Particle Learning and Smoothing

Particle learning (PL) provides state filtering, sequential parameter learning and smoothing in a general class of state space models. Our approach extends existing particle methods by incorporating the estimation of static parameters via a fully-adapted filter that utilizes conditional sufficient statistics for parameters and/or states as particles. State smoothing in the presence of parameter uncertainty is also solved as a by-product of PL. In a number of examples, we show that PL outperforms existing particle filtering alternatives and proves to be a competitor to MCMC.Comment: Published in at http://dx.doi.org/10.1214/10-STS325 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Bis(2-phenyl-4,6-di-2-pyridyl-1,3,5-triazine-κ3 N 4,N 5,N 6)ruthenium(II) bis(hexa­fluoridophosphate)

The asymmetric unit of the title compound, [Ru(C19H13N5)2](PF6)2, consists of an RuII complex cation and two hexa­fluoridophosphate anions. The RuII atom is coordinated by three N atoms from the two outer pyridine and the central triazine rings of each of two tridentate ligands in a distorted octa­hedral environment. The ligands are approximately orthogonal to one another, with a dihedral angle of 88.34 (2)° between planes through the three six-membered rings of the two ligands. The pendant phenyl substituents are almost coplanar with the triazine rings to which they are bound, with dihedral angles of 5.41 (9) and 14.90 (10)°. This is reflected in the previously reported photophysical results with an increased lifetime of the triplet metal to ligand charge transfer (3MLCT) excited state [Fang, Taylor, Hanan, Loiseau, Passalacqua, Campagna, Nierengarten & Van Dorsselaer (2002). J. Am. Chem. Soc. 124, 7912–7913]

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

Fluctuations of radiation from a chaotic laser below threshold

Radiation from a chaotic cavity filled with gain medium is considered. A set of coupled equations describing the photon density and the population of gain medium is proposed and solved. The spectral distribution and fluctuations of the radiation are found. The full noise is a result of a competition between positive correlations of photons with equal frequencies (due to stimulated emission and chaotic scattering) which increase fluctuations, and a suppression due to interaction with a gain medium which leads to negative correlations between photons. The latter effect is responsible for a pronounced suppression of the photonic noise as compared to the linear theory predictions.Comment: 7 pages, 5 figures; expanded version, to appear in Phys. Rev.

Scholarly research productivity among ophthalmology residency graduates

Purpose: The Accreditation Council for Graduate Medical Education (ACGME) requires that ophthalmology residents participate in scholarly activity during residency. However, to our knowledge it is unknown whether research publications during undergraduate, medical school, residency or fellowship training predict future academic publication performance among ophthalmologists. The aim of this study was to (1) measure scholarly research productivity (as measured by the H-index) among ophthalmology residency graduates, as measured by peer-reviewed publication output, and its relation to future publication output, and (2) evaluate whether scholarly impact of academic ophthalmologists is correlated with any specific characteristics.Methods: This study is cross-sectional in nature and included a random sample of 50 ophthalmology residency programs. From each program, a list of graduating residents from years 2013, 2014, and 2015 was compiled and each graduate was search on Scopus, PubMed, and Google Scholar. The publications of each graduate were then identified and data was extracted and collected in a double blind, duplicate fashion by 2 investigators. Research publication output was then stratified and analyzed.Results: Graduates that had a higher mean total publication (M = 9.11, SD=12.91) were significantly more likely to pursue a fellowship than those that did not (M=2.68, SD=3.16) (t234= -3.9, p = .0001). Graduates with more first person publications and higher H-index values were also significantly more likely to pursue fellowships (t234= -3.78, p = 0.0002) (t234= -3.93, p = 0.0001).Graduates that had a higher mean total publication (M = 14.2, SD= 18.19) were more likely to pursue academic careers than those that did not (M=4.57, SD = 4.88) (t234= -6.3, p = 0 .0001). Graduates with more first person publications and higher H-index values were also significantly more likely to pursue academic careers (t234= -5.17, p = 0.001) (t234= -4.84, p <0.0001). Gender proved to not be a significant determination of research pursuit in terms of publication or first person publication numbers (t234= -1.01, p = .3107) (t234= -0.53, p = .5949). However, H-index values for men (M = 3.06, SD= 3.47 ) and women (M = 2.52, SD=2.64) were significantly different (t234= -3.9, p = 0.0406).Conclusion: The positive correlation between the between graduates' research productivity and career and future research outcomes could present an interesting aspect for viewing candidates for fellowship or careers. The correlation demonstrates that students who performed research before and during residency were more productive with research after residency. This could present a positive reason to select an individual for a fellowship or academic program. The lack of research conversely indicates a likelihood of low research productivity. This could potentially negatively impact candidates. The evaluation of an individual's H-value, first-person publications, or total number of publications can then possibly be supplementary for decision making or gauge potential

Insufficient Reporting of Factors Associated with Exercise Referral Scheme Uptake, Attendance, and Adherence: A Systematic Review of Reviews

Background: Exercise Referral Schemes (ERS) are prescribed programmes aimed at tackling physical inactivity and associated non-communicable disease. Inconsistencies in reporting, recording and delivering ERS make it challenging to identify what works, why, and for whom. Methods: PRISMA guided this narrative review of reviews. Fifteen electronic databases were searched for systematic reviews of ERS. Reviewers applied inclusion criteria and quality assessed via the AMSTAR tool. Data on uptake, attendance and adherence were extracted. Results: Eleven reviews met the inclusion criteria. AMSTAR quality was medium. Definitions of uptake varied within reviews. Uptake ranged from 35%-81%. Groups reported as more likely to take up ERS included, (i) females and (ii) older adults. Attendance was defined variably but ranged from 12%-49%. Men were more likely to attend ERS. Effect of medical diagnosis upon uptake and attendance was inconsistent. Exercises prescribed were unreported and therefore, adherence to exercise prescriptions was unreported. The influence of theoretically-informed approaches on uptake, attendance and adherence was generally lacking, however, self-determination, peer support and supervision support were reported as influencing attendance. Conclusions: There was insufficient reporting across studies about uptake, attendance and adherence. Complex interventions like ERS require consistent definitions, recording and reporting of these key facets, but this is not evident from the existing literature