Using simulation studies to evaluate statistical methods

Simulation studies are computer experiments that involve creating data by pseudorandom sampling. The key strength of simulation studies is the ability to understand the behaviour of statistical methods because some 'truth' (usually some parameter/s of interest) is known from the process of generating the data. This allows us to consider properties of methods, such as bias. While widely used, simulation studies are often poorly designed, analysed and reported. This tutorial outlines the rationale for using simulation studies and offers guidance for design, execution, analysis, reporting and presentation. In particular, this tutorial provides: a structured approach for planning and reporting simulation studies, which involves defining aims, data-generating mechanisms, estimands, methods and performance measures ('ADEMP'); coherent terminology for simulation studies; guidance on coding simulation studies; a critical discussion of key performance measures and their estimation; guidance on structuring tabular and graphical presentation of results; and new graphical presentations. With a view to describing recent practice, we review 100 articles taken from Volume 34 of Statistics in Medicine that included at least one simulation study and identify areas for improvement.Comment: 31 pages, 9 figures (2 in appendix), 8 tables (1 in appendix

School that Makes Cent$: Taking CTE Courses

Career and Technical Education (or CTE) classes are a great way to learn skills for a future career. CTE is the practice of teaching career skills to students. By taking a concentration of CTE courses, high school students can graduate with special certifications that make them eligible to work in certain jobs. These certifications can help high school graduates get a head start in college or career. This tip sheet provides high school students with information about what CTE classes are, how to choose a CTE focus for classes and how to request any accommodations that may be needed

I’ve Got My Crew: Inviting Community Partners to Your IEP Meeting

A community partner is a person from an organization outside of a student\u27s high school that can help students plan for life after graduation. A community partner should be a person or organization that can help high school students receiving special education services with their post-high school goals. This tip sheet provides high school students with tips on how to identify community partners, how they can help students, and how to students can include them in the student\u27s Individualized Education Program (IEP) meetings

You Got This: Taking a Leadership Role in Your IEP Meeting

This tip sheet provides tips for how students (ages of 3 to 21) who receive special education services in public schools can take a leadership role in their individualized education programs (IEP) and transition planning. Learn more about IEPs and transition services in our Teens on IEPs: Making My “Transition” Services Work for Me tip sheet. Learn about the Translating Evidence to Support Transitions (TEST) project here

Spectral differences between the radio-loud and radio-quiet low-hard states of GRS 1915+105: possible detection of synchrotron radiation in X-rays

The Galactic microquasar GRS 1915+105 exhibits several episodes of steady X-ray emission characterized by a hard power-law spectrum and intense Quasi Periodic Oscillations. It is known that there are two types of such low-hard states, one with steady radio emission and the other without any significant radio emission. We present the results of a detailed X-ray spectroscopic study of GRS 1915+105, using data from the Rossi X-ray Timing Explorer obtained during various episodes of the low-hard states of the source. We show that there are distinct X-ray spectral differences between the radio-quiet and radio-loud low-hard states of the source. The X-ray spectra of the radio-quiet low-hard state is best described by a model consisting ofa multicolor disk-blackbody and a Comptonized component, whereas the X-ray spectra of radio-loud low-hard state requires a model consisting of three components: a multicolor disk-blackbody, a Comptonized component and a power-law, for statistically and physically acceptable fits. We attempt to model the presence of this additional power-law component as due to synchrotronradiation which is responsible for the radio and infrared radiation from thesource. We show that a simple adiabatically expanding jet model for the synchrotron radiation can account for the observed X-ray flux for reasonable values of the magnetic field and the mass outflow rate. This is the first report of detection of the synchrotron radiation in the X-ray band for this source.Comment: 9 pages 5 figures, Accepted in A&

Tryptic digestion coupled with ambient DESI and LESA mass spectrometry enables identification of skeletal muscle proteins in mixtures and distinguishes between beef, pork, horse, chicken and turkey meat

The use of ambient desorption electrospray ionization (DESI-MS) mass spectrometry and liquid extraction surface analysis mass spectrometry (LESA-MS) is explored for the first time to analyse skeletal muscle proteins obtained from mixture of standard proteins and raw meat. Single proteins and mixtures of up to five proteins (myoglobin, troponin C, actin, BSA, tropomyosin) were deposited onto a polymer surface, followed by in-situ tryptic digestion and comparative analysis using DESI-MS and LESA-MS using tandem electrospray MS. Peptide peaks specific to individual proteins were readily distinguishable with good signal-to-noise ratio in the five-component mixture. LESA-MS gave a more stable analysis and greater sensitivity compared with DESI-MS. Meat tryptic digests were subjected to peptidomics analysis by DESI-MS and LESA-MS. Bovine, horse, pig, chicken and turkey muscle digests were clearly discriminated using multivariate data analysis (MVA) of the peptidomic datasets. The most abundant skeletal muscle proteins were identified and correctly classified according to the species following MS/MS analysis. The study shows, for the first time, that ambient ionization techniques such as DESI-MS and LESA-MS have great potential for species-specific analysis and differentiation of skeletal muscle proteins by direct surface desorption

Ambient DESI and LESA-MS analysis of proteins adsorbed to a biomaterial surface using in-situ surface tryptic digestion

The detection and identification of proteins adsorbed onto biomaterial surfaces under ambient conditions has significant experimental advantages but has proven to be difficult to achieve with conventional measuring technologies. In this study, we present an adaptation of desorption electrospray ionization (DESI) and liquid extraction surface analysis (LESA) mass spectrometry (MS) coupled with in-situ surface tryptic digestion to identify protein species from a biomaterial surface. Cytochrome c, myoglobin, and BSA in a combination of single and mixture spots were printed in an array format onto Permanox slides, followed by in-situ surface digestion and detection via MS. Automated tandem MS performed on surface peptides was able to identify the proteins via MASCOT. Limits of detection were determined for DESI-MS and a comparison of DESI and LESA-MS peptide spectra characteristics and sensitivity was made. DESI-MS images of the arrays were produced and analyzed with imaging multivariate analysis to automatically separate peptide peaks for each of the proteins within a mixture into distinct components. This is the first time that DESI and LESA-MS have been used for the in-situ detection of surface digested proteins on biomaterial surfaces and presents a promising proof of concept for the use of ambient MS in the rapid and automated analysis of surface proteins

Fast Transition between High-soft and Low-soft States in GRS 1915+105: Evidence for a Critically Viscous Accretion Flow

We present the results of a detailed analysis of RXTE observations of class $\omega$ which show an unusual state transition between high-soft and low-soft states in the microquasar GRS 1915+105. Out of about 600 pointed RXTE observations, the source was found to exhibit such state transition only on 16 occasions. An examination of the RXTE/ASM data in conjunction with the pointed observations reveals that these events appeared as a series of quasi-regular dips in two stretches of long duration (about 20 days during each occasions) when hard X-ray and radio flux were very low. The X-ray light curve and color-color diagram of the source during these observations are found to be different from any reported so far. The duration of these dips is found to be of the order of a few tens of seconds with a repetition time of a few hundred seconds. The transition between these dips and non-dips which differ in intensity by a factor of ~ 3.5, is observed to be very fast (~ a few seconds). It is observed that the low-frequency narrow QPOs are absent in the power density spectrum (PDS) of the dip and non-dip regions of class $\omega$ and the PDS is a power law in 0.1 - 10 Hz frequency range. There is a remarkable similarity in the spectral and timing properties of the source during the dip and non-dip regions in these set of observations. These properties of the source are distinctly different from those seen in the observations of other classes. This indicates that the basic accretion disk structure during both dip and non-dip regions of class $\omega$ is similar, but differ only in intensity. To explain these observations, we invoke a model in which the viscosity is very close to critical viscosity and the shock wave is weak or absent.Comment: Replaced with correct figures, Jour. of Astrophysics and Astronomy (accepted

Polychaetes (Perinereis helleri) reared in sand beds filtering nutrients from shrimp (Penaeus monodon) culture ponds can transiently carry IHHNV

A polychaete-assisted sand filter (PASF) system has been developed to help remove nutrients from aquaculture pond wastewater whilst also producing polychaetes that are highly prized as bait by recreational anglers and as a dietary supplement to improve the fecundity of shrimp broodstock. Whilst rearing polychaetes in PASF beds offers potential to reduce impacts of sourcing them from the wild, the use of wastewater from ponds rearing shrimp such as Penaeus monodon will present a biosecurity risk of viruses being transferred to, and potentially amplified in, the worms. To assess such risks for transmitting infectious hypodermal and haematopoietic necrosis virus (IHHNV), groups of 3 or 4 PASF beds seeded with sand worm (Perinereis helleri) juveniles were supplied with wastewater from ponds of P. monodon with either high-load or low-load IHHNV infections. TaqMan real-time qPCR identified low loads of IHHNV (≤878 IHHNV DNA copies 200 ng−1 TNA) in most worms from PASF beds supplied wastewater from the high-load pond. IHHNV was either not detected or detected at the qPCR test sensitivity limits in worms from beds supplied wastewater from the low-load pond. Purging harvested worms of their gut contents in clean filtered seawater for 2 days significantly reduced IHHNV loads. Reverting PASF beds to clean seawater for 8 weeks before harvest also significantly reduced worm loads of IHHNV. Daily additions of a commercial probiotic to the sand bed surface for 4 weeks prior to clean seawater application provided no discernible benefit to IHHNV clearance. While clearly demonstrated to be capable of carrying IHHNV, the remediation measures examined suggest potential to ameliorate the infection transmission risks of P. helleri reared in PASF beds supplied with shrimp pond wastewater as a nutrient source