Biogeographical distribution of house dust mites: database from the literature

There has been a multitude of research into mite fauna with focus on the medical and economic implications of these species, but there is not a recent comprehensive report of all indoor house dust mite fauna worldwide. 347 articles from 1950 to the beginning of 2017 were collected through online searches using Web of Science, Google Scholar, EThOs, ProQuest Dissertations & Theses Global, Summon2.0, Interlibrary loans, and archives in the University of Reading collection, as well as the resources available at the University College of London library. Only mites which were collected from a location where people were living (i.e. sleeping and eating on a regular basis), as well as clothing, were included. Mites identified from other indoor locations, from human sputum after ingestion, or following an allergic reaction or anaphylactic shock were excluded. Specimens which were morphologically identified, as opposed to DNA identified, were incorporated. 531 species were collected from 63 countries worldwide, with the most diverse mite fauna in India (153 species), Japan (112 species), and Brazil (99 species). Dermatophagoides pteronyssinus, Dermatophagoides farinae, and Euroglyphus maynei were the three most common species, collected from 298, 235 and 155 publications respectively. There were some issues with creating this database, including the large discrepancy in the number of studies conducted within one region or country. Therefore the minimal number of studies may not be an accurate representation of all mite fauna in that country. There are many geographical and housing differences between regions within a country, as well as sampling variations. There may also be an issue with species misidentification, particularly pertinent with older publications before more accurate keys had been produced. Some publications also only searched for specific species, so many others may be excluded. Finally, there is a bias towards English-written publications. Research published in certain journals or different languages may have not been encompassed within the online searches. Some information or articles may also be overlooked due to poor translation, as often an English abstract or summary is provided but not the reminder of the publication. Therefore, although this database contains as many publications as possible, some mite fauna may still be missing. However, as this house dust mite fauna database notes specific locations and collection times, it assists with detecting the previously outlined issues of sampling bias and differences between locations

House dust mites and their genetic systems

Despite their medical implications and widespread distribution, there is limited knowledge of house dust mites. I assessed their biogeographical distribution, examined the genetic system of one of the most common species of house dust mite, Dermatophagoides farinae, and modelled different mating systems of mites, with the aim of improving understanding. This included assembling a database of house dust mite diversity, and identifying the most successful protocols for molecular work, which will save researchers time and provide a solid base for future studies. The creation of a house dust mite fauna database through published resources provided a worldwide distribution of all mites collected from homes. This may prove useful in future, particularly by allergists who are focusing on eradicating these mites for the benefit of human health. In addition, this identified the possibility of a latitudinal diversity gradient in house dust mites. Assessing D. farinae mitochondrial and nuclear genome regions through PCR and sequencing has illustrated dissimilarity between populations. This suggested that D. farinae may have been previously misidentified and the examined populations actually represent more than one species. This gives a basis for further analysis with an increased number of populations from a variety of locations. Finally, modelling and comparing different mating systems which may be found in mites, illustrate that despite the benefits of being haplodiploid, it is difficult to transition to this system from diploidy. This indicates that cytoplasmically inherited maternally-transmitted haplodiploidy is not favoured in diploid populations, forming part of the reason why many species are still in the ancestral diploid state

Capability engineering -an analysis of perspectives

The terms "capability" and "capability engineering" are now widely used across industry and in government procurement, but it is clear that different communities use the terms with similar, but distinctly different meanings. Using a soft systems methodological approach, an INCOSE UK working group has identified eight perspectives of capability, which have been related to Ring"s value cycle and the Hitchins" five layer model of systems engineering. It is asserted that capability is the ability to do something and that capability engineering is the overarching approach that links value, purpose, and solution of a systems problem. It is equivalent to layers 1-4 of Hitchins" Five Layer Model and is equivalent to an holistic perspective of systems engineering. There are significant practice and examples of capability engineering from (at least) the UK rail provision, defence, and Information Services and it is the view of the working group that further INCOSE guidance may be needed to ensure engineers are properly equipped to deal with capability and capability engineering.©2011 by Michael Henshaw, Duncan Kemp, Peter Lister, Andrew Daw, Alan Harding, Andrew Farncombe, Malcolm Touchin. Published and used by INCOSE with permission

Incidental findings from cancer next generation sequencing panels

Next-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings

Characterization of 3D PET systems for accurate quantification of myocardial blood flow

Three-dimensional (3D) mode imaging is the current standard for positron emission tomography-computed tomography (PET-CT) systems. Dynamic imaging for quantification of myocardial blood flow (MBF) with short-lived tracers, such as Rb-82- chloride (Rb-82), requires accuracy to be maintained over a wide range of isotope activities and scanner count-rates. We propose new performance standard measurements to characterize the dynamic range of PET systems for accurate quantitative imaging. Methods: 1100-3000 MBq of Rb-82 or N-13-ammonia was injected into the heart wall insert of an anthropomorphic torso phantom. A decaying isotope scan was performed over 5 half-lives on 9 different 3D PET-CT systems and 1 3D/twodimensional (2D) PET-only system. Dynamic images (28x15s) were reconstructed using iterative algorithms with all corrections enabled. Dynamic range was defined as the maximum activity in the myocardial wall with <10% bias, from which corresponding dead-time, count-rates and/or injected activity limits were established for each scanner. Scatter correction residual bias was estimated as the maximum cavity blood-tomyocardium activity ratio. Image quality was assessed via the coefficient of variation measuring non-uniformity of the left ventricle (LV) myocardium activity distribution. Results: Maximum recommended injected activity/body-weight, peak dead-time correction factor, count-rates and residual scatter bias for accurate cardiac MBF imaging were: 3-14 MBq/kg, 1.5-4.0, 22-64 Mcps singles and 4-14 Mcps prompt coincidence count-rates, and 2-10% on the investigated scanners. Non-uniformity of the myocardial activity distribution varied from 3-16%. Conclusion: Accurate dynamic imaging is possible on the 10 3D-PET systems if the maximum injected MBq/kg values are respected to limit peak dead-time losses during the bolus first-pass transit

Suppressing bladder artifacts in bone SPECT of the pelvis.

OBJECTIVE: Bladder-filling reconstruction artifacts have a detrimental effect on the image quality of pelvic bone single photon emission computed tomography (SPECT). Using a simple protocol consisting of forced diuresis coupled with intravenous (IV) hydration, this study was undertaken to obtain an artifact-free pelvic SPECT after discarding the residual urinary activity. METHODS: Thirty patients were enrolled. In group I, pelvic SPECT was performed directly after normal void, whereas in group II, SPECT was preceded by IV injection of 0.5 mg/kg furosemide (maximum 40 mg) coupled with IV infusion of 500 cc of physiologic saline. Bladder-filling reconstruction artifacts were analyzed in group I patients, who had their images reconstructed using both filtered backprojection and iterative algorithms, both qualitatively and quantitatively by means of regions of interest (ROIs) drawn around the artifact-bearing bone areas as well as the corresponding contralateral sites. For group II patients, besides visual analysis, ROIs were placed over the sites corresponding to those of the group I patients. In every patient, total counts of each ROI were normalized to a reference ROI placed over the sacrum, and a ratio was created. RESULTS: Using filtered backprojection, two forms of artifacts were identified in group I patients: first, a streak pattern that extended to the sacro-iliac joint in nine (60%) patients, the hip joint in five (33%), the superior pubic rami in four (27%), the sacrum in three (20%), and the ischium in one (6%); second, a count loss subtype which extended to the hip joints in nine (60%) patients. Corresponding values after iterative reconstruction were two (13%) for the sacro-iliac joint, three (20%) for the hip joint, one (6%) for the superior pubic ramus, and one (6%) for the sacrum. In five (33%) patients, residual count loss artifacts were still identifiable after iterative reconstruction. However in group II, no such effects were observed because the bladder activity reached near background level in 14 (93%) of 15 patients after three successive voids with a 3.5-fold decrease in the mean value of total bladder count in comparison with group I patients. A statistically significant difference was found between artifact- and non-artifact-harboring ROIs in group I whichever the method used for reconstruction, whereas the values of right and left hemi-pelvis ROIs/sacrum in group II were almost identical. CONCLUSIONS: Forced diuresis coupled with parenteral hydration facilitates the acquisition of an artifact-free pelvic SPECT. Especially for clinical questions that focus on femoral heads and pubic bones, applying the aforementioned protocol may improve the diagnostic accuracy of pelvic bone SPECT

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing &amp;gt;3200 variants in &amp;gt;470 genes from &amp;gt;3100 publications