Bulk viscosity of the Lennard-Jones system at the triple point by dynamical Non Equilibrium Molecular Dynamics

Non-equilibrium Molecular Dynamics (NEMD) calculations of the bulk viscosity of the triple point Lennard-Jones fluid are performed with the aim of investigating the origin of the observed disagreement between Green-Kubo estimates and previous NEMD data. We show that a careful application of the Doll's perturbation field, the dynamical NEMD method, the instantaneous form of the perturbation and the "subtraction technique" provides a NEMD estimate of the bulk viscosity at zero field in full agreement with the value obtained by the Green-Kubo formula. As previously reported for the shear viscosity, we find that the bulk viscosity exhibits a large linear regime with the field intensity which confirms the Lennard-Jones fluid as a genuine Newtonian fluid even at triple point.Comment: 27 pages, 11 figure

Uncertainty Quantification for Atlas-Level Cell Type Transfer

Single-cell reference atlases are large-scale, cell-level maps that capture cellular heterogeneity within an organ using single cell genomics. Given their size and cellular diversity, these atlases serve as high-quality training data for the transfer of cell type labels to new datasets. Such label transfer, however, must be robust to domain shifts in gene expression due to measurement technique, lab specifics and more general batch effects. This requires methods that provide uncertainty estimates on the cell type predictions to ensure correct interpretation. Here, for the first time, we introduce uncertainty quantification methods for cell type classification on single-cell reference atlases. We benchmark four model classes and show that currently used models lack calibration, robustness, and actionable uncertainty scores. Furthermore, we demonstrate how models that quantify uncertainty are better suited to detect unseen cell types in the setting of atlas-level cell type transfer.Comment: Workshop paper at the 2022 ICML Workshop on Computational Biolog

Promoter activity of the sea urchin (Paracentrotus lividus) nucleosomal H3 and H2A and linker H1 α-histone genes is modulated by enhancer and chromatin insulator

Core promoters and chromatin insulators are key regulatory elements that may direct a transcriptional enhancer to prefer a specific promoter in complex genetic loci. Enhancer and insulator flank the sea urchin (Paracentrotus lividus) α-histone H2A transcription unit in a tandem repeated cluster containing the five histone genes. This article deals with the specificity of interaction between the H2A enhancer-bound MBF-1 activator and histone gene promoters, and with the mechanism that leads the H1 transcripts to peak at about one-third of the value for nucleosomal H3 and H2A mRNAs. To this end, in vivo competition assays of enhancer and insulator functions were performed. Our evidence suggests that the MBF-1 transcription factor participates also in the expression of the H3 gene and that the sns5 insulator buffers the downstream H1 promoter from the H2A enhancer. Altogether, these results provide a clear demonstration of the enhancer-blocking function of a chromatin insulator in a natural gene context. In addition, they suggest that both the H2A enhancer and the sns5 insulator may account for the diverse accumulation of the linker H1 versus the core nucleosomal histones during early development of the sea urchin embryo

Down regulation of early sea urchin histone H2A gene relies on cis regulative sequences located in the 5’ and 3’ regions and including the enhancer blocker sns

The tandem repeated sea urchin α-histone genes are developmentally regulated by gene-specific promoter elements. Coordinate transcription of the five genes begins after meiotic maturation of the oocyte, continues through cleavage, and reaches its maximum at morula stage, after which these genes are shut off and maintained in a silenced state for the life cycle of the animal. Although cis regulative sequences affecting the timing and the level of expression of these genes have been characterized, much less is known about the mechanism of their repression. Here we report the results of a functional analysis that allowed the identification of the sequence elements needed for the silencing of the α-H2A gene at gastrula stage. We found that important negative regulative sequences are located in the 462 bp sns 5 fragment located in the 3′ region. Remarkably, sns 5 contains the sns enhancer blocking element and the most 3′ H2A codons. In addition, we made the striking observation that inhibition of the anti-enhancer activity of sns, by titration of the binding proteins in microinjected embryos, also affected the capability of sns 5 to down-regulate transgene expression at gastrula stage. A further sequence element essential for repression of the H2A gene was identified upstream of the enhancer, in the 5′ region, and contains four GAGA repeats. Altogether these findings suggest that down-regulation of the α-H2A gene occurs by the functional interaction of the 5′ and 3′ cis sequence elements. These results demonstrate the involvement of a genomic insulator in the silencing of gene expression

Liver enlargement predicts obstructive sleep apnea–hypopnea syndrome in morbidly obese women

Obstructive sleep apnea–hypopnea syndrome (OSAHS) is frequently present in patients with severe obesity, but its prevalence especially in women is not well defined. OSAHS and non-alcoholic fatty liver disease are common conditions, frequently associated in patients with central obesity and metabolic syndrome and are both the result of the accumulation of ectopic fat mass. Identifying predictors of risk of OSAHS may be useful to select the subjects requiring instrumental sleep evaluation. In this cross-sectional study, we have investigated the potential role of hepatic left lobe volume (HLLV) in predicting the presence of OSAHS. OSAHS was quantified by the apnea/hypopnea index (AHI) and oxygen desaturation index in a cardiorespiratory inpatient sleep study of 97 obese women [age: 47 ± 11 years body mass index (BMI): 50 ± 8 kg/m2]. OSAHS was diagnosed when AHI was ≥5. HLLV, subcutaneous and intra-abdominal fat were measured by ultrasound. After adjustment for age and BMI, both HLLV and neck circumference (NC) were independent predictors of AHI. OSAHS was found in 72% of patients; HLLV ≥ 370 cm3 was a predictor of OSAHS with a sensitivity of 66%, a specificity of 70%, a positive and negative predictive values of 85 and 44%, respectively (AUC = 0.67, p < 0.005). A multivariate logistic model was used including age, BMI, NC, and HLLV (the only independent predictors of AHI in a multiple linear regression analyses), and a cut off value for the predicted probability of OSAHS equal to 0.7 provided the best diagnostic results (AUC = 0.79, p < 0.005) in terms of sensitivity (76%), specificity (89%), negative and positive predictive values (59 and 95%, respectively). All patients with severe OSAHS were identified by this prediction model. In conclusion, HLLV, an established index of visceral adiposity, represents an anthropometric parameter closely associated with OSAHS in severely obese women

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.Comment: 23 pages, 12 figure

A multipurpose X-ray fluorescence scanner developed for in situ analysis

Abstract: Over the time, instrument transportability has become more and more important, especially in Cultural Heritage, as often artworks cannot be moved from their site, either because of the size or due to problems with permission issues, or simply because moving them to a laboratory is physically impossible, as e.g. in the case of mural paintings. For this reason, the INFN-CHNet, the network for Cultural Heritage studies of the Italian National Institute of Nuclear Physics (INFN), has developed an XRF scanner for in situ analyses. The instrument is the result of a wide collaboration, where different units of the network have been developing the diverse parts, then merged in a single system. The XRF scanner has been designed to be a four-season and green instrument. The control/acquisition/analysis software has been fully developed by our group, using only open-source software. Other strong points of the system are easiness of use, high portability, good performances and ultra-low radiation dispersion, which allows us to use even when the public can be present. It can run both with mains or on batteries, in the latter case with a maximum runtime longer than 10 h. It has a very low cost, when compared to commercial systems with equivalent performances, and easily replaceable components, which makes it accessible for a much wider portion of the interested community. The system has been thought and designed as an open system, suitable for further development/improvements, that can result interesting for non-conventional XRF analysis. The CHNet XRF scanner has proved to be really very well suited for applications in the Cultural Heritage field, as testified by the many recent applications. This paper describes the present version of our instrument and reports on the tests performed to characterise its main features.Fil: Taccetti, F.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Castelli, L.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Czelusniak, C.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Gelli, N.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Mazzinghi, A.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Palla, L.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Ruberto, C.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Censori, C.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Lo Giudice, A.. Università di Torino; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Re, A.. Università di Torino; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Zafiropulos, D.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Arneodo, F.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Conicella, V.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Di Giovanni, A.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Torres, R.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Castella, F.. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; ArgentinaFil: Mastrangelo, Noemi Elisa. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gallegos, D.. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; ArgentinaFil: Tascon, Marcos. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; Argentina. Universidad Nacional de San Martín. Instituto de Investigación e Ingeniería Ambiental. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación e Ingeniería Ambiental; ArgentinaFil: Marte, F.. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; ArgentinaFil: Giuntini, L.. Università degli Studi di Firenze; Itali

A 20-year H2O maser monitoring program with the Medicina 32-m telescope

The Arcetri/Bologna H2O maser group has been monitoring the 1.3-cm water maser emission from a sample of 43 star-forming regions (SFRs) and 22 late-type stars for about 20 years at a sampling rate of 4-5 observations each year, using the 32-m Medicina Radio Telescope (HPBW 1.‧9 at 22 GHz). For the late-type stars we observe representative samples of OH/IR-stars, Mira's, semi-regular variables, and supergiants. The SFR-sample spans a large interval in FIR luminosity of the associated Young Stellar Object (YSO), from 20 L to 1.5 × 106 L, and offers a unique data base for the study of the long-term (years) variability of the maser emission in regions of star formation. This presentation concerns only the masers in SFRs. The information obtained from single-dish monitoring is complementary to what is extracted from higher-resolution (VLA and VLBI) observations, and can better explore the velocity domain and the long-term variability therein. We characterize the variability of the sources in various ways and we study how it depends on the luminosity and other properties of the associated YSO and its environment

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO