Bsoft: image and molecular processing in electron microscopy

Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages.     

Improved Human Sperm Recovery Using Superoxide Dismutase and Catalase Supplementation in Semen Cryopreservation Procedure

The aim of this work was to evaluate the effects of ROS scavenger supplementation in human semen samples undergoing cryopreservation procedures.After screening out andrological pathologies, we selected 25 male partners of infertile couples with the following semen profile: volume >/= 2.0 ml, normal viscosity, sperm count >/=20 x 10(6)/ml, straight progressive motility (classes 1 and 2) >/= 40% (Mazzilli, Rossi, Delfino and Nofroni (1999) Andrologia 31: 187-194), atypical forms 相似文献   

Automated identification of Fos expression

The concentration of Fos, a protein encoded by the immediate-early gene c-fos, provides a measure of synaptic activity that may not parallel the electrical activity of neurons. Such a measure is important for the difficult problem of identifying dynamic properties of neuronal circuitries activated by a variety of stimuli and behaviours. We employ two-stage statistical pattern recognition to identify cellular nuclei that express Fos in two-dimensional sections of rat forebrain after administration of antipsychotic drugs. In stage one, we distinguish dark-stained candidate nuclei from image background by a thresholding algorithm and record size and shape measurements of these objects. In stage two, we compare performance of linear and quadratic discriminants, nearest-neighbour and artificial neural network classifiers that employ functions of these measurements to label candidate objects as either Fos nuclei, two touching Fos nuclei or irrelevant background material. New images of neighbouring brain tissue serve as test sets to assess generalizability of the best derived classification rule, as determined by lowest cross-validation misclassification rate. Three experts, two internal and one external, compare manual and automated results for accuracy assessment. Analyses of a subset of images on two separate occasions provide quantitative measures of inter- and intra-expert consistency. We conclude that our automated procedure yields results that compare favourably with those of the experts and thus has potential to remove much of the tedium, subjectivity and irreproducibility of current Fos identification methods in digital microscopy.     

核磁共振检测大鼠早期癫痫源性脑损伤的动态发展特征

为探讨癫痫源性脑损伤形成早期不同脑区病理改变和行为发作的动态发展特征 ,本研究对大鼠右背侧海马 (hippocampus,HPC)施加慢性强直电刺激 (6 0Hz,2s,0 .4～ 0 .6mA)诱发癫痫发作 ,1次 /d。每天记录大鼠原发性湿狗样抖动 (wetdogshakes,WEDS)频率 ,分别对大鼠施加电刺激 2、4、6、8和 10d后进行核磁共振成像 (T2 weightedmagneticresonanceimage ,T2 WI)检测 ,并对鼠脑进行了组织学切片鉴定。结果表明 :与空白对照组相比较 ,(1)施加 2d强直电刺激时 ,大鼠双侧背部侧脑室 (lateralventricle,LV)区域呈现对称性T2 WI信号绝对值增加 (n =4,左侧P =0 .0 0 18;右侧P =0 .0 0 10 ) ;施加 6d强直电刺激时 ,大鼠呈现植入电极对侧中、腹部LV区域T2 WI信号值增加 (n =5 ,P =0 .0 0 73;P =0 .0 2 49) ;施加 8d强直电刺激后 ,大鼠仅出现植入电极对侧腹部LV区域T2 WI信号值增加 (n =3,P =0 .0 34 0 ) ;施加 10d强直电刺激后 ,大鼠植入电极同侧腹部LV区域T2 WI信号值增加 (n =4,P =0 .0 10 7) ;(2 )随着强直电刺激天数增加 ,大鼠原发性WEDS频率高峰期出现在第 4个刺激日 ,然后WEDS频率下降 ,与T2 WI信号强度增加之间呈高度负相关关系 (相关系数r =- 0 .987,P <0 .0 2 ) ;(3)组织学切片鉴定 :T2 WI检测LV信号异     

Image processing,diagnostic information extraction and quantitative assessment in pathology

As we enter the information age we hold strong beliefs in the benefits of digital technology applied to pathology: numerical representation offers objectivity . Digital knowledge may indeed lead to significant information discovery, and, processing systems might be designed to allow a true evolution of capabilities. Questions arise whether the methodology underlying quantitative analysis provides the information that we need and whether it is appropriate for some of the problems encountered in diagnostic and prognostic histopathology. While one certainly would not dispute the value of statistical procedures, the clinical needs call for individual patient targeted prognosis.     

Morphological quantification of pellets in Streptomyces hygroscopicus var. geldanus fermentation broths using a flatbed scanner

An image analysis technique has been developed to allow high throughput morphological characterisation of microbial fermentation broths containing spherical pellets greater than 100 m in diameter. Images of stained Streptomyces hygroscopicus var. geldanus culture samples at three different inoculum levels were captured using a flatbed scanner, at a resolution of 21 m per pixel (1200 dots per inch) and subsequently analysed leading to the generation of a morphological profile of each sample. The time taken for image capture and analysis of a prepared sample, containing approx. 2000 particles, was 3 min 6 s.     

Habitat Degradation of Rhinopithecus bieti in Yunnan, China

Black-and-white snub-nosed monkeys (Rhinopithecus bieti) are endemic to the Trans-Himalayas in Northwest Yunnan and Southeast Tibet between the upper Yangtze and Mekong Rivers. Based on field surveys and previous reports, we identified the dark-coniferous forest, the mixed coniferous and broadleaf forest, and oak patches as suitable habitats (SH) for the monkeys. Summer grazing lands (SGL), which were made by local people cutting and burning the dark-coniferous forest at the high altitude belt, replaced SH. To have a general view of the status of the SH in Yunnan, we estimated the areas of SH and SGL from satellite images in 1997, and compared with areas estimated from aerial photo-based maps (ca. 1958). The work resulted in: 1) the area of SH was 4,169 km² in 1997; 2) SGL was 1,923 km²; 3) during the past 40 years, the area of SH decreased by 31% (1,887 km²), and SGL increased by 204% (1,291 km²); and 4) the mean size of forest patches decreased from 15.6 to 5.4 km². In addition, the area of SGL is positively correlated to local human population (R² 0.53), implying that the reduction and fragmentation of habitat for Rhinopithecus bieti is a result of population growth of humans, who mostly employ traditional modes of production. Only 11 monkey groups remained in the changing habitat. Considering that forests at lower elevation were also encroached upon by farmlands in a similar way, the forest ecosystem is highly threatened. The destruction will continue unless there is a change in the mode of production in the region.     

Estimation of the canopy-gap size using two photographs taken at different heights

A new, convenient method to estimate canopy-gap size using a camera is proposed. Canopy-gap size was estimated from two images taken with a vertically mounted, digital camera at high and low points (P_h and P_l) beneath a canopy gap. The actual (A_OBS) and estimated (A_1.0) canopy-gap sizes were highly correlated (R² > 0.93) for 16 canopy gaps in the Cryptomeria japonica D. Don. plantations, and the relationship between A_1.0 and A_OBS was expressed as A_1.0 = 1.16A_OBS. Thus, the method overestimated actual canopy-gap size by an average of 16%.     

A case of chronic cerebral paragonimiasis westermani

We report a chronic cerebral paragonimiasis from a 41-year-old Korean man who complains a headache and weakness of left motor neuron components. Magnetic resonance images of the brain revealed conglomerates of multiple ring-like enhancements in temporo-occipital and frontal lobes of the right hemisphere. An intradermal test for paragonimiasis westermani was positive. The patient was born near an endemic area of paragonimiasis and used to eat boiled or grilled freshwater crayfish in his childhood. Nodules in the brain were resected through craniotomies. The eggs of P. westermani were identified pathologically and parasitologically in the calcified necrotic lesions. Examinations on sputum and fecal specimens for the eggs of P. westermani were shown to be negative and a chest radiograph was normal. It is presumed that the brain lesions were formed by P. westermani approximately 30 years ago.