SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/

Inelastic neutron scattering in random binary alloys : an augmented space approach

Combining the augmented space representation for phonons with a generalized version of Yonezawa-Matsubara diagrammatic technique, we have set up a formalism to seperate the coherent and incoherent part of the total intensity of thermal neutron scattering from disordered alloys. This is done exacly without taking any recourse to mean-field like approximation (as done previously). The formalism includes disorder in masses, force constants and scattering lengths. Implementation of the formalism to realistic situations is performed by an augmented space Block recursion which calculates entire Green matrix and self energy matrix which in turn is needed to evaluate the coherent and incoherent intensities. we apply the formalism to NiPd and NiPt alloys. Numerical results on coherent and incoherent scattering cross sections are presented along the highest symmetry directions. Finally the incoherent intensities are compared with the CPA and also with experiments.Comment: 18 pages, 13 figure

The influence of natural ageing on the artificial ageing response of Al-Si-Cu-Mg casting alloys

The T6 heat treatment is commonly used to increase the strength of gravity cast Al-Si components containingCu and/or Mg. The artificial ageing response is known to be affected by the thermal history, such as solutiontreatment, quench rate, natural ageing and heating rate to the artificial ageing temperature. The influence ofnatural ageing on the artificial ageing response was investigated for three alloys; Al-8Si-0.4Mg, Al-7Si-3Cu andAl-8Si-3Cu-0.4Mg. Natural ageing had a strong influence on the ageing response of the Al-Si-Mg alloy in theunderaged condition and the strength increase was strongly reduced. Despite this, the time to peak yieldstrength as well as its magnitude were not strongly affected by natural ageing. No clear influence of naturalageing was observed for the Al-Si-Cu alloy. For the Al-Si-Cu-Mg alloy the ageing response seems to depend onthe natural ageing time. Natural ageing of 3 weeks shifted the peak yield strength to shorter ageing times andits magnitude was decreased a little compared to direct ageing after quench. Natural ageing of 1 day gave theleast beneficial properties after artificial ageing

Berkeley PHOG: PhyloFacts orthology group prediction web server

Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein–protein interaction and other bioinformatics tasks. We present here the PHOG web server employing a novel algorithm to identify orthologs based on phylogenetic analysis. Results on a benchmark dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and allows users to target different taxonomic distances and precision levels through the use of tree-distance thresholds. For instance, OrthoMCL-DB achieved 76% recall and 66% precision on this dataset; at a slightly higher precision (68%) PHOG achieves 10% higher recall (86%). InParanoid achieved 87% recall at 24% precision on this dataset, while a PHOG variant designed for high recall achieves 88% recall at 61% precision, increasing precision by 37% over InParanoid. PHOG is based on pre-computed trees in the PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species. Predicted orthologs are linked to GO annotations, pathway information and biological literature. The PHOG web server is available at http://phylofacts.berkeley.edu/orthologs/

Anomalous thermal expansion in 1D transition-metal cyanides: what makes the novel trimetallic cyanide Cu1/3Ag1/3Au1/3CN behave differently?

The structural dynamics of a quasi-one-dimensional (1D) mixed-metal cyanide, Cu1/3Ag1/3Au1/3CN, with intriguing thermal properties is explored. All the current known related compounds with straight-chain structures, such as group 11 cyanides CuCN, AgCN, AuCN and bimetallic cyanides MxM’1-xCN (M, M’ = Cu, Ag, Au), exhibit 1D negative thermal expansion (NTE) along the chains and positive thermal expansion (PTE) perpendicular to them. Cu1/3Ag1/3Au1/3CN exhibits similar PTE perpendicular to the chains, however PTE, rather than NTE, is also observed along the chains. In order to understand the origin of this unexpected behavior, inelastic neutron scattering (INS) measurements were carried out, underpinned by lattice-dynamical density-functional-theory (DFT) calculations. Synchrotron-based pair-distribution-function (PDF) analysis and 13C solid-state nuclear-magnetic-resonance (SSNMR) measurements were also performed to build an input structural model for the lattice dynamical study. The results indicate that transverse motions of the metal ions are responsible for the PTE perpendicular to the chains, as is the case for the related group 11 cyanides. However NTE along the chain due to the tension effect of these transverse motions is not observed. As there are different metal-to-cyanide bond lengths in Cu1/3Ag1/3Au1/3CN, the metals in neighboring chains cannot all be truly co-planar in a straight-chain model. For this system, DFT-based phonon calculations predict small PTE along the chain due to low-energy chain-slipping modes induced by a bond-rotation effect on the weak metallophilic bonds. However the observed PTE is greater than that predicted with the straight-chain model. Small bends in the chain to accommodate truly co-planar metals provide an alternative explanation for thermal behavior. These would mitigate the tension effect induced by the transverse motions of the metals and, as temperature increases and the chains move further apart, a straightening could occur resulting in the observed PTE. This hypothesis is further supported by unusual evolution in the phonon spectra, which suggest small changes in local symmetry with temperature

What is known about the health and living conditions of the indigenous people of northern Scandinavia, the Sami?

The Sami are the indigenous ethnic population of northern Scandinavia. Their health condition is poorly known, although the knowledge has improved over the last decade.The aim was to review the current information on mortality, diseases, and risk factor exposure in the Swedish Sami population.Health-related research on Sami cohorts published in scientific journals and anthologies was used to compare the health condition among the Sami and the majority non-Sami population. When relevant, data from the Sami populations in Swedish were compared with corresponding data from Norwegian and Finnish Sami populations.Life expectancy and mortality patterns of the Sami are similar to those of the majority population. Small differences in incidences of cancer and cardiovascular diseases have been reported. The traditional Sami lifestyle seems to contain elements that reduce the risk to develop cancer and cardiovascular diseases, e.g. physical activity, diet rich in antioxidants and unsaturated fatty acids, and a strong cultural identity. Reindeer herding is an important cultural activity among the Sami and is associated with high risks for accidents. Pain in the lower back, neck, shoulders, elbows, and hands are frequent among both men and women in reindeer-herding families. For men, these symptoms are related to high exposure to terrain vehicles, particularly snowmobile, whereas for women psychosocial risk factors seem to more important, e.g. poor social support, high effort, low reward, and high economical responsibilities.Although the health condition of the Sami population appears to be rather similar to that of the general Swedish population, a number of specific health problems have been identified, especially among the reindeer-herding Sami. Most of these problems have their origin in marginalization and poor knowledge of the reindeer husbandry and the Sami culture in the majority population. It is suggested that the most sustainable measure to improve the health among the reindeer-herding Sami would be to improve the conditions of the reindeer husbandry and the Sami culture

Familial liability for eating disorders and suicide attempts : evidence from a population registry in Sweden

Importance: Suicide attempts are common in individuals with eating disorders. More precise understanding of the mechanisms underlying their co-occurrence is needed. Objective: To examine the association between eating disorders and suicide attempts and whether familial risk factors contribute to the association. Design: A cohort design following a Swedish birth cohort 1979-2001 from age 6 until 31/12/2009. Setting: Information was acquired from Swedish national registers. Participants: Individuals born 1979-2001 and living in Sweden before age 6 (N= 2,268,786) were eligible for the study. Each individual was linked to his/her biological full-siblings, maternal half-siblings, paternal half-siblings, full-cousins, and half-cousins. Eating disorders were captured by three variables: any eating disorder, anorexia nervosa (AN), and bulimia nervosa (BN), identified by any lifetime diagnoses recorded in the registers. Suicide attempts were defined as any suicide attempts, including death by suicide, recorded in the registers. We examined the association between eating disorders and death by suicide separately, but were underpowered to explore familial liability for this association. Results: Individuals with any eating disorder had increased risk of suicide attempts (OR=5.28, 95%CI [5.04, 5.54]) and death by suicide (OR=5.39, 95%CI [4.00, 7.25]). The risks attenuated but remained significant after adjusting for comorbid major depressive disorder, anxiety disorders, and substance use disorder. Similar results were found for AN and BN, except that adjusted OR of death by suicide in BN became insignificant, possibly due to insufficient power. Individuals (index) who had a full-sibling with any eating disorder had increased risk of suicide attempts (OR=1.41, 95%CI [1.29, 1.53]). The risk attenuated for any eating disorder in more distant relatives (maternal half-siblings, OR=1.10, 95%CI [0.90, 1.34]; paternal half-siblings, OR=1.21, 95%CI [0.98, 1.49]; full-cousins, OR=1.11, 95%CI [1.06, 1.18]; half-cousins, OR=0.90, 95%CI [0.78, 1.03]). This familial pattern remained stable after adjusting for the index individuals’ eating disorders. Similar patterns were found for AN and BN. Conclusions and Relevance: Our results suggest increased risk of suicide attempts in individuals with lifetime eating disorders and their relatives. The pattern of familial co-aggregation suggests familial liability for the association between eating disorders and suicide. Psychiatric comorbidities partially explain this association, suggesting particularly high-risk presentations.China Scholarship CouncilAmerican Foundation for Suicide PreventionSwedish Initiative for Research on Microdata in the Social and Medical Sciences framework, 340-2013-5867Swedish Research Council, 538-2013Global Foundation for Eating DisordersSwedish Research Council, 538-2013-8864Manuscrip

On the precipitation hardening of selective laser melted AlSi10Mg

Precipitation hardening of selective laser melted AlSi10Mg was investigated in terms of solution heat treatment and aging duration. The influence on the microstructure and hardness was established, as was the effect on the size and density of Si particles. Although the hardness changes according to the treatment duration, the maximum hardening effect falls short of the hardness of the as-built parts with their characteristic fine microstructure. This is due to the difference in strengthening mechanisms

Quasiparticle Effective Mass for the Two- and Three-Dimensional Electron Gas

We calculate the quasiparticle effective mass for the electron gas in two and three dimensions in the metallic region. We employ the single particle scattering potential coming from the Sj\"{o}lander-Stott theory and enforce the Friedel sum rule by adjusting the effective electron mass in a scattering calculation. In 3D our effective mass is a monotonically decreasing function of $r_s$ throughout the whole metallic domain, as implied by the most recent numerical results. In 2D we obtain reasonable agreement with the experimental data, as well as with other calculations based on the Fermi liquid theory. We also present results of a variety of different treatments for the effective mass in 2D and 3D.Comment: 12 pages, 2 figure

The SCottish Alcoholic Liver disease Evaluation: a population-level matched cohort study of hospital-based costs, 1991-2011

Studies assessing the costs of alcoholic liver disease are lacking. We aimed to calculate the costs of hospitalisations before and after diagnosis compared to population controls matched by age, sex and socio-economic deprivation. We aimed to use population level data to identify a cohort of individuals hospitalised for the first time with alcoholic liver disease in Scotland between 1991 and 2011.Incident cases were classified by disease severity, sex, age group, socio-economic deprivation and year of index admission. 5 matched controls for every incident case were identified from the Scottish population level primary care database. Hospital costs were calculated for both cases and controls using length of stay from morbidity records and hospital-specific daily rates by specialty. Remaining lifetime costs were estimated using parametric survival models and predicted annual costs. 35,208 incident alcoholic liver disease hospitalisations were identified. Mean annual hospital costs for cases were 2.3 times that of controls pre diagnosis (£804 higher) and 10.2 times (£12,774 higher) post diagnosis. Mean incident admission cost was £6,663. Remaining lifetime cost for a male, 50-59 years old, living in the most deprived area diagnosed with acoholic liver disease was estimated to be £65,999 higher than the matched controls (£12,474 for 7.43 years remaining life compared to £1,224 for 21.8 years). In Scotland, alcoholic liver disease diagnosis is associated with significant increases in admissions to hospital both before and after diagnosis. Our results provide robust population level estimates of costs of alcoholic liver disease for the purposes of health-care delivery, planning and future cost-effectiveness analyses