The Regulation of Commodity Options

To outline further genetic mechanisms of transformation from follicular lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL), we have performed whole genome array-CGH in 81 tumors from 60 patients [29 de novo DLBCL (dnDLBCL), 31 transformed DLBCL (tDLBCL), and 21 antecedent FL]. In 15 patients, paired tumor samples (primary FL and a subsequent tDLBCL) were available, among which three possessed more than two subsequent tumors, allowing us to follow specific genetic alterations acquired before, during, and after the transformation. Gain of 2p15-16.1 encompassing, among others, the REL, BCL11A, USP34, COMMD1, and OTX1 genes was found to be more common in the tDLBCL compared with dnDLBCL (P < 0.001). Furthermore, a high-level amplification of 2p15-16.1 was also detected in the FL stage prior to transformation, indicating its importance during the transformation event. Quantitative real-time PCR showed a higher level of amplification of REL, USP34, and COMMD1 (all involved in the NF kappa B-pathway) compared with BCL11A, which indicates that the altered genes disrupting the NF kappa B pathway may be the driver genes of transformation rather than the previously suggested BCL11A. Moreover, a 17q21.33 amplification was exclusively found in tDLBCL, never in FL (P < 0.04) or dnDLBCL, indicating an upregulation of genes of importance during the later phase of transformation. Taken together, our study demonstrates potential genomic markers for disease progression to clinically more aggressive forms. We also confirm the importance of the TP53-, CDKN2A-, and NF kappa B-pathways for the transformation from FL to DLBCL

Effects of confinement and crowding on folding of model proteins

We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding scenarios, but both effects are not dramatic. The influence of crowding on folding are studied by placing several identical proteins within the sphere, denaturing them, and then by monitoring refolding. If the interactions between the proteins are dominated by the excluded volume effects, the net folding times are essentially like for a single protein. An introduction of inter-proteinic attractive contacts hinders folding when the strength of the attraction exceeds about a half of the value of the strength of the single protein contacts. The bigger the strength of the attraction, the more likely is the occurrence of aggregation and misfolding

A method to assess the mitochondrial respiratory capacity of complexes I and II from frozen tissue using the Oroboros O2k-FluoRespirometer

High-resolution respirometry methods allow for the assessment of oxygen consumption by the electron transfer systems within cells, tissue samples, and isolated mitochondrial preparations. As mitochondrial integrity is compromised by the process of cryopreservation, these methods have been limited to fresh samples. Here we present a simple method to assess the activity of mitochondria respiratory complexes I and II in previously cryopreserved murine skeletal muscle tissue homogenates, as well as previously frozen D. melanogaster, as a function of oxygen consumption

Testing simplified protein models of the hPin1 WW domain

The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the reliability of the chemically-based Sorenson/Head-Gordon (SHG) model and a standard native centric model in reproducing through molecular dynamics simulations some of the well known features of the folding transition of this small domain. Our results show that the G\={o} model correctly reproduces the cooperative, two-state, folding mechanism of the WW-domain, while the SHG model predicts a transition occurring in two stages: a collapse followed by a structural rearrangement. The lack of a cooperative folding in the SHG simulations appears to be related to the non-funnel shape of the energy landscape featuring a partitioning of the native valley in sub-basins corresponding to different chain chiralities. However the SHG approach remains more reliable in estimating the $\Phi$-values with respect to G\={o}-like description. This may suggest that the WW-domain folding process is stirred by energetic and topological factors as well, and it highlights the better suitability of chemically-based models in simulating mutations.Comment: RevTex4: 12 pages and 13 eps-figure file

Application of reflectance parameters in the estimation of the structural order of coals and carbonaceous materials. Precision and bias of measurements derived from the ICCP structural working group

Optical reflectance of vitrinite is one of the fundamental physical properties that have been used for the study of coal and carbonaceous materials. Organic matter in coals and carbonaceous matter consists mainly of aromatic lamellae, whose dimensions and spatial orientation define its internal structure. Various reflectance parameters describe well the average degree of order of the molecular structure of organic matter. Moreover, reflectance parameters are numerical values which characterize the samples unambiguously, facilitating the comparison of the optical properties of different carbonaceous materials as well as comparison between optical parameters and other physical or chemical factors. The focus of this study is the evaluation of the precision and bias of reflectance measurements (R and R) performed by various analysts in different laboratories in order to check the applicability of reflectance parameters to the estimation of the structural order of coals and carbonaceous materials. Additionally, it was desirable to compare reflectance parameters with other parameters obtained by different analytical methods able to provide structural information. The consistency and repeatability of the reflectance measurements obtained by different participants turned out to enable the drawing of similar conclusions regarding the structural transformation of anthracite during heating. Good correlations were found between the reflectance parameters studied and structural factors obtained by comparative methods. The reflectance parameters examined proved to be very sensitive to any changes of the structural order of coals and carbonaceous materials and seem to be a perfect complement to structural studies made by X-ray diffraction or Raman spectroscopy

p53 is associated with high-risk and pinpointsTP53missense mutations in mantle cell lymphoma

Survival for patients diagnosed with mantle cell lymphoma (MCL) has improved drastically in recent years. However, patients carrying mutations in tumour protein p53 (TP53) do not benefit from modern chemotherapy-based treatments and have poor prognosis. Thus, there is a clinical need to identify missense mutations through routine analysis to enable patient stratification. Sequencing is not widely implemented in clinical practice for MCL, and immunohistochemistry (IHC) is a feasible alternative to identify high-risk patients. The aim of the present study was to investigate the accuracy of p53 as a tool to identify patients withTP53missense mutations and the prognostic impact of overexpression and mutations in a Swedish population-based cohort. In total, 317 cases were investigated using IHC and 255 cases were sequenced, enabling analysis of p53 andTP53status among 137 cases divided over the two-cohort investigated. The accuracy of predicting missense mutations from protein expression was 82%, with sensitivity at 82% and specificity at 100% in paired samples. We further show the impact of p53 expression andTP53mutations on survival (hazard ratio of 3 center dot 1 in univariate analysis for both), and the association to risk factors, such as high MCL International Prognostic Index, blastoid morphology and proliferation, in a population-based setting.Peer reviewe

Micro to nanostructural observations in neutron irradiated nuclear graphites PCEA and PCIB

The neutron irradiation-induced structural changes in nuclear grade graphites PCEA and PCIB were investigated using scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman spectroscopy, transmission electron microscopy (TEM), selected area electron diffraction (SAED) and electron energy loss spectroscopy (EELS). The graphite samples were irradiated at the Advanced Test Reactor at the Idaho National Laboratory. Received doses ranged from 1.5 to 6.8 displacements per atom and irradiation temperatures varied between 350 °C and 670 °C. XRD and Raman measurements provided evidence for irradiation induced crystallite fragmentation, with crystallite sizes reduced by 39–55%. Analysis of TEM images was used to quantify fringe length, tortuosity, and relative misorientation of planes, and indicated that neutron irradiation induced basal plane fragmentation and curvature. EELS was used to quantify the proportion of sp2 bonding and specimen density; a slight reduction in planar-sp2 content (due to the buckling basal planes and the introduction of non-six-membered rings) agreed with the observations from TEM

Modelling hurricane track memory

It has been observed that hurricanes that are close in time often follow similar paths. If this can be shown to be statistically significant, it could have implications for how insurance premiums are calculated in areas of the US prone to hurricanes. We developed two independent path distance metrics and while one suggested that sequential storms within a given hurricane season are more likely to follow each other than any other pair of storms within that season, this conclusion was not supported by the other metric. Some considerations of how local and large scale air pressure gradients might affect hurricane paths were considered. A point vortex model in the presence of a steering flow field was developed and used to simulate the path of two time displaced vortices. In order for the vortices to follow each other they had to be relatively weak compared to the steering flow field. At realistic vortex strength, the trajectories became chaotic. In summary, our metrics provided conflicting evidence towards the no- tion of hurricane track memory. A large-scale steering flow field did not appear to provide sufficient explanation for hurricanes following each other, though this does not preclude hurricane track memory being due to localised physical changes following a large storm

"Pi of the Sky" - all-sky, real-time search for fast optical transients

An apparatus to search for optical flashes in the sky is described. It has been optimized for gamma ray bursts (GRB) optical counterparts. It consists of 2x16 cameras covering all the sky. The sky is monitored continuously and the data are analysed on-line. It has self-triggering capability and can react to external triggers with negative delay. The prototype with two cameras has been installed at Las Campanas (Chile) and is operational from July 2004. The paper presents general idea and describes the apparatus in detail. Performance of the prototype is briefly reviewed and perspectives for the future are outlined

Microscopical characterization of carbon materials derived from coal and petroleum and their interaction phenomena in making steel electrodes, anodes and cathode blocks for the microscopy of Carbon Materials Working Group of the ICCP

This paper describes the evaluation of petrographic textures representing the structural organization of the organic matter derived from coal and petroleum and their interaction phenomena in the making of steel electrodes, anodes and cathode blocks.This work represents the results of the Microscopy of Carbon Materials Working Group in Commission III of the International Committee for Coal and Organic Petrology between the years 2009 and 2013. The round robin exercises were run on photomicrograph samples. For textural characterization of carbon materials the existing ASTM classification system for metallurgical coke was applied.These round robin exercises involved 15 active participants from 12 laboratories who were asked to assess the coal and petroleum based carbons and to identify the morphological differences, as optical texture (isotropic/anisotropic), optical type (punctiform, mosaic, fibre, ribbon, domain), and size. Four sets of digital black and white microphotographs comprising 151 photos containing 372 fields of different types of organic matter were examined. Based on the unique ability of carbon to form a wide range of textures, the results showed an increased number of carbon occurrences which have crucial role in the chosen industrial applications.The statistical method used to evaluate the results was based on the "raw agreement indices". It gave a new and original view on the analysts' opinion by not only counting the correct answers, but also all of the knowledge and experience of the participants. Comparative analyses of the average values of the level of overall agreement performed by each analyst in the exercises during 2009-2013 showed a great homogeneity in the results, the mean value being 90.36%, with a minimum value of 83% and a maximum value of 95%