Encoded evidence: DNA in forensic analysis

Sherlock Holmes said "it has long been an axiom of mine that the little things are infinitely the most important", but never imagined that such a little thing, the DNA molecule, could become perhaps the most powerful single tool in the multifaceted fight against crime. Twenty years after the development of DNA fingerprinting, forensic DNA analysis is key to the conviction or exoneration of suspects and the identification of victims of crimes, accidents and disasters, driving the development of innovative methods in molecular genetics, statistics and the use of massive intelligence databases.     

Fungal genomics: forensic evidence of sexual activity

The genome sequence of the 'asexual' human pathogenic fungus Aspergillus fumigatus suggests it has the capability to undergo mating and meiosis. That this organism engages in clandestine sexual activity is also suggested by observations of two equally distributed complementary mating types in nature, the expression of mating type genes and evidence of recent genome recombination events.     

Linking of digital images to phylogenetic data matrices using a morphological ontology

Images are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.     

Blood analysis using black and white digital images

Image processing offers a powerful tool for medical diagnosis by visual inspection. Our proposed system considers the blood analysis problem. The system processes black and white blood images obtained from a CCD camera through a microscope. Different categories of cells are recognized, counted and classified into white cells, red cells and blood petals. The white cells are further treated for their classification, according to the morphological characteristics of their nuclei. The final classification is printed in special format for the physician.     

微生物组大数据管理与分析

高通量技术的迅猛发展促使微生物生态学研究获得了重大突破,掀起了元基因组学(Metagenomics)研究的热潮。元基因组学通常被定义为对未培养的环境样本中微生物群体的DNA序列分析。随着微生物组学数据的日益剧增,微生物大数据的高效管理与分析越来越受到研究者的关注。如何从海量的微生物组数据中挖掘出具有科研价值的数据信息并应用于实际问题成为当前的研究热点。目前已有很多计算生物学程序工具及数据库用于元基因组数据的分析与管理。本文主要综述了随着高通量测序技术的进步,国际上主要的微生物组计划及微生物组数据平台,如人类微生物组项目(human microbiome project,HMP)、地球微生物组项目(earth microbiome project,EMP)、欧盟的肠道微生物组计划(metagenomics of human intestinal tract,MetaHIT)、MG-RAST、i Microbe、整合微生物组(integration microbial genomes,IMG)以及EBI Metagenomics等;介绍了微生物数据分析的主要流程与工具;提出了建设多源异构的微生物生态数据管理与分析系统的必要性。     

Quantitative densitometry of autoradiograms: digital images representative of optical density

Microcomputer software has been developed to control video acquisitionof 1024 x 1024 digital autoradiogram images which representtrue optical density (OD). Since video cameras are sensitiveto intensity (I), background correction and conversion to ODmust be accomplished in software. The software linearizes cameraoutput against an optical step tablet of known ODs and createsa ‘look-up table’ through which captured imagesare passed. This procedure allows the accurate and rapid conversionof a large number of images. The user is directed through thecalibration and capture procedures; safeguards are includedto ensure that the resultant images are correctly calibrated.The algorithms used in these programs accommodate the limitedcomputing power available in microcomputers. The use of a commerciallyavailable graphics library will enhance the portability to multiplehardware configurations. This software is a low-cost alternativefor the capture of digital images needed for quantitative densitometry. Received on June 20, 1991; accepted on February 17, 1991     

Search images not proven: A reappraisal of recent evidence

It is commonly agreed that predators hunting for cryptic prey have been demonstrated to adopt search images (involving perceptual specialization) for particular prey types. However, a simple alternative strategy, that of an appropriate reduction in search rate, may in many cases have the same effect as adopting a search image. The search image and search rate hypotheses are examined, and a series of critical predictions are proposed to distinguish them. Briefly, the search rate hypothesis predicts: (1) that adjusting search rate for one cryptic prey type will enhance the ability to detect other equally cryptic types (the search image hypothesis predicts that this will interfere with the ability to detect other equally cryptic types); (2) that adjusting search rate for cryptic prey will be achieved by learning to spend longer looking at each patch of the environment, and that the more cryptic the prey the longer will be the viewing time required to effect accurate detection (the search image hypothesis makes no such predictions). Four recent studies purporting to demonstrate search images are re-examined in the light of these predictions, and it is found that the published data fail to distinguish the two hypotheses. In addition, some evidence that is better explained by the search rate hypothesis is discussed. A brief examination of the ecological consequences of the search rate hypothesis shows that, unlike the search image hypothesis, it does not predict apostatic selection. It is therefore argued that the distinction between the two mechanisms explaining how predators ‘learn to see’ cryptic prey is important, but that the critical tests have not yet been made. The existence of search images remains not proven.     

Born‐digital biodiversity data: Millions and billions

Given the dramatic pace of change of our planet, we need rapid collection of environmental data to document how species are coping and to evaluate the impact of our conservation interventions. To address this need, new classes of “born digital” biodiversity records are now being collected and curated many orders of magnitude faster than traditional data. In addition to the millions of citizen science observations of species that have been accumulating over the last decade, the last few years have seen a surge of sensor data, with eMammal's camera trap archive passing 1 million photo‐vouchered specimens and Movebank's animal tracking database recently passing 1.5 billion animal locations. Data from digital sensors have other advantages over visual citizen science observation in that the level of survey effort is intrinsically documented and they can preserve digital vouchers that can be used to verify species identity. These novel digital specimens are leading spatial ecology into the era of Big Data and will require a big tent of collaborating organizations to make these databases sustainable and durable. We urge institutions to recognize the future of born‐digital records and invest in proper curation and standards so we can make the most of these records to inform management, inspire conservation action and tell natural history stories about life on the planet.     

Science,truth, and forensic cultures: The exceptional legal status of DNA evidence

Many epistemological terms, such as investigation, inquiry, argument, evidence, and fact were established in law well before being associated with science. However, while legal proof remained qualified by standards of ‘moral certainty’, scientific proof attained a reputation for objectivity. Although most forms of legal evidence (including expert evidence) continue to be treated as fallible ‘opinions’ rather than objective ‘facts’, forensic DNA evidence increasingly is being granted an exceptional factual status. It did not always enjoy such status. Two decades ago, the scientific status of forensic DNA evidence was challenged in the scientific literature and in courts of law, but by the late 1990s it was being granted exceptional legal status. This paper reviews the ascendancy of DNA profiling, and argues that its widely-heralded objective status is bound up with systems of administrative accountability. The ‘administrative objectivity’ of DNA evidence rests upon observable and reportable bureaucratic rules, records, recording devices, protocols, and architectural arrangements. By highlighting administrative sources of objectivity, this paper suggests that DNA evidence remains bound within the context of ordinary organisational and practical routines, and is not a transcendent source of ‘truth’ in the criminal justice system.     

Subjective interpretation,laboratory error and the value of forensic DNA evidence: Three case studies

This article discusses two factors that may profoundly affect the value of DNA evidence for proving that two samples have a common source: uncertainty about the interpretation of test results and the possibility of laboratory error. Three case studies are presented to illustrate the importance of the analyst's subjective judgments in interpreting some RFLP-based forensic DNA tests. In each case, the likelihood ratio describing the value of DNA evidence is shown to be dramatically reduced by uncertainty about the scoring of bands and the possibility of laboratory error. The article concludes that statistical estimates of the frequency of matching genotypes can be a misleading index of the value of DNA evidence, and that more adequate indices are needed. It also argues that forensic laboratoires should comply with the National Research Council's recommendation that forensic test results be scored in a blind or objective manner.Editor's commentsThe author treats the timely and important issue of laboratory error. Readers will need to read the paper by Lempert in this volume for an alternative interpretation of the 1989 proficiency testing of Cellmark diagnostics.     

Clinical thermometry: possible causes and potential solutions to electronic,digital thermometer inaccuracies

Previous research has indicated that the improvements in safety, speed, and ease of use of the newer electronic, digital oral and tympanic clinical thermometers have been offset by a loss in accuracy and reliability when compared with the traditional glass/mercury oral clinical thermometers. The purpose of this study was to determine possible causes of the relative lack of accuracy and reliability in these thermometers and suggest logical potential solutions. Evidence has been reviewed, which suggests that problems with the tympanic thermometers are the result of the range of normal anatomical variability. The combination of an otoscope with the tympanic thermometers is suggested and discussed as a potential solution. Evidence has been reviewed, which suggests that problems with the newer oral thermometers are the results of the size of the temperature sensors and the speed with which they respond. The small sensor size results in variability in placement relative to the primary heat source. The speed of sensor response results in too great a sensitivity to local, acute vasomotor activity (clinical temperature noise). Potential solutions, including an increase in sensor size and a reduction in response speed are discussed.     

Late Cretaceous incident light reduction: evidence from benthic algae

The Cretaceous-Palaeogene record of benthic marine algae is dominated by two calcified groups: red Corallinales and green Dasycladales. Non-geniculate corallines range to depths of -268 m from tropics to poles. In contrast, dasycladaleans are restricted to shallow, warm waters. During the Maastrichtian, both groups suffered extinction of two-thirds of their species. Extinction among deeper-water species (61-70%) was only slightly less than for shallow-water species (67-79%). This small amount of selectivity between species with very different depth-temperature distributions implicates a factor capable of affecting most of the photic zone. Large-scale reduction in incident light is more likely to have this effect than changes in factors such as temperature or sea level, which would affect shallow water species more intensely than those in deep water. Significant incident light reduction features in both the bolide impact and extensive volcanism hypotheses of Cretaceous-Palaeogene extinction. Dating of this major Late Cretaceous benthic algal extinction event requires further stratigraphic resolution. Available evidence suggests that it occurred in the latter part of the Maastrichtian. Its precise timing could clarify debate concerning the nature and cause of end-Cretaceous mass extinction. Both corallines and dasycladaleans recovered their diversity in Early Palaeocene species radiations.     

Posterior dental size reduction in hominids: The Atapuerca evidence

In order to reassess previous hypotheses concerning dental size reduction of the posterior teeth during Pleistocene human evolution, current fossil dental evidence is examined. This evidence includes the large sample of hominid teeth found in recent excavations (1984–1993) in the Sima de los Huesos Middle Pleistocene cave site of the Sierra de Atapuerca (Burgos, Spain). The lower fourth premolars and molars of the Atapuerca hominids, probably older than 300 Kyr, have dimensions similar to those of modern humans. Further, these hominids share the derived state of other features of the posterior teeth with modern humans, such as a similar relative molar size and frequent absence of the hypoconulid, thus suggesting a possible case of parallelism. We believe that dietary changes allowed size reduction of the posterior teeth during the Middle Pleistocene, and the present evidence suggests that the selective pressures that operated on the size variability of these teeth were less restrictive than what is assumed by previous models of dental reduction. Thus, the causal relationship between tooth size decrease and changes in food-preparation techniques during the Pleistocene should be reconsidered. Moreover, the present evidence indicates that the differential reduction of the molars cannot be explained in terms of restriction of available growth space. The molar crown area measurements of a modern human sample were also investigated. The results of this study, as well as previous similar analyses, suggest that a decrease of the rate of cell proliferation, which affected the later-forming crown regions to a greater extent, may be the biological process responsible for the general and differential dental size reduction that occurred during human evolution. © 1995 Wiley-Liss, Inc.     

Weight reduction in the management of hypertension: epidemiologic and mechanistic evidence

A number of studies have established a close association between increased body mass and elevated blood pressure. The presence of obesity in hypertensive subjects is associated with some hemodynamic, metabolic, and endocrinic characteristics: an increased intravascular volume with a high intracellular body water/interstitial fluid volume ratio, increased cardiac output, stroke volume, and left ventricular work while peripheral resistance was reduced or normal. Weight loss of at least 10 kg can reduce blood pressure independently of changes in sodium intake in obese persons of both sexes with mild, moderate, or severe high blood pressure. The fall in arterial pressure in obese hypertensives after weight loss may reverse many of the previously mentioned altered findings and underscore previous epidemiological studies that have shown that weight control could be an important measure in the treatment of hypertension.