Capturing natural-colour 3D models of insects for species discovery

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3mm to 30mm in length. Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.Comment: 24 pages, 17 figures, PLOS ONE journa

Towards high-throughput 3D insect capture for species discovery and diagnostics

Digitisation of natural history collections not only preserves precious information about biological diversity, it also enables us to share, analyse, annotate and compare specimens to gain new insights. High-resolution, full-colour 3D capture of biological specimens yields color and geometry information complementary to other techniques (e.g., 2D capture, electron scanning and micro computed tomography). However 3D colour capture of small specimens is slow for reasons including specimen handling, the narrow depth of field of high magnification optics, and the large number of images required to resolve complex shapes of specimens. In this paper, we outline techniques to accelerate 3D image capture, including using a desktop robotic arm to automate the insect handling process; using a calibrated pan-tilt rig to avoid attaching calibration targets to specimens; using light field cameras to capture images at an extended depth of field in one shot; and using 3D Web and mixed reality tools to facilitate the annotation, distribution and visualisation of 3D digital models.Comment: 2 pages, 1 figure, for BigDig workshop at 2017 eScience conferenc

The development of performance assessment tools to improve the quality of diagnosis and monitoring of haemoglobinopathy disorders

The haemoglobinopathies are complex inherited disorders of haemoglobin synthesis. Although carriers are generally asymptomatic, homozygous or compound heterozygous inheritance of globin gene mutations may result in severe conditions, identified as a major burden of disease worldwide. The main means of control of the conditions is by carrier screening using specialist laboratory testing, allowing individuals an informed reproductive choice. UK NEQAS Haematology provides a comprehensive external quality assessment service for the haemoglobinopathies and is in a unique position to provide an overview of laboratory performance. The increased emphasis on laboratory quality and a shift in the profile of the participating laboratories from mainly UK-based to more than half non-British Isles in the past decade are drivers for continued improvement in performance assessment methods. The project looked at aspects of performance of both UK NEQAS and the participants. A review of historical quantitation data for haemoglobin (Hb) A2, the standard biomarker for beta thalassaemia carrier identification, showed there remains a need for standardisation between methods of analysis. The survey material distributed for testing was examined to exclude commutability and stability as confounding factors in performance assessment. Changes to Hb A2 performance scoring have been suggested including the identification of one-off analytical EQA errors that could represent misdiagnosis of a beta thalassaemia carrier. In newborn screening, a difference was seen in the sensitivity of different analysers at the low levels of adult haemoglobin (Hb A) seen in a newborn infant with homozygous beta thalassaemia. A significant difference in performance in result interpretation was seen between English NHS laboratories and those outside the British Isles. The scheme should extend performance management in interpretation to all laboratories including the non-British Isles group, to ensure that the scheme remains credible to participants and fulfils its remit to improve performance wherever patients are tested. This will however require the scheme to develop the EQA data capture methods better to reflect current laboratory practice

Rising Sound Intensity: An Intrinsic Warning Cue Activating the Amygdala

Human subjects overestimate the change of rising intensity sounds compared with falling intensity sounds. Rising sound intensity has therefore been proposed to be an intrinsic warning cue. In order to test this hypothesis, we presented rising, falling, and constant intensity sounds to healthy humans and gathered psychophysiological and behavioral responses. Brain activity was measured using event-related functional magnetic resonance imaging. We found that rising compared with falling sound intensity facilitates autonomic orienting reflex and phasic alertness to auditory targets. Rising intensity sounds produced neural activity in the amygdala, which was accompanied by activity in intraparietal sulcus, superior temporal sulcus, and temporal plane. Our results indicate that rising sound intensity is an elementary warning cue eliciting adaptive responses by recruiting attentional and physiological resources. Regions involved in cross-modal integration were activated by rising sound intensity, while the right-hemisphere phasic alertness network could not be supported by this stud

Appendiceal Adenocarcinoma PDX Models Have Improved Tumor Growth in an Orthotopic Tumor Environment

https://openworks.mdanderson.org/sumexp23/1085/thumbnail.jp

Selitrichodes neseri n. sp, a new parasitoid of the eucalyptus gall wasp Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae: Tetrastichinae)

Selitrichodes neseri Kelly & La Salle n. sp. (Hymenoptera: Eulophidae: Tetrastichinae), is described as a parasitoid of the invasive eucalyptus gall wasp Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae: Tetrastichinae), which is causing substantial damage particularly in commercial Eucalyptus plantations. Selitrichodes neseri was originally collected in Australia in 2010 when searching for biological control agents of L. invasa. It has since been reared in quarantine in South Africa where it is being evaluated for release as a biological control agent of L. invasa.The University of Pretoria, Forestry and Agricultural Biotechnology Institute and the Tree Protection Co-operative Programme.http://www.mapress.com/zootaxa/ab201

Full Spectrum Archaeology

Full Spectrum Archaeology (FSA) is an aspiration stemming from the convergence of archaeology’s fundamental principles with international heritage policies and community preferences. FSA encompasses study and stewardship of the full range of heritage resources in accord with the full range of associated values and through the application of treatments selected from the full range of appropriate options. Late modern states, including British Columbia, Canada, nominally embrace de jure heritage policies consonant with international standards yet also resist de facto heritage management practice grounded in professional ethics and local values and preferences. In response, inheritor communities and their allies in archaeology are demonstrating the benefits of FSA and reclaiming control over cultural heritage. Archaeology and heritage management driven by altruistic articulation of communal, educational, scientific and other values further expose shortcomings and vulnerabilities of late modern states as well as public goods in and from FSA

EMQN best practice guidelines for molecular and haematology methods for carrier identification and prenatal diagnosis of the haemoglobinopathies

Haemoglobinopathies constitute the commonest recessive monogenic disorders worldwide, and the treatment of affected individuals presents a substantial global disease burden. Carrier identification and prenatal diagnosis represent valuable procedures that identify couples at risk for having affected children, so that they can be offered options to have healthy offspring. Molecular diagnosis facilitates prenatal diagnosis and definitive diagnosis of carriers and patients (especially ‘atypical’ cases who often have complex genotype interactions). However, the haemoglobin disorders are unique among all genetic diseases in that identification of carriers is preferable by haematological (biochemical) tests rather than DNA analysis. These Best Practice guidelines offer an overview of recommended strategies and methods for carrier identification and prenatal diagnosis of haemoglobinopathies, and emphasize the importance of appropriately applying and interpreting haematological tests in supporting the optimum application and evaluation of globin gene DNA analysis