Evaluation and recommendations for greater accessibility of colour figures in ornithology

People who are colour‐blind or have some form of colour vision deficiency form an invisible minority and scientists should strive to be as inclusive as possible. We reviewed 2873 figures published in 2019 from 1031 scientific papers in 27 ornithological journals to determine those that were colour‐blind compatible, and those that were black‐and‐white printer friendly. About 26% of the published figures were in colour, and while most were colour‐blind compatible, only ~ 60% of them were black‐and‐white printer friendly. Ensuring figures in all forms of scientific communication can be interpreted by readers who are colour‐blind, and can be printed in black‐and‐white will improve the accessibility of ornithological research.     

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.     

Colour model analysis for microscopic image processing

This article presents a comparative study between different colour models (RGB, HSI and CIEL*a*b*) applied to a very large microscopic image analysis. Such analysis of different colour models is needed in order to carry out a successful detection and therefore a classification of different regions of interest (ROIs) within the image. This, in turn, allows both distinguishing possible ROIs and retrieving their proper colour for further ROI analysis. This analysis is not commonly done in many biomedical applications that deal with colour images. Other important aspects is the computational cost of the different processing algorithms according to the colour model. This work takes these aspects into consideration to choose the best colour model tailored to the microscopic stain and tissue type under consideration and to obtain a successful processing of the histological image.     

Time domain analysis of oxygen uptake during pseudorandom binary sequence exercise tests.

Pseudorandom binary sequence (PRBS) exercise tests involve repeated switching between two work rates (WR) according to a computer-generated pattern. This paper presents an approach to analysis of O2 uptake (VO2) in the time domain. First, the autocorrelation function (ACF) of the input WR was recognized to be a triangular-shaped pulse that can be taken to be equivalent to a ramp increase followed by a ramp decrease in WR. Then the cross-correlation function of the input (WR) and the output (VO2) was treated as if it were the response to a triangular-shaped pulse. The cross-correlation function was analyzed by fitting a linear summation of the ramp form of a two-component exponential function to this triangular pulse. VO2 responses of eight subjects were obtained from two different PRBS tests, as well as step changes in WR. The first PRBS test consisted of 15 units, each 30 s in duration. Its ACF had a base width of 60 s. The ramp increase-ramp decrease model fit the data throughout the range of response. The second PRBS test had 63 units, each 5 s in duration; thus its ACF base width was 10 s. Again, the ramp model fit adequately. The data from the second PRBS test could be fit by the impulse form of the two-component exponential equation, although the fit in the first 30 s tended to be poorer. The time constants of VO2 dynamics estimated from step and PRBS tests were not significantly different. PRBS tests can be analyzed in the time domain, and the indicators of system dynamics reflect physiological properties similar to those investigated during step changes in WR.     

SwarmPS: rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.     

In Vitro Import of a Nuclearly Encoded tRNA into the Mitochondrion of Trypanosoma brucei

All of the mitochondrial tRNAs of Trypanosoma brucei have been shown to be encoded in the nucleus and must be imported into the mitochondrion. The import of nuclearly encoded tRNAs into the mitochondrion has been demonstrated in a variety of organisms and is essential for proper function in the mitochondrion. An in vitro import assay has been developed to study the pathway of tRNA import in T. brucei. The in vitro system utilizes crude isolated trypanosome mitochondria and synthetic RNAs transcribed from a cloned nucleus-encoded tRNA gene cluster. The substrate, composed of tRNA(Ser) and tRNA(Leu), is transcribed in tandem with a 59-nucleotide intergenic region. The tandem tRNA substrate is imported rapidly, while the mature-size tRNA(Leu) fails to be imported in this system. These results suggest that the preferred substrate for tRNA import into trypanosome mitochondria is a precursor molecule composed of tandemly linked tRNAs. Import of the tandem tRNA substrate requires (i) a protein component that is associated with the surface of the mitochondrion, (ii) ATP pools both outside and within the mitochondrion, and (iii) a membrane potential. Dissipation of the proton gradient across the inner mitochondrial membrane by treatment with an uncoupling agent inhibits import of the tandem tRNA substrate. Characterization of the import requirements indicates that mitochondrial RNA import proceeds by a pathway including a protein component associated with the outer mitochondrial membrane, ATP-dependent steps, and a mitochondrial membrane potential.     

Reproductive isolation among deep-water cichlid fishes of Lake Malawi differing in monochromatic male breeding dress

Male nuptial colour hues are important for the maintenance of reproductive isolation among cichlid fish species, and environmental changes that lead to narrower light spectra can lead to hybridization. However, cichlid species can naturally co-occur in narrow light spectrum habitats, such as turbid shallow lakes and the deep benthic zones of African rift lakes. Closely related species from narrow light spectrum habitats tend to differ little in the palette of male nuptial colours, thus for these taxa differences in colour patterns may be more important than differences in colour hue for species recognition. To investigate this hypothesis we examined morphometric and genetic differentiation among males of four sympatric putative species within the deep-water genus Diplotaxodon. These taxa live in a narrow-light spectrum environment where only blue light is present, and males differ primarily in 'monochromatic' black, white and silver patterning of the body and fins. Significant genetic differentiation was present among taxa in both microsatellite DNA and mitochondrial DNA, including one pair with no significant morphometric differentiation. Thus, these taxa represent reproductively isolated biological species, a result consistent with male nuptial patterning being important for species recognition and assortative mating. As such, we suggest that narrow-light spectra need not always represent barriers to effective visually mediated mate recognition.     

Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach

Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow.The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR) software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow.     

On the modeling and interpretation of oxygen uptake kinetics from ramp work rate tests

Ramp work rate tests have been used to estimate aerobic parameters in exercise stress testing. Previous studies have suggested an assumption of a linear dynamic system for O2 uptake kinetics. The implication is that model parameters estimated from ramp tests should be similar to those estimated from other dynamic tests. In nine healthy subjects, we found that model parameters used to characterize O2 consumption ramp data were not consistent with those used to characterize step data, when the comparison was made on a subject-to-subject basis. Furthermore the ramp data model parameter values were highly dependent (P less than 0.0001) on the ramp slope. A linear dynamic system interpretation of the ramp data model does not appear to be appropriate, suggesting that caution is needed in the interpretation of ramp data aerobic parameters. The data may be better described by nonlinear or higher order function. Ramp exercise testing is not suitable for assessing dynamic control properties of the cardiorespiratory response to exercise.     

Ultrastructure and functional morphology of a nematalycid mite (Acari: Actinotrichida: Endostigmata: Nematalycidae): adaptations to mesopsammal life*

Nematalycid mites have undergone extreme changes of body shape in adaptating to life in tiny spaces between grains of fine sand. Because of their minute size, the morphology of these organisms can only be reconstructed from ultrathin serial sections. The cuticle forms regular alternating palettes on the surface; such a structure may also function as a plastron. Movement of the body is effected by a continuous secondary muscle layer beneath the epidermis which operates in connection with the cuticular palettes. This movement represents a hitherto unknown mode of reptation, which can be understood as an adaptation to moving among sand particles. The appendages have been reduced to a minute size. The morphology of the digestive tract is described and conclusions are drawn concerning nutrition.     

冷冻电镜单颗粒三维重构密度掩模的自动生成方法研究

冷冻电镜单颗粒三维重构技术是用来解析生物大分子三维结构的常用方法.然而目前在单颗粒三维重构过程中,溶剂平滑操作还存在一定缺陷:没有一款主流的单颗粒三维重构程序能够自动寻找掩模(mask)三维密度图,使得三维重构过程难免受到噪音统计学模型计算偏差的干扰.为解决这一问题,本研究借鉴X射线晶体学中解析优化相位所广泛采用的溶剂平滑方法,采用高斯滤波、坎尼边缘检测、最小误差阈值处理等方法处理重构所得三维密度图,优化溶剂平滑操作,发展在单颗粒三维重构过程中自动寻找mask三维密度图的方法.运用三维密度图傅里叶壳层相关系数(fourier shell correlation,FSC)曲线图、模拟颗粒数据重构角度误差散点图等指标评估此方法的效果.结果表明,自动寻找mask密度图的方法能够较好地找到涵盖分子结构信号区域的mask密度图,较为明显提高三维重构所得密度图分辨率.     

The dynamic dimerization of the yeast ADP/ATP carrier in the inner mitochondrial membrane is affected by conserved cysteine residues

The ADP/ATP carrier (AAC) that facilitates the translocation of ATP made in mitochondria is inserted at the inner mitochondrial membrane by the TIM10-TIM22 protein import system. Here we addressed the state of the AAC precursor during insertion (stage IV of import) and identified residues of the carrier important for dimerization. By a combination of (i) import of a mix of His-tagged and untagged versions of AAC either 35S-labeled or unlabeled, (ii) import of a tandem covalent dimer AAC into wild-type mitochondria, and (iii) import of monomeric AAC into mitochondria expressing only the tandem covalent dimer AAC, we found that the stage IV intermediate is a monomer, and this stage is probably the rate-limiting step of insertion in the membrane. Subsequent dimerization occurs extremely rapidly (within less than a minute). The incoming monomer dimerizes with monomeric endogenous AAC suggesting that the AAC dimer is very dynamic. Conserved Cys residues were found not to affect insertion significantly, but they are crucial for the dimerization process to obtain a functional carrier.     

A Macintosh program for the versatile generation of random nucleic acid sequences and their structural analysis

The program ‘MacStAn’ for the Apple Macintosh generatesrandom sequences and can analyze their tendency to form secondarystructure or translation products as well as their mono-, di-and trinucleotide composition. Generation of random sequencesis versatile in that one can (i) predefine the G + C content,maximal base repetitions and constant regions; (ii) preset theentire dinucleotide composition; or (iii) shuffle an existingsequence. The program constitutes an integrated package witha graphical user interface, fill-featured editing, saving, printing,text import and export, dot plot and sequence alignment.     

Development of a MATLAB based bioprocess simulation tool

A simple user friendly mathematical modelling tool was developed on the basis of MATLAB software. The program system provides the possibility of solving differential equation system with the aid of an easy-to-use graphical surface. It is suitable for bioprocess engineering simulations to describe the dynamic behaviour of a great series of various enzyme, fermentation and environmental bioreaction systems. It is especially beneficial that non-time interventions can also be modelled and graphical representations can be realized on a wide palette.     

PROTEUS: a suite of programs for prediction of structural features of proteins using an Apple lie

We have implemented several algorithms, developed by variousauthors for predicting structural features of proteins fromtheir primary structure, on an Apple lle and collected themin a suite, named PROTEUS. This suite incorporates: (i) methodsfor predicting secondary structure; (ii) the algorithm for computingthe hydropathy profile using one out of five available setsof parameters; (ii) the algorithms for calculating the hydrophobicmoment plot; and (iv) for performing the amphipathic analysisusing one out of four available sets of parameters. The suitehas a utility program for storing on a disk the sequence tobe analysed. As an example, we applied some of the methods includedin PROTEUS to predict the structure of a mitochondnal leaderpeptide. The results suggest the occurrence of structural featurespossibly related to the import of proteins into mitochondria. Received on April 30, 1987; accepted on July 21, 1987     

Design of an automated temperature mapping system for ultrasound or microwave hyperthermia

An automated temperature mapping system was designed to accomplish the following goals: remote control mapping; a maximum position error of 0.5 mm; mapping simultaneously on several channels; real-time screen display on a dedicated computer; to be inexpensive; and have a simple patient interface and set up. A four channel, microstepper system was fabricated for less than $1000 and controlled by an IBM-AT computer. The system utilizes direct drive of Luxtron fibre-optic probes fed through thin flexible Teflon^® tubing which allows for patient movement. The driving and control software were written in the programming language “C”. Mapping parameters for each independent channel include start and stop positions and map increment. The software permits the user to automatically find the maximum temperature along a track in three passes of 2.0, 1.0 and 0.5 mm steps. The latter two passes take five or seven readings centred about the maximum of the previous pass. A high resolution monitor plots the temperatures in real time, overlaying the previous map in a new colour. A screen dump was written to drive a colour printer with the plot information. The computer evaluates each plot to safeguard against any shift in the maximum location. Visualization of orthogonal pullbacks provides rapid feedback and aids in the repositioning of superficial hyperthermia transducers. The time saved over the previous manual mapping methods easily justifies the additional set up time.     

Dynamics of ventilation, circulation, and gas exchange to incremental and decremental ramp exercise.

Transient responses of minute volume (VE), O2 uptake (VO2), CO2 output (VCO2), heart rate (HR), and cardiac output (Q) to a step change and ramp changes with slopes ranging from 33.3 to 14.3 W/min were studied in five healthy human subjects over the load range from 25 to 125 W. The ramp responses were fitted to a first-order model with a pure time delay (td) and a time constant (TC), while most of the step responses fitted better to a second-order model, consisting of a fast and a slow component. No significant asymmetry was observed between the on- and off-responses to step forcing. The mean response time (MRT = td+TC) of the incremental ramp response was prolonged, whereas the MRT of the decremental ramp response was shortened or unchanged, with decreasing ramp slope. The asymmetry was commonly observed in respiratory and gas exchange variables and, to a lesser extent, also in circulatory variables. Neural and humoral factors that might be responsible for this phenomenon are discussed.