189 research outputs found
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
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
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
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
Recommended from our members
Associations of height, body mass index, and weight gain with breast cancer risk in carriers of a pathogenic variant in BRCA1 or BRCA2: the BRCA1 and BRCA2 Cohort Consortium.
INTRODUCTION: Height, body mass index (BMI), and weight gain are associated with breast cancer risk in the general population. It is unclear whether these associations also exist for carriers of pathogenic variants in the BRCA1 or BRCA2 genes. PATIENTS AND METHODS: An international pooled cohort of 8091 BRCA1/2 variant carriers was used for retrospective and prospective analyses separately for premenopausal and postmenopausal women. Cox regression was used to estimate breast cancer risk associations with height, BMI, and weight change. RESULTS: In the retrospective analysis, taller height was associated with risk of premenopausal breast cancer for BRCA2 variant carriers (HR 1.20 per 10 cm increase, 95% CI 1.04-1.38). Higher young-adult BMI was associated with lower premenopausal breast cancer risk for both BRCA1 (HR 0.75 per 5 kg/m2, 95% CI 0.66-0.84) and BRCA2 (HR 0.76, 95% CI 0.65-0.89) variant carriers in the retrospective analysis, with consistent, though not statistically significant, findings from the prospective analysis. In the prospective analysis, higher BMI and adult weight gain were associated with higher postmenopausal breast cancer risk for BRCA1 carriers (HR 1.20 per 5 kg/m2, 95% CI 1.02-1.42; and HR 1.10 per 5 kg weight gain, 95% CI 1.01-1.19, respectively). CONCLUSION: Anthropometric measures are associated with breast cancer risk for BRCA1 and BRCA2 variant carriers, with relative risk estimates that are generally consistent with those for women from the general population
Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study
PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks
Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.
PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks
- …