A Comparative Review of Computational Methods as Applied to Gold(I) Complexes and Mechanisms

In the last two decades, the field of homogeneous gold catalysis has been

extremely active, growing at a rapid pace. Another rapidly-growing field—that of

computational chemistry—has often been applied to the investigation of various gold-

catalyzed reaction mechanisms. Unfortunately, a number of recent mechanistic studies

have utilized computational methods that have been shown to be inappropriate and

inaccurate in their description of gold chemistry. This work presents an overview of

available computational methods with a focus on the approximations and limitations

inherent in each, and offers a review of experimentally-characterized gold(I) complexes

and proposed mechanisms as compared with their computationally-modeled

counterparts. No aim is made to identify a “recommended” computational method for

investigations of gold catalysis; rather, discrepancies between experimentally and

computationally obtained values are highlighted, and the systematic errors between

different computational methods are discussed.

Comparison of two methods for measuring the pubococcygeal line from sagittal-plane magnetic resonance imaging

Aims The pubococcygeal line (PCL) is an important reference line for determining measures of pelvic organ support on sagittal-plane magnetic resonance imaging (MRI); however, there is no consensus on where to place the posterior point of the PCL. As coccyx movement produced during pelvic floor muscle (PFM) contractions may affect other measures, optimal placement of the posterior point is important. This study compared two methods for measuring the PCL, with different posterior points, on T2-weighted sagittal MRI to determine the effect of coccygeal movement on measures of pelvic organ support in older women. Methods MRI of the pelvis was performed in the midsagittal plane, at rest and during PFM contractions, on 47 community-dwelling women 60 and over. The first PCL was measured to the tip of the coccyx (PCLtip) and the second to the sacrococcygeal joint (PCLjnt). Four measures of pelvic organ support were made using each PCL as the reference line: urethrovesical junction height, uterovaginal junction height, M-line and levator plate angle. Results During the PFM contraction the PCLtip shortened and lifted (P < 0.001); the PCLjnt did not change (P > 0.05). The changes in the four measures of pelvic organ support were smaller when measured relative to the PCLtip as compared to those to the PCLjnt (P < 0.001). Conclusions Coccyx movement affected the length and position of the PCLtip, which resulted in underestimates of the pelvic-organ lift produced by the PFM contraction. Therefore, we recommend that the PCL be measured to the sacrococcygeal joint and not to the tip of the coccyx

Particle positions of numerical experiments 1 to 4

In mixed sediment beds, erosion resistance can change relative to that of beds composed of a uniform sediment because of varying textural and/or other grain-size parameters, with effects on pore water flow that are difficult to quantify by means of analogue techniques. To overcome this difficulty, a three-dimensional numerical model was developed using a finite difference method (FDM) flow model coupled with a distinct element method (DEM) particle model. The main aim was to investigate, at a high spatial resolution, the physical processes occurring during the initiation of motion of single grains at the sediment-water interface and in the shallow subsurface of simplified sediment beds under different flow velocities. Increasing proportions of very fine sand (D50=0.08 mm) were mixed into a coarse sand matrix (D50=0.6 mm) to simulate mixed sediment beds, starting with a pure coarse sand bed in experiment 1 (0 wt% fines), and proceeding through experiment 2 (6.5 wt% fines), experiment 3 (10.5 wt% fines), and experiment 4 (28.7 wt% fines). All mixed beds were tested for their erosion behavior at predefined flow velocities varying in the range of U 1-5=10-30 cm/s. The experiments show that, with increasing fine content, the smaller particles increasingly fill the spaces between the larger particles. As a consequence, pore water inflow into the sediment is increasingly blocked, i.e., there is a decrease in pore water flow velocity and, hence, in the flow momentum available to entrain particles. These findings are portrayed in a new conceptual model of enhanced sediment bed stabilization.

Development of release methods for critically endangered freshwater pearl mussels (Margaritifera margaritifera)

Biodiversity loss is a global problem with freshwater bivalves considered amongst the most
endangered biota. The freshwater pearl mussel, Margaritifera margaritifera, is declining
throughout its range owing to habitat degradation and overexploitation. In most of its range,
populations are regarded as reproductively non-functional which has led to the development
of captive breeding programmes. A novel method of releasing M. margaritifera was trialled,
with captive-bred juveniles being released into the rivers caged in ‘mussels silos’ (protective
concrete domes with ventilation creating upwelling to ensure water through flow). We
released 240 juvenile mussels and survival and growth rates were monitored for 18 months
post-release for three size classes: A (13.01-20.00mm); B (10.01-13.00mm); and C (4.01-
10.00mm). We explicitly tested two experimental treatments; one where sediment was added
to each silo (allowing mussels to orientate and burrow) and one without sediment. Survival
by the end of the experiment at month 18 was significantly higher for the largest size class at
97% (though growth was lowest in this cohort), and lowest for the smallest size class at 61%
(though growth was highest in this cohort). Survival and growth were unaffected by the
experimental treatment suggesting that adding sediment offered no advantage. Growth was
positively correlated with both water temperature and the particle size of suspended solids
(both of which were collinear, peaking in summer). There are a large number of ex situ
breeding programmes for freshwater pearl mussels throughout Europe and our finding
suggest that the use of ‘mussel silos’ could be a useful tool to protecting juvenile mussels
allowing them to be released at a relatively early stage of development, minimising the risk of
domestication.

A comparison of three methods for detecting KRAS mutations in formalin-fixed colorectal cancer specimens.

BACKGROUND: KRAS mutation testing is required to select patients with metastatic colorectal cancer (CRC) to receive anti-epidermal growth factor receptor antibodies, but the optimal KRAS mutation test method is uncertain. METHODS: We conducted a two-site comparison of two commercial KRAS mutation kits - the cobas KRAS Mutation Test and the Qiagen therascreen KRAS Kit - and Sanger sequencing. A panel of 120 CRC specimens was tested with all three methods. The agreement between the cobas test and each of the other methods was assessed. Specimens with discordant results were subjected to quantitative massively parallel pyrosequencing (MPP). DNA blends were tested to determine detection rates at 5% mutant alleles. RESULTS: Reproducibility of the cobas test between sites was 98%. Six mutations were detected by cobas that were not detected by Sanger, and five were confirmed by MPP. The cobas test detected eight mutations which were not detected by the therascreen test, and seven were confirmed by MPP. Detection rates with 5% mutant DNA blends were 100% for the cobas and therascreen tests and 19% for Sanger. CONCLUSION: The cobas test was reproducible between sites, and detected several mutations that were not detected by the therascreen test or Sanger. Sanger sequencing had poor sensitivity for low levels of mutation.

Modeling of Turbulent Natural Gas and Biogas Flames of the Delft Jet-in-Hot-Coflow Burner: Effects of Coflow Temperature, Fuel Temperature and Fuel Composition on the Flame Lift-Off Height

The structure of a turbulent non-premixed flame of a biogas fuel in a hot and diluted coflow mimicking moderate and intense low dilution (MILD) combustion is studied numerically. Biogas fuel is obtained by dilution of Dutch natural gas (DNG) with CO2. The results of biogas combustion are compared with those of DNG combustion in the Delft Jet-in-Hot-Coflow (DJHC) burner. New experimental measurements of lift-off height and of velocity and temperature statistics have been made to provide a database for evaluating the capability of numerical methods in predicting the flame structure. Compared to the lift-off height of the DNG flame, addition of 30 % carbon dioxide to the fuel increases the lift-off height by less than 15 %. Numerical simulations are conducted by solving the RANS equations using Reynolds stress model (RSM) as turbulence model in combination with EDC (Eddy Dissipation Concept) and transported probability density function (PDF) as turbulence-chemistry interaction models. The DRM19 reduced mechanism is used as chemical kinetics with the EDC model. A tabulated chemistry model based on the Flamelet Generated Manifold (FGM) is adopted in the PDF method. The table describes a non-adiabatic three stream mixing problem between fuel, coflow and ambient air based on igniting counterflow diffusion flamelets. The results show that the EDC/DRM19 and PDF/FGM models predict the experimentally observed decreasing trend of lift-off height with increase of the coflow temperature. Although more detailed chemistry is used with EDC, the temperature fluctuations at the coflow inlet (approximately 100K) cannot be included resulting in a significant overprediction of the flame temperature. Only the PDF modeling results with temperature fluctuations predict the correct mean temperature profiles of the biogas case and compare well with the experimental temperature distributions.

Population inversion between the sup(3)Hsub(4) and the sup(3)Fsub(4) excited states of Tmsup(3+) investigated by means of numerical solutions of the rate equations system in Tmsup(3+)-doped and Tmsup(3+), Hosup(3+)-codoped fluoride glasses

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Energy transfer rates and population inversion of sup(4)Isub(11/2) excited state of Ersup(3+) investigated by means of numerical solutions of the rate equations system in Er:LiYFsub(4) crystal

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparison of different methods to detect genetic barriers in a small mammal population

Habitat fragmentation and the consequently the loss of connectivity between populations can reduce the individuals interchange and gene flow, increasing the chances of inbreeding, and the increase the risk of local extinction. Landscape genetics is providing more and better tools to identify genetic barriers.. To our knowledge, no comparison of methods in terms of consistency has been made with observed data and species with low dispersal ability. The aim of this study is to examine the consistency of the results of five methods to detect barriers to gene flow in a Mediterranean pine vole population Microtus duodecimcostatus: F-statistics estimations, Non-Bayesian clustering, Bayesian clustering, Boundary detection and Simple/Partial Mantel tests. All methods were consistent in detecting the stream as a non-genetic barrier. However, no consistency in results among the methods were found regarding the role of the highway as a genetic barrier. Fst, Bayesian clustering assignment test and Partial Mantel test identifyed the highway as a filter to individual interchange. The Mantel tests were the most sensitive method. Boundary detection method (Monmonier’s Algorithm) and Non-Bayesian approaches did not detect any genetic differentiation of the pine vole due to the highway. Based on our findings we recommend that the genetic barrier detection in low dispersal ability populations should be analyzed with multiple methods such as Mantel tests, Bayesian clustering approaches because they show more sensibility in those scenarios and with boundary detection methods by having the aim of detect drastic changes in a variable of interest between the closest individuals. Although simulation studies highlight the weaknesses and the strengths of each method and the factors that promote some results, tests with real data are needed to increase the effectiveness of genetic barrier detection.

Case-based reasoning as a tool to improve the usability of numerical models

There may be advantages to be gained by combining Case-Based Reasoning (CBR) techniques with numerical models. In this paper we consider how CBR can be used as a flexible query engine to improve the usability of numerical models. Particularly they can help to solve inverse and mixed problems, and to solve constraint problems. We discuss this idea with reference to the illustrative example of a pneumatic conveyor. We describe a model of the problem of particle degradation in such a conveyor, and the problems faced by design engineers. The solution of these problems requires a system that allows iterative sharing of control between user, CBR system, and numerical model. This multi-initiative interaction is illustrated for the pneumatic conveyor by means of Unified Modeling Language (UML) collaboration and sequence diagrams. We show approaches to the solution of these problems via a CBR tool.

A study of computational methods to analyze gene expression data

The recent advent of new technologies has led to huge amounts of genomic data. With these data come new opportunities to understand biological cellular processes underlying hidden regulation mechanisms and to identify disease related biomarkers for informative diagnostics. However, extracting biological insights from the immense amounts of genomic data is a challenging task. Therefore, effective and efficient computational techniques are needed to analyze and interpret genomic data. In this thesis, novel computational methods are proposed to address such challenges: a Bayesian mixture model, an extended Bayesian mixture model, and an Eigen-brain approach. The Bayesian mixture framework involves integration of the Bayesian network and the Gaussian mixture model. Based on the proposed framework and its conjunction with K-means clustering and principal component analysis (PCA), biological insights are derived such as context specific/dependent relationships and nested structures within microarray where biological replicates are encapsulated. The Bayesian mixture framework is then extended to explore posterior distributions of network space by incorporating a Markov chain Monte Carlo (MCMC) model. The extended Bayesian mixture model summarizes the sampled network structures by extracting biologically meaningful features. Finally, an Eigen-brain approach is proposed to analyze in situ hybridization data for the identification of the cell-type specific genes, which can be useful for informative blood diagnostics. Computational results with region-based clustering reveals the critical evidence for the consistency with brain anatomical structure.