Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories

Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many non-equilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the "weighted ensemble" (WE) simulation protocol [Huber and Kim, Biophys. J., 1996] to generate equilibrium trajectory ensembles and extract non-equilibrium subsets for computing kinetic quantities. States do not need to be chosen in advance. The procedure formally allows estimation of kinetic rates between arbitrary states chosen after the simulation, along with their equilibrium populations. We also describe a related history-dependent matrix procedure for estimating equilibrium and non-equilibrium observables when phase space has been divided into arbitrary non-Markovian regions, whether in WE or ordinary simulation. In this proof-of-principle study, these methods are successfully applied and validated on two molecular systems: explicitly solvated methane association and the implicitly solvated Ala4 peptide. We comment on challenges remaining in WE calculations

On quantitative analysis of interband recombination dynamics: Theory and application to bulk ZnO

The issue of the quantitative analysis of time-resolved photoluminescence experiments is addressed by developing and describing two approaches for determination of unimolecular lifetime, bimolecular recombination coefficient, and equilibrium free-carrier concentration, based on a quite general second-order expression of the electron-hole recombination rate. Application to the case of band-edge emission of ZnO single crystals is reported, evidencing the signature of sub-nanosecond second-order recombination dynamics for optical transitions close to the interband excitation edge. The resulting findings are in good agreement with the model prediction and further confirm the presence, formerly evidenced in literature by non-optical methods, of near-surface conductive layers in ZnO crystals with sheet charge densities of about 3{\div}5*10^13 cm^-2Comment: 4 pages, 5 figure

The kinetic studies of the solvent-promoted aggregation of a steroid-porphyrin derivative

The study of the aggregation of a steroid-functionalised porphyrin derivative shows the formation of chiral suprastuctures. Kinetic studies indicate that the mechanism of the aggregation strongly depends on both the nature of the media and on the concentration of the tetrapyrrolic macrocycle

Pre- and Post-surgical Poor Seizure Control as Hallmark of Malignant Progression in Patients With Glioma?

BackgroundRegarding brain tumor-related epilepsy (BTRE), there is an increasing number of evidence about a relationship between epileptogenesis and oncogenesis. A recent study suggests a role of post-surgery seizure outcome on the survival of patients with low-grade glioma (LGG), underlying the need for a targeted and aggressive epilepsy treatment. ObjectiveThis study aims at investigating the possible correlation between pre- and post-surgical seizure control and tumor progression in patients who underwent surgery for LGG. MethodsWe performed a retrospective analysis of patients affected by LGGs and BTRE, in a single high-volume neurosurgical center. Seizure control was assessed before surgery and at 3 years of follow-up. Patients with histological progression in high-grade glioma (HGG) have been evaluated. Clinical features, pre-surgical electroencephalograms (EEGs), and electrocorticography (ECoG) have been analyzed. ResultsAmong 154 subjects, we collected 32 patients who presented a tumor progression in HGG during the follow-up period. The majority had poor seizure control both pre- and post-surgery, never being in Engel class Ia throughout the whole history of their disease. Almost all patients with poor seizure control had pathological ECoG recording. Clinical features of seizures did not correlate with seizure outcome. On the univariate analysis, the age, the post-operative Engel class, and the extent of resection (EOR) were the prognostic factors significantly associated with oncological outcome; nevertheless, on multivariate analysis, Engel class significance was not confirmed, and the only predicting factor were age and EOR. ConclusionsAlthough not confirmed on multivariate analysis, post-surgical seizure control could be a relevant factor to consider during follow-up of BRTE, in particular, when gross total resection is not achieved. Pathological findings on the ECoG may suggest a "hidden" propensity to malignant progression, strictly related to the persistent neuronal hyper-excitability. Further studies with longer follow-up period are needed to confirm our observations

Predictors of postoperative seizure outcome in low grade glioma: From volumetric analysis to molecular stratification

The importance of the extent of resection (EOR) has been widely demonstrated as the main predictor for survival, nevertheless its effect on tumor related epilepsy is less investigated. A total of 155 patients were enrolled after a first-line surgery for supratentorial Diffuse Low Grade Gliomas (DLGGs). Postoperative seizure outcome was analyzed stratifying the results by tumor volumetric data and molecular markers according to 2016 WHO classification. Receiver operating characteristic (ROC) curves were computed to asses EOR, residual tumor volume, and 06T2T1 MRI index (expressing the tumor growing pattern) corresponding to optimal seizure outcome. A total of 70.97% of patients were seizure-free 18 months after surgery. Better seizure outcome was observed in IDH1/2 mutated and 1p/19q codeleted subgroup. At multivariate analysis, age (p = 0.014), EOR (p = 0.030), 06T2T1 MRI index (p = 0.016) resulted as independent predictors of postoperative seizure control. Optimal parameters to improve postoperative seizure outcome were EOR 65 85%, 06T2T1 MRI index 64 18 cm3, residual tumor volume 64 15 cm3. This study confirms the role of EOR and tumor growing pattern on postoperative seizure outcome independently from the molecular class. Higher 06T2T1 MRI index, representing the infiltrative component of the tumor, is associated with worse seizure outcome and strengthens the evidence of common pathogenic mechanisms underlying tumor growth and postoperative seizure outcome

A new fluorescent oligonucleotide probe for in-situ identification of Microcystis aeruginosa in freshwater.

contaminated water bodies (freshwater, brackish and marine areas). Among 150 known cyanobacteria genera,>40 species are able to produce toxins, which are natural compounds that differ from both a chemical and toxicological point of view and are responsible for acute and chronic poisoning in animals and humans. Among the main classes of cyanotoxins, microcystins are frequently found in the environment. Fast and accurate methods for unequivocally identifying microcystin-producing cyanobacteria, such as Microcystis aeruginosa in water bodies, are necessary to distinguish them from other non-toxic cyanobacteria and to manage and monitor algal blooms. For this purpose, we designed, developed and validated an oligonucleotide probe for FISH (Fluorescence In Situ Hybridization) analysis to detect Microcystis aeruginosa at the species level even at relatively low concentrations in freshwater. The FISH probe, MicAerD03, was designed using the ARB software with the Silva database within the framework of the MicroCoKit project, also with the intention of adding it to the microarray from the EU project, μAQUA, for freshwater pathogens, which had only genus level probes for Microcystis. We tested various fixative methods to minimize the natural autofluorescence from chlorophyll-a and certain accessory pigments (viz., phycobilins and carotenoids). The FISH probe was tested on pure cultures of Microcystis aeruginosa, and then successfully applied to water samples collected from different sampling points of the Tiber River (Italy), using a laser confocal microscope. Subsequently, the probe was also conjugated at the 5′ end with horse-radish peroxidase (HRP-MicAerD03) to apply the CAtalysed Reported Deposition-FISH (CARD-FISH) for increasing the fluorescence signal of the mono-fluorescently labelled probe and make it possible to detect M. aeruginosa using an epifluorescence microscope. Samples taken within the EU MicroCokit project indicated thatmicroarray signals for Microcystis were coming from single cells and not colonial cells. We confirmed this with the CARD-FISH protocol used here to validate the microarray signals for Microcystis detected at the genus level in MicroCokit. This paper provides a new early warning tool for investigating M. aeruginosa at the species level even at low cell concentrations in surface water, which can be added to the μAqua microarray for all freshwater pathogens to complete the probe hierarchy for Microcystis aeruginosa

Characterization of Rotating Cavitation in a Four Bladed Inducer

This work aims to characterize the dynamic behavior of a four bladed inducer and clarify the physical mechanism that leads to the onset of rotating cavitation. The inducer under consideration is representative of a low-pressure liquid oxygen pump (LPOP) inducer of modern design and incorporates several standard design features used in rocket turbopumps to suppress rotating cavitation. The mechanism is characterized based on a combination of two-phase numerical simulations and inducer experiments. Experimental measurements demonstrate a supersynchronous rotating cavity in the periphery of the inducer inlet at frequencies between 1.2 and 1.6 times rotor frequency and a synchronous 2nd spatial harmonic pattern associated with alternate blade cavitation. The analysis indicates a causal link between alternate blade cavitation and rotating cavitation, with a distinct cut-on cut-off behavior. Numerical calculations and high-speed videos elucidate the mechanism of breakdown of alternate blade cavitation and the formation of rotating cavitation. The present work suggests that rotating cavitation is caused by the coupling of the cavities on adjacent blades during alternate blade cavitation. Due to the nearly tangential flow, the vortex lines from one of the non-cavitating blades wrap around the blade leading edge of the adjacent blade, which yields a drop in static pressure and cavity formation. The tip vortex cavity interaction with the leading edge of the blade leads to sheet cavity breakdown with periodic growth and collapse of cavities, creating the apparent super-synchronous rotation of the cavitating region.United States. National Aeronautics and Space Administration (NASA Marshall Space Flight Center

A comparison of magnetic resonance, X-ray and positron emission particle tracking measurements of a single jet of gas entering a bed of particles

Measurements of the lengths of a single jet of gas entering a packed bed were made using magnetic resonance imaging (MRI), positron emission particle tracking (PEPT) and X-ray radiography and the results compared. The experiments were performed using a Perspex bed (50 mm i.d.) of poppy seeds: air at 298 K was admitted to the base of the bed through a single, central orifice, 2 mm in diameter. Poppy seeds (Geldart Group B, measured minimum fluidisation velocity with air at 298 K and 1 atm of 0.13 m/s and particle density ~1060 kg/m3) were used because of their high content of oil, which contains mobile protons and hence is suitable for MRI examination. The lengths of jet measured using the three techniques were in agreement between 50 m/s < Uo < 100 m/s, where Uo is the superficial velocity through the orifice. Below Uo = 50 m/s, X-ray measurements of jet lengths were shorter than those measured using MRI. This was attributed to the minimum diameter of void, found to be 5 mm, detectable in a 50 mm bed using ultra-fast X-ray measurements. PEPT is most commonly used to calculate particle velocities, whilst jet lengths are usually calculated from determinations of voidage. However, the particle locations determined in this work by PEPT were used to calculate a fractional occupancy count, from which a jet length could be inferred.RCUK, OtherThis is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.ces.2014.09.02

Si-compatible candidates for high-K dielectrics with the Pbnm perovskite structure

We analyze both experimentally (where possible) and theoretically from first-principles the dielectric tensor components and crystal structure of five classes of Pbnm perovskites. All of these materials are believed to be stable on silicon and are therefore promising candidates for high-K dielectrics. We also analyze the structure of these materials with various simple models, decompose the lattice contribution to the dielectric tensor into force constant matrix eigenmode contributions, explore a peculiar correlation between structural and dielectric anisotropies in these compounds and give phonon frequencies and infrared activities of those modes that are infrared-active. We find that CaZrO_3, SrZrO_3, LaHoO_3, and LaYO_3 are among the most promising candidates for high-K dielectrics among the compounds we considered.Comment: 17 pages, 9 figures, 4 tables. Supplementary information: http://link.aps.org/supplemental/10.1103/PhysRevB.82.064101 or http://www.physics.rutgers.edu/~sinisa/highk/supp.pd

Could kallikrein-related serine peptidase 3 be an early biomarker of environmental exposure in young women?

Bisphenols and phthalates affect androgen receptor-mediated signaling that directly reg-ulates Kallikrein-Related serine Peptidase 3 (KLK3) secretion, indicating that environmental factors may play a role in KLK3 secretion. With the aim of obtaining preliminary data on whether KLK3 could serve as an early marker of environmental pollution effects, in 61 and 58 healthy women living in a high environmental impact (HEI) and low environmental impact (LEI) area, respectively, serum KLK3 levels at different phases of menstrual cycle were measured. KLK3 values resulted in always being higher in the HEI group with respect to the LEI group. These differences were partic-ularly relevant in the ovulatory phase (cycle day 12°–13°) of the menstrual cycle. The differences in KLK3 values during the three phases of the menstrual cycle were significant in the LEI group dif-ferently from the HEI group. In addition, higher progesterone levels were observed in the LEI group with respect to the HEI group in the luteal phase, indicating an opposite trend of KLK3 and progesterone in this phase of the menstrual cycle. Although changes in KLK3 could also depend on other factors, these preliminary data could be an early indication of an expanding study of the role of biomarkers in assessing early environmental effects for female reproductive health