New algorithm of the high-temperature expansion for the Ising model in three dimensions

New algorithm of the finite lattice method is presented to generate the high-temperature expansion series of the Ising model. It enables us to obtain much longer series in three dimensions when compared not only to the previous algorithm of the finite lattice method but also to the standard graphical method. It is applied to extend the high-temperature series of the simple cubic Ising model from beta^{26} to beta^{46} for the free energy and from beta^{25} to beta^{32} for the magnetic susceptibility.Comment: 3 pages, Lattice2002(spin

Predictive use of the Maximum Entropy Production principle for Past and Present Climates

In this paper, we show how the MEP hypothesis may be used to build simple climate models without representing explicitly the energy transport by the atmosphere. The purpose is twofold. First, we assess the performance of the MEP hypothesis by comparing a simple model with minimal input data to a complex, state-of-the-art General Circulation Model. Next, we show how to improve the realism of MEP climate models by including climate feedbacks, focusing on the case of the water-vapour feedback. We also discuss the dependence of the entropy production rate and predicted surface temperature on the resolution of the model

T2* mapping in an equine articular groove model - visualizing changes in collagen orientation

T2* mapping is promising for the evaluation of articular cartilage collagen. In this work, a groove model in a large animal is used as a model for post-traumatic arthritis. We hypothesized that T2* mapping could be employed to differentiate between healthy and (subtly) damaged cartilage. Eight carpal joints were obtained from four adult Shetland ponies that had been included in the groove study. In this model, grooves were surgically created on the proximal articular surface of the intermediate carpal bone (radiocarpal joint) and the radial facet of the third carpal bone (middle carpal joint) by either coarse disruption or sharp incision. After nine months, T2* mapping of the entire carpal joint was carried out on a 7.0T whole body magnetic resonance imaging (MRI) scanner by means of a gradient echo multi echo sequence. Afterwards, assessment of collagen orientation was carried out based on Picrosirius Red-stained histological sections, visualized by polarized light microscopy (PLM). The average T2* relaxation time in grooved samples was lower than in contralateral control sites. Opposite to the grooved areas, the "kissing sites" had a higher average T2* relaxation time than the grooved sites. PLM showed mild changes in orientation of the collagen fibers, particularly around blunt grooves. This work shows that T2* relaxation times are different in healthy cartilage versus (early) damaged cartilage, as induced by the equine groove model. Additionally, the average T2* relaxation times are different in kissing lesions versus the grooved sites. This article is protected by copyright. All rights reserved

Cytomegalovirus infection does not impact on survival or time to first treatment in patients with chronic lymphocytic leukemia

Human cytomegalovirus (HCMV) is a widely prevalent herpes virus which establishes a state of chronic infection. The establishment of CMV‐specific immunity controls viral reactivation and leads to the accumulation of very large numbers of virus‐specific T cells which come to dominate the immune repertoire. There is concern that this may reduce the immune response to heterologous infections and HCMV infection has been associated with reduced survival in elderly people. Patients with chronic lymphocytic leukemia (B‐CLL) suffer from a state of immune suppression but have a paradoxical increase in the magnitude of the CMV‐specific T cell and humoral immune response. As such, there is now considerable interest in how CMV infection impacts on the clinical outcome of patients with B‐CLL. Utilizing a large prospective cohort of patients with B‐CLL (n = 347) we evaluated the relationship between HCMV seropositivity and patient outcome. HCMV seropositive patients had significantly worse overall survival than HCMV negative patients in univariate analysis (HR = 2.28, 95% CI: 1.34–3.88; P = 0.002). However, CMV seropositive patients were 4 years older than seronegative donors and this survival difference was lost in multivariate modeling adjusted for age and other validated prognostic markers (P = 0.34). No significant difference was found in multivariate modeling between HCMV positive and negative patients in relation to the time to first treatment (HR = 1.12, 95% CI: 0.68–1.84; P = 0.65). These findings in a second independent cohort of 236 B‐CLL patients were validated. In conclusion no evidence that HCMV impacts on the clinical outcome of patients with B‐CLL was found. Am. J. Hematol. 91:776–781, 2016. © 2016 Wiley Periodicals, Inc

Feeder Cells Support the Culture of Induced Pluripotent Stem Cells Even after Chemical Fixation

Chemically fixed mouse embryonic fibroblasts (MEFs), instead of live feeder cells, were applied to the maintenance of mouse induced pluripotent stem (miPS) cells. Formaldehyde and glutaraldehyde were used for chemical fixation. The chemically fixed MEF feeders maintained the pluripotency of miPS cells, as well as their undifferentiated state. Furthermore, the chemically fixed MEF feeders were reused several times without affecting their functions. These results indicate that chemical fixation can be applied to modify biological feeders chemically, without losing their original functions. Chemically fixed MEF feeders will be applicable to other stem cell cultures as a reusable extracellular matrix candidate that can be preserved on a long-term basis

Second law, entropy production, and reversibility in thermodynamics of information

We present a pedagogical review of the fundamental concepts in thermodynamics of information, by focusing on the second law of thermodynamics and the entropy production. Especially, we discuss the relationship among thermodynamic reversibility, logical reversibility, and heat emission in the context of the Landauer principle and clarify that these three concepts are fundamentally distinct to each other. We also discuss thermodynamics of measurement and feedback control by Maxwell's demon. We clarify that the demon and the second law are indeed consistent in the measurement and the feedback processes individually, by including the mutual information to the entropy production.Comment: 43 pages, 10 figures. As a chapter of: G. Snider et al. (eds.), "Energy Limits in Computation: A Review of Landauer's Principle, Theory and Experiments

Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation

Cell differentiation in developing tissues is controlled by a small set of signaling pathways, which must coordinate the timing and levels of activation to ensure robust and precise outcomes. Highly coordinated activation of signaling pathways can result from cross-regulatory interactions in multi-pathway networks. Here we explore the dynamics and function of pathway coordination between the EGFR and DPP pathways during Drosophila wing-vein differentiation. We show that simultaneous activation of both the EGFR and DPP pathways must be maintained for vein cell differentiation and that above-threshold ectopic activation of either pathway is sufficient to drive vein cell differentiation outside the proveins. The joint activation of the EGFR and DPP signaling systems is ensured by a positive feedback loop, in which the two pathways stimulate each other at the level of ligand production

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression