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Transformer-based models have made significant progress in edge detection, but their high computational cost is prohibitive. Recently, vision Mamba have shown excellent ability in efficiently capturing long-range dependencies. Drawing inspiration from this, we propose a novel edge detector with Mamba, termed EDMB, to efficiently generate high-quality multi-granularity edges. In EDMB, Mamba is combined with a global-local architecture, therefore it can focus on both global information and fine-grained cues. The fine-grained cues play a crucial role in edge detection, but are usually ignored by ordinary Mamba. We design a novel decoder to construct learnable Gaussian distributions by fusing global features and fine-grained features. And the multi-grained edges are generated by sampling from the distributions. In order to make multi-granularity edges applicable to single-label data, we introduce Evidence Lower Bound loss to supervise the learning of the distributions. On the multi-label dataset BSDS500, our proposed EDMB achieves competitive single-granularity ODS 0.837 and multi-granularity ODS 0.851 without multi-scale test or extra PASCAL-VOC data. Remarkably, EDMB can be extended to single-label datasets such as NYUDv2 and BIPED. The source code is available at https://github.com/Li-yachuan/EDMB. more...

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/) more...

Bromochloro alkanes (BCAs) have been manufactured for use as flame retardants for decades and preliminary environmental risk screening suggests they are likely to behave similarly to polychlorinated alkanes (PCAs), subclasses of which are restricted as Stockholm Convention Persistent Organic Pollutants (POPs). BCAs have rarely been studied in the environment, though some evidence suggests they may migrate from treated-consumer materials into indoor dust, resulting in human exposure via inadvertent ingestion. In this study, BCA-C14 mixture standards were synthesized and used to validate an analytical method. This method relies on chloride-enhanced liquid chromatography-electrospray ionization-Orbitrap-high resolution mass spectrometry (LC-ESI-Orbitrap-HRMS) and a novel CP-Seeker integration software package for homologue detection and integration. Dust sample preparation via ultrasonic extraction, acidified silica clean-up and fractionation on neutral silica cartridges was found to be suitable for BCAs, with absolute recovery of individual homologues averaging 66 to 78% and coefficients of variation $\le$10% in replicated spiking experiments (n=3). In addition, a total of 59 indoor dust samples from six countries including Australia (n=10), Belgium (n=10), Colombia (n=10), Japan (n=10), Thailand (n=10) and the United States of America (n=9) were analysed for BCAs. BCAs were detected in seven samples from the USA, with carbon chain lengths of C8, C10, C12, C14, C16, C18, C24 to C28, C30 and C31 observed overall, though not detected in samples from any other countries. Bromination of detected homologues in the indoor dust samples ranged from Br1-4 as well as Br7, while chlorine numbers ranged from Cl2-11. BCA-C18 were the most frequently detected, observed in each of the USA samples, while the most prevalent halogenation degrees were homologues of Br2 and Cl4-5. Broad estimations of BCA concentrations in the dust samples indicated that levels may approach those of other flame retardants in at least some instances. These findings suggest that development of quantification strategies and further investigation of environmental occurrence and health implications are needed. more...

We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g. distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust G\=oMartini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based G\=o-like approach for the study of protein-sugar complexes, and also limitations of this approach are discussed. The G\=oMartini approach was first introduced by Poma et al. J. Chem. Theory Comput. 2017, 13(3), 1366-1374 in Martini 2 force field and recently, it has gained the status of gold-standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support to this approach in the context of the biophysical community., Comment: 19 pages, 3 figures more...

Let $X^{1,n}_r$ be the blow-up of $\mathbb{P}^1\times\mathbb{P}^n$ in $r$ general points. We describe the Mori cone of $X^{1,n}_r$ for $r\leq n+2$ and for $r = n+3$ when $n\leq 4$. Furthermore, we prove that $X^{1,n}_{n+1}$ is log Fano and give an explicit presentation for its Cox ring., Comment: 12 pages more...

From viruses to nanoparticles, constructs functionalized with multiple ligands display peculiar binding properties that only arise from multivalent effects. Using statistical mechanical modelling, we describe here how multivalency can be exploited to achieve what we dub range selectivity, that is, binding only to targets bearing a number of receptors within a specified range. We use our model to characterise the region in parameter space where one can expect range selective targeting to occur, and provide experimental support for this phenomenon. Overall, range selectivity represents a potential path to increase the targeting selectivity of multivalent constructs., Comment: Published in Nature Communications. Received: 25 September 2019; Accepted: 28 August 2020; Link to online open-access publisher version: https://www.nature.com/articles/s41467-020-18603-5#citeas more...

The purpose of the present work is the study of reconstruction properties of a new Molecular Breast Imaging (MBI) device for the early diagnosis of breast cancer, in Limited Angle Tomography (LAT), by using two asymmetric detector heads with different collimators. The detectors face each other in anti-parallel viewing direction and, mild-compressing the breast phantom, they are able to reconstruct the inner tumour of the phantoms with only a limited number of projections using a dedicated maximum-likelihood expectation maximization (ML-EM) algorithm. Phantoms, MBI system, as well as Monte Carlo simulator using Geant 4 Application for Tomographic Emission (GATE) software, are briefly described. MBI system's model has been implemented in IDL (Interactive Data Visualization), in order to evaluate the best LAT configuration of the system and its reconstruction ability by varying tumour's size, depth and uptake. LAT setup in real and simulated configurations, as well as the ML-EM method and the preliminary reconstruction results, are discussed., Comment: 10 pages, 10 figures, proceeding conference more...

The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching of proteins, folding and thermal unfolding). Here, we extend the capabilities of the EN model by using a harmonic approximation described by Lennard-Jones (LJ) interactions for far contacts and native contacts obtained from the standard overlap criterion as in the case of Go-like models. While our model is validated against the EN model by reproducing the equilibrium properties for a number of proteins, we also show that the model is suitable for the study of large conformation changes by providing various examples. In particular, this is illustrated on the basis of pulling simulations that predict with high accuracy the experimental data on the rupture force of the studied proteins. Furthermore, in the case of DDFLN4 protein, our pulling simulations highlight the advantages of our model with respect to Go-like approaches, where the latter fail to reproduce previous results obtained by all-atom simulations that predict an additional characteristic peak for this protein. In addition, folding simulations of small peptides yield different folding times for alpha-helix and beta-hairpin, in agreement with experiment, in this way providing further opportunities for the application of our model in studying large conformational changes of proteins. In contrast to the EN model, our model is suitable for both normal mode analysis and molecular dynamics simulation. We anticipate that the proposed model will find applications in a broad range of problems in biology, including, among others, protein folding and thermal unfolding., Comment: 9 pages, 5 figures more...

Samples of two characteristic semiconductor sensor materials, silicon and germanium, have been irradiated with neutrons produced at the RP-10 Nuclear Research Reactor at 4.5 MW. Their radionuclides photon spectra have been measured with high resolution gamma spectroscopy, quantifying four radioisotopes ($^{28}$Al, $^{29}$Al for Si and $^{75}$Ge and $^{77}$Ge for Ge). We have compared the radionuclides production and their emission spectrum data with Monte Carlo simulation results from FLUKA. Thus we have tested FLUKA's low energy neutron library (ENDF/B-VIIR) and decay photon scoring with respect to the activation of these semiconductors. We conclude that FLUKA is capable of predicting relative photon peak amplitudes, with gamma intensities greater than 1%, of produced radionuclides with an average uncertainty of 13%. This work allows us to estimate the corresponding systematic error on neutron activation simulation studies of these sensor materials., Comment: 18 pages, 5 figures; figure added, minor changes, typos corrected more...

Studying atmospheric neutrino oscillations in the few-GeV range with a multimegaton detector promises to determine the neutrino mass hierarchy. This is the main science goal pursued by the future KM3NeT/ORCA water Cherenkov detector in the Mediterranean Sea. In this paper, the processes that limit the obtainable resolution in both energy and direction in charged-current neutrino events in the ORCA detector are investigated. These processes include the composition of the hadronic fragmentation products, the subsequent particle propagation and the photon-sampling fraction of the detector. GEANT simulations of neutrino interactions in seawater produced by GENIE are used to study the effects in the 1 - 20 GeV range. It is found that fluctuations in the hadronic cascade in conjunction with the variation of the inelasticity y are most detrimental to the resolutions. The effect of limited photon sampling in the detector is of significantly less importance. These results will therefore also be applicable to similar detectors/media, such as those in ice., Comment: 37 pages, 28 figures, JHEP published version more...

We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to considerable structural changes on the proteins with evidence suggesting non-alpha helical conformations. Most importantly both aspects lead to a significant improvement on protein stability against thermal denaturation up to 95degC at neutral pH, with little or no evidence of unfolding or reduced enzymatic activity. The latter parameter does indeed exhibit an increase after thermal cycling. Our results suggest that nanoscopic confinement is a promising new avenue for the enhanced long-term storage of proteins. Moreover, our investigations have potentially important implications for the origin of life, since such compartmentalization may well have been critical for ensuring the preservation of primordial functional proteins under relatively harsh conditions, thus playing a key role in the subsequent emergence of primitive life forms., Comment: 16 pages, 6 figures more...