoreline change – and vice versa – than coastal researchers might wish

Simulating the diversity of shapes of the Lyman-α\alpha line

The Ly$\alpha$ line is a powerful probe of distant galaxies, which contains information about inflowing/outflowing gas through which Ly$\alpha$ photons scatter. To develop our understanding of this probe, we post-process a zoom-in radiation-hydrodynamics simulation of a low-mass ($M_* \sim 10^9 M_\odot$) galaxy to construct 22500 mock spectra in 300 directions from $z = 3$ to 4. Remarkably, we show that one galaxy can reproduce the variety of a large sample of spectroscopically observed Ly$\alpha$ line profiles. While most mock spectra exhibit double-peak profiles with a dominant red peak, their shapes cover a large parameter space in terms of peak velocities, peak separation and flux ratio. This diversity originates from radiative transfer effects at ISM and CGM scales, and depends on galaxy inclination and evolutionary phase. Red-dominated lines preferentially arise in face-on directions during post-starburst outflows and are bright. Conversely, accretion phases usually yield symmetric double peaks in the edge-on direction and are fainter. While resonant scattering effects at $< 0.2\times R_{\rm vir}$ are responsible for the broadening and velocity shift of the red peak, the extended CGM acts as a screen and impacts the observed peak separation. The ability of simulations to reproduce observed Ly$\alpha$ profiles and link their properties with galaxy physical parameters offers new perspectives to use Ly$\alpha$ to constrain the mechanisms that regulate galaxy formation and evolution. Notably, our study implies that deeper Ly$\alpha$ surveys may unveil a new population of blue-dominated lines tracing inflowing gas.Comment: Accepted for publication in MNRA

A Multiscale Approach to Shoreline Prediction

ABSTRACT: Shorelines respond to a number of "drivers" operating on a variety of time-scales. For some time-scales (e.g., seasonal), the driver-shoreline relationship is often evident; however, at longer timescales (e.g., multiannual), the shoreline changes may be superimposed on changes at shorter time-scales and thus are diffcult to identify. Here, we predict shoreline evolution from storm events to decadal timescales, using a novel approach based on the Complete Ensemble Empirical Mode Decomposition. This approach identifies and links the primary time-scales in the model drivers (large-scale sea level pressure [SLP] and/or waves) with the same time-scales in the shoreline position. The multiscale approach reproduced shoreline changes at two beaches more skillfully than a common shoreline model when SLP and wave information were used in combination. In addition, the analysis can be applied to climate indices, providing the opportunity to link longer time-scales with climate patterns (e.g., El Niño Southern Oscillation)

Peginterferon Alfa-2a and Ribavirin for 16 or 24 Weeks in HCV Genotype 2 or 3

Background Patients infected with hepatitis C virus (HCV) genotype 2 or 3 have sustained virologic response rates of approximately 80% after receiving treatment with peginterferon and ribavirin for 24 weeks. We conducted a large, randomized, multinational, noninferiority trial to determine whether similar efficacy could be achieved with only 16 weeks of treatment with peginterferon alfa-2a and ribavirin. Methods We randomly assigned 1469 patients with HCV genotype 2 or 3 to receive 180 μg of peginterferon alfa-2a weekly, plus 800 mg of ribavirin daily, for either 16 or 24 weeks. A sustained virologic response was defined as an undetectable serum HCV RNA level (milliliter) 24 weeks after the end of treatment. Results The study failed to demonstrate that the 16-week regimen was noninferior to the 24-week regimen. The sustained virologic response rate was significantly lower in patients treated for 16 weeks than in patients treated for 24 weeks (62% vs. 70%; odds ratio for 16 weeks vs. 24 weeks, 0.67; 95% confidence interval, 0.54 to 0.84; P Conclusions Treatment with peginterferon and ribavirin for 16 weeks in patients infected with HCV genotype 2 or 3 results in a lower overall sustained virologic response rate than treatment with the standard 24-week regimen. (ClinicalTrials.gov number, NCT00077636.

Trend-TDT – a transmission/disequilibrium based association test on functional mini/microsatellites

<p>Abstract</p> <p>Background</p> <p>Minisatellites and microsatellites are associated with human disease, not only as markers of risk but also involved directly in disease pathogenesis. They may play significant roles in replication, repair and mutation of DNA, regulation of gene transcription and protein structure alteration. Phenotypes can thus be affected by mini/microsatellites in a manner proportional to the length of the allele. Here we propose a new method to assess the linear trend toward transmission of shorter or longer alleles from heterozygote parents to affected child.</p> <p>Results</p> <p>This test (trend-TDT) performs better than other TDT (Transmission/Disequilibrium Test) type tests, such as TDT_maxand TDT_L/S, under most marker-disease association models.</p> <p>Conclusion</p> <p>The trend-TDT test is a more powerful association test when there is a biological basis to suspect a relationship between allele length and disease risk.</p

Disambiguation of biomedical text using diverse sources of information

Background: Like text in other domains, biomedical documents contain a range of terms with more than one possible meaning. These ambiguities form a significant obstacle to the automatic processing of biomedical texts. Previous approaches to resolving this problem have made use of various sources of information including linguistic features of the context in which the ambiguous term is used and domain-specific resources, such as UMLS. Materials and methods: We compare various sources of information including ones which have been previously used and a novel one: MeSH terms. Evaluation is carried out using a standard test set (the NLM-WSD corpus). Results: The best performance is obtained using a combination of linguistic features and MeSH terms. Performance of our system exceeds previously published results for systems evaluated using the same data set. Conclusion: Disambiguation of biomedical terms benefits from the use of information from a variety of sources. In particular, MeSH terms have proved to be useful and should be used if available

Both telomeric and non-telomeric DNA damage are determinants of mammalian cellular senescence

<p>Abstract</p> <p>Background</p> <p>Cellular senescence is a state reached by normal mammalian cells after a finite number of cell divisions and is characterized by morphological and physiological changes including terminal cell-cycle arrest. The limits on cell division imposed by senescence may play an important role in both organismal aging and in preventing tumorigenesis. Cellular senescence and organismal aging are both accompanied by increased DNA damage, seen as the formation of γ-H2AX foci (γ-foci), which may be found on uncapped telomeres or at non-telomeric sites of DNA damage. However, the relative importance of telomere- and non-telomere-associated DNA damage to inducing senescence has never been demonstrated. Here we present a new approach to determine accurately the chromosomal location of γ-foci and quantify the number of telomeric versus non-telomeric γ-foci associated with senescence in both human and mouse cells. This approach enables researchers to obtain accurate values and to avoid various possible misestimates inherent in earlier methods.</p> <p>Results</p> <p>Using combined immunofluorescence and telomere fluorescence <it>in situ </it>hybridization on metaphase chromosomes, we show that human cellular senescence is not solely determined by telomeric DNA damage. In addition, mouse cellular senescence is not solely determined by non-telomeric DNA damage. By comparing cells from different generations of telomerase-null mice with human cells, we show that cells from late generation telomerase-null mice, which have substantially short telomeres, contain mostly telomeric γ-foci. Most notably, we report that, as human and mouse cells approach senescence, all cells exhibit similar numbers of total γ-foci per cell, irrespective of chromosomal locations.</p> <p>Conclusion</p> <p>Our results suggest that the chromosome location of senescence-related γ-foci is determined by the telomere length rather than species differences <it>per se</it>. In addition, our data indicate that both telomeric and non-telomeric DNA damage responses play equivalent roles in signaling the initiation of cellular senescence and organismal aging. These data have important implications in the study of mechanisms to induce or delay cellular senescence in different species.</p

Plasmid-Cured Chlamydia caviae Activates TLR2-Dependent Signaling and Retains Virulence in the Guinea Pig Model of Genital Tract Infection

Loss of the conserved “cryptic” plasmid from C. trachomatis and C. muridarum is pleiotropic, resulting in reduced innate inflammatory activation via TLR2, glycogen accumulation and infectivity. The more genetically distant C. caviae GPIC is a natural pathogen of guinea pigs and induces upper genital tract pathology when inoculated intravaginally, modeling human disease. To examine the contribution of pCpGP1 to C. caviae pathogenesis, a cured derivative of GPIC, strain CC13, was derived and evaluated in vitro and in vivo. Transcriptional profiling of CC13 revealed only partial conservation of previously identified plasmid-responsive chromosomal loci (PRCL) in C. caviae. However, 2-deoxyglucose (2DG) treatment of GPIC and CC13 resulted in reduced transcription of all identified PRCL, including glgA, indicating the presence of a plasmid-independent glucose response in this species. In contrast to plasmid-cured C. muridarum and C. trachomatis, plasmid-cured C. caviae strain CC13 signaled via TLR2 in vitro and elicited cytokine production in vivo similar to wild-type C. caviae. Furthermore, inflammatory pathology induced by infection of guinea pigs with CC13 was similar to that induced by GPIC, although we observed more rapid resolution of CC13 infection in estrogen-treated guinea pigs. These data indicate that either the plasmid is not involved in expression or regulation of virulence in C. caviae or that redundant effectors prevent these phenotypic changes from being observed in C. caviae plasmid-cured strains

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Abstract Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I σ70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the α subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the σ70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance.</p