2D与3D景观指数测定山区植被景观格局变化对比分析

植被和土地覆盖变化是环境变化的一个重要因素,同时也是引起景观和生态系统变化的重要原因。景观指数是定量分析植被和土地覆盖变化的重要研究方法之一。以滇西北高山峡谷区为案例区,比较分析传统2D景观指数和3D景观指数进行植被变化定量测定的差异。研究主要选取了基于斑块面积和周长几个常用指数来进行比较分析。研究结果表明在斑块层次上,除了分维数指数,其他指数的三维方法计算值显著地高于二维方法计算值;在类型层次上,三维的类型面积指数、平均斑块面积指数、平均最小邻近距离指数测定的变化值显著大于二维的相应指数测定变化值,但是二维和三维平均形状指数和分维指数测定的植被斑块的平均形状变化结果没有显著差异;在景观层次,只有三维的平均斑块面积和最小邻近距离指数测定的变化结果显著高于二维的平均面积和最小邻近距离指数测定的变化结果,其它指数如形状指数、分维指数、多样性指数和均一度指数等测定出两个不同时期的植被图格局变化结果均无显著差异,主要由于这些指数是采用面积和周长的对数或者比值计算得出,从而缩小了斑块表面面积与平面面积,表面周长与平面周长之间的差异。总体而言,利用二维景观指数在进行定量分析山区植被格局变化时,往往低估了其类型面积、平均斑块面积、斑块邻近距离等指数变化量,而三维景观指数得到相对较精确的变化值。     

The use of PET/CT scanning technique for 3D visualization and quantification of real-time soil/plant interactions

Aims

Conventional methodology using destructive sampling, which is laborious and has poor spatial and temporal resolution, has limited our understanding of soil-plant interactions. New non-invasive tomographic techniques have the potential to significantly improve our knowledge. In this study we demonstrated the simultaneous use of PET (positron emission tomography) and CT (X-ray computed tomography) to (a) non-destructively image a whole plant growing in sand, and (b) to link the observed morphology with recently assimilated C. The PET scanner was used to detect and visualize the location of the short-lived radioisotope ¹¹C (with a half-life of 20.4?min) taken up by the plant through ¹¹C-labelled CO₂. This provided information on carbon translocation and the metabolism of photo-assimilates in the plant as well as root structure. The CT scanners yielded data on soil and root structure.

Methods

A medical PET/CT scanner was used to scan a fodder radish plant growing in a pot with test soil composed of homogenous sand. We constructed an air-plant-soil controller system (APS) to control the environmental conditions, such as CO₂, temperature and light during the experiment. The plant was allowed to assimilate ¹¹CO₂ for 90?min before PET scanning was initiated. We carried out PET scanning for 60?min. Subsequently, the aerial parts of the plant was cut off and the pot was rescanned using a micro-CT scanner to obtain more detailed information on structure of the root system and the growth medium structure.

Results

The acquired PET and CT images gave images clearly visualizing the architecture and morphology of root and soil. Using a CT scanner, we were able to detect the main taproot located at 0 to 30?mm depth. With the PET scanner, we were able to measure a signal down to 82?mm below the surface of the sand. We found the highest concentration of ¹¹C at the position of the main root. The PET images, at different time intervals, showed the translocation and metabolisation of photo-assimilates from top to root. Using the micro-CT scanner (voxel size of 90?μm), we were able to detect roots down to 100?mm depth. These findings correlated the PET signals measured down to 82?mm depth.

Conclusions

We conclude that the simultaneous use of PET and CT technologies was successfully applied for soil-plant studies. The combined PET/CT technology has potential to provide new fundamental insight into soil-plant interactions and especially into the effect of abiotic stresses in spite of the limitation due to spatial resolution.     

A novel staining method for quantification and 3D visualisation of capillaries and muscle fibres

The aim of this study was to introduce a combined fluorescent staining that clearly demonstrates capillaries and distinguishes them from the basal lamina of muscle fibres in skeletal muscle tissue. The triple staining with CD31, Griffonia (Bandeira) simplicifolia lectin (GSL I) and laminin efficiently distinguishes vascular endothelium from the basal lamina of skeletal muscle fibres in physiological and pathological conditions. The presented triple staining method has several advantages, which facilitate quantitative analysis of the capillary network, and its relation to individual muscle fibres.     

A flow cytometric technique for quantification and differentiation of bacteria in bulk tank milk

AIMS: The present study describes a flow cytometric technique for quantification and differentiation of bacteria in bulk tank milk according to the main cause of elevated counts. METHODS AND RESULTS: A total of 75 Danish bulk tank milk samples exceeding the grading level of 3.0 x 10(4) CFU ml(-1) were examined by both flow cytometry and traditional microbiological analyses. The correlation coefficient (r) between the two methods was 0.71. For the differential analyses of the dominant bacterial populations four different parameters were used to give a species-characteristic pattern. The four parameters were as follows: staining with Oregon Green conjugated wheat germ agglutinin that binds to the cell wall of bacteria, staining with hexidium iodide that binds to all bacterial DNA, the flow cytometric forward scatter and the flow cytometric side scatter. Three regions in the flow cytometric plot were defined: region 1 includes bacteria mainly associated with poor hygiene, region 2 includes psychrotrophic hygiene bacteria and region 3 includes bacteria mainly related to mastitis. The ability of the flow cytometric technique to predict the main cause of elevated bacterial counts on routine samples was examined. Comparing these results with results obtained by traditional microbiological analyses for identification showed that for 81% of the samples the two techniques agreed on the main cause of an elevated bacterial count. CONCLUSIONS: The ability of the presented flow cytometric technique to enumerate and differentiate bacteria in bulk tank milk according to the main cause of elevated counts was demonstrated. SIGNIFICANCE AND IMPACT OF THE STUDY: This study described the first step in development of a technique suitable for routine analyses of bulk tank milk samples. A technique indicating the main cause of an elevated count will enable the farmer to eliminate the contamination source within a short time limit.     

A simple impregnation technique for thin and semithin enterochromaffin cells in sections

Constant, intense and precise impregnation of enterochromaffin (EC) cells was achieved simply by floating thin or semithin sections of gut mucosa, fixed in osmium tetroxide or in glutaraldehyde with postfixation in osmium, on a silver nitrate or proteinate solution. EC cells alone showed impregnation in the light microscope. In the electron microscope, impregnation affected not only the secretory granules of EC cells but also, although much more faintly, those of other, non-EC cells (D, X, D1, G and other cells). Lysosomes also showed partial or total reactivity. Oxidation reduced but did not entirely suppress EC cell staining and had no effect on non-EC endocrine cell staining. Since the reaction did not occur with glutaraldehyde alone, osmium appeared to be a crucial component of the process. These findings should be borne in mind in applying Thiery's method for vicinal glycol groups to the type of study material used in these experiments.     

A simple impregnation technique for thin and semithin enterochromaffin cells in sections

Summary Constant, intense and precise impregnation of enterochromaffin (EC) cells was achieved simply by floating thin or semithin sections of gut mucosa, fixed in osmium tetroxide or in glutaraldehyde with postfixation in osmium, on a silver nitrate or proteinate solution. EC cells alone showed impregnation in the light microscope. In the electron microscope, impregnation affected not only the secretory granules of EC cells but also, although much more faintly, those of other, non-EC cells (D, X, D₁, G and other cells). Lysosomes also showed partial or total reactivity. Oxidation reduced but did not entirely suppress EC cell staining and had no effect on non-EC endocrine cell staining. Since the reaction did not occur with glutaraldehyde alone, osmium appeared to be a crucial component of the process. These findings should be borne in mind in applying Thiery's method for vicinal glycol groups to the type of study material used in these experiments.     

Single camera photogrammetric technique for restricted 3D motion analysis

The purpose of this study was to use a single camera to determine the true elbow flexion angle with the arm plane oriented arbitrarily with respect to the camera. A mathematical theory was developed and a mechanical arm model was constructed to validate the theory. A static weightlifting skill was analysed to investigate the viability of the technique on the human subject. The validation of the theory showed the error associated with the elbow flexion angle was reduced from as high as 108° when uncorrected to within 3° when corrected by the technique. The elbow flexion angle of the human arm can be calculated to within 6° of error for static weightlifting skill analysis.     

A new in vivo technique for determination of femoro-tibial and femoro-patellar 3D kinematics in total knee arthroplasty

Aim was to develop an in vivo technique which allows determination of femoro-tibial and of femoro-patellar 3D-kinematics in TKA simultaneously. The knees of 20 healthy volunteers and of eight patients with TKA (PCR, rotating platform) were investigated. Kinematics analysis was performed in an open MR-system at different flexion angles with external loads being applied. The TKA components were identified using a 3D-fitting technique, which allows an automated 3D-3D-registration of the TKA. Femoro-patellar and femoro-tibial 3D-kinematics were analyzed by image postprocessing. The validity of the postprocessing technique demonstrated a coefficient of determination of 0.98 for translation and of 0.97 for rotation. The reproducibility yielded a coefficient of variation (CV%) for patella kinematics between 0.17% (patello-femoral angle) and 6.8% (patella tilt). The femoro-tibial displacement also showed a high reproducibility with CV% of 4.0% for translation and of 7.1% for rotation. While in the healthy knees the typical screw-home mechanism was observed, a paradoxical anterior translation of the femur relative to the tibia combined with an external rotation occurred after TKA. Fifty percent of the TKA's experienced a condylar lift-off of >1mm predominately on the medial side. Regarding patellar kinematics significant changes were found in both planes in TKA with an increased patella height in the sagittal plane and patella tilt and shift in the transversal plane. The results demonstrate that the presented 3D MR-open based method is highly reproducible and valid for image acquisition and postprocessing and provides--for the first time--in vivo data of 3D-kinematics of the tibio-femoral and simultaneously of the patello-femoral joint during knee flexion.     

A new in vivo technique for determination of 3D kinematics and contact areas of the patello-femoral and tibio-femoral joint

Patello-femoral disorders are often caused by changes of patello-femoral and/or tibio-femoral kinematics. However, until now there has been no quantitative in vivo technique, that is able to obtain 3D kinematics and contact areas of all knee compartments simultaneously on a non-invasive basis. The aim of this study was therefore to develop and apply a technique which allows for determination of 3D kinematics and contact areas of the patello-femoral and tibio-femoral joint during different knee flexion angles and under neuromuscular activation patterns. One knee of each of the 10 healthy volunteers was examined in an open MR system under flexing isometric muscle activity at 30 degrees and 90 degrees. Three-dimensional kinematics and contact areas of the patello-femoral and tibio-femoral joints were analyzed by 3D image postprocessing. The reproducibility of the imaging technique yielded a coefficient of variation of 4.6% for patello-femoral, 4.7% for femoro-tibial displacement and 8.6% for contact areas. During knee flexion (30-90 degrees ), patella tilt (opened to medial) decreased (8.8+/-3.4 degrees vs. 4.6+/-3.1 degrees, p<0.05), while lateral patellar shift increased significantly (1.6+/-2.3mm vs. 3.4+/-3.0mm, p<0.05). Furthermore, a significant posterior translation and external rotation of the femur relative to the tibia was observed. Patello-femoral contact areas increased significantly in size (134+/-60mm(2) vs. 205+/-96 mm(2)) during knee flexion. This technique shows a high reproducibility and provides physiologic in vivo data of 3D kinematics and contact areas of the patello-femoral and the tibio-femoral joint during knee flexion. This allows for advanced in vivo diagnostics, and may help to improve therapy of patello-femoral disorders in the future.     

Validation of 3D spino-pelvic muscle reconstructions based on dedicated MRI sequences for fat-water quantification

ObjectivesTo evaluate a protocol, including MRI acquisition with dedicated sequences for fat-water quantification and semi-automatic segmentation, for 3D geometry measurement and fat infiltration of key muscles of the spino-pelvic complex.Materials and methodsMRI protocol: two axial acquisitions from the thoraco-lumbar region to the patella were obtained: one T1-weighted and one based on the Dixon method, permitted to evaluate the proportion of fat inside each muscle. Muscle reconstruction: with Muscl’X software, 3D reconstructions of 18 muscles or groups of muscles were obtained identifying their contours on a limited number of axial images 3D references were obtained only on T1 acquisitions identifying the contour of the muscles on all axial images. Evaluation: for two volunteers, three operators completed reconstructions three times across three sessions. Each reconstruction was projected on the reference to calculate the ‘point to surface’ error. Mean and maximal axial section, muscle volume, and muscle length calculated from the reconstructions were compared to reference values, and intra- and inter-operator variability for those parameters were evaluated.Results2xRMS ‘point to surface’ error was below 3 mm, on average. The agreement between the two methods was variable between muscles [–4.50; 8.00%] for the mean axial section, the length and the volume. Intra- and inter-operator variability were less than 5% and comparison of variability for the Fat and T1 reconstructions did not reveal any significant differences.DiscussionExcellent inter- and intra-operator reliability was demonstrated for 3D muscular reconstruction using the DPSO method and Dixon images that allowed generation of patient-specific musculoskeletal models.     

An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays

A flat microdevice which incorporates a thin-film amorphous silicon (a-Si:H) photodetector with an upper layer of functionalized SiO₂ is used to quantify the density of both immobilized and hybridized DNA oligonucleotides labeled with a fluorophore. The device is based on the photoconductivity of hydrogenated amorphous silicon in a coplanar electrode configuration. Excitation, with near UV/blue light, of a single-stranded DNA molecule tagged with the fluorophore 1-(3-(succinimidyloxycarbonyl)benzyl)-4-(5-(4-methoxyphenyl)oxazol-2-yl) pyridinium bromide (PyMPO), results in the emission of visible light. The emitted light is then converted into an electrical signal in the photodetector, thus allowing the optoelectronic detection of the DNA molecules. The detection limit of the present device is of the order of 1 × 10¹² molecules/cm² and is limited by the efficiency of the filtering of the excitation light. A surface density of 33.5 ± 4.0 pmol/cm² was measured for DNA covalently immobilized to the functionalized SiO₂ thin film and a surface density of 3.7 ± 1.5 pmol/cm² was measured for the complementary DNA hybridized to the bound DNA. The detection concept explored can enable on-chip electronic data acquisition, improving both the speed and the reliability of DNA microarrays.     

A themogravimetric analysis for poly(3-hydroxybutyrate) quantification

Summary A simple and quick thermogravimetric analysis method has been suggested for poly(3-hydroxybutyrate) [PHB] quantification. During the analysis, a rapid thermal degradation of PHB occurred in the range of 250 to 320 °C. From the gravimetric change during the thermal degradation, we could quantify PHB contents of various samples. Due to the simultaneous thermal degradation of cellular materials, the PHB contents were estimated slightly higher than those by gas chromatographic analysis. We have proposed a way to compensate for such errors using a linear correlation to allow accurate determination of PHB contents.     

Membrane filter technique for the quantification of stressed fecal coliforms in the aquatic environment.

A two-layer membrane filtration (MF) medium (injury-mitigating MF [IM-MF]) and a procedure for the enumeration of injured fecal coliforms are described. These procedures included the addition of glycerol and acetate plus reducing agents to both layers of a two-layer medium and rinsing of the filter with a rich resuscitation medium. Some changes in incubation time and temperatures were used. This method was compared with the multiple-tube fermentation most-probable-number procedure and the one-step M-FC agar-membrane filter method (direct M-FC) in terms of fecal coliform recovery from various aquatic environments that cause bacterial injury. With chlorinated sewage effluents, results of the IM-MF technique were equal to or greater than the most probable number in 9 of 18 trials and were 1.3 to 19 times greater than the M-FC method. When sewage samples were chlorinated in the laboratory, fecal coliform counts with IM-MF equaled or exceeded the most probable number in 7 of 15 trials and always exceeded the M-FC. M-FC was exceeded by IM-MF in 30 of 33 trials with clean mountain stream water. Fecal coliform bacteria that were exposed to low levels of an iodophore in the laboratory produced IM-MF counts 3 to 10 times greater than those with M-FC. A biochemical rationale for the formation of the IM-MF medium is discussed.     

Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analog. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyze bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance toward the discovery of the mechanisms of microbial colonisation of the rhizosphere.     

Functional morphology of synarthrial articulations in the crinoid stem

Synarthrial fulcral ridges are found in crinoid columnals from the mid-Ordovician to the present and in all four subclasses. Similar articulations did not become common in the cirri until the Mesozoic. Synarthrial stem articulations fall into two broad groups. Type I articulations have a fulcral ridge in the centre of the articular facet. In elliptical ossicles this ridge corresponds to either the long (IA) or short (IB) axis of the facet. Although both are functionally similar, Type IA ossicles are more common. Type II articulations have an excentric fulcral ridge, parallel to either the long (IIA) or short (IIB) axis of the articular facet. Type IIA articulations are found in crinoid stems capable of coiling. Type II articulations are particularly common in the cirri of articulates and are well adapted for attachment to hard and soft substrates. Columnals with Type I articulations often have divergent fulcra, giving the stem flexibility in all directions, but this feature is not seen in cirri or in coiled stems, where it would impair normal functions. Only the cirri of isocrinids and comatulids are muscular, so the movement of columns with fulcra must be passive.