A conjectured scenario for order-parameter fluctuations in spin glasses

We study order-parameter fluctuations (OPF) in disordered systems by considering the behavior of some recently introduced paramaters $G,G_c$ which have proven very useful to locate phase transitions. We prove that both parameters G (for disconnected overlap disorder averages) and $G_c$ (for connected disorder averages) take the respective universal values 1/3 and 13/31 in the $T\to 0$ limit for any {\em finite} volume provided the ground state is {\em unique} and there is no gap in the ground state local-field distributions, conditions which are met in generic spin-glass models with continuous couplings and no gap at zero coupling. This makes $G,G_c$ ideal parameters to locate phase transitions in disordered systems much alike the Binder cumulant is for ordered systems. We check our results by exactly computing OPF in a simple example of uncoupled spins in the presence of random fields and the one-dimensional Ising spin glass. At finite temperatures, we discuss in which conditions the value 1/3 for G may be recovered by conjecturing different scenarios depending on whether OPF are finite or vanish in the infinite-volume limit. In particular, we discuss replica equivalence and its natural consequence $\lim_{V\to\infty}G(V,T)=1/3$ when OPF are finite. As an example of a model where OPF vanish and replica equivalence does not give information about G we study the Sherrington-Kirkpatrick spherical spin-glass model by doing numerical simulations for small sizes. Again we find results compatible with G=1/3 in the spin-glass phase.Comment: 18 pages, 9 postscript figure

Scaling approach to order-parameter fluctuations in disordered frustrated systems

We present a constructive approach to obtain information about the compactness and shape of large-scale lowest excitations in disordered systems by studying order-parameter fluctuations (OPF) at low temperatures. We show that the parameter $G$ which measures OPF is 1/3 at T=0 provided the ground state is unique and the probability distribution for the lowest excitations is gapless and with finite weight at zero-excitation energy. We then apply zero-temperature scaling to describe the energy and volume spectra of the lowest large-scale excitations which scale with the system size and have a weight at ze ro energy $\hat{P}_v(0)\sim l^{-\theta'}$ with $v=l^d$. A low-temperature expansion reveals that, OPF vanish like $L^{-\theta}$, if $\theta> 0$ and remain finite for space filling lowest excitations with $\theta=0$. The method can be extended to extract information about the shape and fractal surface of the large-scale lowest excitations.Comment: 4 pages, REVTeX. Some modifications; final version accepted for publication in J. Phys. A: Math. and General (Letters

Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer

Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eightythree genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes

Modelling adult Aedes aegypti and Aedes albopictus survival at different temperatures in laboratory and field settings.

BACKGROUND: The survival of adult female Aedes mosquitoes is a critical component of their ability to transmit pathogens such as dengue viruses. One of the principal determinants of Aedes survival is temperature, which has been associated with seasonal changes in Aedes populations and limits their geographical distribution. The effects of temperature and other sources of mortality have been studied in the field, often via mark-release-recapture experiments, and under controlled conditions in the laboratory. Survival results differ and reconciling predictions between the two settings has been hindered by variable measurements from different experimental protocols, lack of precision in measuring survival of free-ranging mosquitoes, and uncertainty about the role of age-dependent mortality in the field. METHODS: Here we apply generalised additive models to data from 351 published adult Ae. aegypti and Ae. albopictus survival experiments in the laboratory to create survival models for each species across their range of viable temperatures. These models are then adjusted to estimate survival at different temperatures in the field using data from 59 Ae. aegypti and Ae. albopictus field survivorship experiments. The uncertainty at each stage of the modelling process is propagated through to provide confidence intervals around our predictions. RESULTS: Our results indicate that adult Ae. albopictus has higher survival than Ae. aegypti in the laboratory and field, however, Ae. aegypti can tolerate a wider range of temperatures. A full breakdown of survival by age and temperature is given for both species. The differences between laboratory and field models also give insight into the relative contributions to mortality from temperature, other environmental factors, and senescence and over what ranges these factors can be important. CONCLUSIONS: Our results support the importance of producing site-specific mosquito survival estimates. By including fluctuating temperature regimes, our models provide insight into seasonal patterns of Ae. aegypti and Ae. albopictus population dynamics that may be relevant to seasonal changes in dengue virus transmission. Our models can be integrated with Aedes and dengue modelling efforts to guide and evaluate vector control, better map the distribution of disease and produce early warning systems for dengue epidemics

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences

Femtosecond double-pulse laser ablation and deposition of Co-doped ZnS thin films

Nanostructured thin films of Co-doped zinc sulfide were synthesized through femtosecond pulsed laser deposition. The scheme involved ablation of physically mixed Co and ZnS with pairs of ultrashort pulses separated in time in the 0-300 ps range. In situ monitorization of the deposition process was carried out through a simultaneous reflectivity measurement. The crystallinity of generated nanoparticles and the inclusion of Co in the ZnS lattice is demonstrated by transmission electron microscopy and energy dispersive X-ray microanalysis (TEM-EDX) characterization. Surface morphology, Raman response, and photoluminescence of the films have also been assessed. The role of interpulse temporal separation is most visible in the thickness of the films obtained at the same total fluence, with much thicker films deposited with short delays than with individual uncoupled pulses. The proportion of Co in the synthesized doped ZnS nanoparticles is found to be substantially lower than the original proportion, and practically independent on interpulse delay

Exploring the Role of Mutations in Fanconi Anemia Genes in Hereditary Cancer Patients

Fanconi anemia (FA) is caused by biallelic mutations in FA genes. Monoallelic mutations in five of these genes (BRCA1, BRCA2, PALB2, BRIP1 and RAD51C) increase the susceptibility to breast/ovarian cancer and are used in clinical diagnostics as bona-fide hereditary cancer genes. Increasing evidence suggests that monoallelic mutations in other FA genes could predispose to tumor development, especially breast cancer. The objective of this study is to assess the mutational spectrum of 14 additional FA genes (FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FANCP, FANCQ, FANCR and FANCU) in a cohort of hereditary cancer patients, to compare with local cancer-free controls as well as GnomAD. A total of 1021 hereditary cancer patients and 194 controls were analyzed using our next generation custom sequencing panel. We identified 35 pathogenic variants in eight genes. A significant association with the risk of breast cancer/breast and ovarian cancer was found for carriers of FANCA mutations (odds ratio (OR) = 3.14 95% confidence interval (CI) 1.4-6.17, p = 0.003). Two patients with early-onset cancer showed a pathogenic FA variant in addition to another germline mutation, suggesting a modifier role for FA variants. Our results encourage a comprehensive analysis of FA genes in larger studies to better assess their role in cancer risk

An apoplastic fluid extraction method for the characterization of grapevine leaves proteome and metabolome from a single sample

The analysis of complex biological systems keeps challenging researchers. The main goal of systems biology is to decipher interactions within cells, by integrating datasets from large scale analytical approaches including transcriptomics, proteomics and metabolomics andmore specialized ‘OMICS’ such as epigenomics and lipidomics. Studying different cellular compartments allows a broader understanding of cell dynamics. Plant apoplast, the cellular compartment external to the plasma membrane including the cell wall, is particularly demanding to analyze. Despite our knowledge on apoplast involvement on several processes from cell growth to stress responses, its dynamics is still poorly known due to the lack of efficient extraction processes adequate to each plant system.Analyzing woody plants such as grapevine raises even more challenges. Grapevine is among the most important fruit crops worldwide and awider characterization of its apoplast is essential for a deeper understanding of its physiology and cellular mechanisms. Here, we describe, for the first time, a vacuum-infiltrationcentrifugationmethod that allows a simultaneous extraction of grapevine apoplastic proteins and metabolites from leaves on a single sample, compatible with high-throughput mass spectrometry analyses. The extracted apoplast from two grapevine cultivars, Vitis vinifera cv ‘Trincadeira’ and ‘Regent’, was directly used for proteomics and metabolomics analysis. The proteome was analyzed by nanoLC-MS/MS and more than 700 common proteinswere identified, with highly diverse biological functions. The metabolome profile through FT-ICR-MS allowed the identification of 514 unique putative compounds revealing a broad spectrum of molecular classesinfo:eu-repo/semantics/publishedVersio