Ontogeny of a subtidal point bar in the microtidal Venice Lagoon (Italy) revealed by three-dimensional architectural analyses

Sedimentological and architectural features of meandering subtidal channels are relatively unexplored, and their deposits are commonly investigated based on facies models set up for intertidal meandering channels. The Venice Lagoon (northern Adriatic Sea, Italy) is affected by a micro-tidal regime and hosts a dense network of active and buried tidal channels. It represents an excellent natural laboratory to improve the current knowledge on subtidal meander morphodynamics and related deposits. In this study, the integration of high-resolution geophysical images and core data allows reconstruction of the architectural three-dimensional model of a meandering subtidal palaeochannel, which is buried below a modern subtidal flat. The study palaeochannel was 35 m wide and 3 m deep, and formed three adjacent meander bends and related point bars. A detailed three-dimensional architectural reconstruction was carried out for deposits associated with one of these meander bends, that was crossed by a minor, low-sinuosity channel with two minor bank-attached bars. This reconstruction highlights that the study point bar has a horseshoe shape, which arose from the onset of bar accretion from an already-sinuous channel. Reconstructed growth stages of the studied bends show that point-bar accretion can follow different styles of planform transformation, also experiencing simultaneously landward (or seaward) deposition according to the dominant flow direction (i.e. local tidal asymmetry). The analyses show that planform transformations occurred in parallel with elevation changes of the related channel thalweg, which shaped pools with geometry varying with the radius of curvature of the bend. The present study highlights the relevance of high-resolution three-dimensional reconstructions to link palaeomorphodynamic processes with related sedimentary products

An experimental study of droplet-particle collisions

When spray drying a liquid slurry such as milk, collisions between droplets, partially dried particles and completely dry particles are important because coalescence, agglomeration and breakup events influence the size and morphology of the produced powder. When modelling such a spray drying process, it is therefore important to be able to predict the outcomes of individual binary collisions. Both binary dry particle collisions and binary droplet collisions have individually been thoroughly researched over the years due to their widespread occurrence. The importance of understanding binary particle-droplet collisions has been emphasized more recently. However, the number of available studies is limited and simulation studies usually focus on relatively high capillary number. A theory explaining the transition between different regimes is still lacking. The goal of this study is to provide an experimental data set at low capillary number. These results can be used to validate future theories and simulations. To produce and record particle-droplet collisions, an experimental setup that enables synchronized release of both a particle and a droplet was used. One single hanging droplet was released from above onto a particle that initially was held in place by vacuum suction. A high speed camera was synchronized with the setup, and recorded the collisions. Image files were then analysed in Matlab to find velocities and sizes of the particle and droplet before and after impact. The contrast of particle and droplet against the illuminated background was a key factor in succeeding with this. Different collision outcomes were identified as either agglomeration (merging), where the whole droplet would stick to the surface of the particle, or a stretching separation (breaking), where the droplet collides with the particle in an oblique position and stretches out until a part of the droplet detaches from the liquid sticking to the particle. The formation of satellite droplets, i.e. droplets with a radius significantly smaller than the leaving droplet, was also detected. The relation of these collision outcomes to impact conditions such as Weber number and impact parameter was reviewed and put into regime maps

Mean Field Theory of the Localization Transition

A mean field theory of the localization transition for bosonic systems is developed. Localization is shown to be sensitive to the distribution of the random site energies. It occurs in the presence of a triangular distribution, but not a uniform one. The inverse participation ratio, the single site Green's function, the superfluid order parameter and the corresponding susceptibility are calculated, and the appropriate exponents determined. All of these quantities indicate the presence of a new phase, which can be identified as the {\it Bose-glass}.Comment: 4 pages, Revtex, 2 figures appende

Outcome comparison between radiation therapy and surgery as primary treatment for dogs with periarticular histiocytic sarcoma: An Italian Society of Veterinary Oncology study

Localized histiocytic sarcoma may occur as a primary lesion in periarticular tissues of large appendicular joints. Treatment options for the primary lesion include radical surgical excision, radiation therapy (RT), or both, in combination with chemotherapy for potential systemic metastases. In an effort to better characterize the time to progression (TTP) following surgical vs non-surgical approaches for periarticular histiocytic sarcoma (PAHS), a contemporary European population of affected dogs was retrospectively surveyed. Medical records were queried for newly-diagnosed PAHS cases undergoing surgery (predominantly limb amputation) or RT followed by systemic chemotherapy. Of 49 dogs, 34 underwent RT and 15 underwent surgery. All dogs received adjuvant chemotherapy. There was no statistically significant difference in TTP or overall survival between groups. The median TTP was 336 days for the operated dogs and 217 days for the irradiated dogs (P =.117). The median overall survival time was 398 days for the operated dogs and 240 days for the irradiated dogs (P =.142). On multi-variable analysis, the variables significantly associated with an increased risk of both tumour progression and tumour-related death were regional lymph node and distant metastasis at admission. Survival and local control rates following RT may be comparable to radical resection. These data may better inform shared decision-making processes between multi-disciplinary care providers and owners

NETTAB 2012 on “Integrated Bio-Search”

The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement

Onset of Superfluidity in 4He Films Adsorbed on Disordered Substrates

We have studied 4He films adsorbed in two porous glasses, aerogel and Vycor, using high precision torsional oscillator and DC calorimetry techniques. Our investigation focused on the onset of superfluidity at low temperatures as the 4He coverage is increased. Torsional oscillator measurements of the 4He-aerogel system were used to determine the superfluid density of films with transition temperatures as low as 20 mK. Heat capacity measurements of the 4He-Vycor system probed the excitation spectrum of both non-superfluid and superfluid films for temperatures down to 10 mK. Both sets of measurements suggest that the critical coverage for the onset of superfluidity corresponds to a mobility edge in the chemical potential, so that the onset transition is the bosonic analog of a superconductor-insulator transition. The superfluid density measurements, however, are not in agreement with the scaling theory of an onset transition from a gapless, Bose glass phase to a superfluid. The heat capacity measurements show that the non-superfluid phase is better characterized as an insulator with a gap.Comment: 15 pages (RevTex), 21 figures (postscript

Benchmarking of cell type deconvolution pipelines for transcriptomics data

Many computational methods have been developed to infer cell type proportions from bulk transcriptomics data. However, an evaluation of the impact of data transformation, pre-processing, marker selection, cell type composition and choice of methodology on the deconvolution results is still lacking. Using five single-cell RNA-sequencing (scRNA-seq) datasets, we generate pseudo-bulk mixtures to evaluate the combined impact of these factors. Both bulk deconvolution methodologies and those that use scRNA-seq data as reference perform best when applied to data in linear scale and the choice of normalization has a dramatic impact on some, but not all methods. Overall, methods that use scRNA-seq data have comparable performance to the best performing bulk methods whereas semi-supervised approaches show higher error values. Moreover, failure to include cell types in the reference that are present in a mixture leads to substantially worse results, regardless of the previous choices. Altogether, we evaluate the combined impact of factors affecting the deconvolution task across different datasets and propose general guidelines to maximize its performance. Inferring cell type proportions from transcriptomics data is affected by data transformation, normalization, choice of method and the markers used. Here, the authors use single-cell RNAseq datasets to evaluate the impact of these factors and propose guidelines to maximise deconvolution performance

NKG2A is a late immune checkpoint on CD8 T cells and marks repeated stimulation and cell division

The surface inhibitory receptor NKG2A forms heterodimers with the invariant CD94 chain and is expressed on a subset of activated CD8 T cells. As antibodies to block NKG2A are currently tested in several efficacy trials for different tumor indications, it is important to characterize the NKG2A(+) CD8 T cell population in the context of other inhibitory receptors. Here we used a well-controlled culture system to study the kinetics of inhibitory receptor expression. Naive mouse CD8 T cells were synchronously and repeatedly activated by artificial antigen presenting cells in the presence of the homeostatic cytokine IL-7. The results revealed NKG2A as a late inhibitory receptor, expressed after repeated cognate antigen stimulations. In contrast, the expression of PD-1, TIGIT and LAG-3 was rapidly induced, hours after first contact and subsequently down regulated during each resting phase. This late, but stable expression kinetics of NKG2A was most similar to that of TIM-3 and CD39. Importantly, single-cell transcriptomics of human tumor-infiltrating lymphocytes (TILs) showed indeed that these receptors were often coexpressed by the same CD8 T cell cluster. Furthermore, NKG2A expression was associated with cell division and was promoted by TGF-beta in vitro, although TGF-beta signaling was not necessary in a mouse tumor model in vivo. In summary, our data show that PD-1 reflects recent TCR triggering, but that NKG2A is induced after repeated antigen stimulations and represents a late inhibitory receptor. Together with TIM-3 and CD39, NKG2A might thus mark actively dividing tumor-specific TILs.Experimental cancer immunology and therap