A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals

Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.

The extrusion of continuous lengths of YBa2Cu3O7-x wire using hydroxypropyl methylcellulose

Wires of YBa2Cu3O7-x were fabricated by extrusion using a hydroxypropyl methylcellulose (HPMC) binder. As little as 2 wt.% binder was added to an oxide prepared by a novel co-precipitation process, to produce a plastic mass which readily gave continuous extrusion of long lengths of wire in a reproducible fashion. Critical temperatures of 92K were obtained for wires given optimum high-temperature heat treatments. Critical current densities greater than 1000 A cm-1 were measured at 77.3K using heat treatments at around 910°C for 10h. These transport critical current densities, measured on centimeter-long wires, were obtained with microstructures showing a relatively dense and uniform distribution of randomly oriented, small YBa2Cu3O7-x grains. © 1993.

Engine performance characteristics for biodiesels of different degrees of saturation and carbon chain lengths

This experimental study examines the effect on performance and emission outputs of a compression ignition engine operating on biodiesels of varying carbon chain length and the degree of unsaturation. A well-instrumented, heavy-duty, multi-cylinder, common-rail, turbo-charged diesel engine was used to ensure that the results contribute in a realistic way to the ongoing debate about the impact of biofuels. Comparative measurements are reported for engine performance as well as the emissions of NOx, particle number and size distribution, and the concentration of the reactive oxygen species (which provide a measure of the toxicity of emitted particles). It is shown that the biodiesels used in this study produce lower mean effective pressure, somewhat proportionally with their lower calorific values; however, the molecular structure has been shown to have little impact on the performance of the engine. The peak in-cylinder pressure is lower for the biodiesels that produce a smaller number of emitted particles, compared to fossil diesel, but the concentration of the reactive oxygen species is significantly higher because of oxygen in the fuels. The differences in the physicochemical properties amongst the biofuels and the fossil diesel significantly affect the engine combustion and emission characteristics. Saturated short chain length fatty acid methyl esters are found to enhance combustion efficiency, reduce NOx and particle number concentration, but results in high levels of fuel consumption.

The increased risks of death and extra lengths of hospital and ICU stay from hospital-acquired bloodstream infections : a case-control study

Objectives Hospital-acquired bloodstream infections are known to increase the risk of death and prolong hospital stay, but precise estimates of these two important outcomes from well-designed studies are rare, particularly for non-intensive care unit (ICU) patients. We aimed to calculate accurate estimates, which are vital for estimating the economic costs of hospital-acquired bloodstream infections.

Repeatability and comparison of peripheral eye lengths with two instruments

Purpose: To assess intrasessional and intersessional repeatability of two commercial partial coherence interferometry instruments for measuring peripheral eye lengths and to investigate the agreement between the two instruments. Methods: Central and peripheral eye lengths were determined with the IOLMaster (Carl-Zeiss Meditec AG, Jena, Germany) and the Lenstar (Haag Streit, Bern, Switzerland) in seven adults. Measurements were performed out to 35° and 30° from fixation for horizontal and vertical visual fields, respectively, in 5° intervals. An external fixation target at optical infinity was used. At least four measurements were taken at each location for each instrument, and measurements were taken at two sessions. Results: The mean intrasessional SDs for the IOLMaster along both the horizontal and vertical visual fields were 0.04 ± 0.04 mm; corresponding results for the Lenstar were 0.02 ± 0.02 mm along both fields. The intersessional SDs for the IOLMaster for the horizontal and vertical visual fields were ±0.11 and ±0.08 mm, respectively; corresponding limits for the Lenstar were ±0.05 and ±0.04 mm. The intrasessional and intersessional variability increased away from fixation. The mean differences between the two instruments were 0.01 ± 0.07 mm and 0.02 ± 0.07 mm in the horizontal and vertical visual fields, but the lengths with the Lenstar became greater than those with the IOLMaster as axial length increased (rate of approximately 0.016 mm/mm). Conclusions: Both the IOLMaster and the Lenstar demonstrated good intrasessional and intersessional repeatability for peripheral eye length measurements, with the Lenstar showing better repeatability. The Lenstar would be expected to give a slightly greater range of eye lengths than the IOLMaster across the visual field.

The long and short of it: branch lengths and the problem of placing the New Zealand short-tailed bat.

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous–Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

The Long and Short of It: Branch Lengths and the Problem of Placing the New Zealand Short-Tailed Bat, Mystacina

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

Genetics of path lengths in brain connectivity networks: HARDI-based maps in 457 adults

Brain connectivity analyses are increasingly popular for investigating organization. Many connectivity measures including path lengths are generally defined as the number of nodes traversed to connect a node in a graph to the others. Despite its name, path length is purely topological, and does not take into account the physical length of the connections. The distance of the trajectory may also be highly relevant, but is typically overlooked in connectivity analyses. Here we combined genotyping, anatomical MRI and HARDI to understand how our genes influence the cortical connections, using whole-brain tractography. We defined a new measure, based on Dijkstra's algorithm, to compute path lengths for tracts connecting pairs of cortical regions. We compiled these measures into matrices where elements represent the physical distance traveled along tracts. We then analyzed a large cohort of healthy twins and show that our path length measure is reliable, heritable, and influenced even in young adults by the Alzheimer's risk gene, CLU.

Change to costs and lengths of stay in the emergency department and the Brisbane protocol: An observational study

- Objective To compare health service cost and length of stay between a traditional and an accelerated diagnostic approach to assess acute coronary syndromes (ACS) among patients who presented to the emergency department (ED) of a large tertiary hospital in Australia. - Design, setting and participants This historically controlled study analysed data collected from two independent patient cohorts presenting to the ED with potential ACS. The first cohort of 938 patients was recruited in 2008–2010, and these patients were assessed using the traditional diagnostic approach detailed in the national guideline. The second cohort of 921 patients was recruited in 2011–2013 and was assessed with the accelerated diagnostic approach named the Brisbane protocol. The Brisbane protocol applied early serial troponin testing for patients at 0 and 2 h after presentation to ED, in comparison with 0 and 6 h testing in traditional assessment process. The Brisbane protocol also defined a low-risk group of patients in whom no objective testing was performed. A decision tree model was used to compare the expected cost and length of stay in hospital between two approaches. Probabilistic sensitivity analysis was used to account for model uncertainty. - Results Compared with the traditional diagnostic approach, the Brisbane protocol was associated with reduced expected cost of $1229 (95% CI −$1266 to $5122) and reduced expected length of stay of 26 h (95% CI −14 to 136 h). The Brisbane protocol allowed physicians to discharge a higher proportion of low-risk and intermediate-risk patients from ED within 4 h (72% vs 51%). Results from sensitivity analysis suggested the Brisbane protocol had a high chance of being cost-saving and time-saving. - Conclusions This study provides some evidence of cost savings from a decision to adopt the Brisbane protocol. Benefits would arise for the hospital and for patients and their families.

A Raman spectroscopic study of the uranyl mineral rutherfordine – revisited

The molecular structure of the uranyl mineral rutherfordine has been investigated by the measurement of the NIR and Raman spectra and complemented with infrared spectra including their interpretation. The spectra of the rutherfordine show the presence of both water and hydroxyl units in the structure as evidenced by IR bands at 3562 and 3465 cm-1 (OH) and 3343, 3185 and 2980 cm-1 (H2O). Raman spectra show the presence of four sharp bands at 3511, 3460, 3329 and 3151 cm-1. Corresponding molecular water bending vibrations were only observed in both Raman and infrared spectra of one of two studied rutherfordine samples. The second rutherfordine sample studied contained only hydroxyl ions in the equatorial uranyl plane and did not contain any molecular water. The infrared spectra of the (CO3)2- units in the antisymmetric stretching region show complexity with three sets of carbonate bands observed. This combined with the observation of multiple bands in the (CO3)2- bending region in both the Raman and IR spectra suggests that both monodentate and bidentate (CO3)2- units may be present in the structure. This cannot be exactly proved and inferred from the spectra; however, it is in accordance with the X-ray crystallographic studies. Complexity is also observed in the IR spectra of (UO2)2+ antisymmetric stretching region and is attributed to non-identical UO bonds. U-O bond lengths were calculated using wavenumbers of the 3 and 1 (UO2)2+ and compared with data from X-ray single crystal structure analysis of rutherfordine. Existence of solid solution having a general formula (UO2)(CO3)1-x(OH)2x.yH2O ( x, y  0) is supported in the crystal structure of rutherfordine samples studied.

Cyclic strain disrupts endothelial network formation on Matrigel

Most forms of tissue healing depend critically on revascularisation. In soft tissues and in vitro, mechanical stimuli have been shown to promote vessel-forming activity. However, in bone defects, increased interfragmentary motion impairs vascular regeneration. Because these effects seem contradictory, we aimed to determine whether a range of mechanical stimuli exists in which angiogenesis is favoured. A series of cyclic strain magnitudes were applied to a Matrigel-based “tube formation” assay and the total lengths of networks formed by human microvascular endothelial cells measured at 24 h. Network lengths were reduced at all strain levels, compared to unstretched controls. However, the levels of pro-angiogenic matrix metalloproteases-2 and -9 in the corresponding conditioned media were unchanged by strain, and vascular endothelial growth factor was uniformly elevated in stretched conditions. By repeating the assay with the addition of conditioned media from mesenchymal stem cells cultivated in similar conditions, paracrine stimuli were shown to increase network lengths, but not to alter the negative effect of cyclic stretching. Together, these results demonstrate that directly applied periodic strains can inhibit endothelial organisation in vitro, and suggest that this may be due to physical disruption rather than biochemical modulation. Most importantly, the results indicate that the straining of endothelial cells and their assembly into vascular-like structures must be studied simultaneously to adequately characterise the mechanical influence on vessel formation.

Cellular senescence and longevity of osteophyte-derived mesenchymal stem cells compared to patient-matched bone marrow stromal cells

This study aimed to determine the cellular aging of osteophyte-derived mesenchymal cells (oMSCs) in comparison to patient-matched bone marrow stromal cells (bMSCs). Extensive expansion of the cell cultures was performed and early and late passage cells (passages 4 and 9, respectively) were used to study signs of cellular aging, telomere length, telomerase activity, and cell-cycle-related gene expression. Our results showed that cellular aging was more prominent in bMSCs than in oMSCs, and that oMSCs had longer telomere length in late passages compared with bMSCs, although there was no significant difference in telomere lengths in the early passages in either cell type. Telomerase activity was detectable only in early passage oMSCs and not in bMSCs. In osteophyte tissues telomerase-positive cells were found to be located perivascularly and were Stro-1 positive. Fifteen cell-cycle regulator genes were investigated and only three genes (APC, CCND2, and BMP2) were differentially expressed between bMSC and oMSC. Our results indicate that oMSCs retain a level of telomerase activity in vitro, which may account for the relatively greater longevity of these cells, compared with bMSCs, by preventing replicative senescence. J. Cell. Biochem. 108: 839-850, 2009. (c) 2009 Wiley-Liss, Inc.

A fully Bayesian approach to inference for Coxian phase-type distributions with covariate dependent mean

Phase-type distributions represent the time to absorption for a finite state Markov chain in continuous time, generalising the exponential distribution and providing a flexible and useful modelling tool. We present a new reversible jump Markov chain Monte Carlo scheme for performing a fully Bayesian analysis of the popular Coxian subclass of phase-type models; the convenient Coxian representation involves fewer parameters than a more general phase-type model. The key novelty of our approach is that we model covariate dependence in the mean whilst using the Coxian phase-type model as a very general residual distribution. Such incorporation of covariates into the model has not previously been attempted in the Bayesian literature. A further novelty is that we also propose a reversible jump scheme for investigating structural changes to the model brought about by the introduction of Erlang phases. Our approach addresses more questions of inference than previous Bayesian treatments of this model and is automatic in nature. We analyse an example dataset comprising lengths of hospital stays of a sample of patients collected from two Australian hospitals to produce a model for a patient's expected length of stay which incorporates the effects of several covariates. This leads to interesting conclusions about what contributes to length of hospital stay with implications for hospital planning. We compare our results with an alternative classical analysis of these data.

Raman spectroscopic study of the uranyl mineral natrouranospinite (Na2,Ca)[(UO2)(AsO4)]2•5H2O

Raman spectra of natrouranospinite complemented with infrared spectra were studied and related to the structure of the mineral. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (AsO4)3- units and of water molecules. U-O bond lengths in uranyl and O-H…O hydrogen bond lengths were calculated from the Raman and infrared spectra.