Coetzee on South Africa's Past: Remembering in the Time of Forgetting

As an intellectual figure in South Africa, J. M. Coetzee has consistently engaged with the politics of the past, particularly the contemporary ethical ramifications of the colonial past, alongside the more recent and bitter history of oppression under apartheid. As archaeologists, we aim to excavate these engagements through his novels and essays, particularly his long-standing concerns with the Khoekhoe communities of the Cape. In South Africa today, the tensions between remembering and forgetting are palpable and, in the aftermath of the Truth and Reconciliation Commission (TRC), we suggest that not all forgetting can be cast as therapeutic. Throughout his complex relationships with the nation's history, Coetzee foregrounds the colonial past and reiterates the ethical responsibilities of remembering so that the patterns of the past are not repeated.     

基于不同分类模型的基因芯片癌症诊断方法研究

基因芯片技术的发展为生物信息学带来了机遇,使在基因表达水平上进行癌症诊断成为可能。但基因芯片数据高维小样本的特征也使传统机器学习方法面临挑战。本文利用真实的基因表达数据,测试了目前主要的分类方法和降维方法在癌症诊断方面的效果,通过实验对比发现：基于线性核函数的支持向量机可以有效地分类肿瘤与非肿瘤的基因表达,从而为癌症诊断提供借鉴。     

Hidden pattern discovery on event related potential EEG signals

EEG signals are important to capture brain disorders. They are useful for analyzing the cognitive activity of the brain and diagnosing types of seizure and potential mental health problems. The Event Related Potential can be measured through the EEG signal. However, it is always difficult to interpret due to its low amplitude and sensitivity to changes of the mental activity. In this paper, we propose a novel approach to incrementally detect the pattern of this kind of EEG signal. This approach successfully summarizes the whole stream of the EEG signal by finding the correlations across the electrodes and discriminates the signals corresponding to various tasks into different patterns. It is also able to detect the transition period between different EEG signals and identify the electrodes which contribute the most to these signals. The experimental results show that the proposed method allows the significant meaning of the EEG signal to be obtained from the extracted pattern.     

Apartheid's end: South Africa's transition from racial domination

South Africa's transition to inclusive democracy does not conform to the prevalent theories of either revolution, or élite controlled ‘pact‐making’ as in Brazil. As a country long divided between supporters and opponents of racial domination, the loyalty of the former prevented a revolutionary overthrow, and the resistance of the latter drove and impinged upon negotiations. To account for South Africa's transition, we must take cognizance of the history of racial domination as the central impediment to democracy in that country. I argue that such racial domination was encoded as a means of unifying white ethnic groups, previously at war. Over the course of this century, amidst ongoing tension, intra‐white conflict was diminished with policies unifying whites on racial grounds. But such policies, excluding blacks, provoked massive resistance. When white unity had been more largely achieved, and the nation‐state and its economy threatened by growing protest by the majority, apartheid was ended. This process conforms with the seminal argument of Dunkwart Rustow (1970), that democracy can be achieved only with greater ‘national unity’ gained through contestation.     

Use of direct gradient analysis to study the climate-vegetation relationships in Galicia,Spain

This paper reports a bioclimatic analysis of plant species in Galicia, NW Spain. A set of floristic data obtained from 150 plots located at euclimatopes (sites with monitored climate) was analysed using direct gradient analysis and clustering with respect to the 8 climatic variables thought to play a major role in regulating the distribution of the species considered in the study area. Principal component analysis (PCA) and hierarchical clustering were based on a matrix of species by climatic variables. Indicator taxa for the variables were identified on the basis of their Indicator values (Brisse & Grandjouan 1978) and grouped by cluster analysis. The groups produced were compatible with the results of principal component analysis and the frequential analysis of the species, which identified their phytoclimatic nature. The groups were then characterized by determining their climatic positions and indicator values with respect to the chief climatic variables. The first three PCA axes, which were associated with Oceanity, Mean minimum temperatures and the temperature range in the coldest month, together accounted for 97.2% of the variance of the data.     

Volatile constituents and antimicrobial activities of nine South African liverwort species

The volatile constituents of nine liverworts species (Asterella marginata, Dumortiera hirsuta, Fossombronia swaziensis, Marchantia pappeana, Marchantia polymorpha subsp. ruderalis, Pallavicinia lyellii, Plagiochasma rupestre, Riccia albolimbata and Symphyogyna podophylla) from South Africa were determined by gas chromatography. Where possible the volatile constituents identified were compared to those reported for the same species from other countries. Among the analysed liverworts, the chemical compositions of A. marginata, F. swaziensis, M. pappeana, and R. albolimbata are reported for the first time. Each of the analysed liverwort species produced its own characteristic components. Thujopsanes, chamigranes and cuparanes were found to be the most characteristic components of M. polymorpha subsp. ruderalis. The presence of dumortane-type sesquiterpenoids in D. hirsuta indicated that this species is similar in chemistry to an Argentinean sample. This is one of only a handful of reports on the presence of this sesquiterpene-type in liverworts. Simple thallose liverworts, S. podophylla and P. lyellii, were characterized by the presence of labdane-type diterpenoids. In addition, the antimicrobial activities of chloroform:methanol (1:1) extracts of the liverworts were evaluated against several important human pathogens using the serial dilution assay. Four of the liverwort species were active against Pseudomonas aeruginosa with MIC values ranging from 0.50 to 1.0 mg/mL. Some activity (MIC value of 1.0 mg/mL) was also recorded for the crude extracts of P. lyellii and M. pappeana against Escherichia coli. The extract of S. podophylla displayed the best activity towards the yeast Cryptococcus neoformans (MIC = 1.0 mg/mL). Although approximately 300 liverwort species occur in southern Africa, a Scopus search confirmed that this is the first report of the volatile profiles and biological properties of species from the region.     

The taxonomic status of the Black Sea and Marmara Sea populations of the Broadnosed Pipefish Syngnathus cf. argentatus Pallas (Teleostei: Syngnathidae) based on morphological and molecular characters

As the Black Sea and Marmara Sea population of the Broadnosed Pipefish Syngnathus cf. argentatus show some morphological differences from the Mediterranean Sea populations, some authors regard it as an endemic species Syngnathus argentatus Pallas, 1814, while others consider it as a synonym of S. typhle Linnaeus, 1758. The aim of this study is to compare the populations of the Black Sea and Sea of Marmara with the Aegean Sea population, using a combination of morphological and molecular characters, in order to clarify their taxonomic status. Sampling was carried out at three stations in the Black Sea, two in the Sea of Marmara and three in the Aegean Sea, and a total of 24 morphometric and 6 meristic characters were examined. Metric data were analysed by Principal Component Analysis (PCA) and phylogenetic relationships between the populations were analysed using both cytochrome oxidase subunit 1 (COI) gene and cytochrome b (cyt-b) gene sequences. Although constant differences were observed in snout depths between the Black Sea/Marmara Sea and the Aegean Sea populations, other morphological features and genetic analysis did not enable these populations to be differentiated. These findings indicate that S. argentatus is a synonym of S. typhle.     

Local ecological footprint using Principal Component Analysis: A case study of localities in Andalusia (Spain)

The quantity and quality of available information is one of the major constraints for the calculation of the ecological footprint, particularly for sub-national or sub-regional territorial levels. At the national or even regional level, the information that allows for computing the ecological footprint is generally available. However, when trying to calculate the footprint for lower-level territorial realities (e.g., cities or municipalities), this information is insufficient or non-existent. In this article, we propose an indirect method for calculating the ecological footprint of such territorial spaces through Principal Component Analysis. The case study utilises the ecological footprint of Andalusia (a Spanish region) as a starting point for footprint assignment to each of the 771 municipalities included in the Andalusian region. A set of variables related to the consumption levels in these municipalities has been utilised and is expressed in physical units. These variables make it possible to obtain a weighting factor to determine the ecological footprint of each municipality. This procedure also makes it possible to identify which variables or indicators have the greatest impact on the ecological footprint for a given territory. According to the results, the method also shows how inappropriate it is to consider the population as a way to distribute the ecological footprint; there are relevant differences between the weight of the population in municipalities and their generated footprint. There are also significant differences between the magnitude of economic indicators, such as GDP, and the estimated ecological footprint; for municipalities with higher income levels, the ecological impact is more than proportional to the weight of the monetary indicators.     

Multivariate analysis of climatic patterns of the Meditrranean basin

Climatic data from 444 weather-recording stations in the Mediterranean basin are examined by cluster analysis and principal component analysis. The application of numerical clustering distinguished several groups of climatic stations clearly interpretable in geographic and climatic terms. The hierarchical structure of the dendrograms could be used to identify at different scales uniform climatic regions. The complementary application of principal component analysis produced an ordination of climatic types, which clearly showed the main trends of variation in the precipitation and temperature patterns.     

响应面结合主成分分析方法优化黄瓜种子GA3包衣浓度和贮藏时间组合

采用响应面结合主成分分析方法优化黄瓜种子GA_3包衣浓度和贮藏时间的组合.采用响应面试验设计的二因素14个组合对黄瓜种子GA_3浓度和贮藏时间进行处理,然后进行发芽试验.对得到的苗高、叶绿素含量和根系活力指数进行主成分分析,对得到的主成分向量进行响应面分析,找到了提高黄瓜幼苗苗高、叶绿素含量和根系活力的最佳处理组合.     

73份亚洲水稻恢复系农艺性状的主成分与聚类分析

选取来自亚洲主要产稻国家的73份恢复系资源,种植在四川省德阳市和泸州市2个环境下,根据株高、单株有效穗、千粒重、单株生物量、单株稻谷产量、每穗实粒数、每穗颖花数、每日稻谷产量、每日生物量、结实率、收获指数等11个性状进行主成分与聚类分析。结果表明:通过主成分分析,将11个性状简化为4个主成分,即稻谷产量因子、生物产量因子、穗数因子和粒重因子,以上因子提供的信息量占总信息量的87.640%(德阳)和88.861%(泸州)。利用4个主成分因子进行系统聚类,在2个环境下,73份资源均聚为4大类,其中来自中国60.71%的资源聚在Ⅰ类群,主要特点是千粒重大,株高偏高,产量较高。来自印度45.45%的资源聚在Ⅱ类群,主要特点是千粒重偏小,产量、收获指数等性状均较高。4类群间差异明显,分类结果与地理来源基本一致。     

Landmark based geometric morphometric analysis of wing shape in Sibiricobombus Vogt (Hymenoptera: Apidae: Bombus Latreille)

B. (Sibiricobombus) niveatus and B. (Sibiricobombus) vorticosus are analyzed and compared with selected species of the subgenera Melanobombus and Mendacibombus. Different geometric morphometric methods based on wings landmark data show that there are no morphological differences between B. niveatus and B. vorticosus. These results support the hypothesis that B. niveatus and B. vorticosus should be regarded as conspecific. On the other hand, the wing shapes show significant differences among the bumblebee species and subgenera that are coherent with their specific and subgeneric status. This approach may help future studies not only by contributing towards solving problems in systematics but also in understanding the flight mechanism of bumblebees. It also supports studies on the evolution of crossvein structure and on aerodynamics of different wing shapes in insects.     

The Influence of Selected Environmental Variables on Fish Assemblage Structure in a Range of Southeast African Estuaries

This study compared the ichthyofaunal assemblages in 10 Eastern Cape Province, South Africa, estuaries to identify whether there were any structural variations between the assemblages and to determine the environmental and physical factors linked to these variations. Species belonging to both the marine migrant and estuarine resident groups, by consistent representation within each estuary grouping, were responsible for the separation of fish assemblage structures between the different types of systems. The data further revealed that fish assemblages in the three main types of estuaries investigated were distinct, linked primarily to estuary mouth status and estuary size.     

Multi-scale determinants of dung beetle assemblage structure across abiotic gradients of the Kalahari–Nama Karoo ecotone, South Africa

Aim Changing conditions across spatial gradients are primary determinants of biotic regions, local habitats, and distributional edges. We investigate how a climatic gradient and edaphic mosaic interact as multi‐scale drivers of spatial patterns in scarabaeine dung beetles. The patterns are tested for congruency with ecoregion and floral boundaries over the same gradient, as responses to physical factors often differ among higher taxa. Location Southern Africa and the Nama Karoo–Kalahari ecotone, Northern Cape, South Africa. Methods Data consisted of the climatic distributions of 104 species and their abundances at 223 sites in two ecoregions/floral biomes, four bioregions, and 13 vegetation units. Factor analyses determined the biogeographical composition of the species, and regional‐ to local‐scale patterns in species abundance structure. Hierarchical analysis of oblique factors determined the proportional contribution of spatial variance to patterns. One‐way anova was used to test for significant separation of patterns along factor axes. Stepwise multiple regression was used to determine correlations of five physical attributes with species richness, Shannon‐Wiener diversity, and factor loadings for the study sites. Results Four biogeographical influences overlap in the study region, although rank contribution declines from south‐west arid through north‐east savanna to widespread and south‐east highland taxa. Species abundance structure comprises five subregional patterns, two centred to the north‐east (Kalahari, Isolated Kalahari Dune) dominated by Kalahari influence, and three to the south‐west (Nama Karoo subdivisions: Bushmanland, ‘Upper’, ‘Stony Prieska’) dominated by south‐west arid influence. Kalahari deep sands are characterized especially by a warmer, moister climate, whereas the Nama Karoo mosaic of deep or stony soils is characterized especially by north‐west aridity (Bushmanland), south‐east cooler temperatures (‘Upper’), or excessively stony soils (‘Stony Prieska’). Four of the subregional patterns each comprised three localized patterns related primarily to relative stoniness, edge effects from geographical position, or incidence of rainfall. Species richness and diversity declined with decreasing rainfall and increasing stoniness. Main conclusions Climatic and edaphic factors are important multi‐scale determinants of spatial patterns in dung beetle assemblage structure, with edaphic factors becoming more important at local spatial scales. The patterns are roughly congruent with the Kalahari Savanna–Nama Karoo ecotone at the floral biome or ecoregion scale, but show limited coincidence with finer‐scale floral classification.     

South African populations of Littorina rudis

Littorina rudis was collected from stands of Spartina capensis in saltmarsh habitats within Langebaan and knysna lagoon, Cape Province. It was absent from rocky sores and from saltmarshes east of Knysna. The shell, radular and penial morphology are described. L. rudis from both localities bore tessellated colour patterns similar to those of British saltmarsh ecotypes. The Knysna population contained individuals with a unique amber background colour. The shells from Knysna and Langebaan were very thin in accordance with the sheltered habitats. The number of embryos carried in the brood puch was similar in both countries. Sexual maturity was attained at about 4 mm shell length; the male and female modal sizes were 4.9 mm and 5.1 mm respectively at Langebaan. No. published records were found for L. rudis in South West Africa. Some possible origins of the South African L. rudis populations are discussed.     

Suitability of Kinect for measuring whole body movement patterns during exergaming

Exergames provide a challenging opportunity for home-based training and evaluation of postural control in the elderly population, but affordable sensor technology and algorithms for assessment of whole body movement patterns in the home environment are yet to be developed. The aim of the present study was to evaluate the use of Kinect, a commonly available video game sensor, for capturing and analyzing whole body movement patterns. Healthy adults (n=20) played a weight shifting exergame under five different conditions with varying amplitudes and speed of sway movement, while 3D positions of ten body segments were recorded in the frontal plane using Kinect and a Vicon 3D camera system. Principal Component Analysis (PCA) was used to extract and compare movement patterns and the variance in individual body segment positions explained by these patterns. Using the identified patterns, balance outcome measures based on spatiotemporal sway characteristics were computed. The results showed that both Vicon and Kinect capture >90% variance of all body segment movements within three PCs. Kinect-derived movement patterns were found to explain variance in trunk movements accurately, yet explained variance in hand and foot segments was underestimated and overestimated respectively by as much as 30%. Differences between both systems with respect to balance outcome measures range 0.3–64.3%. The results imply that Kinect provides the unique possibility of quantifying balance ability while performing complex tasks in an exergame environment.     

Vector space classification of DNA sequences

Revisiting the problem of intron-exon identification, we use a principal component analysis (PCA) to classify DNA sequences and present first results that validate our approach. Sequences are translated into document vectors that represent their word content; a principal component analysis then defines Gaussian-distributed sequence classes. The classification uses word content and variation of word usage to distinguish sequences. We test our approach with several data sets of genomic DNA and are able to classify introns and exons with an accuracy of up to 96%. We compare the method with the best traditional coding measure, the non-overlapping hexamer frequency count, and find that the PCA method produces better results. We also investigate the degree of cross-validation between different data sets of introns and exons and find evidence that the quality of a data set can be detected.     

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1^T, B. betae PL7HG1^T, B. ganzhouense CCBAU 51670 ^T, B. cytisi CTAW11^T and B. rifense CTAW71^T) resulted in values well below 95–96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14AB^T (=LMG 31415 ^T = SARCC-753 ^T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.     

The biology of Dendropoma corallinaceum and Serpulorbis natalensis, two South African vermetid gastropods

D. corallinacewn forms sheet-like colonies at Mean Low Water (MLW) on exposed rocky shores: S. natalensis forms loose aggregations under stones below MLW in more sheltered situations. Both species released young from July— December. D. corallinaceun has single embryos in capsules brooded free in the mantle cavity; S. natalensis has 20–40 embryos per capsule, the latter being attached to the roof of the shell and hanging through a dorsal slit in the mantle. The morphology of the crawling young is similar in both species, resembling adult errant prosobranchs. D. corallinaceum has a stouter, more streamlined protoconch than S. natalensis correlated with the more turbulent water of its habitat. The crawling young secrete a sticky mucous trail for adhesion to the substratum. They are strongly photopositive until settlement. D. corallinaceum can settle within 24 hours but may delay settlement to 4–5 days if suitable substrata are absent. Metamorphosis is complete 2 days after settlement. D. corallinaceum prefer to settle on Lithothamnion which is easily eroded by the radula to provide a groove for rapid, firm attachments to the substratum. Both species feed from mucous nets, S. natalensis having a slower feeding rhythm commensurate with its larger size. Contiguous pairs of S. natalensis have synchronised feeding rhythms, probably to reduce mutual net robbing. Particles are also filtered out of suspension; many particles are rejected in the pseudofaeces but some are ingested. D. corallinaceum and S. natalensis have many similar ecologically equivalent species throughout the warm temperate and tropical seas of the world.