Monte Carlo simulation of size-effects on thermal conductivity in a 2-dimensional Ising system

A model based on microcanonical Monte Carlo method is used to study the application of the temperature gradient along a two-dimensional (2D) Ising system. We estimate the system size effects on thermal conductivity, $K$, for a nano-scale Ising layer with variable size. It is shown that $K$ scales with size as $K=cL^\alpha$ where $\alpha$ varies with temperature. Both the Metropolis and Cruetz algorithms have been used to establish the temperature gradient. Further results show that the average demon energy in the presence of an external magnetic field is zero for low temperatures.Comment: 10 pages, 7 figures, to appear in Physica

The Zebrafish equivalent of Alzheimer's disease-associated PRESENILIN Isoform PS2V regulates inflammatory and other responses to hypoxic stress

Dominant mutations in the PRESENILIN genes PSEN1 and PSEN2 cause familial Alzheimer's disease (fAD) that usually shows onset before 65 years of age. In contrast, genetic variation at the PSEN1 and PSEN2 loci does not appear to contribute to risk for the sporadic, late onset form of the disease (sAD), leading to doubts that these genes play a role in the majority of AD cases. However, a truncated isoform of PSEN2, PS2V, is upregulated in sAD brains and is induced by hypoxia and high cholesterol intake. PS2V can increase γ-secretase activity and suppress the unfolded protein response (UPR), but detailed analysis of its function has been hindered by lack of a suitable, genetically manipulable animal model since mice and rats lack this PRESENILIN isoform. We recently showed that zebrafish possess an isoform, PS1IV, that is cognate to human PS2V. Using an antisense morpholino oligonucleotide, we can block specifically the induction of PS1IV that normally occurs under hypoxia. Here, we exploit this ability to identify gene regulatory networks that are modulated by PS1IV. When PS1IV is absent under hypoxia-like conditions, we observe changes in expression of genes controlling inflammation (particularly sAD-associated IL1B and CCR5), vascular development, the UPR, protein synthesis, calcium homeostasis, catecholamine biosynthesis, TOR signaling, and cell proliferation. Our results imply an important role for PS2V in sAD as a component of a pathological mechanism that includes hypoxia/oxidative stress and support investigation of the role of PS2V in other diseases, including schizophrenia, when these are implicated in the pathology.Esmaeil Ebrahimie, Seyyed Hani Moussavi Nik, Morgan Newman, Mark Van Der Hoek and Michael Lardell

Correlation Between Intra-Abdominal Free Fluid and Solid Organ Injury in Blunt Abdominal Trauma

Background: In previous studies, the diagnostic value of Focused Assessment with Sonography for Trauma (FAST) has been evaluated but few studies have been performed on the relationship between the amount of free intra-abdominal fluid and organ injury in blunt abdominal trauma. To select patients with a higher probability of intra-abdominal injuries, several scoring systems have been proposed based on the results of FAST. Objectives: The aim of this study was to determine the prognostic value of FAST according to the Huang scoring system and to propose a cut-off point for predicting the presence of intra-abdominal injuries on the Computed Tomography (CT) scan. The correlation between age and Glasgow Coma Scale (GCS) and the presence of intra-abdominal injuries on the CT scan was also assessed. Patients and Methods: This study was performed on 200 patients with severe blunt abdominal trauma who had stable vital signs. For all patients, FAST-ultrasound was performed by a radiologist and the free fluid score in the abdomen was calculated according to the Huang score. Immediately, an intravenous contrast-enhanced abdominal CT scan was performed in all patients and abdominal solid organ injuries were assessed. Results were analyzed using Kruskal-Wallis test, Mann-Whitney test and ROC curves. The correlation between age and GCS and the presence of intra-abdominal injuries on CT-scan was also evaluated. Results: The mean age of the patients was 29.6 ± 18.3 years and FAST was positive in 67% of the subjects. A significant correlation was seen between the FAST score and the presence of organ injury on CT scan (P < 0.001). Considering the cut-off point of 3 for the free fluid score (with a range of 0-8), sensitivity, specificity, positive predictive value and negative predictive value were calculated to be 0.83, 0.98, 0.93, and 0.95, respectively. Age and GCS showed no significant correlation with intra-abdominal injuries. Conclusions: It seems that FAST examination for intra-abdominal fluid in blunt trauma patients can predict intra-abdominal injuries with very high sensitivity and specificity. Using the scoring system can more accurately determine the probability of the presence of abdominal injuries with a cut-off point of three

Routine Chest Computed Tomography and Patient Outcome in Blunt Trauma

Background: Computerized Tomography (CT) scan is gaining more importance in the initial evaluation of patients with multiple trauma, but its effect on the outcome is still unclear. Until now, no prospective randomized trial has been performed to define the role of routine chest CT in patients with blunt trauma. Objectives: In view of the considerable radiation exposure and the high costs of CT scan, the aim of this study was to assess the effects of performing the routine chest CT on the outcome as well as complications in patients with blunt trauma. Patients and Methods: After approval by the ethics board committee, 100 hemodynamically stable patients with high-energy blunt trauma were randomly divided into two groups. For group one (control group), only chest X-ray was requested and further diagnostic work-up was performed by the decision of the trauma team. For group two, a chest X-ray was ordered followed by a chest CT, even if the chest X-ray was normal. Injury severity, total hospitalization time, Intensive Care Unit (ICU) admission time, duration of mechanical ventilation and complications were recorded. Data were evaluated using t-test, Man-Whitney and chi-squared test. Results: No significant differences were found regarding the demographic data such as age, injury severity and Glasgow Coma Scale (GCS). Thirty-eight percent additional findings were seen in chest CT in 26% of the patients of the group undergoing routine chest CT, leading to 8% change in management. The mean of in-hospital stay showed no significant difference in both groups with a P value of 0.098. In addition, the mean ICU stay and ventilation time revealed no significant differences (P values = 0.102 and 0.576, respectively). Mortality rate and complications were similar in both groups. Conclusions: Performing the routine chest CT in high-energy blunt trauma patients (with a mean injury severity of 9), although leading to the diagnosis of some occult injuries, has no impact on the outcome and does not decrease the in-hospital stay and ICU admission time. It seems that performing the routine chest CT in these patients may lead to overtreatment of nonsignificant injuries. The decision about performing routine CT scan in a trauma center should be made cautiously, considering the detriments and benefits

Lithium Phthalocyanine: A Probe for Electron Paramagnetic Resonance Oximetry in Viable Biological Systems.

Lithium phthalocyanine (LiPc) is a prototype of another generation of synthetic, metallic-organic, paramagnetic crystallites that appear very useful for in vitro and in vivo electron paramagnetic resonance oximetry. The peak-to-peak line width of the electron paramagnetic resonance spectrum of LiPc is a linear function of the partial pressure of oxygen (pO2); this linear relation is independent of the medium surrounding the LiPc. It has an extremely exchange-narrowed spectrum (peak-to-peak line width = 14 mG in the absence of O2). Physicochemically LiPc is very stable; its response to pO2 does not change with conditions and environments (e.g., pH, temperature, redox conditions) likely to occur in viable biological systems. These characteristics provide the sensitivity, accuracy, and range to measure physiologically and pathologically pertinent O2 tensions (0.1-50 mmHg; 1 mmHg = 133 Pa). The application of LiPc in biological systems is demonstrated in measurements of pO2 in vivo in the heart, brain, and kidney of rats

Peptidoglycan Remodeling and Conversion of an Inner Membrane into an Outer Membrane during Sporulation

Two hallmarks of the Firmicute phylum, which includes the Bacilli and Clostridia classes, are their ability to form endospores and their “Gram-positive” single-membraned, thick-cell-wall envelope structure. Acetonema longum is part of a lesser-known family (the Veillonellaceae) of Clostridia that form endospores but that are surprisingly “Gram negative,” possessing both an inner and outer membrane and a thin cell wall. Here, we present macromolecular resolution, 3D electron cryotomographic images of vegetative, sporulating, and germinating A. longum cells showing that during the sporulation process, the inner membrane of the mother cell is inverted and transformed to become the outer membrane of the germinating cell. Peptidoglycan persists throughout, leading to a revised, “continuous” model of its role in the process. Coupled with genomic analyses, these results point to sporulation as a mechanism by which the bacterial outer membrane may have arisen and A. longum as a potential “missing link” between single- and double-membraned bacteria

Identification and expression analysis of the zebrafish orthologues of the mammalian MAP1LC3 gene family

Autophagy is the principle pathway within cells involved in clearing damaged proteins and organelles. Therefore autophagy is necessary to maintain the turnover balance of peptides and homoeostasis. Autophagy occurs at basal levels under normal conditions but can be upregulated by chemical inducers or stress conditions. The zebrafish (Danio rerio) serves as a versatile tool to understand the functions of genes implicated in autophagy. We report the identification of the zebrafish orthologues of mammalian genes MAP1LC3A (map1lc3a) and MAP1LC3B (map1lc3b) by phylogenetic and conserved synteny analysis and we examine their expression during embryonic development. The zebrafish map1lc3a and map1lc3b genes both show maternally contributed transcripts in early embryogenesis. However, levels of map1lc3a transcript steadily increase until at least 120h post-fertilisation while the levels of map1lc3b show a more variable pattern across developmental time. We have also validated the LC3I ratio/LC3I immunoblot autophagy assay in the presence of chloroquine (a lysosomal proteolysis inhibitor). We found that the LC3II/LC3I ratio is significantly increased in the presence of sodium azide with chloroquine supporting that hypoxia induces autophagy in zebrafish. This was supported by our qPCR assay that showed increased map1lc3a transcript levels in the presence of sodium azide. In contrast, levels of map1lc3b transcripts were reduced in the presence of rapamycin but the decrease in the presence of sodium azide did not reach statistical significance. Our study supports the use of zebrafish for analysing the interplay between hypoxia, development and autophagy.Swamynathan Ganesan, Seyyed Hani Moussavi Nik, Morgan Newman, Michael Lardell

Gene Ontology-based analysis of zebrafish’ omics data using the web tool Comparative Gene Ontology

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: ‘‘Molecular Function,’’ ‘‘Biological Process,’’ and ‘‘Cellular Component.’’ GOanalysis can assist in revealing functionalmechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 (www.comparativego.com). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.Esmaeil Ebrahimie, Mario Fruzangohar, Seyyed Hani Moussavi-Nik, and Morgan Newma

Antarctic Supraglacial Lake Identification Using Landsat-8 Image Classification

Surface meltwater generated on ice shelves fringing the Antarctic Ice Sheet can drive ice-shelf collapse, leading to ice sheet mass loss and contributing to global sea level rise. A quantitative assessment of supraglacial lake evolution is required to understand the influence of Antarctic surface meltwater on ice-sheet and ice-shelf stability. Cloud computing platforms have made the required remote sensing analysis computationally trivial, yet a careful evaluation of image processing techniques for pan-Antarctic lake mapping has yet to be performed. This work paves the way for automating lake identification at a continental scale throughout the satellite observational record via a thorough methodological analysis. We deploy a suite of different trained supervised classifiers to map and quantify supraglacial lake areas from multispectral Landsat-8 scenes, using training data generated via manual interpretation of the results from k-means clustering. Best results are obtained using training datasets that comprise spectrally diverse unsupervised clusters from multiple regions and that include rock and cloud shadow classes. We successfully apply our trained supervised classifiers across two ice shelves with different supraglacial lake characteristics above a threshold sun elevation of 20°, achieving classification accuracies of over 90% when compared to manually generated validation datasets. The application of our trained classifiers produces a seasonal pattern of lake evolution. Cloud shadowed areas hinder large-scale application of our classifiers, as in previous work. Our results show that caution is required before deploying ‘off the shelf’ algorithms for lake mapping in Antarctica, and suggest that careful scrutiny of training data and desired output classes is essential for accurate results. Our supervised classification technique provides an alternative and independent method of lake identification to inform the development of a continent-wide supraglacial lake mapping product