Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics.

In the last years, it has been proved that some viruses are able to re-structure chromatin organization and alter the epigenomic landscape of the host genome. In addition, they are able to affect the physical mechanisms shaping chromatin 3D structure, with a consequent impact on gene activity. Here, we investigate with polymer physics genome re-organization of the host genome upon SARS-CoV-2 viral infection and how it can impact structural variability within the population of single-cell chromatin configurations.

Prevalence and Characterization of Staphylococcus aureus Isolated from Meat and Milk in Northeastern Italy.

Staphylococcus aureus is a pathogenic microorganism often found in animal-derived foods and is known for its ability to readily develop resistance to antibiotic treatments. This study was designed to determine the prevalence of S. aureus strains in raw milk and meat in Italy and to evaluate their antibiotic resistance profiles and biofilm production.

Propagation of Orientation Across Lengthscales in Sheared Self-Assembling Hierarchical Suspensions via Rheo-PLI-SAXS.

Simultaneous rheological, polarized light imaging, and small-angle X-ray scattering experiments (Rheo-PLI-SAXS) are developed, thereby providing unprecedented level of insight into the multiscale orientation of hierarchical systems in simple shear. Notably, it is observed that mesoscale alignment in the flow direction does not develop simultaneously across nano-micro lengthscales in sheared suspensions of rod-like chiral-nematic (meso) phase forming cellulose nanocrystals. Rather, with increasing shear rate, orientation is observed first at mesoscale and then extends to the nanoscale, with influencing factors being the aggregation state of the hierarchy and concentration.

Molecular signatures associated with venous thromboembolism in children with acute lymphoblastic leukemia.

Background: Venous thromboembolism (VTE) is a frequent complication of childhood acute lymphoblastic leukemia (ALL).

Objectives: We aimed to identify molecular markers and signatures of leukemia microenvironment associated with VTE in childhood ALL, by dual-omics approach of gene expression (GEP) and DNA-methylation profiling.

Patients/methods: Eligible children were aged 1-21 years old with newly diagnosed ALL enrolled on the Dana Farber Cancer Institute 16-001 trial with available RNA sequencing data from bone marrow at diagnosis.

A Multiscale Perspective on Chromatin Architecture through Polymer Physics.

The spatial organization of chromatin within the eukaryotic nucleus is critical in regulating key cellular functions, such as gene expression, and its disruption can lead to disease. Advances in experimental techniques, such as Hi-C and microscopy, have significantly enhanced our understanding of chromatin's intricate and dynamic architecture, revealing complex patterns of interaction at multiple scales. Along with experimental methods, physics-based computational models, including polymer phase separation and loop-extrusion mechanisms, have been developed to explain chromatin structure in a principled manner.

Enhancing Direction-of-Arrival Estimation with Multi-Task Learning.

There are numerous methods in the literature for Direction-of-Arrival (DOA) estimation, including both classical and machine learning-based approaches that jointly estimate the Number of Sources (NOS) and DOA. However, most of these methods do not fully leverage the potential synergies between these two tasks, which could yield valuable shared information. To address this limitation, in this article, we present a multi-task Convolutional Neural Network (CNN) capable of simultaneously estimating both the NOS and the DOA of the signal.

Search for Soft Unclustered Energy Patterns in Proton-Proton Collisions at 13 TeV.

The first search for soft unclustered energy patterns (SUEPs) is performed using an integrated luminosity of 138  fb^{-1} of proton-proton collision data at sqrt[s]=13  TeV, collected in 2016-2018 by the CMS detector at the LHC. Such SUEPs are predicted by hidden valley models with a new, confining force with a large 't Hooft coupling. In events with boosted topologies, selected by high-threshold hadronic triggers, the multiplicity and sphericity of clustered tracks are used to reject the background from standard model quantum chromodynamics.

Extracellular Histones Profiles of Pediatric H3K27-Altered Diffuse Midline Glioma.

Background: Diffuse midline glioma, H3 K27-altered (DMG) is a fatal tumour that arises in the midline structures of the brain. When located in the pons, it is more commonly referred to as diffuse intrinsic pontine glioma (DIPG). DMG/DIPG is usually diagnosed when children are < 10 years, and it has a median overall survival of < 12 months after diagnosis.

An integrated view of the structure and function of the human 4D nucleome.

The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales.

Search for the Z Boson Decay to ττμμ in Proton-Proton Collisions at sqrt[s]=13 TeV.

The first search for the Z boson decay to ττμμ at the CERN LHC is presented, based on data collected by the CMS experiment at the LHC in proton-proton collisions at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 138  fb^{-1}. The data are compatible with the predicted background. For the first time, an upper limit at the 95% confidence level of 6.

Enhancing the light yield of He:CF based gaseous detector.

The CYGNO experiment aims to build a large ( m ) directional detector for rare event searches, such as nuclear recoils (NRs) induced by dark matter (DM), such as weakly interactive massive particles (WIMPs). The detector concept comprises a time projection chamber (TPC), filled with a He:CF 60/40 scintillating gas mixture at room temperature and atmospheric pressure, equipped with an amplification stage made of a stack of three gas electron multipliers (GEMs) which are coupled to an optical readout. The latter consists in scientific CMOS (sCMOS) cameras and photomultipliers tubes (PMTs).

Observation of the decay.

Using proton-proton collision data corresponding to an integrated luminosity of collected by the CMS experiment at , the decay is observed for the first time, with a statistical significance exceeding 5 standard deviations. The relative branching fraction, with respect to the decay, is measured to be , where the first uncertainty is statistical, the second is systematic, and the third is related to the uncertainties in and .

Observation of Enhanced Long-Range Elliptic Anisotropies Inside High-Multiplicity Jets in pp Collisions at sqrt[s]=13 TeV.

A search for collective effects inside jets produced in proton-proton collisions is performed via correlation measurements of charged particles using the CMS detector at the CERN LHC. The analysis uses data collected at a center-of-mass energy of sqrt[s]=13  TeV, corresponding to an integrated luminosity of 138  fb^{-1}. Jets are reconstructed with the anti-k_{T} algorithm with a distance parameter of 0.

ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway.

Repurposing an organelle for specialized metabolism provides an avenue for fermentable, unicellular organisms such as Saccharomyces cerevisiae to mimic compartmentalization of metabolic pathways within different plant tissues. Peroxisomes are attractive organelles for repurposing as they are not required for yeast viability when grown on glucose and can efficiently compartmentalize heterologous enzymes to enable physical separation of cytosolic native metabolism and peroxisomal engineered metabolism. However, when not required, peroxisomes are repressed, leading to low functional capacities for heterologous proteins.

A Convolutional Framework for Color Constancy.

We introduce a convolutional framework (CF) for computational color constancy, building upon the established low-level image feature-based framework, which utilized simple image statistics for illuminant estimation. Our framework expands upon this through an end-to-end learnable neural architecture. This adaptation enables the learning and usage of advanced filters that are not restricted to Gaussian kernels operating on individual color channels, thus generalizing the capabilities of the original framework.

Measurement of Energy Correlators inside Jets and Determination of the Strong Coupling α_{S}(m_{Z}).

Energy correlators that describe energy-weighted distances between two or three particles in a hadronic jet are measured using an event sample of sqrt[s]=13  TeV proton-proton collisions collected by the CMS experiment and corresponding to an integrated luminosity of 36.3  fb^{-1}. The measured distributions are consistent with the trends in the simulation that reveal two key features of the strong interaction: confinement and asymptotic freedom.

Observation of the ϒ(3S) Meson and Suppression of ϒ States in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV.

The production of ϒ(2S) and ϒ(3S) mesons in lead-lead (Pb-Pb) and proton-proton (pp) collisions is studied in their dimuon decay channel using the CMS detector at the LHC. The ϒ(3S) meson is observed for the first time in Pb-Pb collisions, with a significance above 5 standard deviations. The ratios of yields measured in Pb-Pb and pp collisions are reported for both the ϒ(2S) and ϒ(3S) mesons, as functions of transverse momentum and Pb-Pb collision centrality.

Ultrasensitive Raman Detection of Biomolecular Conformation at the Attomole Scale using Chiral Nanophotonics.

Understanding the function of a biomolecule hinges on its 3D conformation or secondary structure. Chirally sensitive, optically active techniques based on the differential absorption of UV-vis circularly polarized light excel at rapid characterisation of secondary structures. However, Raman spectroscopy, a powerful method for determining the structure of simple molecules, has limited capacity for structural analysis of biomolecules because of intrinsically weak optical activity, necessitating millimolar (mM) sample quantities.

Search for Narrow Trijet Resonances in Proton-Proton Collisions at sqrt[s]=13 TeV.

The first search for singly produced narrow resonances decaying to three well-separated hadronic jets is presented. The search uses proton-proton collision data corresponding to an integrated luminosity of 138  fb^{-1} at sqrt[s]=13  TeV, collected at the CERN LHC. No significant deviations from the background predictions are observed between 1.