Signature Of Transition Research Articles

Longitudinal 1H NMR-Based Metabolomics in Saliva Unveils Signatures of Transition from Acute to Post-Acute Phase of SARS-CoV-2 Infection

COVID-19 can range from a mild to severe acute respiratory syndrome and also could result in multisystemic damage. Additionally, many people develop post-acute symptoms associated with immune and metabolic disturbances in response to viral infection, requiring longitudinal and multisystem studies to understand the complexity of COVID-19 pathophysiology. Here, we conducted a 1H Nuclear Magnetic Resonance metabolomics in saliva of symptomatic subjects presenting mild and moderate respiratory symptoms to investigate prospective changes in the metabolism induced after acute-phase SARS-CoV-2 infection. Saliva from 119 donors presenting non-COVID and COVID-19 respiratory symptoms were evaluated in the acute phase (T1) and the post-acute phase (T2). We found two clusters of metabolite fluctuation in the COVID-19 group. Cluster 1, metabolites such as glucose, (CH3)3 choline-related metabolites, 2-hydroxybutyrate, BCAA, and taurine increased in T2 relative to T1, and in cluster 2, acetate, creatine/creatinine, phenylalanine, histidine, and lysine decreased in T2 relative to T1. Metabolic fluctuations in the COVID-19 group were associated with overweight/obesity, vaccination status, higher viral load, and viral clearance of the respiratory tract. Our data unveil metabolic signatures associated with the transition to the post-acute phase of SARS-CoV-2 infection that may reflect tissue damage, inflammatory process, and activation of tissue repair cascade. Thus, they contribute to describing alterations in host metabolism that may be associated with prolonged symptoms of COVID-19.

Decorin as a key marker of desmoplastic cancer-associated fibroblasts mediating first-line immune checkpoint blockade resistance in metastatic gastric cancer.

Gastric cancer (GC) remains a significant cause of cancer-related mortality worldwide. Despite the transformative impact of immune checkpoint blockade (ICB) therapies across various cancers, only a minority of patients with metastatic GC (mGC) benefit, emphasizing the urgent need for precise biomarkers to predict therapeutic responses and optimize patient selection. In this multi-omics study, we conducted whole exome and transcriptome sequencing on 12 tumors from mGC patients treated with nivolumab as first-line therapy. To validate our findings, we performed whole transcriptome sequencing on 17 additional tumors and analyzed 45 tumors from public dataset (PRJEB25780) of patients who received ICB therapy as second or third-line treatment. Comprehensive multi-omics analyses were conducted using single-cell RNA sequencing (n = 5, GSE167297) and spatial transcriptome sequencing (n = 2, independent internal dataset). ICB-sensitive tumors exhibited robust activation of the interferon response pathway, while ICB-resistant tumors displayed epithelial-mesenchymal transition signatures. Intriguingly, at the single-cell level, genes associated with ICB sensitivity were predominantly expressed in immune cells, whereas genes associated with resistance were primarily found in cancer-associated fibroblasts (CAFs), particularly the desmoplastic CAF (dCAF) subtype. We identified DCN as a hallmark dCAF marker, and high DCN expression was inversely correlated with PD-L1 levels, ICB resistance, and poor prognosis in mGC (log-rank p = 0.027). This study elucidates the critical influence of the tumor microenvironment, specifically dCAFs, in mediating ICB resistance in mGC. Our findings highlight DCN as a representative marker for dCAF and a promising negative predictive biomarker for ICB response. These findings highlight the complex stromal-immune interactions and open avenues for personalized treatment for mGC.

Covariant formulation of spinodal decomposition in rapidly expanding quark gluon plasma

Quantum chromodynamics (QCD) is expected to have a first order phase transition between the confined hadron gas and the deconfined quark gluon plasma at high baryon densities. This will result in phase boundary effects in the metastable and unstable regions. It is important to include these effects in phenomenological models of heavy ion collisions to identify experimental signatures of a phase transition. This requires building intuition on phase separation in rapidly expanding fluids. In this work we present the covariant equations of relativistic hydrodynamics with a phase boundary, provide prescriptions to extend the equation of state to metastable and unstable regions, and show the effects of spinodal separation in a Bjorken flow. Published by the American Physical Society 2024

Quantum steering ellipsoids and quantum obesity in critical systems

Abstract Quantum obesity (QO) is a novel function introduced to quantify quantum correlations that go beyond traditional measures like entanglement, while also functioning as an entanglement witness. One of the key strengths of QO lies in its analyticity for arbitrary states of bipartite systems, making it a more accessible and versatile tool compared to other measures of quantum correlations, such as quantum discord. In this work, we highlight the importance of QO as a fundamental quantity for identifying signatures of quantum phase transitions, which are critical changes in the ground state of quantum systems driven by quantum fluctuations. We introduce a mechanism based on local filtering operations designed to enhance the critical behavior of QO near phase transition points, providing a deeper understanding of these phenomena. Furthermore, we present a theorem that characterizes how QO transforms under local quantum operations and classical communications (LOCC), which broadens its applicability to a wider range of quantum systems. This opens new avenues for exploring quantum criticality and other novel quantum phenomena by leveraging the analytically computable, pairwise QO, thus offering both theoretical insights and practical applications in quantum information science.

Topological phase transitions via attosecond x-ray absorption spectroscopy

We present a numerical experiment that demonstrates the possibility to capture topological phase transitions via an x-ray absorption spectroscopy scheme. We consider a Chern insulator whose topological phase is tuned via a second-order hopping. We perform time-dynamics simulations of the out-of-equilibrium laser-driven electron motion that enables us to model a realistic attosecond spectroscopy scheme. In particular, we use an ultrafast scheme with a circularly polarized IR pump pulse and an attosecond x-ray probe pulse. A laser-induced dichroism-type spectrum shows a clear signature of the topological phase transition. We are able to connect these signatures with the Berry structure of the system. This work extend the applications of attosecond absorption spectroscopy to systems presenting a non-trivial topological phase.

Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) is a progressive and rapidly fatal disease with an intricate etiology. Identifying biomarkers for early PAH lesions based on the exploration of subtle biological processes is significant for timely diagnosis and treatment. In the present study, nine distinct cell populations identified based on gene expression profiles revealed high heterogeneity in cell composition ratio, biological function, distribution preference, and communication patterns in PAH. Notably, compared to other cells, endothelial cells (ECs) showed prominent variation in multiple perspectives. Further analysis demonstrated the endothelial-to-mesenchymal transition (EndMT) in ECs and identified a subgroup exhibiting a contrasting phenotype. Based on these findings, a machine-learning integrated program consisting of nine learners was developed to create a PAH Endothelial-to-mesenchymal transition Signature (PETS). This study identified cell populations underlying EndMT and furnished a potential tool that might be valuable for PAH diagnosis and new precise therapies.

Dynamical signatures of discontinuous phase transitions: How phase coexistence determines exponential versus power-law scaling

Dynamical signatures of discontinuous phase transitions: How phase coexistence determines exponential versus power-law scaling

Superconductor to metal quantum phase transition with magnetic field in Josephson coupled lead islands on Graphene

Abstract Superconductor-to-metal transition with magnetic field and gate-voltage is studied in a Josephson junction array comprising of randomly distributed lead islands on exfoliated single-layer graphene. The superconductivity onset temperature at low magnetic-fields is fitted to the Werthamer-Helfand-Hohenberg theory to model the temperature dependence of the upper critical field. The magnetoresistance in the intermediate temperature and field regime is described using thermally activated flux flow dictated by field dependent activation barrier. The barrier also depends on the gate voltage which dictates the inter-island Josephson coupling and disorder. The magnetoresistance near the upper critical field at low temperatures shows signatures of a gate dependent continuous quantum phase transition between superconductor and metal. The finite size scaling analysis shows that this transition belongs to the $(2+1)$D-XY universality class without disorder.

Signature of pressure-induced topological phase transition in ZrTe5

The layered van der Waals material ZrTe5 is known as a candidate topological insulator (TI), however its topological phase and the relation with other properties such as an apparent Dirac semimetallic state is still a subject of debate. We employ a semiclassical multicarrier transport (MCT) model to analyze the magnetotransport of ZrTe5 nanodevices at hydrostatic pressures up to 2 GPa. The temperature dependence of the MCT results between 10 and 300 K is assessed in the context of thermal activation, and we obtain the positions of conduction and valence band edges in the vicinity of the chemical potential. We find evidence of the closing and re-opening of the band gap with increasing pressure, which is consistent with a phase transition from weak to strong TI. This matches expectations from ab initio band structure calculations, as well as previous observations that CVT-grown ZrTe5 is a weak TI in ambient conditions.

Characterizing metabolome signature of colostrum, transition and mature milk of indigenous cows (Bos indicus) adapted to high altitude environment of Leh-Ladakh

This study has identified 46 metabolites in colostrum, transition milk and mature milk of unique indigenous high altitude adapted Ladakhi cows using 1D 1H 800 MHz NMR spectroscopy. The multivariate analysis revealed that UDP-galactose, UDP-glucose, citrate, creatine phosphate, myo-inositol, lactose, 2-oxoglutarate, valine, maltose, leucine, dimethylamine, and choline with high VIP scores could differentiate the colostrum, transition and mature milk in separate clusters. . Highly enriched metabolites in colostrum such as UDP-galactose, UDP-glucose play crucial roles in cell growth, differentiation, and defense responses. Similarly, the presence of branched chain amino acids in colostrum could be linked to mammary gland development, N-acetylglucosamine, N-acetyl carnitine, choline etc. in high concentration in colostrum l might be helping in growth and development of neonatal calves of Ladakhi cows under hypoxia environment. Overall, this study has helped to characterize the metabolomic signatures of milk/colostrum of Ladakhi cows adapted to high altitude and cold desert of Leh-Ladakh.

Use of HSP105 in the Differential Diagnosis of Basaloid Skin Tumors: A Study of 73 Cases.

Basaloid skin tumors include subtypes of basal cell carcinoma (BCC) and the basaloid variant of squamous cell carcinoma (SCC). Due to their similarity in pathology and clinical presentation, their diagnosis is not straightforward. The aim of this study was to analyze the immunohistochemical expression of HSP105 in basaloid skin tumors, which include BCC, basosquamous carcinoma (BSC), metatypical basal cell carcinoma (MBCC), basaloid squamous cell carcinoma (BSCC), BCC with squamous differentiation as well as conventional SCC. This retrospective study included 17 cases of BCC, 11 cases of BSC, 8 instances of MBCC, 10 cases of BCC with squamous differentiation, 8 cases of BSCC, and 19 cases of SCC. Their clinical characteristics were summarized, and the paraffin blocks of tumor biopsy specimens were collected for HSP105 immunostaining. In contrast to the BCC group, which stained predominantly negative, SCC stained diffusely positive for HSP105. BSCs showed some areas of HSP105 positivity with a transitional expression signature. HSP105 was only weakly positive in a few cases of MBCC. Although BSCC was stained positive for HSP105, the HSCORE was significantly lower than that of the classic SCC. In BCC with squamous differentiation, focal staining for HSP105 was only seen in the area of squamous differentiation. There was a difference in immunohistochemical staining of HSP105 in basaloid skin tumors which helps in differential diagnosis. Differentiation between BCC, SCC, BSCC, MBCC, and BCC with squamous differentiation can be aided by immunohistochemistry using HSP105.

Attribute-Based Designated Combiner Transitive Signature Scheme

Transitive signatures allow any entity to obtain a valid signature of (i,k) by combining signatures of (i,j) and (j,k). However, the traditional transitive signature scheme does not offer fine-grained control over the combiner. To address this issue, we propose a formal definition of the attribute-based designated combiner transitive signature (ABDCTS) and its security model, where only entities whose inherent attributes meet the access policy can combine signatures. By introducing the fine-grained access control structure, control over the combiner is achieved. To demonstrate the feasibility of our primitive, this paper presents the first attribute-based designated combiner transitive signature scheme. Under an adaptive chosen-message attack, we prove its security based on the one-more CDH problem and the co-CDH problem, and that its algorithms have robustness.

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants.

The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g. polyploidy, engorged nutritional rewards, and dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g. plant fragment degradation, ant-farmer communication, and antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: (i) free-living to ant-cultivated: loss of genes conferring stress response and detoxification; (ii) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis; and (iii) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by 3 leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes toward long-term ecological resilience of farming systems that have thrived across millennia.

Intrinsic dipole Hall effect in twisted MoTe2: magnetoelectricity and contact-free signatures of topological transitions

We discover an intrinsic dipole Hall effect in a variety of magnetic insulating states at integer fillings of twisted MoTe2 moiré superlattice, including topologically trivial and nontrivial ferro-, antiferro-, and ferri-magnetic configurations. The dipole Hall current, in linear response to in-plane electric field, generates an in-plane orbital magnetization M∥ along the field, through which an AC field can drive magnetization oscillation up to THz range. Upon the continuous topological phase transitions from trivial to quantum anomalous Hall states in both ferromagnetic and antiferromagnetic configurations, the dipole Hall current and M∥ have an abrupt sign change, enabling contact-free detection of the transitions through the magnetic stray field. In configurations where the linear response is forbidden by symmetry, the dipole Hall current and M∥ appear as a crossed nonlinear response to both in-plane and out-of-plane electric fields. These magnetoelectric phenomena showcase fascinating functionalities of insulators from the interplay between magnetism, topology, and electrical polarization.

Death-associated protein kinase 3 modulates migration and invasion of triple-negative breast cancer cells.

Sixteen patient-derived xenografts (PDXs) were analyzed using a mass spectrometry (MS)-based kinase inhibitor pull-down assay (KIPA), leading to the observation that death-associated protein kinase 3 (DAPK3) is significantly and specifically overexpressed in the triple-negative breast cancer (TNBC) models. Validation studies confirmed enrichment of DAPK3 protein, in both TNBC cell lines and tumors, independent of mRNA levels. Genomic knockout of DAPK3 in TNBC cell lines inhibited in vitro migration and invasion, along with down-regulation of an epithelial-mesenchymal transition (EMT) signature, which was confirmed in vivo. The kinase and leucine-zipper domains within DAPK3 were shown by a mutational analysis to be essential for functionality. Notably, DAPK3 was found to inhibit the levels of desmoplakin (DSP), a crucial component of the desmosome complex, thereby explaining the observed migration and invasion effects. Further exploration with immunoprecipitation-mass spectrometry (IP-MS) identified that leucine-zipper protein 1 (LUZP1) is a preferential binding partner of DAPK3. LUZP1 engages in a leucine-zipper domain-mediated interaction that protects DAPK3 from proteasomal degradation. Thus, the DAPK3/LUZP1 heterodimer emerges as a newly discovered regulator of EMT/desmosome components that promote TNBC cell migration.

Circulating Exosomes Studied by Label-free Proteomics Analysis Reveal Transition Signatures from Diabetes Mellitus to Diabetic Kidney Disease

Background: Diabetic kidney disease (DKD) is a common microvascular complication of diabetic mellitus (DM). At present, the early diagnosis of DKD mainly depends on microalbuminuria, which is prone to be affected by confounding factors such as urinary tract infections. Methods: To identify the more stable early diagnosis markers, the whole proteome in the circulating exosomes from controls, DM patients, and DKD patients was quantified by label-free proteomics analysis and then validated with parallel reaction monitoring. Results: Three hundred ninety-one quantitative proteins were detected, and the expression trends of 7 proteins in the validation phase were consistent with that in the discovery phase. The expression level assessment results revealed that the expression of EFEMP1 and ApoA4 in the DKD group was significantly higher than those in DM and controls. Correlation analysis showed that EFEMP1 and APOA4 were positively correlated with urinary microalbumin and urinary albumin creatinine ratio and had excellent diagnostic values for distinguishing DKD from DM and controls. Conclusions: ApoA4 and EFEMP1 could serve as the early diagnosis markers of DKD. These findings provide a possibility for the development of a clinical diagnostic index that can efficiently distinguish DKD from DM in the near future.

Hidden collective oscillations in a disordered mean-field spin model with non-reciprocal interactions

Abstract We study the effect of introducing separable quenched disorder on a non-equilibrium mean-field spin model exhibiting a phase transition to an oscillating state in the absence of disorder, due to non-reciprocal interactions. In the disordered model, the magnetisation and its time derivative no longer carry the signature of the phase transition to an oscillating state. However, thanks to the separable (Mattis-type) form of the disorder, the presence of oscillations can be revealed by introducing a specific, disorder-dependent observable. We also introduce generalised linear and non-linear susceptibilities associated either with the magnetisation or with its time derivative. While linear susceptibilities show no sign of a phase transition, the third-order susceptibilities present a clear signature of the onset of an oscillating phase. In addition, we show that the overlap distribution also provides evidence for the presence of oscillations, without explicit knowledge of the disorder.

Jamming is a first-order transition with quenched disorder in amorphous materials sheared by cyclic quasistatic deformations

Jamming is an athermal transition between flowing and rigid states in amorphous systems such as granular matter, colloidal suspensions, complex fluids and cells. The jamming transition seems to display mixed aspects of a first-order transition, evidenced by a discontinuity in the coordination number, and a second-order transition, indicated by power-law scalings and diverging lengths. Here we demonstrate that jamming is a first-order transition with quenched disorder in cyclically sheared systems with quasistatic deformations, in two and three dimensions. Based on scaling analyses, we show that fluctuations of the jamming density in finite-sized systems have important consequences on the finite-size effects of various quantities, resulting in a square relationship between disconnected and connected susceptibilities, a key signature of the first-order transition with quenched disorder. This study puts the jamming transition into the category of a broad class of transitions in disordered systems where sample-to-sample fluctuations dominate over thermal fluctuations, suggesting that the nature and behavior of the jamming transition might be better understood within the developed theoretical framework of the athermally driven random-field Ising model.

On a Signature of Phase Transition in Heavy Ion Nuclear Matter

On a Signature of Phase Transition in Heavy Ion Nuclear Matter

Signatures of hadron-quark phase transition through the r-mode instability in twin stars

Signatures of hadron-quark phase transition through the r-mode instability in twin stars