Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Immunologic Markers and Cirrhosis in Individuals from a Prospective Chronic Hepatitis C Cohort

Simple Summary To date: no prospective cohort studies have been used to investigate the role of circulating immunologic markers as they relate to the progression of liver disease in those chronically infected with hepatitis C (HCV). Using data/samples from a prospective cohort of chronically HCV-infected individuals, we sampled 68 individuals who developed cirrhosis, 91 controls who did not develop cirrhosis, and 94 individuals who developed hepatocellular carcinoma (HCC). Using baseline plasma, we examined levels of 102 markers in individuals who developed cirrhosis vs. controls and those who developed HCC vs. cirrhosis. The findings from this study highlight the important role of immunological markers in predicting HCV-related cirrhosis. Abstract Background: Chronic hepatitis C virus (HCV) infection can affect immune response and inflammatory pathways, leading to severe liver diseases such as cirrhosis and hepatocellular carcinoma (HCC). Methods: In a prospective cohort of chronically HCV-infected individuals, we sampled 68 individuals who developed cirrhosis, 91 controls who did not develop cirrhosis, and 94 individuals who developed HCC. Unconditional odds ratios (ORs) from polytomous logistic regression models and canonical discriminant analyses (CDAs) were used to compare categorical (C) baseline plasma levels for 102 markers in individuals who developed cirrhosis vs. controls and those who developed HCC vs. cirrhosis. Leave-one-out cross validation was used to produce receiver operating characteristic curves to assess predictive ability of markers. Lastly, biological pathways were assessed in association with cirrhotic development compared to controls. Results: After multivariable adjustment, DEFA-1 (OR: C2v.C1 = 7.73; p < 0.0001), ITGAM (OR: C2v.C1 = 4.03; p = 0.0002), SCF (OR: C4v.C1 = 0.19; p-trend = 0.0001), and CCL11 (OR: C4v.C1 = 0.31; p-trend= 0.002) were all associated with development of cirrhosis compared to controls; these markers, together with clinical/demographics variables, improved prediction of cirrhosis from 55.7% (in clinical/demographic-only model) to 74.9% accuracy. A twelve-marker model based on CDA results further increased prediction of cirrhosis to 88.0%. While six biological pathways were found to be associated with cirrhosis, cell adhesion was the only pathway associated with cirrhosis after Bonferroni correction. In contrast to cirrhosis, DEFA-1 and ITGAM levels were inversely associated with HCC risk. Conclusions: Pending validation, these findings highlight the important role of immunological markers in predicting HCV-related cirrhosis even 11 years post-enrollment.
Baryogenesis from the Berry phase

The spontaneous baryogenesis scenario explains how a baryon asymmetry can develop while baryon violating interactions are still in thermal equilibrium. However, generation of the chemical potential from the derivative coupling is dubious since the chemical potential may not appear after the Legendre transformation. The geometric phase (Pancharatnam-Berry phase) results from the geometrical properties of the parameter space of the Hamiltonian, which is calculated from the Berry connection. In this paper, using the formalism of the Berry phase, we show that the chemical potential defined by the Berry connection is consistent with the Legendre transformation. The framework of the Berry phase is useful in explaining the mathematical background of the spontaneous baryogenesis and also in calculating the asymmetry of the nonthermal particle production in time-dependent backgrounds. Using the formalism, we show that the mechanism can be extended to more complex situations.
A Review of Current Evidence on the Relationship between Phosphate Metabolism and Metabolic Syndrome

Phosphorus, present as phosphate in biological systems, is an essential mineral for various biological activities and biochemical processes. Numerous studies have indicated that disturbed phosphate balance may contribute to the development of metabolic syndrome (MetS). However, no consistent result was found on the association between phosphorus intake and serum phosphate concentration with MetS. It is believed that both positive and negative impacts of phosphorus/phosphate co-exist in parallel during MetS condition. Reduced phosphate level contributed to the development of obesity and hyperglycaemia. Low phosphate is believed to compromise energy production, reduce exercise capacity, increase food ingestion, and impair glucose metabolism. On the other hand, the effects of phosphorus/phosphate on hypertension are rather complex depending on the source of phosphorus and subjects’ health conditions. Phosphorus excess activates sympathetic nervous system, renin-angiotensin-aldosterone system, and induces hormonal changes under pathological conditions, contributing to the blood pressure-rising effects. For lipid metabolism, adequate phosphate content ensures a balanced lipid profile through regulation of fatty acid biosynthesis, oxidation, and bile acid excretion. In conclusion, phosphate metabolism serves as a potential key feature for the development and progression of MetS. Dietary phosphorus and serum phosphate level should be under close monitoring for the management of MetS.
Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization

Human–wildlife coexistence may increase the potential risk of direct transmission of emergent or re-emergent zoonotic pathogens to humans. Intending to assess the occurrence of three important foodborne pathogens in wild animals of two wildlife conservation centers in Portugal, we investigated 132 fecal samples for the presence of Escherichia coli (Shiga toxin-producing E. coli (STEC) and non-STEC), Salmonella spp. and Campylobacter spp. A genotypic search for genes having virulence and antimicrobial resistance (AMR) was performed by means of PCR and Whole-Genome Sequencing (WGS) and phenotypic (serotyping and AMR profiles) characterization. Overall, 62 samples tested positive for at least one of these species: 27.3% for STEC, 11.4% for non-STEC, 3.0% for Salmonella spp. and 6.8% for Campylobacter spp. AMR was detected in four E. coli isolates and the only Campylobacter coli isolated in this study. WGS analysis revealed that 57.7% (30/52) of pathogenic E. coli integrated genetic clusters of highly closely related isolates (often involving different animal species), supporting the circulation and transmission of different pathogenic E. coli strains in the studied areas. These results support the idea that the health of humans, animals and ecosystems are interconnected, reinforcing the importance of a One Health approach to better monitor and control public health threats.
New inhibitors for dicarbonyl/L-xylulose reductase in Caenorhabditis elegans

Dicarbonyl/L-xylulose reductase (DCXR) is an enzyme reducing dicarbonyl (-CO-) groups in single sugar molecules and participates in the sugar metabolism of several sugar metabolism cycles in different living organisms (humans, other animals, fungi, and microorganisms). Caenorhabditis elegans, a model organism, has a unique DCXR (referred to as Ce DCXR) which plays a biochemical function similar to its homologs in the other organisms. However, the catalytic regulation of the enzyme has not been fully elucidated yet. Therefore, in this study, we investigated the chemicals which could inhibit the enzyme and found three inhibitor compounds including hexanoic acid, phosphoenolpyruvic acid, and DL-α-aminobutyrate hydrochloride for the enzyme. Because these inhibitors and their derivatives suppressed DCXRs in humans, mice, rabbits, and rats, they possibly inhibit the DCXR homologs at least in other animals. If the inhibitors and their derivatives are components in pharmaceutical products, foods, and drinks, they may come into cells, interact with DCXRs and inactivate them, causing toxicity for the host organisms.
Does the SN rate explain the very high energy cosmic rays in the central 200 pc of our Galaxy

The High Energy Stereoscopic System (H.E.S.S.) collaboration revealed the presence of a very high energy (VHE) diffuse emission in the inner 100 pc of the Galaxy in close correlation with the central molecular zone (CMZ). Recently, they deduced from this emission a cosmic ray (CR) overdensity in the region with a local peak towards the Galactic Centre (GC) and proposed a diffusive scenario with a stationary source at the GC to explain it. However, the high supernovae (SN) rate in the GC must also create a sustained CR injection in the region via the shocks produced at the time of their explosion. Considering a typical diffusion coefficient close to the interstellar medium (ISM) value yields a diffuse escape time much lower than the recurrence time between each SN explosion, showing that a steady-state model will fail to reproduce the data. This work aims to study the impact of the spatial and temporal distribution of SNs in the CMZ on the VHE emission morphology and spectrum: we build a 3D model of VHE CR injection and diffusive propagation with a realistic gas distribution. We show that a peaked γ-ray profile towards the GC can be obtained using realistic SN spatial distribution taking into account the central massive star cluster. We conclude that the contribution of SNs cannot be neglected, in particular at large longitudes; however, an additional CR injection at the GC is required to reproduce the very central excess.
Causal structure in categorical quantum mechanics

Categorical quantum mechanics is a way of formalising the structural features of quantum theory using category theory. It uses compound systems as the primitive notion, which is formalised by using symmetric monoidal categories. This leads to an elegant formalism for describing quantum protocols such as quantum teleportation. In particular, categorical quantum mechanics provides a graphical calculus that exposes the information flow of such protocols in an intuitive way. However, the graphical calculus also reveals surprising features of these protocols; for example, in the quantum teleportation protocol, information appears to flow `backwards-in-time'. This leads to question of how causal structure can be described within categorical quantum mechanics, and how this might lead to insight regarding the structural compatibility between quantum theory and relativity. This thesis is concerned with the project of formalising causal structure in categorical quantum mechanics. We begin by studying an abstract view of Bell-type experiments, as described by `no-signalling boxes', and we show that under time-reversal no-signalling boxes generically become signalling. This conflicts with the underlying symmetry of relativistic causal structure. This leads us to consider the framework of categorical quantum mechanics from the perspective of relativistic causal structure. We derive the properties that a symmetric monoidal category must satisfy in order to describe systems in such a background causal structure. We use these properties to define a new type of category, and this provides a formal framework for describing protocols in spacetime. We explore this new structure, showing how it leads to an understanding of the counter-intuitive information flow of protocols in categorical quantum mechanics. We then find that the formal properties of our new structure are naturally related to axioms for reconstructing quantum theory, and we show how a reconstruction scheme based on purification can be formalised using the structures of categorical quantum mechanics. Finally, we discuss the philosophical aspects of using category theory to describe fundamental physics. We consider a recent argument that category-theoretic formulations of physics, such as categorical quantum mechanics, can be used to support a variant of structural realism. We argue against this claim. The work of this thesis suggests instead that the philosophy of categorical quantum mechanics is subtler than either operationalism or realism.
On the physical connections between galaxies of different types

Galaxies can be classified in two broad sequences which are likely to reflect their formation mechanism. The ‘main sequence’, consisting of spirals, irregulars and all dwarf galaxies, is probably produced by gas settling within dark matter haloes. We show that the sizes and surface densities along this sequence are primarily determined by the distributions of the angular momentum and formation time of dark haloes. They are well reproduced by current cosmogonies provided that galaxies form late, at z ≲ 2. In this scenario, dwarf ellipticals were small ‘discs’ at z ∼ 1 and become ‘ellipticals’ after they fall into cluster environments. The strong clustering of dwarf ellipticals is then a natural by-product of the merging and transformation process. The number of dwarf galaxies predicted in a cluster such as Virgo is in good agreement with the observed number. On the other hand, the ‘giant branch’, consisting of giant ellipticals and bulges, is probably produced by the merging of disc galaxies. Based on the observed phase-space densities of galaxies, we show that the main bodies of all giant ellipticals can be produced by dissipationless mergers of high-redshift discs. However, high-redshift discs, although denser than present-day ones, are still not compact enough to produce the high central phase-space density of some low-luminosity ellipticals. Dissipation must have occurred in the central parts of these galaxies during the merger which formed them.
Trends in Using Antibiotics in the Era of National Health Insurance in the City of Manado

Introduction: Antibiotic use needs to be monitored. Its irrational use causes resistance. Research aims to determine trends in antibiotic use. Methods: Observational research with retrospective data collection. Cross-sectional research design. Data about the availability of antibiotics from 2014 to 2017 in hospitals, health offices and PHCs in the city of Manado. Results: Trends of antibiotics used in PHC and health office in 2014–2017 were betalactam, macrolide, sulfamethoxazole-trimethoprim, and quinolone groups. Trends in secondary hospital were betalactam, sulfamethoxazole-trimethoprim, and quinolone groups. Trends in tertiary hospital are betalactam, quinolones, and other groups. Conclusion: Based on the data of five major antibiotics use in Manado City, there was a change in the pattern of antibiotic use, and this pattern tended to increase.
A Monte Carlo Approach to Magnetar-powered Transients. II. Broad-lined Type Ic Supernovae Not Associated with GRBs

Broad-lined type Ic supernovae (SNe Ic-BL) are a subclass of rare core-collapse SNe whose energy source is debated in the literature. Recently, a series of investigations on SNe Ic-BL with the magnetar (plus 56Ni) model were carried out. Evidence for magnetar formation was found for the well-observed SNe Ic-BL 1998bw and 2002ap. In this paper, we systematically study a large sample of SNe Ic-BL not associated with gamma-ray bursts (GRBs). We use photospheric velocity data determined in a homogeneous way. We find that the magnetar+56Ni model provides a good description of the light curves and velocity evolution of our sample of SNe Ic-BL, although some SNe (not all) can also be described by the pure-magnetar model or by the two-component pure-56Ni model (three out of 12 are unlikely to be explained by two-component model). In the magnetar+56Ni model, the amount of 56Ni required to explain their luminosity is significantly reduced, and the derived initial explosion energy is, in general, in accordance with neutrino heating. Some correlations between different physical parameters are evaluated, and their implications regarding magnetic field amplification and the total energy reservoir are discussed.
The Kinematics and Metallicity of the M31 Globular Cluster System

With the ultimate aim of distinguishing between various models describing the formation of galaxy halos (e.g., radial or multiphase collapse and random mergers), we have completed a spectroscopic study of the globular cluster system of M31. We present the results of deep intermediate-resolution fiber-optic spectroscopy of several hundred of the M31 globular clusters using the Wide Field Fibre Optic Spectrograph at the William Herschel Telescope in La Palma, Canary Islands. These observations have yielded precise radial velocities (±12 km s-1) and metallicities (±0.26 dex) for over 200 members of the M31 globular cluster population out to a radius of 1. °5 from the galaxy center. Many of these clusters have no previous published radial velocity or [Fe/H] estimates, and the remainder typically represent significant improvements over earlier determinations. We present analyses of the spatial, kinematic, and metal abundance properties of the M31 globular clusters. We find that the abundance distribution of the cluster system is consistent with a bimodal distribution with peaks at [Fe/H] ∼ -1.4 and -0.5. The metal-rich clusters demonstrate a centrally concentrated spatial distribution with a high rotation amplitude, although this population does not appear significantly flattened and is consistent with a bulge population. The metal-poor clusters tend to be less spatially concentrated and are also found to have a strong rotation signature.
Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.
Stabilization of Nanometre-Size Particle Beams in the Final Focus System of the Compact LInear Collider (CLIC)

The Compact LInear Collider (CLIC) study at the European Organization for Nuclear Research (CERN) is developing the design of a 3 TeV ee linear collider. The discovery reach of this machine depends on obtaining a luminosity of 10 cms, which will be done by colliding beams with transverse spot sizes in the nanometre range (≈ 60 × 0.7 nm). Tolerances on fast mechanical stability of the focusing quadrupoles reach the 0.2 nm level. The serious concern of magnet stabilization for future linear colliders has been addressed by building a CERN test stand on magnet stability, bringing together state-of-the-art stabilization technology, latest equipment for vibration measurements and realistic magnet prototypes. For the first time an accelerator magnet was successfully stabilized to the sub-nanometre level, reducing its vibrations level by one order of magnitude with respect to the supporting ground. The best measurements indicate transverse RMS vibration amplitudes (above 4 Hz) of (0.79±0.08) nm horizontally and (0.43±0.04) nm vertically, maintained to a maximum of less than (1.47±0.15) nm and (1.00±0.10) nm, respectively, over a period of several days. Detailed simulations of time-dependent luminosity, which use a model for magnet displacements based on measured vibration spectra, show that approximately 70% of the CLIC goal luminosity can be achieved with the demonstrated performance in the CERN test stand. This indicates the basic feasibility of colliding nanometre-size beams in CLIC. Geneva, Switzerland 1 June 2004 PhD thesis presented at the University of Lausanne (CH), High Energy Physics Institute (IPHE), in December 2003. Work was carried out at CERN from January 2001 to December 2003, in the framework of the CLIC Stability Study Team.
Disentangling the Circumnuclear Environs of Centaurus A. III. An Inner Molecular Ring, Nuclear Shocks, and the CO to Warm H2 Interface

We present the distribution and kinematics of the molecular gas in the circumnuclear disk (CND; 400 pc × 200 pc) of Centaurus A with resolutions of ∼5 pc (0.″3) and shed light onto the mechanism feeding the active galactic nucleus (AGN) using CO(3–2), HCO+(4–3), HCN(4–3), and CO(6–5) observations obtained with ALMA. Multiple filaments or streamers of tens to a hundred parsec scale exist within the CND, which form a ring-like structure with an unprojected diameter of 9″ × 6″ (162 pc × 108 pc) and a position angle P.A. ≃ 155°. Inside the nuclear ring, there are two leading and straight filamentary structures with lengths of about 30–60 pc at P.A. ≃ 120° on opposite sides of the AGN, with a rotational symmetry of 180° and steeper position–velocity diagrams, which are interpreted as nuclear shocks due to non-circular motions. Along the filaments, and unlike other nearby AGNs, several dense molecular clumps present low HCN/HCO+(4–3) ratios (≲0.5). The filaments abruptly end in the probed transitions at r ≃ 20 pc from the AGN, but previous near-IR H2(J = 1–0)S(1) maps show that they continue in an even warmer gas phase (T ∼ 1000 K), winding up in the form of nuclear spirals, and forming an inner ring structure with another set of symmetric filaments along the N–S direction and within r ≃ 10 pc. The molecular gas is governed primarily by non-circular motions, being the successive shock fronts at different scales where loss of angular momentum occurs, a mechanism that may feed efficiently powerful radio galaxies down to parsec scales.
On Convergence Rates of Empirical Bayes Procedures

Empirical Bayes procedures are commonly used based on the supposed asymptotic equivalence with fully Bayesian procedures, which, however, has not so far received full theoretical support in terms of uncertainty quantification. In this note, we provide some results on contraction rates of empirical Bayes posterior distributions which are illustrated in nonparametric curve estimation using Dirichlet process mixture models.