Nuclear Overlap Research Articles

Structural requirements for the specific binding of CRABP2 to cyclin D3.

Cellular retinoic acid binding protein 2 (CRABP2) transports retinoic acid from the cytoplasm to the nucleus where it then transfers its cargo to retinoic acid receptor-containing complexes leading to activation of gene transcription. We demonstrate using purified proteins that CRABP2 is also a cyclin D3-specific binding protein and that the CRABP2 cyclin D3 binding site and the proposed CRABP2 nuclear localization sequence overlap. Both sequences are within the helix-loop-helix motif that forms a lid to the retinoic acid binding pocket. Mutations within this sequence that block both cyclin D3 and retinoic acid binding promote formation of a CRABP2 structure in which the retinoic acid binding pocket is occupied by an alternative lid conformation. Structural and functional analysis of CRABP2 and cyclin D3 mutants combined with AlphaFold models of the ternary CDK4/6-cyclin D3-CRABP2 complex supports the identification of an α-helical protein binding site on the cyclin D3 C-terminal cyclin box fold.

Lepton pair photoproduction in hadronic heavy-ion collisions with nuclear overlap

Lepton pair photoproduction in hadronic heavy-ion collisions with nuclear overlap

Robust nuclei segmentation with encoder‐decoder network from the histopathological images

AbstractNuclei segmentation is a prerequisite and an essential step in cancer detection and prognosis. Automatic nuclei segmentation from the histopathological images is challenging due to nuclear overlap, disease types, chromatic stain variability, and cytoplasmic morphology differences. Furthermore, it is demanding to develop a single accurate method for segmenting nuclei of different organs because of the diversity in nuclei size, shape, and appearance across the various organs. To address these challenges, we developed a robust Encoder‐Decoder network for nuclei segmentation from the multi‐organ histopathological images. In this approach, we utilize a pre‐trained EfficientNet‐B4 as an Encoder subnetwork and design a new Decoder subnetwork architecture. Additionally, we have applied morphological operation‐based post‐processing to improve the segmentation results. The performance of our approach has been evaluated on three public datasets, namely, Kumar, TNBC, and CPM‐17 datasets, which contain histopathological images of seven organs, one organ, and four organs, respectively. The proposed method achieved an aggregated Jacquard index of 0.636, 0.611, and 0.706 on Kumar, TNBC, and CPM‐17 datasets, respectively. Our proposed approach also shows superiority over the existing methods.

Autophagy inhibitors 3-MA and BAF may attenuate hippocampal neuronal necroptosis after global cerebral ischemia-reperfusion injury in male rats by inhibiting the interaction of the RIP3/AIF/CypA complex.

Our previous study found that receptor interacting protein 3 (RIP3) and apoptosis-inducing factor (AIF) were involved in neuronal programmed necrosis during global cerebral ischemia-reperfusion (I/R) injury. Here, we further studied its downstream mechanisms and the role of the autophagy inhibitors 3-methyladenine (3-MA) and bafilomycin A1 (BAF). A 20-min global cerebral I/R injury model was constructed using the 4-vessel occlusion (4-VO) method in male rats. 3-MA and BAF were injected into the lateral ventricle 1 h before ischemia. Spatial and activation changes of proteins were detected by immunofluorescence (IF), and protein interaction was determined by immunoprecipitation (IP). The phosphorylation of H2AX (γ-H2AX) and activation of mixed lineage kinase domain-like protein (p-MLKL) occurred as early as 6 h after reperfusion. RIP3, AIF, and cyclophilin A (CypA) in the neurons after I/R injury were spatially overlapped around and within the nucleus and combined with each other after reperfusion. The survival rate of CA1 neurons in the 3-MA and BAF groups was significantly higher than that in the I/R group. Autophagy was activated significantly after I/R injury, which was partially inhibited by 3-MA and BAF. Pretreatment with both 3-MA and BAF almost completely inhibited nuclear translocation, spatial overlap, and combination of RIP3, AIF, and CypA proteins. These findings suggest that after global cerebral I/R injury, RIP3, AIF, and CypA translocated into the nuclei and formed the DNA degradation complex RIP3/AIF/CypA in hippocampal CA1 neurons. Pretreatment with autophagy inhibitors could reduce neuronal necroptosis by preventing the formation of the RIP3/AIF/CypA complex and its nuclear translocation.

Coherent J/ψ photoproduction and polarization in peripheral Pb−Pb collisions

Photonuclear reactions are induced by the strong electromagnetic field generated by ultrarelativistic heavy-ion collisions. These processes have been extensively studied in ultraperipheral collisions, where the impact parameter is larger than twice the nuclear radius. In recent years, the observation of coherent J/ψ photoproduction at very low transverse momentum has been claimed in nucleus−nucleus (A−A) collisions with nuclear overlap, based on the measurement of an excess in the J/ψ yield with respect to hadroproduction expectations. Such quarkonium measurements can help to constrain the nuclear gluon distribution at low Bjorken-x and high energy. The photoproduced quarkonium is expected to preserve the polarization of the incoming photon due to the s-channel helicity conservation. In this contribution, we report on the new preliminary measurements of the y-differential cross section and the first polarization analysis of coherently photoproduced J/ψ in peripheral Pb−Pb collisions with the ALICE detector at forward rapidity in the dimuon decay channel. Comparison with models will be shown when available.

Photoproduction of low-pT J/ψ from peripheral to central Pb–Pb collisions at 5.02 TeV

An excess of J/ψ yield at very low transverse momentum (pT<0.3 GeV/c), originating from coherent photoproduction, is observed in peripheral and semicentral hadronic Pb–Pb collisions at a center-of-mass energy per nucleon pair of sNN=5.02 TeV. The measurement is performed with the ALICE detector via the dimuon decay channel at forward rapidity (2.5<y<4). The nuclear modification factor at very low pT and the coherent photoproduction cross section are measured as a function of centrality down to the 10% most central collisions. These results extend the previous study at sNN=2.76 TeV, confirming the clear excess over hadronic production in the pT range 0−0.3 GeV/c and the centrality range 70–90%, and establishing an excess with a significance greater than 5σ also in the 50–70% and 30–50% centrality ranges. The results are compared with earlier measurements at sNN=2.76 TeV and with different theoretical predictions aiming at describing how coherent photoproduction occurs in hadronic interactions with nuclear overlap.

The Accurate Interpretation and Clinical Significance of Morphological Features of Fine Needle Aspiration Cells in Papillary Thyroid Carcinoma.

Papillary thyroid carcinoma (PTC) is the most common malignant neoplasm of the thyroid gland; fine needle aspiration cytology is the most basic and reliable diagnostic method before PTC operation. However, it is not clear which cell morphological changes can be used as a reliable standard for the diagnosis of PTC. A retrospective analysis was performed on 337 patients with PTC confirmed by postoperative histology. An additional 197 randomly selected patients with benign thyroid lesions were included in the study and used as a control group. True papillary arrangements, swirl arrangements, and escape arrangements had high specificity, all of which were 100%, but only swirl arrangements had ideal sensitivity (77.61%). The nuclear volume characteristics had a high sensitivity of more than 90%, but the specificities of both nuclear crowding and nuclear overlap were too low, only 16.34% and 23.35%. The sensitivities of five nuclear structural characteristics were more than 90%, but only the specificity of intranuclear cytoplasmic pseudoinclusions (INCIs) reached 100%, nuclear contour irregularity and pale nuclei with powdery chromatin also had ideal interpretation value except for grooves and marginally placed micronucleoli. Although the sensitivity of psammoma bodies (PBs) was low, the specificity was 100%. In terms of preparation methods, the method of liquid-based preparation (LBP) is obviously better than that of conventional smears. The diagnostic efficiency by the combined detection method of parallel tests showed that without reducing the specificity, the sensitivity increased with the increase of the number of morphological characteristics and finally reached 98.81%. The INCIs and swirl arrangements are the most common and important indicators for the diagnosis of PTC, whereas papillary-like arrangements, the crowding and overlap of nuclear, grooves, marginally placed micronucleoli, and multinucleated giant cells are of little significance for the diagnosis of PTC.

Probing initial geometrical anisotropy and final azimuthal anisotropy in heavy-ion collisions at Large Hadron Collider energies through event-shape engineering

Anisotropic flow is accredited to have effects from the initial state geometry and fluctuations in the nuclear overlap region. The elliptic flow (${v}_{2}$) and triangular flow (${v}_{3}$) coefficients of the final state particles are expected to have influenced by eccentricity (${ϵ}_{2}$) and triangularity (${ϵ}_{3}$) of the participants, respectively. In this work, we study ${v}_{2}$, ${v}_{3}$, ${ϵ}_{2}$, ${ϵ}_{3}$, and the correlations among them with respect to event topology in the framework of a multiphase transport model (AMPT). We use transverse spherocity and reduced flow vector as event shape classifiers in this study. Transverse spherocity has the unique ability to separate events based on geometrical shapes, i.e., jetty and isotropic, which pertain to pQCD and non-pQCD domains of particle production in high-energy physics, respectively. We use the two-particle correlation method to study different anisotropic flow coefficients. We confront transverse spherocity with a more widely used event shape classifier--reduced flow vector (${q}_{n}$) and they are found to have significant (anti)correlations among them. We observe significant spherocity dependence on ${v}_{2}$, ${v}_{3}$, and ${ϵ}_{2}$. This work also addresses transverse momentum dependent crossing points between ${v}_{2}$ and ${v}_{3}$, which varies for different centrality and spherocity percentiles.

Jet Tomography in Heavy-Ion Collisions with Deep Learning

Deep learning techniques have the power to identify the degree of modification of high energy jets traversing deconfined QCD matter on a jet-by-jet basis. Such knowledge allows us to study jets based on their initial, rather than final, energy. We show how this new technique provides unique access to the genuine configuration profile of jets over the transverse plane of the nuclear collision, both with respect to their production point and their orientation. By effectively removing the selection biases induced by final-state interactions, one can analyze the potential azimuthal anisotropies of jet production associated to initial-state effects. Additionally, we demonstrate the capability of our new method to locate with precision the production point of a dijet pair in the nuclear overlap region, in what constitutes an important step forward toward the long term quest of using jets as tomographic probes of the quark-gluon plasma.

Coherent photoproduction processes in hadronic heavy-ion collisions

Recently, significant abnormal enhancements in &lt;i&gt;J&lt;/i&gt;/&lt;i&gt;ψ&lt;/i&gt; and dilepton production have been observed in peripheral heavy-ion collisions at very low transverse momentum by the STAR, ALICE and ATLAS Collaborations. The observed excesses cannot be explained by hadronic production combined with the cold and hot medium effects, though it can be well described by coherent photoproduction calculations with nuclear overlap. These experimental and theoretical results provide evidence of coherent photoproduction in hadronic heavy-ion collisions, which suggest novel probes for detecting the properties of quark-gluon plasma (QGP). In this work, we review recent experimental and theoretical progress regarding coherent photoproduction in hadronic heavy-ion collisions.

Thermodynamic and transport properties of matter formed in pp, p-Pb, Xe–Xe and Pb–Pb collisions at the Large Hadron Collider using color string percolation model

To have a better understanding of the matter formed in ultra-relativistic collisions, using the color string percolation model, we have estimated initial energy density, mean free path, squared speed of sound, shear viscosity to entropy density ratio (η/s), bulk viscosity to entropy density ratio and bulk modulus for pp, p-Pb, Xe–Xe and Pb–Pb collisions at the Large Hadron Collider (LHC). These observables are studied as a function of final state charged particle multiplicity density normalized by nuclear overlap area and initial state percolation temperature. The results from this work are compared with the results from well known QCD models and with the transport properties of matter found in day-to-day life. These observables allow us to conclude an array of important findings about the matter formed in high-energy collisions at the LHC. For the high-multiplicity events, the estimated η/s are comparable with that is observed for heavy-ion collisions, which is an indication of a strongly coupled quark gluon plasma. This makes LHC high-multiplicity pp collision events as probable candidates for the search of quark-gluon plasma droplets.

Quarkonium measurements in nucleus-nucleus collisions with ALICE

Heavy quarks are produced in the early stages of nucleus-nucleus collisions and can therefore provide important insight into the Quark–Gluon Plasma (QGP). Quarkonia are proposed as crucial probes to study the QGP. The extent of the medium modification for heavy-quark quarkonium production in heavy-ion collisions is measured in terms of a nuclear modification factor RAA, defined as the quarkonium yield in heavy-ion collisions divided by the relative quarkonium cross section in pp collisions scaled by the nuclear overlap function. A possible path-length dependent quarkonium dissociation, as well as a contribution of (re-)generation of quarkonia from heavy quarks in the medium, would lead to an azimuthal anisotropy of quarkonium production relative to the reaction plane. In this contribution, the recent ALICE measurements of quarkonia in Pb–Pb collisions at sNN=5.02TeV will be discussed for both mid- and forward rapidity. The dependence of RAA on centrality and pT for J/ψ, ϒ(1S), ϒ(2S), as well as the J/ψ elliptic flow ν2 will be shown. Comparisons between the experimental data and the current theoretical model calculations will be also discussed.

Influence of quark content and collision geometry on proton production in heavy ion collisions

Proton production have been preivously measured in PHENIX experiment in Au+Au collisions at . It was obtained that protons yields are enhanced over all mesons yields. This phenomenon was called “baryon puzzle”. This paper presents mesurements of protons in asymmetric Cu+Au collisions at in order to investigate influence of collision geometry. Results in Cu+Au and Au+Au systems were found to be in agreement at similar number of participants, which might indicate that proton production in heavy-ion collision scales with the average size of the nuclear overlap region and do not depends on the details of its shape. ln order to investigate influence of quark content on production of protons consisting of three quarks comparison with φ, π 0 -mesons (quark-antiquark pairs) was provided in Cu+Au collisions at the collision energy of 200 GeV. Such information can improve our understanding of quark-gluon plasma and recombination model.

Production of K*(892)° mesons in Cu+Au collisions at = 200 GeV and U+U collisions at = 192 GeV

Studying the properties and evolution of the QGP is one of the main goals in modern heavy ion physics. Due to strange quark content K*0 meson is a good probe for the study of QGP formed in heavy-ion collisions. K *0-meson production was previously measured by PHENIX in symmetric Cu+Cu collisions at = 200 GeV and U+U collisions at = 200 GeV. K *0-meson production in asymmetric Cu+Au collisions at = 200 GeV and U+U collisions at = 200 GeV and spherically asymmetric uranium nuclei at = 200 GeV and U+U collisions at = 192 GeV was performed for continuation the study of the QGP properties. This report presents invariant transverse momentum spectra and nuclear modification factors of K *0-mesons which were measured in Cu+Au collisions at the energy of = 200 GeV and U+U collisions at = 200 GeV and U+U collisions at the energy of = 200 GeV and U+U collisions at = 192 GeV. In results, K *0-mesons yields are less suppressed than the yields of non-strange mesons, which might indicate that additional particle production mechanisms are involved in the K *0-meson production. The production of the K *0-mesons in Cu+Cu, Cu+Au, and U+U collisions scales with Npart and seems to depend on nuclear overlap size, but not on its geometry.

Pulmonary sclerosing pneumocytoma: Cytomorphology and immunoprofile.

Sclerosing pneumocytoma (SP) is a rare, benign pulmonary neoplasm. To the authors' knowledge, the current study is the first to evaluate the cytomorphology and immunoprofile of SP in a series. A total of 9 fine-needle aspiration cases of SP (7 of which were computed tomography guided and 2 of which were endobronchial ultrasound guided) including histopathology and immunohistochemistry were collected from 5 institutions. The female-to-male ratio was 3.5:1, and the mean age of the patients was 54years (range, 27-73years). All cases presented as lung nodules, with a mean size of 2.2cm (range, 1.1-5cm), and were interpreted as atypical on rapid on-site evaluation. The final diagnoses were favor adenocarcinoma (1 case), well-differentiated lung adenocarcinoma (2 cases), low-grade epithelial neoplasm (2 cases), and sclerosing pneumocytoma (4 cases). Samples were moderately cellular, and consisted of round epithelioid cells with clear cell features, columnar cells, and spindle cells. A papillary arrangement with prominent hyalinized fibrovascular cores was the most common architectural pattern, followed by flat sheets and acinar formations. Tumor cells demonstrated mild, focally moderate nuclear pleomorphism with prominent nucleoli, hyperchromasia, nuclear elongation, nuclear overlap, and occasional nuclear inclusions and grooves. The background consisted of foamy macrophages (9 cases), hemosiderin pigment (6 cases), and lymphoid aggregates (3 cases) with no mitoses and/or necrosis. The surface cells and underlying round cells were positive for both thyroid transcription factor 1 and epithelial membrane antigen in all cases, which was the most notable immunohistochemical finding. Cytomorphological findings of SP overlap with those of well-differentiated lung adenocarcinoma. Awareness of these cytomorphologic findings and the distinct immunoprofile of the 2 cell types found in SP should prevent a misdiagnosis and aggressive treatment.

Photoproduction of J/ψ in non-single-diffractive p+p collisions * * Supported by the National Natural Science Foundation of China (11775213, 11505180, 11675168), the U.S. DOE Office of Science (DE-SC0012704) and MOST (2016YFE0104800)

Significant enhancements of production at very low transverse momenta were recently observed by the ALICE and STAR collaborations in peripheral hadronic A+A collisions. The anomalous excess points to coherent photon-nucleus interactions in violent hadronic heavy-ion collisions, which were conventionally studied only in ultra-peripheral collisions. Assuming that the coherent photoproduction is the underlying mechanism responsible for the excess observed in peripheral A+A collisions, its contribution in p+p collisions with nuclear overlap, i.e. non-single-diffractive collisions, is of particular interest. In this paper, we perform a calculation of exclusive photoproduction in non-single-diffractive p+p collisions at the RHIC and LHC energies based on the pQCD motivated parametrization using the world-wide experimental data, which could be further employed to improve the precision of the phenomenological calculations for photoproduction in A+A collisions. The differential rapidity and transverse momentum distributions of from photoproduction are presented. In comparison with the production from hadronic interactions, we find that the contribution of photoproduction is negligible.

Erratum: Improved Monte Carlo Glauber predictions at present and future nuclear colliders [Phys. Rev. C 97 , 054910 (2018)

We present the results of an improved Monte Carlo Glauber (MCG) model of relevance for collisions involving nuclei at center-of-mass energies of BNL RHIC ($\sqrt{s_{\rm NN}}=0.2$ TeV), CERN LHC ($\sqrt{s_{\rm NN}}=2.76$-$8.8$ TeV), and proposed future hadron colliders ($\sqrt{s_{\rm NN}}\approx 10$-$63$ TeV). The inelastic pp cross sections as a function of $\sqrt{s_{\rm NN}}$ are obtained from a precise data-driven parametrization that exploits the many available measurements at LHC collision energies. We describe the nuclear transverse profile with two separated 2-parameter Fermi distributions for protons and neutrons to account for their different densities close to the nuclear periphery. Furthermore, we model the nucleon degrees of freedom inside the nucleus through a lattice with a minimum nodal separation, combined with a "recentering and reweighting" procedure, that overcomes some limitations of previous MCG approaches. The nuclear overlap function, number of participant nucleons and binary nucleon-nucleon collisions, participant eccentricity and triangularity, overlap area and average path length are presented in intervals of percentile centrality for lead-lead (PbPb) and proton-lead (pPb) collisions at all collision energies. We demonstrate for collisions at $\sqrt{s_{\rm NN}}=5.02$ TeV that the central values of the Glauber quantities change by up to 7%, in a few bins of reaction centrality, due to the improvements implemented, though typically remain within the previously assigned systematic uncertainties, while their associated uncertainties are generally smaller (mostly below 5%) at all centralities than for earlier calculations. Tables for all quantities versus centrality at present and foreseen collision energies involving Pb nuclei, as well as for collisions of XeXe at $\sqrt{s_{\rm NN}}=5.44$, and AuAu and CuCu at $\sqrt{s_{\rm NN}}=0.2$ TeV, are provided.

Non-Markovian dynamics of the electronic subsystem in a laser-driven molecule: Characterization and connections with electronic-vibrational entanglement and electronic coherence

Non-Markovian quantum evolution of the electronic subsystem in a laser-driven molecule is characterized through the appearance of negative decoherence rates in the canonical form of the electronic master equation. For a driven molecular system described in a bipartite Hilbert space $\mathcal{H}={\mathcal{H}}_{el}⨂{\mathcal{H}}_{\mathrm{vib}}$ of dimension $2\ifmmode\times\else\texttimes\fi{}{N}_{v}$, we derive the canonical form of the electronic master equation, deducing the canonical measures of non-Markovianity and the Bloch volume of accessible states. We find that one of the decoherence rates is always negative, accounting for the inherent non-Markovian character of the electronic evolution in the vibrational environment. Enhanced non-Markovian behavior, characterized by two negative decoherence rates, appears if there is a coupling between the electronic states $g,\phantom{\rule{0.16em}{0ex}}e$, such that the evolution of the electronic populations obeys $d({P}_{g}{P}_{e})/dt&gt;0$. Non-Markovianity of the electronic evolution is analyzed in relation to temporal behaviors of the electronic-vibrational entanglement and electronic coherence, showing that enhanced non-Markovian behavior accompanies entanglement increase. Taking as an example the coupling of two electronic states by a laser pulse in the ${\mathrm{Cs}}_{2}$ molecule, we analyze non-Markovian dynamics under laser pulses of various strengths, finding that the weaker pulse stimulates the bigger amount of non-Markovianity. Our results show that increase of the electronic-vibrational entanglement over a time interval is correlated to the growth of the total amount of non-Markovianity calculated over the same interval using canonical measures and connected with the increase of the Bloch volume. After the pulse, non-Markovian behavior is correlated to electronic coherence, such that vibrational motion in the electronic potentials which diminishes the nuclear overlap, implicitly increasing the linear entropy of entanglement, brings a memory character to dynamics.

Production of π0 and η mesons in Cu+Au collisions at sNN=200GeV

Production of π0 and η mesons has been measured at midrapidity in Cu+Au collisions at sNN=200GeV. Measurements were performed in π0(η)→γγ decay channel in the 1(2)−20GeV/c transverse momentum range. A strong suppression is observed for π0 and η meson production at high transverse momentum in central Cu+Au collisions relative to the p+p results scaled by the number of nucleon-nucleon collisions. In central collisions the suppression is similar to Au+Au with comparable nuclear overlap. The η/π0 ratio measured as a function of transverse momentum is consistent with mT-scaling parametrization down to pT=2GeV/c, its asymptotic value is constant and consistent with Au+Au and p+p and does not show any significant dependence on collision centrality. Similar results were obtained in hadron-hadron, hadron-nucleus, and nucleus-nucleus collisions as well as in e+e− collisions in a range of collision energies sNN=3−1800 GeV. This suggests that the quark-gluon-plasma medium produced in Cu+Cu collisions either does not affect the jet fragmentation into light mesons or it affects the π0 and η the same way.Received 4 June 2018DOI:https://doi.org/10.1103/PhysRevC.98.054903Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Funded by SCOAP3.Published by the American Physical SocietyPhysics Subject Headings (PhySH)Research AreasRelativistic heavy-ion collisionsPhysical SystemsLight mesonsPionsTechniquesHadron collidersNuclear Physics

Recent PHENIX Results on High-pT π0 and η Production in Cu+Au and U+U Collisions

One of the key signatures of the Quark-Gluon Plasma (QGP), is the modification of hadron transverse momentum differential cross-sections in heavy-ion collisions as compared to p+p collisions. Suppression of hadron production at high transverse momenta (pT) in heavy ion collisions has been explained by the energy loss of the partons produced in the hard scattering processes that traverse the deconfined quantum chromodynamics (QCD) matter. Recent RHIC runs with asymmetric Cu+Au collisions and non-spherical nuclear U+U collisions provide the means to systematically study suppression pattern of hadrons in different nuclear overlap geometry and different energy density and surface biases compared to Au+Au collisions. These studies provide an important input to improve theoretical description of parton energy loss in QGP. In this proceeding, we present results from π0 and η production in Cu+Au and U+U systems and discuss how these results further our understanding of parton energy loss.