Fourier domain mode locking laser sweeping based on optical parametric amplification

We present a Fourier domain mode locked (FDML) laser scanning from 1516 to 1550 nm and 1567 to 1597 nm using optical parametric amplifier (OPA) as the gain medium. The output power of -4.85 dBm with sweep rate of 39.6 kHz is achieved. © 2010 IEEE.published_or_final_versionThe 2010 Conference on Optical Fiber Communication (OFC), collocated National Fiber Optic Engineers Conference (OFC/NFOEC), San Diego, CA., 21-25 March 2010. In Proceedings of OFC/NFOEC, 2010, p. 1-

Acoustic Disturbances in Galaxy Clusters

Galaxy cluster cores are pervaded by hot gas which radiates at far too high a rate to maintain any semblance of a steady state; this is referred to as the cooling flow problem. Of the many heating mechanisms that have been proposed to balance radiative cooling, one of the most attractive is dissipation of acoustic waves generated by Active Galactic Nuclei (AGN). Fabian (2005) showed that if the waves are nearly adiabatic, wave damping due to heat conduction and viscosity must be well below standard Coulomb rates in order to allow the waves to propagate throughout the core. Because of the importance of this result, we have revisited wave dissipation under galaxy cluster conditions in a way that accounts for the self limiting nature of dissipation by electron thermal conduction, allows the electron and ion temperature perturbations in the waves to evolve separately, and estimates kinetic effects by comparing to a semi-collisionless theory. While these effects considerably enlarge the toolkit for analyzing observations of wavelike structures and developing a quantitative theory for wave heating, the drastic reduction of transport coefficients proposed in Fabian (2005) remains the most viable path to acoustic wave heating of galaxy cluster cores

Prime movers : mechanochemistry of mitotic kinesins

Mitotic spindles are self-organizing protein machines that harness teams of multiple force generators to drive chromosome segregation. Kinesins are key members of these force-generating teams. Different kinesins walk directionally along dynamic microtubules, anchor, crosslink, align and sort microtubules into polarized bundles, and influence microtubule dynamics by interacting with microtubule tips. The mechanochemical mechanisms of these kinesins are specialized to enable each type to make a specific contribution to spindle self-organization and chromosome segregation

Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm

Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation, and they usually assume that the two alleles in a heterozygous individual are sampled with equal probability. This is generally false for structural variants detected with paired ends or split reads. Therefore, the population genetics of structural variants cannot be studied, unless a painstaking and potentially biased genotyping is performed first. Results We present svgem, an expectation-maximization implementation to estimate allele and genotype frequencies, calculate genotype posterior probabilities, and test for Hardy-Weinberg equilibrium and for population differences, from the numbers of times the alleles are observed in each individual. Although applicable to single nucleotide variation, it aims at bi-allelic structural variation of any type, observed by either split reads or paired ends, with arbitrarily high allele sampling bias. We test svgem with simulated and real data from the 1000 Genomes Project. Conclusions svgem makes it possible to use low-coverage sequencing data to study the population distribution of structural variants without having to know their genotypes. Furthermore, this advance allows the combined analysis of structural and nucleotide variation within the same genotype-free statistical framework, thus preventing biases introduced by genotype imputation

Transcriptional activity and strain-specific history of mouse pseudogenes

Abstract: Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes

Recent Progress in Modeling the Macro- and Micro-Physics of Radio Jet Feedback in Galaxy Clusters

Peer reviewed: TrueFunder: Science and Technology Facilities CouncilFunder: Yushan Scholar Program of the Ministry of Education (MoE) of TaiwanRadio jets and the lobes they inflate are common in cool-core clusters and are known to play a critical role in regulating the heating and cooling of the intracluster medium (ICM). This is an inherently multi-scale problem, and much effort has been made to understand the processes governing the inflation of lobes and their impact on the cluster, as well as the impact of the environment on the jet–ICM interaction, on both macro- and microphysical scales. The developments of new numerical techniques and improving computational resources have seen simulations of jet feedback in galaxy clusters become ever more sophisticated. This ranges from modeling ICM plasma physics processes such as the effects of magnetic fields, cosmic rays, and viscosity to including jet feedback in cosmologically evolved cluster environments in which the ICM thermal and dynamic properties are shaped by large-scale structure formation. In this review, we discuss the progress made over the last ∼decade in capturing both the macro- and microphysical processes in numerical simulations, highlighting both the current state of the field, as well as the open questions and potential ways in which these questions can be addressed in the future.</jats:p

Powering of Hα Filaments by Cosmic Rays

Cluster cool cores possess networks of line-emitting filaments. These filaments are thought to originate via uplift of cold gas from cluster centers by buoyant active galactic nuclei (AGN) bubbles, or via local thermal instability in the hot intracluster medium (ICM). Therefore, the filaments are either the signatures of AGN feedback or feeding of supermassive black holes. Despite being characterized by very short cooling times, the filaments are significant H$\alpha$ emitters, which suggests that some process continuously powers these structures. Many cool cores host diffuse radio mini halos and AGN injecting radio plasma, suggesting that cosmic rays (CRs) and magnetic fields are present in the ICM. We argue that the excitation of Alfv\'en waves by CR streaming, and the replenishment of CR energy via accretion onto the filaments of high plasma-$\beta$ ICM characterized by low CR pressure support, can provide the adequate amount of heating to power and sustain the emission from these filaments. This mechanism does not require the CRs to penetrate the filaments even if the filaments are magnetically isolated from the ambient ICM and it may operate irrespectively of whether the filaments are dredged up from the center or form in situ in the ICM. This picture is qualitatively consistent with non-thermal line ratios seen in the cold filaments. Future X-ray observations of the iron line complex with XARM, Lynx, or Athena could help to test this model by providing constraints on the amount of CRs in the hot plasma that is cooling and accreting onto the filaments

Acoustic Disturbances in Galaxy Clusters

Galaxy cluster cores are pervaded by hot gas which radiates at far too high a rate to maintain any semblance of a steady state; this is referred to as the cooling flow problem. Of the many heating mechanisms that have been proposed to balance radiative cooling, one of the most attractive is dissipation of acoustic waves generated by Active Galactic Nuclei (AGN). Fabian (2005) showed that if the waves are nearly adiabatic, wave damping due to heat conduction and viscosity must be well below standard Coulomb rates in order to allow the waves to propagate throughout the core. Because of the importance of this result, we have revisited wave dissipation under galaxy cluster conditions in a way that accounts for the self limiting nature of dissipation by electron thermal conduction, allows the electron and ion temperature perturbations in the waves to evolve separately, and estimates kinetic effects by comparing to a semi-collisionless theory. While these effects considerably enlarge the toolkit for analyzing observations of wavelike structures and developing a quantitative theory for wave heating, the drastic reduction of transport coefficients proposed in Fabian (2005) remains the most viable path to acoustic wave heating of galaxy cluster cores

Powering of Hα Filaments by Cosmic Rays

Cluster cool cores possess networks of line-emitting filaments. These filaments are thought to originate via uplift of cold gas from cluster centers by buoyant active galactic nuclei (AGN) bubbles, or via local thermal instability in the hot intracluster medium (ICM). Therefore, the filaments are either the signatures of AGN feedback or feeding of supermassive black holes. Despite being characterized by very short cooling times, the filaments are significant Hα emitters, which suggests that some process continuously powers these structures. Many cool cores host diffuse radio mini halos and AGN injecting radio plasma, suggesting that cosmic rays (CRs) and magnetic fields are present in the ICM. We argue that the excitation of Alfv ́en waves by CR streaming, and the replenishment of CR energy via accretion onto the filaments of high plasma-β ICM characterized by low CR pressure support, can provide the adequate amount of heating to power and sustain the emission from these filaments. This mechanism does not require the CRs to penetrate the filaments even if the filaments are magnetically isolated from the ambient ICM and it may operate irrespectively of whether the filaments are dredged up from the center or form in situ in the ICM. This picture is qualitatively consistent with non-thermal line ratios seen in the cold filaments. Future X-ray observations of the iron line complex with XARM, Lynx, or Athena could help to test this model by providing constraints on the amount of CRs in the hot plasma that is cooling and accreting onto the filaments