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Portal Rodent Trapping Forecasts for May 2017

Weecology Group
Predictions and 90% prediction intervals on the Portal rodent trapping results for 5/26 - 5/28/2017. Predictions are made for the next 12 months, by species and for total of all rodents, on all plots and on only the long-term controls. Details of the models used can be found at https://github.com/weecology/portalPredictions .

A Unified Analysis of Structured Sonar-Terrain Data Using Bayesian Functional Mixed Models

Hongxiao Zhu, Philip Caspers, Jeffrey S. Morris, Xiaowei Wu & Rolf Müller
Sonar emits pulses of sound and uses the reflected echoes to gain information about target objects. It offers a low cost, complementary sensing modality for small robotic platforms. Although existing analytical approaches often assume independence across echoes, real sonar data can have more complicated structures due to device setup or experimental design. In this article, we consider sonar echo data collected from multiple terrain substrates with a dual-channel sonar head. Our goals are to identify...

A Unified Analysis of Structured Sonar-Terrain Data Using Bayesian Functional Mixed Models

Hongxiao Zhu, Philip Caspers, Jeffrey S. Morris, Xiaowei Wu & Rolf Müller
Sonar emits pulses of sound and uses the reflected echoes to gain information about target objects. It offers a low cost, complementary sensing modality for small robotic platforms. Although existing analytical approaches often assume independence across echoes, real sonar data can have more complicated structures due to device setup or experimental design. In this article, we consider sonar echo data collected from multiple terrain substrates with a dual-channel sonar head. Our goals are to identify...

Precision Matrix Estimation With ROPE

M. O. Kuismin, J. T. Kemppainen & M. J. Sillanpää
It is known that the accuracy of the maximum likelihood-based covariance and precision matrix estimates can be improved by penalized log-likelihood estimation. In this article, we propose a ridge-type operator for the precision matrix estimation, ROPE for short, to maximize a penalized likelihood function where the Frobenius norm is used as the penalty function. We show that there is an explicit closed form representation of a shrinkage estimator for the precision matrix when using a...

Group-Wise Principal Component Analysis for Exploratory Data Analysis

José Camacho, Rafael A. Rodríguez-Gómez & Edoardo Saccenti
In this article, we propose a new framework for matrix factorization based on principal component analysis (PCA) where sparsity is imposed. The structure to impose sparsity is defined in terms of groups of correlated variables found in correlation matrices or maps. The framework is based on three new contributions: an algorithm to identify the groups of variables in correlation maps, a visualization for the resulting groups, and a matrix factorization. Together with a method to...

Plot-specific vegetation measurements

Benjamin Sulman
Measurements of mycorrhizal association, fine root production, leaf production, wood production, NPP, rhizosphere volume, and root exudation used to drive and evaluate the FUN-CORPSE model.

FUN-CORPSE model output

Benjamin Sulman
Output from FUN-CORPSE model simulations used in Ecology Letters (2017) paper

Characterization of Nanosized Silica Size Standards

Shigeru Kimoto, William D. Dick, Ben Hunt, Wladyslaw W. Szymanski, Peter H. McMurry, Daryl L. Roberts & David Y. H. Pui
Nanosized silica size standards produced with a sol-gel synthesis process were evaluated for particle size, effective density and refractive index in this study. Particle size and effective density measurements were conducted following protocol from the National Institute of Advanced Industrial Science and Technology (AIST) in Japan. Particle sizes were measured via electrical mobility analysis using a differential mobility analyzer (DMA) at sheath flow rates (Qsh) of 3.0 and 6.0 L/min and a constant aerosol flow rate...

Characterization of Nanosized Silica Size Standards

Shigeru Kimoto, William D. Dick, Ben Hunt, Wladyslaw W. Szymanski, Peter H. McMurry, Daryl L. Roberts & David Y. H. Pui
Nanosized silica size standards produced with a sol-gel synthesis process were evaluated for particle size, effective density and refractive index in this study. Particle size and effective density measurements were conducted following protocol from the National Institute of Advanced Industrial Science and Technology (AIST) in Japan. Particle sizes were measured via electrical mobility analysis using a differential mobility analyzer (DMA) at sheath flow rates (Qsh) of 3.0 and 6.0 L/min and a constant aerosol flow rate...

Sample size for comparing negative binomial rates in noninferiority and equivalence trials with unequal follow-up times

Yongqiang Tang
We derive the sample size formulae for comparing two negative binomial rates based on both the relative and absolute rate difference metrics in noninferiority and equivalence trials with unequal follow-up times, and establish an approximate relationship between the sample sizes required for the treatment comparison based on the two treatment effect metrics. The proposed method allows the dispersion parameter to vary by treatment groups. The accuracy of these methods is assessed by simulations. It is...

Sample size for comparing negative binomial rates in noninferiority and equivalence trials with unequal follow-up times

Yongqiang Tang
We derive the sample size formulae for comparing two negative binomial rates based on both the relative and absolute rate difference metrics in noninferiority and equivalence trials with unequal follow-up times, and establish an approximate relationship between the sample sizes required for the treatment comparison based on the two treatment effect metrics. The proposed method allows the dispersion parameter to vary by treatment groups. The accuracy of these methods is assessed by simulations. It is...

Introduction to Dynamic Modeling of Infectious Diseases

Steven Bellan & Juliet Pulliam
An introduction to infectious disease transmission modeling. Goals are for audience to be able to:
1. Understand the natural history of infection
2. Explain SIR model formulation Define the basic reproduction number (R0)
3. Calculate vaccinated proportion needed for pathogen elimination
4.Explain the effect of demography on epidemics

An efficient and catalyst free methylthiolation of 4-(bromomethyl)-2H-chromen-2-ones with DMSO

Bahubali M. Chougala, Samundeeswari S, Megharaja Holiyachi, Nirmala S. Naik, Lokesh A. Shastri & Vinay A Sunagar
The first simple, metal free, and efficient protocol has been established for the methylthiolation of structurally diverse 4-bromomethyl-2H-chromen-2-ones using dimethyl sulfoxide (DMSO) as methylthiolation source at higher temperature. The experimental method is highly economical and provides excellent yields of highly pure products which do not require further purification. All novel 4-[(methylthio)methyl]-2H-chromen-2-ones were characterized by 1H, 13C NMR, and single-crystal X-ray analysis.

An efficient and catalyst free methylthiolation of 4-(bromomethyl)-2H-chromen-2-ones with DMSO

Bahubali M. Chougala, Samundeeswari S, Megharaja Holiyachi, Nirmala S. Naik, Lokesh A. Shastri & Vinay A Sunagar
The first simple, metal free, and efficient protocol has been established for the methylthiolation of structurally diverse 4-bromomethyl-2H-chromen-2-ones using dimethyl sulfoxide (DMSO) as methylthiolation source at higher temperature. The experimental method is highly economical and provides excellent yields of highly pure products which do not require further purification. All novel 4-[(methylthio)methyl]-2H-chromen-2-ones were characterized by 1H, 13C NMR, and single-crystal X-ray analysis.

Design, synthesis, crystal structure and insecticidal evaluation of novel arylpyrazole derivatives containing cyhalothroyl thiourea moiety

Zhen-Yu Han, Wen-Yuan Wu, Fu-Li Chen, Xi-Lin Guan, Xiao-Huan Fu, Peng Jiang & Rong Wan
On the basis of the commercial insecticide Fipronil, a series of novel arylpyrazole derivatives containing the cyhalothroyl thiourea moiety were designed and synthesized via the key intermediate 5-amino-3-cyano-1-(substituted phenyl) pyrazole. The structures of target compounds were characterized by 1H NMR, FT-IR, elemental analysis and single crystal X-ray diffraction analysis. Their insecticidal activities against Culex pipiens and Musca domestica were evaluated. The results of bioassays indicated that title compounds exhibited satisfactory insecticidal activities. Among those, Compound...

Design, synthesis, crystal structure and insecticidal evaluation of novel arylpyrazole derivatives containing cyhalothroyl thiourea moiety

Zhen-Yu Han, Wen-Yuan Wu, Fu-Li Chen, Xi-Lin Guan, Xiao-Huan Fu, Peng Jiang & Rong Wan
On the basis of the commercial insecticide Fipronil, a series of novel arylpyrazole derivatives containing the cyhalothroyl thiourea moiety were designed and synthesized via the key intermediate 5-amino-3-cyano-1-(substituted phenyl) pyrazole. The structures of target compounds were characterized by 1H NMR, FT-IR, elemental analysis and single crystal X-ray diffraction analysis. Their insecticidal activities against Culex pipiens and Musca domestica were evaluated. The results of bioassays indicated that title compounds exhibited satisfactory insecticidal activities. Among those, Compound...

Research Data Management Teaching Toolkit

Kevin Read & Alisa Surkis
This teaching toolkit is designed to be used for a one hour introductory data management class for biomedical researchers. It consists of an instructional guide for teaching the material, a PowerPoint presentation with a script in the accompanying notes to each slide, and a separate evaluation form. This material is built on training material provided in the BD2K funded online research data management educational modules that are freely available here: http://bit.ly/RDM_Modules

Research Data Management Teaching Toolkit

Kevin Read & Alisa Surkis
This teaching toolkit is designed to be used for a one hour introductory data management class for biomedical researchers. It consists of an instructional guide for teaching the material, a PowerPoint presentation with a script in the accompanying notes to each slide, and a separate evaluation form. This material is built on training material provided in the BD2K funded online research data management educational modules that are freely available here: http://bit.ly/RDM_Modules

Outback Interviews

John Rovers
These are interviews (blinded as to identity) of individuals working in an Aboriginal Health Service in Outback Australia. The data was used to create a model for drug procurement, storage and distribution in a rural and remote population living several hundred miles from the nearest pharmacy

Outback Interviews

John Rovers
These are interviews (blinded as to identity) of individuals working in an Aboriginal Health Service in Outback Australia. The data was used to create a model for drug procurement, storage and distribution in a rural and remote population living several hundred miles from the nearest pharmacy

A state-of-the-art machine learning pipeline for the analysis of spatial proteomics data

Laurent Gatto, Lisa M. Breckels, Thomas Naake, Samual Wieczorek, Thomas Burger & Kathryn S. Lilley
Poster presented at the HUPO conference in 2014

Organelle proteomics, or spatial proteomics, is the systematic study of proteins and their assignment to subcellular niches including organelles. pRoloc and pRolocGUI are R/Bioconductor packages that implement all the necessary tools for the sound and reproducible analysis and interactive exploration of spatial proteomics data from any type of experiment such as LOPIT, PCP or PCP-SILAC.

A state-of-the-art machine learning pipeline for the analysis of spatial proteomics data

Laurent Gatto, Lisa M. Breckels, Thomas Naake, Samual Wieczorek, Thomas Burger & Kathryn S. Lilley
Poster presented at the HUPO conference in 2014

Organelle proteomics, or spatial proteomics, is the systematic study of proteins and their assignment to subcellular niches including organelles. pRoloc and pRolocGUI are R/Bioconductor packages that implement all the necessary tools for the sound and reproducible analysis and interactive exploration of spatial proteomics data from any type of experiment such as LOPIT, PCP or PCP-SILAC.

The SIR Model Family

Jonathan Dushoff
An introduction to the susceptible-infected-recovered compartmental model of infectious disease transmission.

pRoloc - A unifying bioinformatics framework for organelle proteomics

Laurent Gatto, Lisa M. Breckels, Matthew W.B. Trotter & Kathryn S. Lilley
Poster presented at the HUPO conference in 2011

Reliably resolving protein localisation is not a trivial task, and requires (1) flexible, yet powerful data (and meta-data) structures, with handling and transformation capabilities, (2) efficient processing algorithms and (3) customisable data visualisation. So far, several data analysis strategies for MS-based approaches have been described in the literature, but no comparison has been attempted due to their diverse and ill-documented nature. pRoloc aims at filling this gap to...

pRoloc - A unifying bioinformatics framework for organelle proteomics

Laurent Gatto, Lisa M. Breckels, Matthew W.B. Trotter & Kathryn S. Lilley
Poster presented at the HUPO conference in 2011

Reliably resolving protein localisation is not a trivial task, and requires (1) flexible, yet powerful data (and meta-data) structures, with handling and transformation capabilities, (2) efficient processing algorithms and (3) customisable data visualisation. So far, several data analysis strategies for MS-based approaches have been described in the literature, but no comparison has been attempted due to their diverse and ill-documented nature. pRoloc aims at filling this gap to...

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