32,587 research outputs found

    Quantum Bochkov-Kuzovlev Work Fluctuation Theorems

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    The quantum version of the Bochkov-Kuzovlev identity is derived on the basis of the appropriate definition of work as the difference of the measured internal energies of a quantum system at the beginning and at the end of an external action on the system given by a prescribed protocol. According to the spirit of the original Bochkov-Kuzovlev approach, we adopt the "exclusive" viewpoint, meaning that the coupling to the external work-source is {\it not} counted as part of the internal energy. The corresponding canonical and microcanonical quantum fluctuation theorems are derived as well, and are compared to the respective theorems obtained within the "inclusive" approach. The relations between the quantum inclusive-work ww, the exclusive-work w0w_0 and the dissipated-work wdisw_{dis}, are discussed and clarified. We show by an explicit example that w0w_0 and wdisw_{dis} are distinct stochastic quantities obeying different statistics.Comment: 16 page

    Anomalous electrical and frictionless flow conductance in complex networks

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    We study transport properties such as electrical and frictionless flow conductance on scale-free and Erdos-Renyi networks. We consider the conductance G between two arbitrarily chosen nodes where each link has the same unit resistance. Our theoretical analysis for scale-free networks predicts a broad range of values of G, with a power-law tail distribution \Phi_{SF}(G) \sim G^{g_G}, where g_G = 2\lambda - 1, where \lambda is the decay exponent for the scale-free network degree distribution. We confirm our predictions by simulations of scale-free networks solving the Kirchhoff equations for the conductance between a pair of nodes. The power-law tail in \Phi_{SF}(G) leads to large values of G, thereby significantly improving the transport in scale-free networks, compared to Erdos-Renyi networks where the tail of the conductivity distribution decays exponentially. Based on a simple physical 'transport backbone' picture we suggest that the conductances of scale-free and Erdos-Renyi networks can be approximated by ck_Ak_B/(k_A+k_B) for any pair of nodes A and B with degrees k_A and k_B. Thus, a single quantity c, which depends on the average degree of the network, characterizes transport on both scale-free and Erdos-Renyi networks. We determine that c tends to 1 for increasing , and it is larger for scale-free networks. We compare the electrical results with a model for frictionless transport, where conductance is defined as the number of link-independent paths between A and B, and find that a similar picture holds. The effects of distance on the value of conductance are considered for both models, and some differences emerge. Finally, we use a recent data set for the AS (autonomous system) level of the Internet and confirm that our results are valid in this real-world example.Comment: 8 pages, 11 figure

    Transport of multiple users in complex networks

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    We study the transport properties of model networks such as scale-free and Erd\H{o}s-R\'{e}nyi networks as well as a real network. We consider the conductance GG between two arbitrarily chosen nodes where each link has the same unit resistance. Our theoretical analysis for scale-free networks predicts a broad range of values of GG, with a power-law tail distribution ő¶SF(G)‚ąľG‚ąígG\Phi_{\rm SF}(G)\sim G^{-g_G}, where gG=2őĽ‚ąí1g_G=2\lambda -1, and őĽ\lambda is the decay exponent for the scale-free network degree distribution. We confirm our predictions by large scale simulations. The power-law tail in ő¶SF(G)\Phi_{\rm SF}(G) leads to large values of GG, thereby significantly improving the transport in scale-free networks, compared to Erd\H{o}s-R\'{e}nyi networks where the tail of the conductivity distribution decays exponentially. We develop a simple physical picture of the transport to account for the results. We study another model for transport, the \emph{max-flow} model, where conductance is defined as the number of link-independent paths between the two nodes, and find that a similar picture holds. The effects of distance on the value of conductance are considered for both models, and some differences emerge. We then extend our study to the case of multiple sources, where the transport is define between two \emph{groups} of nodes. We find a fundamental difference between the two forms of flow when considering the quality of the transport with respect to the number of sources, and find an optimal number of sources, or users, for the max-flow case. A qualitative (and partially quantitative) explanation is also given

    Severe congenital microcephaly with AP4M1 mutation, a case report

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    Background: Autosomal recessive defects of either the B1, E1, M1 or S1 subunit of the Adaptor Protein complex-4 (AP4) are characterized by developmental delay, severe intellectual disability, spasticity, and occasionally mild to moderate microcephaly of essentially postnatal onset. Case presentation: We report on a patient with severe microcephaly of prenatal onset, and progressive spasticity, developmental delay, and severe intellectual deficiency. Exome sequencing showed a homozygous mutation in AP4M1, causing the replacement of an arginine by a stop codon at position 338 of the protein (p.Arg338X). The premature stop codon truncates the Mu homology domain of AP4M1, with predicted loss of function. Exome analysis also showed heterozygous variants in three genes, ATR, MCPH1 and BLM, which are known causes of autosomal recessive primary microcephaly. Conclusions: Our findings expand the AP4M1 phenotype to severe microcephaly of prenatal onset, and more generally suggest that the AP4 defect might share mechanisms of prenatal neuronal depletion with other genetic defects of brain development causing congenital, primary microcephaly

    Tuning and optimization for a variety of many-core architectures without changing a single line of implementation code using the Alpaka library

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    We present an analysis on optimizing performance of a single C++11 source code using the Alpaka hardware abstraction library. For this we use the general matrix multiplication (GEMM) algorithm in order to show that compilers can optimize Alpaka code effectively when tuning key parameters of the algorithm. We do not intend to rival existing, highly optimized DGEMM versions, but merely choose this example to prove that Alpaka allows for platform-specific tuning with a single source code. In addition we analyze the optimization potential available with vendor-specific compilers when confronted with the heavily templated abstractions of Alpaka. We specifically test the code for bleeding edge architectures such as Nvidia's Tesla P100, Intel's Knights Landing (KNL) and Haswell architecture as well as IBM's Power8 system. On some of these we are able to reach almost 50\% of the peak floating point operation performance using the aforementioned means. When adding compiler-specific #pragmas we are able to reach 5 TFLOPS/s on a P100 and over 1 TFLOPS/s on a KNL system.Comment: Accepted paper for the P\^{}3MA workshop at the ISC 2017 in Frankfur

    Associations of clock genes polymorphisms with soft tissue sarcoma susceptibility and prognosis

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    BACKGROUND: Dysfunction of the circadian clock and polymorphisms of some circadian genes have been linked to cancer development and progression. We investigated the relationship between circadian genes germline variation and susceptibility or prognosis of patients with soft tissue sarcoma. PATIENTS AND METHODS: We considered the 14 single nucleotide polymorphisms (SNPs) of 6 core circadian genes that have a minor allele frequency >\u20095% and that are known to be associated with cancer risk or prognosis. Genotyping was performed by q-PCR. Peripheral blood and clinic-pathological data were available for 162 patients with liposarcoma or leiomyosarcoma and 610 healthy donors. Associations between the selected clock genes polymorphisms and sarcoma susceptibility or prognosis were tested assuming 3 models of inheritance: additive, recessive and dominant. Subgroup analysis based on sarcoma histotype was performed under the additive genetic model. Multivariate logistic regression and multivariate Cox proportional hazard regression analyses were utilized to assess the association between SNPs with patient susceptibility and survival, respectively. Pathway variation analysis was conducted employing the Adaptive Rank Truncated Product method. RESULTS: Six out of the 14 analyzed SNPs were statistically significantly associated with susceptibility or prognosis of soft tissue sarcoma (P <\u20090.05). The present analysis suggested that carriers of the minor allele of the CLOCK polymorphism rs1801260 (C) or of PER2 rs934945 (T) had a reduced predisposition to sarcoma (26% and 35% respectively with the additive model) and liposarcoma (33% and 41% respectively). The minor allele (A) of NPAS2 rs895520 was associated with an increased predisposition to sarcoma of 33% and leiomyosarcoma of 44%. RORA rs339972 C allele was associated with a decreased predisposition to develop sarcoma assuming an additive model (29%) and leiomyosarcoma (36%). PER1 rs3027178 was associated with a reduced predisposition only in liposarcoma subgroup (32%). rs7602358 located upstream PER2 was significantly associated with liposarcoma survival (HR: 1.98; 95% CI 1.02-3.85; P\u2009=\u20090.04). Germline genetic variation in the circadian pathway was associated with the risk of developing soft tissue sarcoma (P\u2009=\u20090.035). CONCLUSIONS: Genetic variation of circadian genes appears to play a role in the determinism of patient susceptibility and prognosis. These findings prompt further studies to fully dissect the molecular mechanisms

    Evidence that the 36kb plasmid of Brachyspira hyodysenteriae contributes to virulence

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    Swine dysentery (SD) results from infection of the porcine large intestine with the anaerobic intestinal spirochaete Brachyspira hyodysenteriae. Recently the genome of virulent Australian B. hyodysenteriae strain WA1 was sequenced, and a 36. kilobase (kb) circular plasmid was identified. The plasmid contained 31 genes including six rfb genes that were predicted to be involved with rhamnose biosynthesis, and others associated with glycosylation. In the current study a set of PCRs was developed to amplify portions of nine of the plasmid genes. When used with DNA extracted from virulent strain B204, PCR products were generated, but no products were generated with DNA from avirulent strain A1. Analysis of the DNA using pulsed field gel electrophoresis (PFGE) identified a plasmid band in strains WA1 and B204, but not in strain A1. These results demonstrate that strain A1 does not contain the plasmid, and suggests that lack of the plasmid may explain why this strain is avirulent. To determine how commonly strains lacking plasmids occur, DNA was extracted from 264 Australian field isolates of B. hyodysenteriae and subjected to PCRs for three of the plasmid genes. Only one isolate (WA400) that lacked the plasmid was identified, and this absence was confirmed by PFGE analysis of DNA from the isolate and further PCR testing. To assess its virulence, 24 pigs were experimentally challenged with cultures of WA400, and 12 control pigs were challenged with virulent strain WA1 under the same conditions. Significantly fewer (P= 0.03) of the pigs challenged with WA400 became colonised and developed SD (13/24; 54%) compared to the pigs infected with WA1 (11/12; 92%). Gross lesions in the pigs colonised with WA400 tended to be less extensive than those in pigs colonised with WA1, although there were no obvious differences at the microscopic level. The results support the likelihood that plasmid-encoded genes of B. hyodysenteriae are involved in colonisation and/or disease expression

    Multi-locus analysis of genomic time series data from experimental evolution.

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    Genomic time series data generated by evolve-and-resequence (E&amp;R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. We first use simulated data to demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&amp;R experiments with requisite power. We also explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate. Then, we apply our method to analyze genome-wide data from a real E&amp;R experiment designed to study the adaptation of D. melanogaster to a new laboratory environment with alternating cold and hot temperatures
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