Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance

OBJECTIVES: The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods. METHODS: Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied. RESULTS: Using a z score value of 3 as the cut-off, 98.11% - 100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06% - 100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly-p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively. CONCLUSIONS: Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide

Abdo-Man: a 3D-printed anthropomorphic phantom for validating quantitative SIRT

BACKGROUND: The use of selective internal radiation therapy (SIRT) is rapidly increasing, and the need for quantification and dosimetry is becoming more widespread to facilitate treatment planning and verification. The aim of this project was to develop an anthropomorphic phantom that can be used as a validation tool for post-SIRT imaging and its application to dosimetry. METHOD: The phantom design was based on anatomical data obtained from a T1-weighted volume-interpolated breath-hold examination (VIBE) on a Siemens Aera 1.5 T MRI scanner. The liver, lungs and abdominal trunk were segmented using the Hermes image processing workstation. Organ volumes were then uploaded to the Delft Visualization and Image processing Development Environment for smoothing and surface rendering. Triangular meshes defining the iso-surfaces were saved as stereo lithography (STL) files and imported into the Autodesk® Meshmixer software. Organ volumes were subtracted from the abdomen and a removable base designed to allow access to the liver cavity. Connection points for placing lesion inserts and filling holes were also included. The phantom was manufactured using a Stratasys Connex3 PolyJet 3D printer. The printer uses stereolithography technology combined with ink jet printing. Print material is a solid acrylic plastic, with similar properties to polymethylmethacrylate (PMMA). RESULTS: Measured Hounsfield units and calculated attenuation coefficients of the material were shown to also be similar to PMMA. Total print time for the phantom was approximately 5 days. Initial scans of the phantom have been performed with Y-90 bremsstrahlung SPECT/CT, Y-90 PET/CT and Tc-99m SPECT/CT. The CT component of these images compared well with the original anatomical reference, and measurements of volume agreed to within 9 %. Quantitative analysis of the phantom was performed using all three imaging techniques. Lesion and normal liver absorbed doses were calculated from the quantitative images in three dimensions using the local deposition method. CONCLUSIONS: 3D printing is a flexible and cost-efficient technology for manufacture of anthropomorphic phantom. Application of such phantoms will enable quantitative imaging and dosimetry methodologies to be evaluated, which with optimisation could help improve outcome for patients

Electrical conductivity during incipient melting in the oceanic low-velocity zone

International audienceThe low-viscosity layer in the upper mantle, the asthenosphere, is a requirement for plate tectonics1. The seismic low velocities and the high electrical conductivities of the asthenosphere are attributed either to subsolidus, water-related defects in olivine minerals2, 3, 4 or to a few volume per cent of partial melt5, 6, 7, 8, but these two interpretations have two shortcomings. First, the amount of water stored in olivine is not expected to be higher than 50 parts per million owing to partitioning with other mantle phases9 (including pargasite amphibole at moderate temperatures10) and partial melting at high temperatures9. Second, elevated melt volume fractions are impeded by the temperatures prevailing in the asthenosphere, which are too low, and by the melt mobility, which is high and can lead to gravitational segregation11, 12. Here we determine the electrical conductivity of carbon-dioxide-rich and water-rich melts, typically produced at the onset of mantle melting. Electrical conductivity increases modestly with moderate amounts of water and carbon dioxide, but it increases drastically once the carbon dioxide content exceeds six weight per cent in the melt. Incipient melts, long-expected to prevail in the asthenosphere10, 13, 14, 15, can therefore produce high electrical conductivities there. Taking into account variable degrees of depletion of the mantle in water and carbon dioxide, and their effect on the petrology of incipient melting, we calculated conductivity profiles across the asthenosphere for various tectonic plate ages. Several electrical discontinuities are predicted and match geophysical observations in a consistent petrological and geochemical framework. In moderately aged plates (more than five million years old), incipient melts probably trigger both the seismic low velocities and the high electrical conductivities in the upper part of the asthenosphere, whereas in young plates4, where seamount volcanism occurs6, a higher degree of melting is expected

Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Peer reviewe

The joint IAEA, EANM, and SNMMI practical guidance on peptide receptor radionuclide therapy (PRRNT) in neuroendocrine tumours

Peptide receptor radionuclide therapy (PRRNT) is a molecularly targeted radiation therapy involving the systemic administration of a radiolabelled peptide designed to target with high affinity and specificity receptors overexpressed on tumours. PRRNT employing the radiotagged somatostatin receptor agonists (90)Y-DOTATOC ([(90)Y-DOTA(0),Tyr(3)]-octreotide) or (177)Lu-DOTATATE ([(177)Lu-DOTA(0),Tyr(3),Thr(8)]-octreotide or [(177)Lu-DOTA(0),Tyr(3)]-octreotate) have been successfully used for the past 15 years to target metastatic or inoperable neuroendocrine tumours expressing the somatostatin receptor subtype 2. Accumulated evidence from clinical experience indicates that these tumours can be subjected to a high absorbed dose which leads to partial or complete objective responses in up to 30 % of treated patients. Survival analyses indicate that patients presenting with high tumour receptor expression at study entry and receiving (177)Lu-DOTATATE or (90)Y-DOTATOC treatment show significantly higher objective responses, leading to longer survival and improved quality of life. Side effects of PRRNT are typically seen in the kidneys and bone marrow. These, however, are usually mild provided adequate protective measures are undertaken. Despite the large body of evidence regarding efficacy and clinical safety, PRRNT is still considered an investigational treatment and its implementation must comply with national legislation, and ethical guidelines concerning human therapeutic investigations. This guidance was formulated based on recent literature and leading experts’ opinions. It covers the rationale, indications and contraindications for PRRNT, assessment of treatment response and patient follow-up. This document is aimed at guiding nuclear medicine specialists in selecting likely candidates to receive PRRNT and to deliver the treatment in a safe and effective manner. This document is largely based on the book published through a joint international effort under the auspices of the Nuclear Medicine Section of the International Atomic Energy Agency

Mineral nutrition of vegetable crops: XXV - Mineral nutrition of new zealand spinach plant (Tetragonia expansa Murr.)

The present work was carried out in order to study: a - the effect of omission and presence of the macronutrients and boron on the growth of the plants; b - deficiency symptoms of macronutrients, as well of boron; c - the effect of the deficiency of each nutrient on the chemical composition of the plants. Young spinach plants were grown in pots containing pure quartz sand. Several times a day the plants were irrigated by percolation with nutrient solutions. The treatments were: complete solution and deficient solution, in which each one of the macronutrients was omitted as well boron. Soon as the malnutrition symptoms appered, the plants were harvested and analysed chemically. - symptoms of malnutrition are easily observed for N, K, Ca and B. - symptoms of malnutrition for P, S and Mg are not easily identified. - the nutrient content, in dry matter, in deficient leaves and healthy leaves is:O trabalho teve como objetivo estudar alguns aspectos da nutrição mineral do espinafre (Tetragonia expansa Murr.) no que concerne: 1 - Efeitos da omissão dos macronutrientes e do boro, na obtenção de um quadro sintomatológico; 2 - Efeitos das carências na produção de matéria seca e composição química da planta. Mudas com trinta dias de idade foram transplantadas para soluções nutritivas carentes nos macronutrientes e/ou em boro. A coleta das plantas foi realizada quando os sintomas de deficiência se tornaram evidentes. No material seco procedeu-se a análise química. Os dados mostram que: 1 - os sintomas visuais de deficiência de N, K, Ca e B apresentam-se bem definidos; sendo que os de P, Mg e S são de difícil caracterização ; 2 - os teores dos nutrientes em plantas sadias e deficientes são

Barriers to Physical Activity and Healthy Eating As Perceived by Parents in Lompoc: Focus Group Results

Dear members of the Lompoc Valley Community Healthcare Organization, Community Health for Lompoc Valley Community Health Center, Lompoc Valley Partners and Lompoc Valley Healthy Kids Initiative, On behalf of Cal Poly’s emerging Center for Obesity Prevention and Education (COPE), I would like to begin by expressing my gratitude to Dr. Steve McDowell and Ms. Judy Taggart for inviting our research team to partner with your community in this exciting project. It is clear to our research team that the community health agencies have invested a tremendous amount of time, energy and money in planning and implementing changes designed to improve the health of children and families in Lompoc. By actively seeking input from the recipients of the Lompoc region medical and educational services and by conducting focus groups on the topic of food, physical activity and current family practices, we have a better understanding of the fundamental beliefs and perceptions of your clients. Unlike questionnaires, the qualitative data generated by focus groups provides information not only on what they do, but why they do it. Also, participating in the focus group sessions, it was clear that your clients felt a sense of value, pride and investment in helping their community. It was a very empowering and enlightening experience for all of us. The following report includes a summary of our procedures, questionnaires and forms, and participants. Data generated from the transcripts have been carefully reviewed and analyzed by four researchers, then synthesized into this final report. Over one hundred sixty-five hours were required for the analysis and report phases alone. We encourage you to examine the information contained in this report with a positive perspective. For example, we are aware that many changes in Lompoc were already in the works (such as park improvements), but weak communication lines left the community members unaware of the level of commitment by the city and health agencies and of the forward progress that was occurring. Language posed a problem for non-English speakers. And participants reported not reading the newspaper, but relying on the TV. Recognizing this cluster of facts then enables your agencies to develop an effective communication campaign to resolve the issue. Later, when unveiling new programs or playgrounds, you now have an opportunity to give credit to the community members who invested their time and expressed their concerns/wishes, thereby empowering and rewarding those clients. Utilizing the information contained in this report will enable your Healthy Kids Initiative members to better understand perceived barriers. More importantly, you will be able to identify opportunities and strategies that address these perceptions in terms that are meaningful to your clients. Targeting your audience members through specific messages, approaches, and services will allow you to increase the likelihood of success. We hope that your actions will set precedence for the central coast region and inspire other agencies to become familiar with qualitative research methods when problem solving. If we can be of further assistance in addressing the solutions, please do not hesitate to call. At Cal Poly, besides further developing our qualitative research team, we are strengthening our educational program capabilities for developing targeted nutrition and physical activity interventions, and have hired a new education technology specialist for film, media, and public service announcement campaigns and outreach. On behalf of our entire research team, we wish you continued success on your quest for improved and responsive health for the Lompoc community. And in the future, we hope opportunities to collaborate continue on a regular basis. Should you have any questions after reading the report, or wish to further discuss a topic, please do not hesitate to contact me. Also, I would be happy to present a PowerPoint presentation of the report findings to your staff or community members. Sincerely, Ann Yelmokas McDermott, PhD, MS, LDN Director, the emerging Center for Obesity Prevention and Education Associate Professor, Kinesiology Cal Poly San Luis Obispo, CA 93407 Office: 805-756-6447 Cell: 617-869-3878 [email protected]