Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev.

Relaxation and Metastability in the RandomWalkSAT search procedure

An analysis of the average properties of a local search resolution procedure for the satisfaction of random Boolean constraints is presented. Depending on the ratio alpha of constraints per variable, resolution takes a time T_res growing linearly (T_res \sim tau(alpha) N, alpha < alpha_d) or exponentially (T_res \sim exp(N zeta(alpha)), alpha > alpha_d) with the size N of the instance. The relaxation time tau(alpha) in the linear phase is calculated through a systematic expansion scheme based on a quantum formulation of the evolution operator. For alpha > alpha_d, the system is trapped in some metastable state, and resolution occurs from escape from this state through crossing of a large barrier. An annealed calculation of the height zeta(alpha) of this barrier is proposed. The polynomial/exponentiel cross-over alpha_d is not related to the onset of clustering among solutions.Comment: 23 pages, 11 figures. A mistake in sec. IV.B has been correcte

Concentration in saliva and antibacterial effect of xylitol chewing gum : in vivo and In vitro study

Purpose. The saliva concentration of xylitol released from two chewing gums was recorded, the first containing xylitol as the only sweetener (100% xylitol) and the second containing only 22% of the polyol. In addition, the in vitro antibacterial effect of the two chewing gums was evaluated. Materials and Methods. The salivary concentration of Xylitol in 32 subjects was determined before and at 0.30, 1.00, 2.00, 5.00, and 10.00 min while using the chewing gums, and at 15.00, 20.00, and 25.00 min after the gums were discarded. In vitro antibacterial activity was determined on a pooled subgingival plaque sample obtained from four patients with periodontal disease. Cariogenic and periodontal bacteria were evaluated before and 15 min, 60 min, and 24 h after gum contact. Results. Using the 100% xylitol chewing gum, saliva levels increased bimodally, one peak after 30 s (1.49 \ub1 1.41 log\u3bcg/L) and a second one at a 10-min evaluation (1.41 \ub1 1.11 log\u3bcg/L); the 22% chewing gum peaked only two minute after contact (1.21 \ub1 1.24 log\u3bcg/L). Overall, a statistically significantly higher salivary concentration of xylitol was detected using the 100% xylitol gum. All bacteria decreased after the addition of the two chewing gums; the 100% gum achieved a greater decrease than the 22% gum. Conclusion. The use of both chewing gums increased the concentrations of xylitol in saliva, with a statistically significantly higher concentration using the 100% xylitol gum. Cariogenic and periodontal bacteria were reduced by both chewing gums; 100% xylitol gum produced the highest and longest lasting effect. This study opens up to the use of xylitol against periodontal disease

Electronic structure study by means of X-ray spectroscopy and theoretical calculations of the "ferric star" single molecule magnet

The electronic structure of the single molecule magnet system M[Fe(L)2]3*4CHCl3 (M=Fe,Cr; L=CH3N(CH2CH2O)2) has been studied using X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, soft X-ray emission spectroscopy, and density functional calculations. There is good agreement between theoretical calculations and experimental data. The valence band mainly consists of three bands between 2 eV and 30 eV. Both theory and experiments show that the top of the valence band is dominated by the hybridization between Fe 3d and O 2p bands. From the shape of the Fe 2p spectra it is argued that Fe in the molecule is most likely in the 2+ charge state. Its neighboring atoms (O,N) exhibit a magnetic polarisation yielding effective spin S=5/2 per iron atom, giving a high spin state molecule with a total S=5 effective spin for the case of M = Fe.Comment: Fig.2 replaced as it will appear in J. Chem. Phy

Adaptive cluster expansion for the inverse Ising problem: convergence, algorithm and tests

We present a procedure to solve the inverse Ising problem, that is to find the interactions between a set of binary variables from the measure of their equilibrium correlations. The method consists in constructing and selecting specific clusters of variables, based on their contributions to the cross-entropy of the Ising model. Small contributions are discarded to avoid overfitting and to make the computation tractable. The properties of the cluster expansion and its performances on synthetic data are studied. To make the implementation easier we give the pseudo-code of the algorithm.Comment: Paper submitted to Journal of Statistical Physic

Rupture history of the 1997 Umbria-Marche (Central Italy) main shocks from the inversion of GPS, DInSAR and near field strong motion data

We investigate the rupture history of the three largest magnitude earthquakes of the 1997 Umbria-Marche sequence by inverting GPS, DInSAR and near-source strong motion waveforms. We use the frequency domain inversion procedure proposed by Cotton and Campillo (1995) and calculate the Green s functions for a layered halfspace using the discrete wavenumber and reflectivity methods. We first invert GPS measurements and DInSAR interferograms to image the coseismic slip distribution on the fault planes in a layered half space for the two earthquakes that occurred on September 26, 1997 at 00:33 UTC (Mw = 5.7) and 09:40 UTC (Mw = 6.0) near Colfiorito. We also invert DInSAR interferograms to infer the slip distribution during the subsequent earthquake that occurred on October 14, 1997 at 15:23 UTC (Mw = 5.6) in the SE section of the seismogenic zone near Sellano. We also explore the set of acceptable solutions using a genetic algorithm to have information on the available resolution of geodetic data. The slip models obtained by geodetic data inversion are used to perform a forward modeling of strong motion waveforms for all three events. We adopt a constant rupture velocity of 2.6 km/s and a constant rise time of 1 s. Our results show that these rupture models provide an acceptable fit to recorded waveforms. Finally, we invert the recorded ground displacements, collected during the September 26th 09:40 main shock and the October 14th Sellano earthquake, to constrain the rupture history. We use the geodetic slip distribution as starting model for the iterative inversion procedure. The retrieved rupture models are consistent with those inferred from geodetic data and yield a good fit to recorded seismograms. These rupture models are characterized by a heterogeneous slip distribution and an evident rupture directivity in agreement with previous observations

Optimized hybrid ensemble learning approaches applied to very short-term load forecasting

The significance of accurate short-term load forecasting (STLF) for modern power systems’ efficient and secure operation is paramount. This task is intricate due to cyclicity, non-stationarity, seasonality, and nonlinear power consumption time series data characteristics. The rise of data accessibility in the power industry has paved the way for machine learning (ML) models, which show the potential to enhance STLF accuracy. This paper presents a novel hybrid ML model combining Gradient Boosting Regressor (GBR), Extreme Gradient Boosting (XGBoost), k-Nearest Neighbors (kNN), and Support Vector Regression (SVR), examining both standalone and integrated, coupled with signal decomposition techniques like STL, EMD, EEMD, CEEMDAN, and EWT. Through Automated Machine Learning (AutoML), these models are integrated and their hyperparameters optimized, predicting each load signal component using data from two sources: The National Operator of Electric System (ONS) and the Independent System Operators New England (ISO-NE), boosting prediction capacity. For the 2019 ONS dataset, combining EWT and XGBoost yielded the best results for very short-term load forecasting (VSTLF) with an RMSE of 1,931.8 MW, MAE of 1,564.9 MW, and MAPE of 2.54%. These findings highlight the necessity for diverse approaches to each VSTLF problem, emphasizing the adaptability and strength of ML models combined with signal decomposition techniques

Interventional Ultrasound in Dermatology: A Pictorial Overview Focusing on Cutaneous Melanoma Patients

Cutaneous melanoma incidence is increasing worldwide, representing an aggressive tumor when evolving to the metastatic phase. High-resolution ultrasound (US) is playing a growing role in the assessment of newly diagnosed melanoma cases, in the locoregional staging prior to the sentinel lymph-node biopsy procedure, and in the melanoma patient follow-up. Additionally, US may guide a number of percutaneous procedures in the melanoma patients, encompassing diagnostic and therapeutic modalities. These include fine needle cytology, core biopsy, placement of presurgical guidewires, aspiration of lymphoceles and seromas, and electrochemotherapy

1-Benzoyl-3-[3-cyano-8-methyl-4-(1-methyl-1H-pyrrol-2-yl)-5,6,7,8-tetra­hydro­quinolin-2-yl]thio­urea

In the N-substituted benzoyl­thio­urea, C24H23N5OS, the benzoyl­thio­urea unit is non-planar (r.m.s. deviation = 0.126 Å). The aliphatic part of the tetra­hydro­quinoline fused-ring system is disordered over two positions in a 0.592 (5):0.408 (5) ratio. The pyridine and pyrrole rings are twisted by 55.2 (1)° in order to avoid crowding of their respective substituents. Pairs of mol­ecules are linked by N—H⋯N hydrogen bonds, forming centrosymmetric dimers. Furthermore, an intra­molecular N—H⋯O hydrogen bond stabilizes the mol­ecular conformation

Approximation schemes for the dynamics of diluted spin models: the Ising ferromagnet on a Bethe lattice

We discuss analytical approximation schemes for the dynamics of diluted spin models. The original dynamics of the complete set of degrees of freedom is replaced by a hierarchy of equations including an increasing number of global observables, which can be closed approximately at different levels of the hierarchy. We illustrate this method on the simple example of the Ising ferromagnet on a Bethe lattice, investigating the first three possible closures, which are all exact in the long time limit, and which yield more and more accurate predictions for the finite-time behavior. We also investigate the critical region around the phase transition, and the behavior of two-time correlation functions. We finally underline the close relationship between this approach and the dynamical replica theory under the assumption of replica symmetry.Comment: 21 pages, 5 figure