~(12)C~(6+)离子束辐照紫苏干种子当代效应；Effects of Irradiation with ~(12)C~(6+) Ions on M1 Characters of Perilla frutescens(L.) Britt

利用兰州重离子研究装置(HIRFL)提供的12C6+离子束辐照紫苏干种子(辐照剂量为40,80和120Gy,剂量率4Gy/min),探讨了重离子束辐照对紫苏M1代的生物学效应。结果发现,经不同剂量的12C6+离子束辐照后,紫苏种子的发芽率、发芽势、存活率、株高、分枝数、单株产量和千粒重等生物学性状均发生了变化,其中发芽势、单株产量和千粒重随辐照剂量的提高而降低,且有明显的剂量效应关系,但发芽率、大田成活率、株高和分枝数却随辐照剂量的增大,呈现出明显的"抛物线"趋势;紫苏幼苗根尖细胞的微核率和染色体畸变率随辐照剂量增加呈线性增加关系。这表明:12C6+重离子束辐照紫苏种子,具有明显的当代损伤效应,在本试验剂量范围内,低剂量辐照对发芽率和成活率有促进作用。

Growth characters and photosynthetic capacity of Gracilaria lemaneiformis as a biofilter in a shellfish farming area in Sanggou Bay, China

Experiments on growth characters and ecological functions of the macroalgae Gracilaria lemaneiformis, collected from south China, were conducted in polyculture areas of kelp and filter-feeding bivalve in Sanggou Bay in Weihai City, Shandong, in north China from May 2002 to May 2003. The results of 116 days cultivation showed that the average wet weight of alga increased 89 times from 0.1 to 8.9 kg rope(-1), with an average specific growth rate ( based on wet weight) of 3.95% per day. The most favorable water layer for its growth was 1.0 - 1.8 m below the surface in July and August, with an average specific growth rate of 8.2% per day in 30-day experiments. Photosynthetic activity changed seasonally, with an average of 7.3 mg O-2 g dw(-1) h(-1). The maximum rate (14.4 mg O-2 g dw(-1) h(-1)) was recorded in July, or 19.3 mg CO2 g dw(-1) h(-1), while the minimum (0.40 mg CO2 g dw(-1) h(-1)) was in April. This study indicated that the culture of G. lemaneiformis is an effective way to improve water quality where scallops are cultivated intensively.

左中部梭状回枕颞沟内皮质对汉字加工的必要性、选择性和作用性质

A number of functional neuroimaging studies with skilled readers consistently showed activation to visual words in the left mid-fusiform cortex in occipitotemporal sulcus (LMFC-OTS). Neuropsychological studies also showed that lesions at left ventral occipitotemporal areas result in impairment in visual word processing. Based on these empirical observations and some theoretical speculations, a few researchers postulated that the LMFC-OTS is responsible for instant parallel and holistic extraction of the abstract representation of letter strings, and labeled this piece of cortex as “visual word form area” (VWFA). Nonetheless, functional neuroimaging studies alone is basically a correlative rather than causal approach, and lesions in the previous studies were typically not constrained within LMFC-OTS but also involving other brain regions beyond this area. Given these limitations, it remains unanswered for three fundamental questions: is LMFC-OTS necessary for visual word processing? is this functionally selective for visual word processing while unnecessary for processing of non-visual word stimuli? what are its function properties in visual word processing? This thesis aimed to address these questions through a series of neuropsychological, anatomical and functional MRI experiments in four patients with different degrees of impairments in the left fusiform gyrus. Necessity: Detailed analysis of anatomical brain images revealed that the four patients had differential foci of brain infarction. Specifically, the LMFC-OTS was damaged in one patient, while it remained intact in the other three. Neuropsychological experiments showed that the patient with lesions in the LMFC-OTS had severe impairments in reading aloud and recognizing Chinese characters, i.e., pure alexia. The patient with intact LMFC-OTS but information from the left visual field (LVF) was blocked due to lesions in the splenium of corpus callosum, showed impairment in Chinese characters recognition when the stimuli were presented in the LVF but not in the RVF, i.e. left hemialexia. In contrast, the other two patients with intact LMFC-OTS had normal function in processing Chinese characters. The fMRI experiments demonstrated that there was no significant activation to Chinese characters in the LMFC-OTS of the pure alexic patient and of the patient with left hemialexia when the stimuli were presented in the LVF. On the other hand, this patient, when Chinese characters were presented in right visual field, and the other two with intact LMFC-OTS had activation in the LMFC-OTS. These results together point to the necessity of the LMFC-OTS for Chinese character processing. Selectivity: We tested selectivity of the LMFC-OTS for visual word processing through systematically examining the patients’ ability for processing visual vs. auditory words, and word vs. non-word visual stimuli, such as faces, objects and colors. Results showed that the pure alexic patients could normally process auditory words (expression, understanding and repetition of orally presented words) and non-word visual stimuli (faces, objects, colors and numbers). Although the patient showed some impairments in naming faces, objects and colors, his performance scores were only slightly lower or not significantly different relative to those of the patients with intact LMFC-OTS. These data provide compelling evidence that the LMFC-OTS is not requisite for processing non-visual word stimuli, thus has selectivity for visual word processing. Functional properties: With tasks involving multiple levels and aspects of word processing, including Chinese character reading, phonological judgment, semantic judgment, identity judgment of abstract visual word representation, lexical decision, perceptual judgment of visual word appearance, and dictation, copying, voluntary writing, etc., we attempted to reveal the most critical dysfunction caused by damage in the LMFC-OTS, thus to clarify the most essential function of this region. Results showed that in addition to dysfunctions in Chinese character reading, phonological and semantic judgment, the patient with lesions at LMFC-OTS failed to judge correctly whether two characters (including compound and simple characters) with different surface features (e.g., different fonts, printed vs. handwritten vs. calligraphy styles, simplified characters vs. traditional characters, different orientations of strokes or whole characters) had the same abstract representation. The patient initially showed severe impairments in processing both simple characters and compound characters. He could only copy a compound character in a stroke-by-stroke manner, but not by character-by-character or even by radical-by-radical manners. During the recovery process, namely five months later, the patient could complete the abstract representation tasks of simple characters, but showed no improvement for compound characters. However, he then could copy compound characters in a radical-by-radical manner. Furthermore, it seems that the recovery of copying paralleled to that of judgment of abstract representation. These observations indicate that lesions of the LMFC-OTS in the pure alexic patients caused several damage in the ability of extracting the abstract representation from lower level units to higher level units, and the patient had especial difficulty to extract the abstract representation of whole character from its secondary units (e.g., radicals or single characters) and this ability was resistant to recover from impairment. Therefore, the LMFC-OTS appears to be responsible for the multilevel (particularly higher levels) abstract representations of visual word form. Successful extraction seems independent on access to phonological and semantic information, given the alexic patient showed severe impairments in reading aloud and semantic processing on simple characters while maintenance of intact judgment on their abstract representation. However, it is also possible that the interaction between the abstract representation and its related information e.g. phonological and semantic information was damaged as well in this patient. Taken together, we conclude that: 1) the LMFC-OTS is necessary for Chinese character processing, 2) it is selective for Chinese character processing, and 3) its critical function is to extract multiple levels of abstract representation of visual word and possibly to transmit it to phonological and semantic systems.

Agency and animation: the performance of interactive game characters

As an animator and practice-based researcher with a background in games development, I am interested in technological change in the video game medium, with a focus on the tools and technologies that drive game character animation and interactive story. In particular, I am concerned with the issue of ‘user agency’, or the ability of the end user to affect story development—a key quality of the gaming experience and essential to the aesthetics of gaming, which is defined in large measure by its interactive elements. In this paper I consider the unique qualities of the video game1 as an artistic medium and the impact that these qualities have on the production of animated virtual character performances. I discuss the somewhat oppositional nature of animated character performances found in games from recent years, which range from inactive to active—in other words, low to high agency. Where procedural techniques (based on coded rules of movement) are used to model dynamic character performances, the user has the ability to interactively affect characters in real-time within the larger sphere of the game. This game play creates a high degree of user agency. However, it lacks the aesthetic nuances of the more crafted sections of games: the short cut-scenes, or narrative interludes where entire acted performances are mapped onto game characters (often via performance capture)2 and constructed into relatively cinematic representations. While visually spectacular, cut-scenes involve minimal interactivity, so user agency is low. Contemporary games typically float between these two distinct methods of animation, from a focus on user agency and dynamically responsive animation to a focus on animated character performance in sections where the user is a passive participant. We tend to think of the majority of action in games as taking place via playable figures: an avatar or central character that represents a player. However, there is another realm of characters that also partake in actions ranging from significant to incidental: non-playable characters, or NPCs, which populate action sequences where game play takes place as well as cut scenes that unfold without much or any interaction on the part of the player. NPCs are the equivalent to supporting roles, bit characters, or extras in the world of cinema. Minor NPCs may simply be background characters or enemies to defeat, but many NPCs are crucial to the overall game story. It is my argument that, thus far, no game has successfully utilized the full potential of these characters to contribute toward development of interactive, high performance action. In particular, a type of NPC that I have identified as ‘pivotal’3—those constituting the supporting cast of a video game—are essential to the telling of a game story, particularly in genres that focus on story and characters: adventure games, action games, and role-playing games. A game story can be defined as the entirety of the narrative, told through non-interactive cut-scenes as well a interactive sections of play, and development of more complex stories in games clearly impacts the animation of NPCs. I argue that NPCs in games must be capable of acting with emotion throughout a game—in the cutscenes, which are tightly controlled, but also in sections of game play, where player agency can potentially alter the story in real-time. When the animated performance of NPCs and user agency are not continuous throughout the game, the implication is that game stories may be primarily told through short movies within games, making it more difficult to define video games animation as a distinct artistic medium.

Cancer Risk Assessment Related to Anatomical Tissue Types

H. Strange, W. He, E. Denton and R. Zwiggelaar, 'Cancer Risk Assessment Related to Anatomical Tissue Types', Proceedings of the Twelfth Annual Conference on Medical Image Understanding and Analysis, 2008, p.138. Sponsorship: EPSRC

Anatomical identification of extracellularly recorded cells in large-scale multielectrode recordings.

This study combines for the first time two major approaches to understanding the function and structure of neural circuits: large-scale multielectrode recordings, and confocal imaging of labeled neurons. To achieve this end, we develop a novel approach to the central problem of anatomically identifying recorded cells, based on the electrical image: the spatiotemporal pattern of voltage deflections induced by spikes on a large-scale, high-density multielectrode array. Recordings were performed from identified ganglion cell types in the macaque retina. Anatomical images of cells in the same preparation were obtained using virally transfected fluorescent labeling or by immunolabeling after fixation. The electrical image was then used to locate recorded cell somas, axon initial segments, and axon trajectories, and these signatures were used to identify recorded cells. Comparison of anatomical and physiological measurements permitted visualization and physiological characterization of numerically dominant ganglion cell types with high efficiency in a single preparation.

Phenex: ontological annotation of phenotypic diversity.

BACKGROUND: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. CONCLUSIONS/SIGNIFICANCE: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

Micro-Anatomical Quantitative Imaging Towards Enabling Automated Diagnosis of Thick Tissues at the Point of Care

Histopathology is the clinical standard for tissue diagnosis. However, histopathology has several limitations including that it requires tissue processing, which can take 30 minutes or more, and requires a highly trained pathologist to diagnose the tissue. Additionally, the diagnosis is qualitative, and the lack of quantitation leads to possible observer-specific diagnosis. Taken together, it is difficult to diagnose tissue at the point of care using histopathology.

Several clinical situations could benefit from more rapid and automated histological processing, which could reduce the time and the number of steps required between obtaining a fresh tissue specimen and rendering a diagnosis. For example, there is need for rapid detection of residual cancer on the surface of tumor resection specimens during excisional surgeries, which is known as intraoperative tumor margin assessment. Additionally, rapid assessment of biopsy specimens at the point-of-care could enable clinicians to confirm that a suspicious lesion is successfully sampled, thus preventing an unnecessary repeat biopsy procedure. Rapid and low cost histological processing could also be potentially useful in settings lacking the human resources and equipment necessary to perform standard histologic assessment. Lastly, automated interpretation of tissue samples could potentially reduce inter-observer error, particularly in the diagnosis of borderline lesions.

To address these needs, high quality microscopic images of the tissue must be obtained in rapid timeframes, in order for a pathologic assessment to be useful for guiding the intervention. Optical microscopy is a powerful technique to obtain high-resolution images of tissue morphology in real-time at the point of care, without the need for tissue processing. In particular, a number of groups have combined fluorescence microscopy with vital fluorescent stains to visualize micro-anatomical features of thick (i.e. unsectioned or unprocessed) tissue. However, robust methods for segmentation and quantitative analysis of heterogeneous images are essential to enable automated diagnosis. Thus, the goal of this work was to obtain high resolution imaging of tissue morphology through employing fluorescence microscopy and vital fluorescent stains and to develop a quantitative strategy to segment and quantify tissue features in heterogeneous images, such as nuclei and the surrounding stroma, which will enable automated diagnosis of thick tissues.

To achieve these goals, three specific aims were proposed. The first aim was to develop an image processing method that can differentiate nuclei from background tissue heterogeneity and enable automated diagnosis of thick tissue at the point of care. A computational technique called sparse component analysis (SCA) was adapted to isolate features of interest, such as nuclei, from the background. SCA has been used previously in the image processing community for image compression, enhancement, and restoration, but has never been applied to separate distinct tissue types in a heterogeneous image. In combination with a high resolution fluorescence microendoscope (HRME) and a contrast agent acriflavine, the utility of this technique was demonstrated through imaging preclinical sarcoma tumor margins. Acriflavine localizes to the nuclei of cells where it reversibly associates with RNA and DNA. Additionally, acriflavine shows some affinity for collagen and muscle. SCA was adapted to isolate acriflavine positive features or APFs (which correspond to RNA and DNA) from background tissue heterogeneity. The circle transform (CT) was applied to the SCA output to quantify the size and density of overlapping APFs. The sensitivity of the SCA+CT approach to variations in APF size, density and background heterogeneity was demonstrated through simulations. Specifically, SCA+CT achieved the lowest errors for higher contrast ratios and larger APF sizes. When applied to tissue images of excised sarcoma margins, SCA+CT correctly isolated APFs and showed consistently increased density in tumor and tumor + muscle images compared to images containing muscle. Next, variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82% and 75%. The utility of this approach was further tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78% and 82%. The results indicate that SCA+CT can accurately delineate APFs in heterogeneous tissue, which is essential to enable automated and rapid surveillance of tissue pathology.

Two primary challenges were identified in the work in aim 1. First, while SCA can be used to isolate features, such as APFs, from heterogeneous images, its performance is limited by the contrast between APFs and the background. Second, while it is feasible to create mosaics by scanning a sarcoma tumor bed in a mouse, which is on the order of 3-7 mm in any one dimension, it is not feasible to evaluate an entire human surgical margin. Thus, improvements to the microscopic imaging system were made to (1) improve image contrast through rejecting out-of-focus background fluorescence and to (2) increase the field of view (FOV) while maintaining the sub-cellular resolution needed for delineation of nuclei. To address these challenges, a technique called structured illumination microscopy (SIM) was employed in which the entire FOV is illuminated with a defined spatial pattern rather than scanning a focal spot, such as in confocal microscopy.

Thus, the second aim was to improve image contrast and increase the FOV through employing wide-field, non-contact structured illumination microscopy and optimize the segmentation algorithm for new imaging modality. Both image contrast and FOV were increased through the development of a wide-field fluorescence SIM system. Clear improvement in image contrast was seen in structured illumination images compared to uniform illumination images. Additionally, the FOV is over 13X larger than the fluorescence microendoscope used in aim 1. Initial segmentation results of SIM images revealed that SCA is unable to segment large numbers of APFs in the tumor images. Because the FOV of the SIM system is over 13X larger than the FOV of the fluorescence microendoscope, dense collections of APFs commonly seen in tumor images could no longer be sparsely represented, and the fundamental sparsity assumption associated with SCA was no longer met. Thus, an algorithm called maximally stable extremal regions (MSER) was investigated as an alternative approach for APF segmentation in SIM images. MSER was able to accurately segment large numbers of APFs in SIM images of tumor tissue. In addition to optimizing MSER for SIM image segmentation, an optimal frequency of the illumination pattern used in SIM was carefully selected because the image signal to noise ratio (SNR) is dependent on the grid frequency. A grid frequency of 31.7 mm-1 led to the highest SNR and lowest percent error associated with MSER segmentation.

Once MSER was optimized for SIM image segmentation and the optimal grid frequency was selected, a quantitative model was developed to diagnose mouse sarcoma tumor margins that were imaged ex vivo with SIM. Tumor margins were stained with acridine orange (AO) in aim 2 because AO was found to stain the sarcoma tissue more brightly than acriflavine. Both acriflavine and AO are intravital dyes, which have been shown to stain nuclei, skeletal muscle, and collagenous stroma. A tissue-type classification model was developed to differentiate localized regions (75x75 µm) of tumor from skeletal muscle and adipose tissue based on the MSER segmentation output. Specifically, a logistic regression model was used to classify each localized region. The logistic regression model yielded an output in terms of probability (0-100%) that tumor was located within each 75x75 µm region. The model performance was tested using a receiver operator characteristic (ROC) curve analysis that revealed 77% sensitivity and 81% specificity. For margin classification, the whole margin image was divided into localized regions and this tissue-type classification model was applied. In a subset of 6 margins (3 negative, 3 positive), it was shown that with a tumor probability threshold of 50%, 8% of all regions from negative margins exceeded this threshold, while over 17% of all regions exceeded the threshold in the positive margins. Thus, 8% of regions in negative margins were considered false positives. These false positive regions are likely due to the high density of APFs present in normal tissues, which clearly demonstrates a challenge in implementing this automatic algorithm based on AO staining alone.

Thus, the third aim was to improve the specificity of the diagnostic model through leveraging other sources of contrast. Modifications were made to the SIM system to enable fluorescence imaging at a variety of wavelengths. Specifically, the SIM system was modified to enabling imaging of red fluorescent protein (RFP) expressing sarcomas, which were used to delineate the location of tumor cells within each image. Initial analysis of AO stained panels confirmed that there was room for improvement in tumor detection, particularly in regards to false positive regions that were negative for RFP. One approach for improving the specificity of the diagnostic model was to investigate using a fluorophore that was more specific to staining tumor. Specifically, tetracycline was selected because it appeared to specifically stain freshly excised tumor tissue in a matter of minutes, and was non-toxic and stable in solution. Results indicated that tetracycline staining has promise for increasing the specificity of tumor detection in SIM images of a preclinical sarcoma model and further investigation is warranted.

In conclusion, this work presents the development of a combination of tools that is capable of automated segmentation and quantification of micro-anatomical images of thick tissue. When compared to the fluorescence microendoscope, wide-field multispectral fluorescence SIM imaging provided improved image contrast, a larger FOV with comparable resolution, and the ability to image a variety of fluorophores. MSER was an appropriate and rapid approach to segment dense collections of APFs from wide-field SIM images. Variables that reflect the morphology of the tissue, such as the density, size, and shape of nuclei and nucleoli, can be used to automatically diagnose SIM images. The clinical utility of SIM imaging and MSER segmentation to detect microscopic residual disease has been demonstrated by imaging excised preclinical sarcoma margins. Ultimately, this work demonstrates that fluorescence imaging of tissue micro-anatomy combined with a specialized algorithm for delineation and quantification of features is a means for rapid, non-destructive and automated detection of microscopic disease, which could improve cancer management in a variety of clinical scenarios.

Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.

Identificación de tubérculos andinos (Oxalis tuberosa, Ullucus tuberosus y Tropaeolum tuberosum) : mediante caracteres anatómicos y exomorfológicos

p.141-153

Morphological and molecular characters reveal differentiation in a Neotropical social bee, Melipona beecheii (Apidae : Meliponini)

Morphometrics and DNA microsatellites were used to analyse the genetic structure of populations of the stingless bee M. beecheii from two extremes of its geographic range. The results showed that populations from Costa Rica and Yucatan exhibit substantial phenotypic and molecular differentiation. Bees from Yucatan were smaller and paler than those from Costa Rica. The value of multilocus F-ST = 0.280 (P <0.001) confirmed that there were significant molecular genetic differences between the two populations. Populations showed significant deviation from Hardy Weinberg equilibrium and the values of FIS (the inbreeding coefficient) were positive for Costa Rica = 0.416 and the Yucatan Peninsula = 0.193, indicating a lack of heterozygotes in both populations possibly due to inbreeding. The DNA sequence of 678 bp of the mitochondrial gene COI differed between populations by 1.2%. The results of this study should be considered in conservation programmes, particularly with regard to the movement of colonies between regions.