Genetic affinities of the Andaman Islanders,a vanishing human population

BACKGROUND: The Andaman Islands in the Bay of Bengal are inhabited by hunter-gatherers of unknown origin, now on the verge of extinction. The Andamanese and other Asian small-statured peoples, traditionally known as "Negritos," resemble African pygmies. However, it is generally believed that they descend from the early Australo-Melanesian settlers of Southeast Asia and that their resemblance to some Africans is due to adaptation to a similar environment, rather than shared origins.RESULTS: We analyzed mitochondrial DNA (mtDNA) sequences and RFLP polymorphisms, and Y chromosome biallelic markers and microsatellites, in present-day Andamanese of the Onge, Jarawa, and Great Andamanese tribes, and of inhabitants of the neighboring Nicobar Islands. We also analyzed mtDNA sequences from Andamanese hair samples collected by an ethnographer during 1906-1908. Living Andamanese exhibit low genetic variability that is consistent with their small population size and reproductive isolation.CONCLUSIONS: Our data indicate that the Andamanese have closer affinities to Asian than to African populations and suggest that they are the descendants of the early Palaeolithic colonizers of Southeast Asia. In contrast, the Nicobarese have genetic affinities to groups widely distributed throughout Asia today, presumably descended from Neolithic agriculturalists.     

Time to move: winds and the political economy of space in Andamanese culture

Seasons, or temporal duration, for Andamanese are created by the flow of winds through the Andamanese cultural construct of space, which is neither fixed nor constant. In order to organize the space for society, Andaman islanders have to move constantly out from the place where the winds are. Winds associated with temperamental spirits are powerful aspects of nature that culture has to negotiate. Within this worldview where winds affect individual body condition and the capacity to continue hunting and gathering, Andaman islanders negotiate space by creating conditions that invite winds to structure and sustain life. For this purpose, smells are ritualized and wind movements are manipulated. As a result, seasons are distinguished either by winds that are spirit-given, or by a lack of winds caused by islanders' actions. Based on ethnographic data from the Ongees and Jarwas, this analysis will focus on how various forms of movement in Andamanese culture are negotiated according to a political economy of winds and smells. The worldview of the Andaman islanders, within which winds are so central, has major implications for government authorities, who are keen to confine the translocating Jarwas to a specific and permanent location. But is this possible for the Andamanese, for whom space, like time, changes by the presence and absence of winds?     

Ethnobotanical studies of the negrito islanders of Andaman Islands,India—the Great Andamanese

This paper deals with ethnobotany of the Great Andamanese tribe. Brief accounts of Andaman geography, ethnology, and previous ethnobotanical studies are given. Plants used in everyday life, such as for bows and arrows, canoes, fibers, food, medicines, rituals, musical instruments, tools, and shelter, are described and discussed. Scientific and vernacular names, uses, and ethnobotanical importance are listed.     

Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic

In view of the geographically closest location to Andaman archipelago,Myanmar was suggested to be the origin place of aboriginal Andamanese.However,for lacking any genetic information from this region,which has prevented to resolve the dispute on whether the aboriginal Andamanese were originated from mainland India or Myanmar.To solve this question and better understand the origin of the aboriginal Andamanese,we screened for haplogroups M31(from which Andaman-specific lineage M31a1 branched off)and M32 among 846mitochondrial DNAs(mtDNAs)sampled across Myanmar.As a result,two Myanmar individuals belonging to haplogroup M31 were identified,and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations.Since no root lineages of haplogroup M31 or M32 were observed in Myanmar,it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese.To get further insight into the origin of this unique population,the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations,and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India.Time estimation results further indicated that the Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum(LGM),a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.     

Red cell genetic abnormalities, beta-globin gene haplotypes, and APOB polymorphism in the Great Andamanese, a primitive Negrito tribe of Andaman and Nicobar Islands, India.

The Great Andamanese are a primitive Negrito tribe of the Andaman and Nicobar Islands, India, with a total population of 37. We studied 29 individuals from eight families from this population for abnormal hemoglobins, G6PD deficiency, DNA haplotypes, and apolipoprotein B (APOB, gene) polymorphism. Hb E was detected in five individuals, the prevalence of Hb E heterozygotes being 14.3%. One individual had beta-thalassemia trait. One female was G6PD deficient and showed the G6PD Orissa mutation. Haplotype analysis of the beta-globin gene cluster showed that the betaE chromosomes were linked to two haplotypes (- - - - - + + and + + - + + + +) representing the framework 1 gene, whereas the betaA chromosomes showed eight different haplotypic patterns corresponding to framework 1 and 3 genes. APOB polymorphism analysis showed that the 631-base-pair (bp) allele was the predominant one with a high homozygosity rate, which could be due to the higher rate of inbreeding in this isolated group. The presence of Hb E and our findings on haplotype analysis supports the hypothesis that the Great Andamanese are reasonably believed to be the surviving representatives of the Negrito race that once flourished in the entire Southeast Asian region in ancient times.     

TreeSnatcher: coding trees from images

TreeSnatcher is a GUI-driven JAVA application for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes the topology and the metrics of a tree depicted. The analysis is carried out in a multiple-stage process using algorithms from image analysis. In the end, TreeSnatcher produces a Newick tree code that represents the tree structure optionally including branch lengths. TreeSnatcher can process trees with 100 leaves or more in a few seconds. AVAILABILITY: TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher.     

Chimpanzees as an outgroup for the examination of human dental evolution

In the assessment of human origins, chimpanzees (Pan troglodytes, henceforth called Pan) represent the best hominoid outgroup for comparisons. Such an outgroup roots the "anatomically modern" human population cluster, or continuum. This study incorporates chimpanzees into a worldwide modern human database of quantified complete tooth variables (approximately 30 per tooth; e.g., root, pulp, enamel) in an attempt to develop a more accurate phylogeny of the hominoid continuum, with only intervening extinct hominids missing. Canonical discriminate analysis was performed mainly among Liberian common chimpanzees and global samples of humans. The first canonical variable explained 70% of the total variance and showed a tight cluster of humans, with chimpanzees as a distant outgroup. Within the human community, first non-San Bushman, sub-Saharan Africans and Andamanese, and then, close in, Australian aborigines were positioned towards Pan. Their relative orientation suggested an African human origin with the first branch within sub-Saharan Africa: sub-Saharan Africans and San Bushmen. Next, Andamanese Negritos, and then Australian aborigines, formed the early first surviving modern human lineage to leave Africa. Thin enamel and big teeth with relatively large roots characterized Pan nonmolar teeth. Humans showed a generalized sexual dimorphism for all teeth, with males having bigger teeth, bigger relative roots, and thinner enamel than females, while only Pan canines had significant and impressive sexual dimorphism. Interestingly, Pan molars were not larger than human molars. The data suggest that although hominids underwent two dental macroevolutionary events, the lineage leading to modern humans only experienced anterior tooth-size reduction. The suggested evolutionary significance of the observed total tooth variation is discussed.     

The genetic origins of the Andaman Islanders

Mitochondrial sequences were retrieved from museum specimens of the enigmatic Andaman Islanders to analyze their evolutionary history. D-loop and protein-coding data reveal that phenotypic similarities with African pygmoid groups are convergent. Genetic and epigenetic data are interpreted as favoring the long-term isolation of the Andamanese, extensive population substructure, and/or two temporally distinct settlements. An early colonization featured populations bearing mtDNA lineage M2, and this lineage is hypothesized to represent the phylogenetic signal of an early southern movement of humans through Asia. The results demonstrate that Victorian anthropological collections can be used to study extinct, or seriously admixed populations, to provide new data about early human origins.     

Axes, planes and tubes, or the geometry of embryogenesis

The paper presents selected figures of chick embryogenesis as depicted in the classic studies of Caspar Friedrich Wolff (1734–1794), Christian Heinrich Pander (1794–1865) and Karl Ernst von Baer (1792–1786). My main objective here is (1) to demonstrate how the imagery of Wolff, Pander and Baer attempted to project an image of a 3-dimensional rotating body into static figures on paper by means of linear contours, and (2) to ponder on the efficacy and pervasiveness of dots, lines and arrows for depicting embryogenesis.     

PupDB: a database of pupylated proteins

Background

Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.

Results

TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees.

Conclusions

Although illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format.     

Balancing acts: Picturing perspiration in the long eighteenth century

This essay examines the historical fortunes of an image that throughout the seventeenth and eighteenth centuries became a landmark of the medical doctrine and practice of static medicine advanced by the physician Santorio Santorio (1561-1636). The image depicted a man sitting on a large Roman steelyard, which allowed the weighing of bodily discharges and gave guidance on the intake of food. Well into the eighteenth century, the image of the weight-watching man accompanied Santorio's work on the art of static medicine and, most likely, contributed to its success. It appeared in a variety of medical works and navigated across competing medical theories and different medical genres, while remaining largely unscathed. This essay explores the success and the historical agency of this image. Focusing on the history of its copies and variants, it investigates how the image came to symbolize the attempt to transform dietetics into an experimental practice, and accordingly preserve its pivotal significance in the medical world.     

Shape from texture

A central goal for visual perception is the recovery of the three-dimensional structure of the surfaces depicted in an image. Crucial information about three-dimensional structure is provided by the spatial distribution of surface markings, particularly for static monocular views: projection distorts texture geometry in a manner tha depends systematically on surface shape and orientation. To isolate and measure this projective distortion in an image is to recover the three dimensional structure of the textured surface. For natural textures, we show that the uniform density assumption (texels are uniformly distributed) is enough to recover the orientation of a single textured plane in view, under perspective projection. Furthermore, when the texels cannot be found, the edges of the image are enough to determine shape, under a more general assumption, that the sum of the lengths of the contours on the world plane is about the same everywhere. Finally, several experimental results for synthetic and natural images are presented.     

CircHIPK3 sponges miR‐558 to suppress heparanase expression in bladder cancer cells

Correction to: EMBO Reports (2017) 18(9): 1646–1659. DOI: 10.15252/embr.201643581 ¦ Published online 9 August 2017The authors contacted the journal after being alerted to issues in the figures. The authors state that while preparing the figures, images were mislabelled leading to partial duplications in two figure panels. The authors requested to withdraw the affected panels and to replace them with correct representative images that had been generated at the time of the original experimentation. The panels listed below are therefore withdrawn and replaced. The related source data are published with this note.Figure 4DThe transwell assay image for UMUC3 cells showing invasion behaviour upon miR‐558 mimic treatment (“miR‐558”) had been incorrect. An image showing the invasion behaviour of UMUC3 cells upon depletion of circHIPK3 (“si‐circHIPK3#1”) showing the same cells as depicted in Fig 2H was erroneously used. A representative image of the correct data is now displayed in the paper.Figure 4EThe transwell assay image for UMUC3 cells showing migration behaviour upon treatment with an miR‐588 anti‐miR (“anti‐miR‐558”) had been incorrect. An image showing the migration behaviour of UMUC3 cells upon circHIPK3 overexpression (“circHIPK3”) showing the same cells as those depicted in Fig 2D was erroneously used. A representative image of the correct data is now displayed in the paper.Figure 5CThe Western blot image showing the β‐actin loading control for T24T cells had been incorrect. A representative image of the correct data is now displayed in the paper.Figure 5FThe image for UMUC3 cells showing tube formation upon treatment with a control mimic and overexpression of circHIPK3 “mimicNC+circHIPK3” had been incorrect. A representative image of the correct data is now displayed in the paper.The figure issues described above are herewith corrected. The authors state that the errors do not affect the results or conclusions of the study and apologize for any confusion these errors may have caused. Figure 4D. Original. Figure 4D. Corrected. Figure 4E. Original. Figure 4E. Corrected. Figure 5C. Original. Figure 5C. Corrected. Figure 5F. Original. Figure 5F. Corrected.      

广州市主城区树冠覆盖景观格局梯度

城市树冠覆盖是城市森林在小尺度上的景观表达,是衡量城市森林生态功能服务质量的重要指标.通过在ArcGIS9.2中对广州市中心城区的高分辨率航片进行目视解译,对形成的树冠覆盖专题图分析并生成栅格数据,利用Fragstats3.3软件分别选择标准方法和移动窗口方法分析研究区景观格局特征.其中基于移动窗口法形成了一系列基于所选择格局特征的连续栅格表面,每一个栅格单元代表的是设定的移动窗口半径尺度下景观类型的格局特征.分析表明,研究区景观格局呈现明显的空间异质性梯度特征.基于样带区尺度效应分析的结果表明,粒度3-5m和移动窗口半径400-600m可适合于研究区的景观格局梯度分析,选择的景观指数能够形成较为平滑的栅格表面.基于移动窗口的分析结果以连续变量图的形式对景观格局空间异质性进行可视化表达,能够为小尺度上的城市森林景观格局优化提供重要的参考.     

基于微血栓运动分析的微血管特征结构自动提取

提出了一种基于微血栓运动分析的微血管特征结构自动提取策略。提出用灰度梯度直方图统计来自动选阈的快速阈值值化算法,检测形态复杂的微血管图像边缘,抑制次要的微血管,采用低阈值双窗二次角点选择策略选取边缘曲线角点。通过微血管显微图像及其二值化图像分析,建立反映含微血栓的微血管特征结构模型,利用微血管的先验知识,给出提取微血管特征结构的算法,最后给出微血管显微图像结构的提取结果,实验证明该算法是十分有效的。含微血栓的微血管的特征结构建立,复杂的微血栓的匹配和识别问题将得到简化,微血管及微血栓的形态变化及运动估算任务得以减轻。该研究对于脑微循环障碍和老年病的基础医学研究和临床实践具有十分重要的意义。     

Blind subjects construct conscious mental images of visual scenes encoded in musical form.

Blind (previously sighted) subjects are able to analyse, describe and graphically represent a number of high-contrast visual images translated into musical form de novo. We presented musical transforms of a random assortment of photographic images of objects and urban scenes to such subjects, a few of which depicted architectural and other landmarks that may be useful in navigating a route to a particular destination. Our blind subjects were able to use the sound representation to construct a conscious mental image that was revealed by their ability to depict a visual target by drawing it. We noted the similarity between the way the visual system integrates information from successive fixations to form a representation that is stable across eye movements and the way a succession of image frames (encoded in sound) which depict different portions of the image are integrated to form a seamless mental image. Finally, we discuss the profound resemblance between the way a professional musician carries out a structural analysis of a musical composition in order to relate its structure to the perception of musical form and the strategies used by our blind subjects in isolating structural features that collectively reveal the identity of visual form.     

Spontaneous discrimination of possible and impossible objects by newly hatched chicks

Four-month-old infants can integrate local cues provided by two-dimensional pictures and interpret global inconsistencies in structural information to discriminate between possible and impossible objects. This leaves unanswered the issue of the relative contribution of maturation of biologically predisposed mechanisms and of experience with real objects, to the development of this capability. Here we show that, after exposure to objects in which junctions providing cues to global structure were occluded, day-old chicks selectively approach the two-dimensional image that depicted the possible rather than the impossible version of a three-dimensional object, after restoration of the junctions. Even more impressively, completely naive newly hatched chicks showed spontaneous preferences towards approaching two-dimensional depictions of structurally possible rather than impossible objects. These findings suggest that the vertebrate brain can be biologically predisposed towards approaching a two-dimensional image representing a view of a structurally possible three-dimensional object.     

Olfaction spontaneously highlights visual saliency map

Attention is intrinsic to our perceptual representations of sensory inputs. Best characterized in the visual domain, it is typically depicted as a spotlight moving over a saliency map that topographically encodes strengths of visual features and feedback modulations over the visual scene. By introducing smells to two well-established attentional paradigms, the dot-probe and the visual-search paradigms, we find that a smell reflexively directs attention to the congruent visual image and facilitates visual search of that image without the mediation of visual imagery. Furthermore, such effect is independent of, and can override, top-down bias. We thus propose that smell quality acts as an object feature whose presence enhances the perceptual saliency of that object, thereby guiding the spotlight of visual attention. Our discoveries provide robust empirical evidence for a multimodal saliency map that weighs not only visual but also olfactory inputs.     

Individual filamentous phage imaged by electron holography

An in-line electron hologram of an individual f1.K phage was recorded with a purpose-built low energy electron point source (LEEPS) microscope. Cryo-microscopic methods were employed to prepare the specimen so that a single phage could be presented to the coherent low energy electrons: An aqueous phage suspension was applied to a thin carbon membrane with micro-machined slits. The membrane was rapidly cooled to freeze the remaining water as an amorphous ice sheet, which was then sublimated at low temperatures and pressures to leave individual free-standing phages suspended across slits. An image of a phage particle, depicted as the amplitude of the object wave, was reconstructed numerically from a digitized record of the hologram, obtained using 88 eV coherent electrons. The reconstructed image shows a single phage suspended across a slit in a supporting carbon membrane, magnified by a factor of 100,000. The width and shape in the reconstructed image compared well with a TEM image of the same filament. It is thus possible to record and reconstruct electron holograms of an individual phage. The challenge now is to improve the resolution of reconstructed images obtained by this method and to extend these structural studies to other biological molecules.