Assembling genomes using short-read sequencing technology

Short-read sequencing technology can bring gigabase genome assemblies in under a million dollars

Edge effects in graphene nanostructures: II. Semiclassical theory of spectral fluctuations and quantum transport

We investigate the effect of different edge types on the statistical properties of both the energy spectrum of closed graphene billiards and the conductance of open graphene cavities in the semiclassical limit. To this end, we use the semiclassical Green's function for ballistic graphene flakes that we have derived in Reference 1. First we study the spectral two point correlation function, or more precisely its Fourier transform the spectral form factor, starting from the graphene version of Gutzwiller's trace formula for the oscillating part of the density of states. We calculate the two leading order contributions to the spectral form factor, paying particular attention to the influence of the edge characteristics of the system. Then we consider transport properties of open graphene cavities. We derive generic analytical expressions for the classical conductance, the weak localization correction, the size of the universal conductance fluctuations and the shot noise power of a ballistic graphene cavity. Again we focus on the effects of the edge structure. For both, the conductance and the spectral form factor, we find that edge induced pseudospin interference affects the results significantly. In particular intervalley coupling mediated through scattering from armchair edges is the key mechanism that governs the coherent quantum interference effects in ballistic graphene cavities

Symmetry Classes in Graphene Quantum Dots: Universal Spectral Statistics, Weak Localization, and Conductance Fluctuations

We study the symmetry classes of graphene quantum dots, both open and closed, through the conductance and energy level statistics. For abrupt termination of the lattice, these properties are well described by the standard orthogonal and unitary ensembles. However, for smooth mass confinement, special time-reversal symmetries associated with the sublattice and valley degrees of freedom are critical: they lead to block diagonal Hamiltonians and scattering matrices with blocks belonging to the unitary symmetry class even at zero magnetic field. While the effect of this structure is clearly seen in the conductance of open dots, it is suppressed in the spectral statistics of closed dots, because the intervalley scattering time is shorter than the time required to resolve a level spacing in the closed systems but longer than the escape time of the open systems.Comment: 4 pages, 4 figures, RevTex, submitted to Phys. Rev. Let

Effect of oxygen supply on metabolism of immobilized and suspended Escherichia coli

The effect of reduced oxygen supply on the production of a recombinant protein (plasmid-encoded β-galactosidase) was investigated in Escherichia coli. A novel modified bubble tank reactor was used to provide a direct comparison between immobilized and suspended cells in identical environments except for the immobilization matrix. Decreased oxygen supply led to increased β-galactosidase synthesis by both immobilized and suspended cells. Immobilized cells produced similar amounts of β-galactosidase as the suspended cells. Lactose consumption and acetate production, on a per cell basis, were significantly higher in immobilized cells, suggesting that immobilized cells utilized fermentative metabolism. However, a transport analysis of the immobilized cell system showed that immobilized cells were not subject to either external or internal mass transfer gradients.The effect of reduced oxygen supply on the production of a recombinant protein (plasmid-encoded β-galactosidase) was investigated in Escherichia coli. A novel modified bubble tank reactor was used to provide a direct comparison between immobilized and suspended cells in identical environments except for the immobilization matrix. Decreased oxygen supply led to increased β-galactosidase synthesis by both immobilized and suspended cells. Immobilized cells produced similar amounts of β-galactosidase as the suspended cells. Lactose consumption and acetate production, on a per cell basis, were significantly higher in immobilized cells, suggesting that immobilized cells utilized fermentative metabolism. However, a transport analysis of the immobilized cell system showed that immobilized cells were not subject to either external or internal mass transfer gradients

Semiclassical approach to the ac-conductance of chaotic cavities

We address frequency-dependent quantum transport through mesoscopic conductors in the semiclassical limit. By generalizing the trajectory-based semiclassical theory of dc quantum transport to the ac case, we derive the average screened conductance as well as ac weak-localization corrections for chaotic conductors. Thereby we confirm respective random matrix results and generalize them by accounting for Ehrenfest time effects. We consider the case of a cavity connected through many leads to a macroscopic circuit which contains ac-sources. In addition to the reservoir the cavity itself is capacitively coupled to a gate. By incorporating tunnel barriers between cavity and leads we obtain results for arbitrary tunnel rates. Finally, based on our findings we investigate the effect of dephasing on the charge relaxation resistance of a mesoscopic capacitor in the linear low-frequency regime

Density of states in d-wave superconductors disordered by extended impurities

The low-energy quasiparticle states of a disordered d-wave superconductor are investigated theoretically. A class of such states, formed via tunneling between the Andreev bound states that are localized around extended impurities (and result from scattering between pair-potential lobes that differ in sign) is identified. Its (divergent) contribution to the total density of states is determined by taking advantage of connections with certain one-dimensional random tight-binding models. The states under discussion should be distinguished from those associated with nodes in the pair potential.Comment: 5 pages, 1 figur

Probing d-wave pairing correlations in the pseudogap regime of the cuprate superconductors via low-energy states near impurities

The issue of probing the pseudogap regime of the cuprate superconductors, specifically with regard to the existence and nature of superconducting pairing correlations of d-wave symmetry, is explored theoretically. It is shown that if the d-wave correlations believed to describe the superconducting state persist into the pseudogap regime, but with pair-potential phase-fluctuations that destroy their long-range nature, then the low-energy quasiparticle states observed near extended impurities in the truly superconducting state should also persist as resonances in the pseudogap regime. The scattering of quasiparticles by these phase-fluctuations broadens what was (in the superconducting state) a sharp peak in the single-particle spectral function at low energy, as we demonstrate within the context of a simple model. This peak and its broadening is, in principle, accessible via scanning tunneling spectroscopy near extended impurities in the pseudogap regime. If so, such experiments would provide a probe of the extent to which d-wave superconducting correlations persist upon entering the pseudogap regime, thus providing a stringent diagnostic of the phase-fluctuation scenario.Comment: 8 pages, 2 figure

Lower vitamin D is associated with metabolic syndrome and insulin resistance in systemic lupus: data from an international inception cohort

OBJECTIVES: Vitamin D (25(OH)D) deficiency and metabolic syndrome (MetS) may both contribute to increased cardiovascular risk in systemic lupus erythematosus (SLE). We aimed to examine the association of demographic factors, SLE phenotype, therapy and vitamin D levels with MetS and insulin resistance. METHODS: The Systemic Lupus International Collaborating Clinics (SLICC) enrolled patients recently diagnosed with SLE (<15 months) from 33 centres across 11 countries from 2000. Clinical, laboratory and therapeutic data were collected. Vitamin D level was defined according to tertiles based on distribution across this cohort, which were set at T1 (10-36 nmol/l), T2 (37-60 nmol/l) and T3 (61-174 nmol/l). MetS was defined according to the 2009 consensus statement from the International Diabetes Federation. Insulin resistance was determined using the HOMA-IR model. Linear and logistic regressions were used to assess the association of variables with vitamin D levels. RESULTS: Of the 1847 patients, 1163 (63%) had vitamin D measured and 398 (34.2%) subjects were in the lowest 25(OH)D tertile. MetS was present in 286 of 860 (33%) patients whose status could be determined. Patients with lower 25(OH)D were more likely to have MetS and higher HOMA-IR. The MetS components, hypertension, hypertriglyceridemia and decreased HDL were all significantly associated with lower 25(OH)D. Increased average glucocorticoid exposure was associated with higher insulin resistance. CONCLUSIONS: MetS and insulin resistance are associated with lower vitamin D in patients with SLE. Further studies could determine whether vitamin D repletion confers better control of these cardiovascular risk factors and improve long-term outcomes in SLE

The views and experiences of fathers regarding their young child's intellectual and developmental disability diagnosis: Findings from a qualitative study

AIMS AND OBJECTIVES: To report the views and experiences of fathers following their child's diagnosis of an intellectual and developmental disability (IDD). BACKGROUND: There is a growing interest in understanding the experiences of fathers of children with IDD given the transformation of the structural change of fathers' roles within the family and wider society. DESIGN: A qualitative design was used to elicit the view and experiences of fathers. METHODS: A total of ten Irish fathers participated in face-to-face interviews. The data were thematically analysed. The COREQ guidelines for reporting qualitative studies were used in the development of this paper. RESULTS: The key themes that emerged were (a) the confirmation of the child's diagnosis (b) the impact of the diagnosis and (c) father's motivation to participate in disability research. CONCLUSIONS: This study informs and develops a further understanding of the international evidence base of fathers receiving a confirmation of a child's diagnosis of an intellectual and developmental disability, the impact of the diagnosis on fathers and their motivation to share their stories to add to the disability research. Health and social care practitioners have important contributions to make in meeting the needs of fathers. There are specific areas to consider in terms of practice, education and research that require further attention and development to ensure fathers' distinct needs regarding their child's diagnosis of IDD are known and responded to effectively. RELEVANCE TO CLINICAL PRACTICE: This study highlights that when the child's disability is confirmed, fathers experience a diverse range of mixed emotions. Health and social care practitioners including nurses need to be aware of the impact of the diagnosis upon fathers. There is scope to develop the knowledge, skills and confidence of health and social care practitioners regarding the experiences of fathers and how they can further support fathers and their families during the critical time of a disability disclosure

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis