Derivation of the PHD filter based on direct Kullback-Leibler divergence minimisation

In this paper, we provide a novel derivation of the probability hypothesis density (PHD) filter without using probability generating functionals or functional derivatives. The PHD filter fits in the context of assumed density filtering and implicitly performs Kullback-Leibler divergence (KLD) minimisations after the prediction and update steps. The novelty of this paper is that the KLD minimisation is performed directly on the multitarget prediction and posterior densities

Nitrogen oxidation consortia dynamics influence the performance of full-scale rotating biological contactors.

Ammonia oxidising microorganisms (AOM) play an important role in ammonia removal in wastewater treatment works (WWTW) including rotating biological contactors (RBCs). Environmental factors within RBCs are known to impact the performance of key AOM, such that only some operational RBCs have shown ability for elevated ammonia removal. In this work, long-term treatment performance of seven full-scale RBC systems along with the structure and abundance of the ammonia oxidising bacteria (AOB) and archaea (AOA) communities within microbial biofilms were examined. Long term data showed the dominance of AOB in most RBCs, although two RBCs had demonstrable shift toward an AOA dominated AOM community. Next Generation Sequencing of the 16S rRNA gene revealed diverse evolutionary ancestry of AOB from RBC biofilms while nitrite-oxidising bacteria (NOBs) were similar to reference databases. AOA were more abundant in the biofilms subject to lower organic loading and higher oxygen concentration found at the distal end of RBC systems. Modelling revealed a distinct nitrogen cycling community present within high performing RBCs, linked to efficient control of RBC process variables (retention time, organic loading and oxygen concentration). We present a novel template for enhancing the resilience of RBC systems through microbial community analysis which can guide future strategies for more effective ammonia removal. To best of the author's knowledge, this is the first comparative study reporting the use of next generation sequencing data on microbial biofilms from RBCs to inform effluent quality of small WWTW

Spontaneous bacterial peritonitis from Salmonella: an unusual bacterium with unusual presentation

Spontaneous bacterial peritonitis (SBP) is a common cause of morbidity and mortality in patients with advanced cirrhosis and portal hypertension. While gram-negative rods and Enterococcus species are the common offending organisms, Salmonella has also been recognized as a rare and atypical offending organism. Atypical features of Salmonella SBP include both its occurrence in cirrhotic patients with immunosuppressive state and its lack of typical neutroascitic response. Diagnosis is often delayed as it requires confirmation from ascitic fluid culture. We report a case of Salmonella SBP occurring in a patient with decompensated cryptogenic cirrhosis with concurrent low-grade non-Hodgkin lymphoma and prior treatment with rituximab. Physicians should be aware of the atypical presentation, especially in cirrhotic patients who are immunosuppressed

Challenges in Survey Research

While being an important and often used research method, survey research has been less often discussed on a methodological level in empirical software engineering than other types of research. This chapter compiles a set of important and challenging issues in survey research based on experiences with several large-scale international surveys. The chapter covers theory building, sampling, invitation and follow-up, statistical as well as qualitative analysis of survey data and the usage of psychometrics in software engineering surveys.Comment: Accepted version of chapter in the upcoming book on Contemporary Empirical Methods in Software Engineering. Update includes revision of typos and additional figures. Last update includes fixing two small issues and typo

Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Results Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. Conclusions The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions

Separation of Oligosaccharides from Lotus Seeds via Medium-pressure Liquid Chromatography Coupled with ELSD and DAD

peer-reviewedLotus seeds were identified by the Ministry of Public Health of China as both food and medicine. One general function of lotus seeds is to improve intestinal health. However, to date, studies evaluating the relationship between bioactive compounds in lotus seeds and the physiological activity of the intestine are limited. In the present study, by using medium pressure liquid chromatography coupled with evaporative light-scattering detector and diode-array detector, five oligosaccharides were isolated and their structures were further characterized by electrospray ionization-mass spectrometry and gas chromatography-mass spectrometry. In vitro testing determined that LOS3-1 and LOS4 elicited relatively good proliferative effects on Lactobacillus delbrueckii subsp. bulgaricus. These results indicated a structure-function relationship between the physiological activity of oligosaccharides in lotus seeds and the number of probiotics applied, thus providing room for improvement of this particular feature. Intestinal probiotics may potentially become a new effective drug target for the regulation of immunity

Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA

In eukaryotes, the Cdt1-bound replicative helicase core MCM2-7 is loaded onto DNA by the ORC-Cdc6 ATPase to form a prereplicative complex (pre-RC) with an MCM2-7 double hexamer encircling DNA. Using purified components in the presence of ATP-γS, we have captured in vitro an intermediate in pre-RC assembly that contains a complex between the ORC-Cdc6 and Cdt1-MCM2-7 heteroheptamers called the OCCM. Cryo-EM studies of this 14-subunit complex reveal that the two separate heptameric complexes are engaged extensively, with the ORC-Cdc6 N-terminal AAA+ domains latching onto the C-terminal AAA+ motor domains of the MCM2-7 hexamer. The conformation of ORC-Cdc6 undergoes a concerted change into a right-handed spiral with helical symmetry that is identical to that of the DNA double helix. The resulting ORC-Cdc6 helicase loader shows a notable structural similarity to the replication factor C clamp loader, suggesting a conserved mechanism of action

Genetic diversity in peripheral and central populations of the Cantabrian endemism <i>Genista legionensis</i> (Pau) M. Laínz (Fabaceae)

The impact of habitat fragmentation and isolation on the genetic diversity of populations has attracted much attention in studies of plant conservation. The central-peripheral population hypothesis predicts that peripheral populations have reduced genetic variability, so it is often assumed that they deserve higher conservation priority over central populations. In this work, using amplified fragment length polymorphism (AFLP), we studied the genetic diversity of central and peripheral populations of the Cantabrian endemism Genista legionensis (Fabaceae). At the species level, percentage of polymorphic bands, Nei heterozygosity and Shannon information index were PPB = 89.21%, Hε = 0.246 and I = 0.377, respectively. The study revealed that peripheral populations were smaller in number, with lower levels of genetic diversity compared to the central populations. Furthermore, analysis of molecular variance (AMOVA) indicated that most of the variability was partitioned among populations, also supported by principal coordinates analysis. This study indicates that the decrease in diversity from central to peripheral populations could be explained as a result of edge effect and fragmentation through the enhanced inbreeding and genetic drift, and thus supported the view that habitat fragmentation and related edge effect reduce the population genetic diversity. However, the presence of discriminating fragments in the peripheral populations suggests their conservation in order to preserve the genetic diversity in the Cantabrian endemism G. legionensis.El impacto de la fragmentación del hábitat y el aislamiento sobre la diversidad genética de las poblaciones, han despertado mucha atención en estudios de conservación de plantas. La hipótesis de la población centro-periferia predice que las poblaciones periféricas reducen la variabilidad genética, por lo que a menudo se asume que merecen una mayor prioridad de conservación respecto a las poblaciones centrales. En este trabajo, hemos empleado los polimorfismos en longitud de fragmentos amplificados (AFLP), para estudiar la diversidad genética de las poblaciones centrales y periféricas del endemismo cantábrico Genista legionensis (Fabaceae). A nivel de especie, el porcentaje de bandas polimórficas, la heterocigosidad de Nei y el índice de Shannon fueron PPB = 89,21%, Hε = 0,246 y I = 0,377, respectivamente. El estudio reveló que las poblaciones periféricas fueron menores en número, con niveles más bajos de diversidad genética si las comparamos con las poblaciones centrales. Además, el análisis molecular de la varianza (AMOVA) indicó que la mayor parte de la variabilidad tuvo lugar entre las poblaciones, también apoyado por el aná - lisis de coordenadas principales. Este estudio indica que la disminución de la diversidad desde el centro hasta las poblaciones periféricas, puede deberse a un efecto de borde y fragmentación acompañado de endogamia y deriva génica, y por ello apoya la idea de que la fragmentación del hábitat y el efecto borde están relacionados con una reducción de la diversidad genética poblacional. Sin embargo, la presencia de fragmentos discriminantes en las poblaciones periféricas sugiere su conservación a fin de preservar la diversidad genética del endemismo Cantábrico G. legionensis

Evaluating predictive pharmacogenetic signatures of adverse events in colorectal cancer patients treated with fluoropyrimidines

The potential clinical utility of genetic markers associated with response to fluoropyrimidine treatment in colorectal cancer patients remains controversial despite extensive study. Our aim was to test the clinical validity of both novel and previously identified markers of adverse events in a broad clinical setting. We have conducted an observational pharmacogenetic study of early adverse events in a cohort study of 254 colorectal cancer patients treated with 5-fluorouracil or capecitabine. Sixteen variants of nine key folate (pharmacodynamic) and drug metabolising (pharmacokinetic) enzymes have been analysed as individual markers and/or signatures of markers. We found a significant association between TYMP S471L (rs11479) and early dose modifications and/or severe adverse events (adjusted OR = 2.02 [1.03; 4.00], p = 0.042, adjusted OR = 2.70 [1.23; 5.92], p = 0.01 respectively). There was also a significant association between these phenotypes and a signature of DPYD mutations (Adjusted OR = 3.96 [1.17; 13.33], p = 0.03, adjusted OR = 6.76 [1.99; 22.96], p = 0.002 respectively). We did not identify any significant associations between the individual candidate pharmacodynamic markers and toxicity. If a predictive test for early adverse events analysed the TYMP and DPYD variants as a signature, the sensitivity would be 45.5 %, with a positive predictive value of just 33.9 % and thus poor clinical validity. Most studies to date have been under-powered to consider multiple pharmacokinetic and pharmacodynamic variants simultaneously but this and similar individualised data sets could be pooled in meta-analyses to resolve uncertainties about the potential clinical utility of these markers

Metabolic suppression in thecosomatous pteropods as an effect of low temperature and hypoxia in the eastern tropical North Pacific

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Marine Biology 159 (2012): 1955-1967, doi:10.1007/s00227-012-1982-x.Many pteropod species in the eastern tropical north Pacific Ocean migrate vertically each day, transporting organic matter and respiratory carbon below the thermocline. These migrations take species into cold (15-10ºC) hypoxic water (< 20 µmol O2 kg-1) at depth. We measured the vertical distribution, oxygen consumption and ammonia excretion for seven species of pteropod, some of which migrate and some which remain in oxygenated surface waters throughout the day. Within the upper 200 meters of the water column, changes in water temperature result in a ~60-75% reduction in respiration for most species. All three species tested under hypoxic conditions responded to low O2 with an additional ~35-50% reduction in respiratory rate. Combined, low temperature and hypoxia suppress the metabolic rate of pteropods by ~80-90%. These results shed light on the ways in which expanding regions of hypoxia and surface ocean warming may impact pelagic ecology.This work was funded by National Science Foundation grants to K. Wishner and B. Seibel (OCE – 0526502 and OCE – 0851043) and to K. Daly (OCE – 0526545), the University of Rhode Island, and the Rhode Island Experimental Program to Stimulate Competitive Research Fellowship program.2013-06-3