Quantifying the performance of two different types of commercial software programs for 3D patient dose reconstruction for prostate cancer patients: Machine log files vs. machine log files with EPID images

We clarified the reconstructed 3D dose difference between two different commercial software programs (Mobius3D v2.0 and PerFRACTION v1.6.4).Five prostate cancer patients treated with IMRT (74 Gy/37 Fr) were studied. Log files and cine EPID images were acquired for each fraction. 3D patient dose was reconstructed using log files (Mobius3D) or log files with EPID imaging (PerFRACTION). The treatment planning dose was re-calculated on homogeneous and heterogeneous phantoms, and log files and cine EPID images were acquired. Measured doses were compared with the reconstructed point doses in the phantom. Next, we compared dosimetric metrics (mean dose for PTV, rectum, and bladder) calculated by Mobius3D and PerFRACTION for all fractions from five patients.Dose difference at isocenter between measurement and reconstructed dose for two software programs was within 3.0% in both homogeneous and heterogeneous phantoms. Moreover, the dose difference was larger using skip arc plan than that using full arc plan, especially for PerFRACTION (e.g., dose difference at isocenter for PerFRACTION: 0.34% for full arc plan vs. −4.50% for skip arc plan in patient 1).For patients, differences in dosimetric parameters were within 1% for almost all fractions. PerFRACTION had wider range of dose difference between first fraction and the other fractions than Mobius3D (e.g., maximum difference: 0.50% for Mobius3D vs. 1.85% for PerFRACTION), possibly because EPID may detect some types of MLC positioning errors such as miscalibration errors or mechanical backlash which cannot be detected by log files, or that EPID data might include image acquisition failure and image noise.     

潜蝇属六种的摩擦发音器(双翅目：潜蝇科)(英文)

本文对我国潜蝇属Ａｇｒｏｍｙｚａ６种（其中２种为国内新纪录）的摩擦发间器特征作为扫描电镜观察。首次提出了多个形态用语,并试以音锉分类为６种潜蝇作出检索表。对潜蝇科内两类音锉型的关系作了图解。     

Theory of single-file noise

A general theoretical approach to the analysis of electric fluctuations generated by the so-called single-file diffusion through narrow channels is presented. The formalism is a slight extension of an approach to electric fluctuations in discrete transport systems with negligible interactions between the particles recently developed by one of the authors. In the single-file transport mechanism interactions between the particles must be taken into account. Three main results of principal interest are: (a) the electric fluctuations around stationary states (at equilibrium and non-equilibrium) are determined by the time-dependent solutions of the macroscopic single-file transport equations, (b) as a direct consequence of the interactions between the ions in the single-file transport the macroscopic time-dependent current and the autocorrelation function of the microscopic current fluctuations can exhibit damped oscillatory behavior, and the current noise spectrum can show peaking, (c) the number of binding sites for the ions within the pores seems to have a strong influence on the oscillatory behavior: with increasing number of binding sites the damping of the oscillations decreases and the peaking of the spectrum becomes stronger.     

Recent advances in quantitative colocalization analysis: Focus on neuroscience

Quantitative colocalization analysis is an advanced digital imaging tool to characterize the spatial expression of molecules of interest in immunofluorescence images obtained using confocal microscopes. It began from simple pixel counting and, with introduction of specialized algorithms, transformed into a powerful image analyzing technique capable of identifying the exact locations of various molecules in tissues and cells and describing their subtle changes in dynamics. Applications of quantitative colocalization in the field of neuroscience proved to be particularly informative by helping to obtain observations not otherwise achievable using other techniques. In this article, we review the background and applicability of quantitative colocalization with special focus on neuroscience research.     

The redox state and the phosphorylation state of the mannitol-specific carrier of the E. coli phosphoenolpyruvate-dependent phosphotransferase system

This review summarizes the recent developments in identifying the activity-linked cysteine as one of the phosphorylation sites on the mannitol-specific EII of the E. coli phosphoenolpyruvate-dependent mannitol transport system. Two phosphorylation sites have been identified, one being the HPr/P-HPr exchange site, the other being the mannitol/mannitol-P exchange site. The activity-linked cysteine and the second phosphorylation site are located in the same 14 residue peptide. Phosphorylation of the second site and phosphoryl group transfer to mannitol do not occur as long as the activity-linked cysteine is oxidized or alkylated.A kinetic scheme has been developed which accounts for the relationships between the redox state, the phosphorylation state and the activity of the carrier. Kinetics of the individual reactions determine whether the enzyme cycles through an oxidized/reduced state during a cycle of phosphorylation/dephosphorylation.Abbreviations DTT Dithiothreitol - glc glucose - mtl mannitol - mtl-P mannitol Phosphate - frc fructose - bgl -glucoside - nag N-acetylglucosamine - PTS Phosphoenolpyruvate-dependent Phosphotransferase System - PEP Phosphoenolpyruvate - P-enolpyruvate Phosphoenolpyruvate     

ABI sequencing analysis

The ABI Sequencing Analysis application is designed specifically for the analysis of data produced by the ABI DNA Sequencer. The ABI sequencer is a laser-based instrument that utilizes fluorescent labels to analyze the products of a sequencing reaction as they migrate through a gel. After the data are collected from a sequencing run, the Analysis program identifies and tracks the sample lanes of the gel and subsequently normalizes and integrates the raw data into a chromatogram of the final sequence. For the use, there are basically two types of files that can be manipulated to potentially improve the analysis results. The Gel File consists of a computer generated image of the sequencing gel with the fluorescent DNA banding patterns. This image allows the user to view and edit the tracking lines generated and used by Analysis to collect data points for each sample. Individual Sample Files are stored for each of the samples analyzed and include the chromatogram, raw data, and annotations and information regarding the sample and sequence run. Generally, the products of a sequencing reaction are easily resolved and the Analysis software interprets the correct nucleotide sequence. Ambiguous base calls tend to occur near the end of the sequence and may be either edited or deleted by the user before exporting the data for further comparisons or alignments. Occasionally the tracking lines within the gel image may need to be adjusted or moved. The sample data are then reextracted from the Gel File and analyzed again. This review explains the general operation of Analysis in terms of viewing and editing a chromatogram, retracking the lanes of a Gel File, and analyzing the final sample data. The three versions 1.2.1, 2.1.2, and 3.3 are discussed.     

Modelling publication bias and p-hacking

Publication bias and p-hacking are two well-known phenomena that strongly affect the scientific literature and cause severe problems in meta-analyses. Due to these phenomena, the assumptions of meta-analyses are seriously violated and the results of the studies cannot be trusted. While publication bias is very often captured well by the weighting function selection model, p-hacking is much harder to model and no definitive solution has been found yet. In this paper, we advocate the selection model approach to model publication bias and propose a mixture model for p-hacking. We derive some properties for these models, and we compare them formally and through simulations. Finally, two real data examples are used to show how the models work in practice.     

create: a software to create input files from diploid genotypic data for 52 genetic software programs

create is a Windows program for the creation of new and conversion of existing data input files for 52 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, genetic data analysis, and specialized applications. create is able to read in data from text, Microsoft Excel and Access sources and allows the user to specify columns containing individual and population identifiers, birth and death data, sex data, relationship information, and spatial location data. create's only constraints on source data are that one individual is contained in one row, and the genotypic data is contiguous. create is available for download at http://www.lsc.usgs.gov/CAFL/Ecology/Software.html.     

Husbandry of the little file snake,Acrochordus granulatus

Aquatic snakes of the family Acrochordidae are unusual in terms of appearance, biology, and natural history. In spite of many attractive and fascinating features, there are few zoological exhibits of acrochordid snakes, and as a result many aspects of their husbandry are poorly understood. The present paper summarizes aspects of acrochordid biology related to health and welfare of captive snakes, with emphasis on the little file snake, Acrochordus granulatus. Several key points emerge having crucial relevance to successful husbandry. (1) File snakes are sensitive to low temperatures and to rapid thermal change. Captive snakes do well when maintained at water temperatures of 27–30°C and will not thrive if water temperatures are below 25°C. (2) File snakes can be kept in either fresh water or seawater. Snakes in sea or brackish water dehydrate, however, and must be allowed to drink fresh water periodically. If snakes from marine populations are maintained in saline water, 60–70% seawater is recommended. In all cases, water should be filtered or changed periodically to maintain quality. (3) File snakes feed almost exclusively on fishes which are usually captured in body coils. Snakes are more inclined to feed well if live prey are offered in shallow water where they are more easily captured. (4) File snakes are nocturnal and prefer quiescent seclusion within darkened refugia during daylight hours. Providing snakes with refugia such as sections of PVC pipe (which simulate burrows) helps reduce stress and improves the chances of snakes feeding regularly. (5) Snakes tend to burrow, and they locomote by crawling as well as by swimming. Use of sharp or rough materials in aquaria should be avoided because of possible skin abrasion which increases permeability and provides sites for bacterial infection. © 1996 Wiley-Liss, Inc.     

A parallel programming interface for out-of-core cluster applications

Clusters of workstations are a practical approach to parallel computing that provide high performance at a low cost for many scientific and engineering applications. In order to handle problems with increasing data sets, methods supporting parallel out-of-core computations must be investigated. Since writing an out-of-core version of a program is a difficult task and virtual memory systems do not perform well in some cases, we have developed a parallel programming interface and the support library to provide efficient and convenient access to the out-of-core data. This paper focuses on how these components extend the range of problem sizes that can be solved on the cluster of workstations. Execution time of Jacobi iteration when using our interface, virtual memory and PVFS are compared to characterize the performance for various problem sizes, and it is concluded that our new interface significantly increases the sizes of problems that can be efficiently solved. Jianqi Tang received B.Sc. and M.Sc. from Harbin Institute of Technology in 1997 and 1999 respectively, both in computer application. Currently, she is a Ph.D. candidate at the Department of Computer Science and engineering, Harbin Institute of Technology. She has participated in several National research projects. Her research interests include parallel computing, parallel I/O and grid computing. Binxing Fang received M.Sc. in 1984 from Tsinghua University and Ph.D. from Harbin Institute of Technology in 1989, both in computer science. From 1990 to 1993 he was with National University of Defense Technology as a postdoctor. Since 1984, he is a faculty member at the Department of Computer Science and engineering of Harbin Institute of Technology, where he is presently a Professor. He is a Member of the National Information Expert Consultant Group and a Standing Member of the Council of Chinese Society of Communications. His research efforts focus on parallel computing, computer network and information security. Professor Fang has implemented over 30 projects from the state and ministry/province. Mingzeng Hu was born in 1935. He has been with the Department of Computer Science and engineering in Harbin Institute of Technology since 1958, where he is currently a Professor. He was a visiting scholar in the Siemens Company, Germany from 1978 to 1979, a visiting associate professor in Chiba University, Japan from 1984 to 1985, and a visiting professor in York University, Canada from 1989 to 1995. He is the Director of the National Key Laboratory of Computer Information Content Security. He is also a Member of 3rd Academic Degree Committee under the State Council of China. Professor Hu’s research interests include high performance computer architecture and parallel processing technology, fault tolerant computing, network system, VL design, and computer system security technology. He has implemented many projects from the state and ministry/province and has won several Ministry Science and Technology Progress Awards. He published over 100 papers in core journals home and abroad and one book. Professor Hu has supervised over 20 doctoral students. Hongli Zhang received M.Sc in computer system software in 1996 and Ph.D. in computer architecture in 1999 from Harbin Institute of Technology. Currently, she is an Associate Professor at the Department of Computer Science and engineering, Harbin Institute of Technology. Her research interests include computer network security and parallel computing.