Machine learning for detection of 3D features using sparse x-ray tomographic reconstruction.

In many inertial confinement fusion (ICF) experiments, the neutron yield and other parameters cannot be completely accounted for with one and two dimensional models. This discrepancy suggests that there are three dimensional effects that may be significant. Sources of these effects include defects in the shells and defects in shell interfaces, the fill tube of the capsule, and the joint feature in double shell targets. Due to their ability to penetrate materials, x rays are used to capture the internal structure of objects. Methods such as computational tomography use x-ray radiographs from hundreds of projections, in order to reconstruct a three dimensional model of the object. In experimental environments, such as the National Ignition Facility and Omega-60, the availability of these views is scarce, and in many cases only consists of a single line of sight. Mathematical reconstruction of a 3D object from sparse views is an ill-posed inverse problem. These types of problems are typically solved by utilizing prior information. Neural networks have been used for the task of 3D reconstruction as they are capable of encoding and leveraging this prior information. We utilize half a dozen, different convolutional neural networks to produce different 3D representations of ICF implosions from the experimental data. Deep supervision is utilized to train a neural network to produce high-resolution reconstructions. These representations are used to track 3D features of the capsules, such as the ablator, inner shell, and the joint between shell hemispheres. Machine learning, supplemented by different priors, is a promising method for 3D reconstructions in ICF and x-ray radiography, in general.

Use of computer vision for analysis of image datasets from high temperature plasma experiments.

Great strides have been made in improving the quality of x-ray radiographs in high energy density plasma experiments, enabled in part by innovations in engineering and manufacturing of integrated circuits and materials. As a consequence, the radiographs of today are filled with a great deal of detail, but few of these features are extracted in a systematic way. Analysis techniques familiar to plasma physicists tend toward brittle 1D lineout or Fourier transform type analyses. The techniques applied to process our data have not kept pace with improvements in the quality of our data. Fortunately, the field of computer vision has a wealth of tools to offer, which have been widely used in industrial imaging and, more recently, adopted in biological imaging. We demonstrate the application of computer vision techniques to the analysis of x-ray radiographs from high energy density plasma experiments, as well as give a brief tutorial on the computer vision techniques themselves. These tools robustly extract 2D contours of shocks, boundaries of inhomogeneities, and secondary flows, thereby allowing for increased automation of analysis, as well as direct and quantitative comparisons with simulations.

Metabolite activity in the anterior cingulate cortex during a painful stimulus using functional MRS.

To understand neurochemical brain responses to pain, proton magnetic resonance spectroscopy (1H-MRS) is used in humans in vivo to examine various metabolites. Recent MRS investigations have adopted a functional approach, where acquisitions of MRS are performed over time to track task-related changes. Previous studies suggest glutamate is of primary interest, as it may play a role during cortical processing of noxious stimuli. The objective of this study was to examine the metabolic effect (i.e., glutamate) in the anterior cingulate cortex during noxious stimulation using fMRS. The analysis addressed changes in glutamate and glutamate + glutamine (Glx) associated with the onset of pain, and the degree by which fluctuations in metabolites corresponded with continuous pain outcomes. Results suggest healthy participants undergoing tonic noxious stimulation demonstrated increased concentrations of glutamate and Glx at the onset of pain. Subsequent reports of pain were not accompanied by corresponding changes in glutamate of Glx concentrations. An exploratory analysis on sex revealed large effect size changes in glutamate at pain onset in female participants, compared with medium-sized effects in male participants. We propose a role for glutamate in the ACC related to the detection of a noxious stimulus.

Soft x-ray spectrum unfold of K-edge filtered x-ray diode arrays using cubic splines.

Cubic spline interpolation is able to recover temporally and spectrally resolved soft x-ray fluxes from an array of K-edge filtered x-ray diodes without the need for a priori assumptions about the spectrum or the geometry of the emitting volume. The mathematics of the cubic spline interpolation is discussed in detail. The analytic nature of the cubic spline solution allows for analytical error propagation, and the method of calculating the error for radiation temperature, spectral power, and confidence intervals of the unfolded spectrally resolved flux is explained. An unfold of a blackbody model demonstrates the accuracy of the cubic spline unfold. Tests of cubic spline performance using spectrally convolved detailed atomic model simulation results have been performed to measure the method's ability to conserve spectral power to within a factor of 2 or better in line-dominated regimes. The unfold is also demonstrated to work when information from the x-ray diode array is limited due to high signal-to-noise ratios or the lack of signal due to over-attenuation or over-filtration of the x-ray diode signal. The robustness of the unfold with respect to background subtraction and raw signal processing, signal alignment between diode traces, limited signal information, and initial conditions is discussed. Results from an example analysis of a halfraum drive are presented to demonstrate the capabilities of the unfold in comparison with previously established methods.

Goth migration induced changes in the matrilineal genetic structure of the central-east European population.

For years, the issues related to the origin of the Goths and their early migrations in the Iron Age have been a matter of hot debate among archaeologists. Unfortunately, the lack of new independent data has precluded the evaluation of the existing hypothesis. To overcome this problem, we initiated systematic studies of the populations inhabiting the contemporary territory of Poland during the Iron Age. Here, we present an analysis of mitochondrial DNA isolated from 27 individuals (collectively called the Mas-VBIA group) excavated from an Iron Age cemetery (dated to the 2nd-4th century A.D.) attributed to Goths and located near Maslomecz, eastern Poland. We found that Mas-VBIA has similar genetic diversity to present-day Asian populations and higher diversity than that of contemporary Europeans. Our studies revealed close genetic links between the Mas-VBIA and two other Iron Age populations from the Jutland peninsula and from Kowalewko, located in western Poland. We disclosed the genetic connection between the Mas-VBIA and ancient Pontic-Caspian steppe groups. Similar connections were absent in the chronologically earlier Kowalewko and Jutland peninsula populations. The collected results seem to be consistent with the historical narrative that assumed that the Goths originated in southern Scandinavia; then, at least part of the Goth population moved south through the territory of contemporary Poland towards the Black Sea region, where they mixed with local populations and formed the Chernyakhov culture. Finally, a fraction of the Chernyakhov population returned to the southeast region of present-day Poland and established the archaeological formation called the "Maslomecz group".

Reply to 'Thomson scattering in inhomogeneous plasmas: The Role of the Fluctuation-Dissipation Theorem'.

In a comment on our article "Theory of Thomson scattering in inhomogeneous media", V. V. Belyi asserts that there is an inconsistency in our method of applying gradient effects via the dielectric superposition principle, in violation of the fluctuation-dissipation theorem; and that his Klimontovich-Langevin formulation would be more appropriate to our application. While we agree that a generalization, along the lines of Belyi's work, would be required for strongly coupled systems, for the weakly coupled systems which we considered, these corrections are not necessary and our approach is still appropriate.Replying to: V. Belyi, Sci. Rep. 8 (2018); https://doi.org/10.1038/s41598-018-25319-6 .

MR-compatibility of a high-resolution small animal PET insert operating inside a 7 T MRI.

A full-ring PET insert consisting of 16 PET detector modules was designed and constructed to fit within the 114 mm diameter gradient bore of a Bruker 7 T MRI. The individual detector modules contain two silicon photomultiplier (SiPM) arrays, dual-layer offset LYSO crystal arrays, and high-definition multimedia interface (HDMI) cables for both signal and power transmission. Several different RF shielding configurations were assessed prior to construction of a fully assembled PET insert using a combination of carbon fibre and copper foil for RF shielding. MR-compatibility measurements included field mapping of the static magnetic field (B 0) and the time-varying excitation field (B 1) as well as acquisitions with multiple pulse sequences: spin echo (SE), rapid imaging with refocused echoes (RARE), fast low angle shot (FLASH) gradient echo, and echo planar imaging (EPI). B 0 field maps revealed a small degradation in the mean homogeneity (+0.1 ppm) when the PET insert was installed and operating. No significant change was observed in the B 1 field maps or the image homogeneity of various MR images, with a 9% decrease in the signal-to-noise ratio (SNR) observed only in EPI images acquired with the PET insert installed and operating. PET detector flood histograms, photopeak amplitudes, and energy resolutions were unchanged in individual PET detector modules when acquired during MRI operation. There was a small baseline shift on the PET detector signals due to the switching amplifiers used to power MRI gradient pulses. This baseline shift was observable when measured with an oscilloscope and varied as a function of the gradient duty cycle, but had no noticeable effect on the performance of the PET detector modules. Compact front-end electronics and effective RF shielding led to minimal cross-interference between the PET and MRI systems. Both PET detector and MRI performance was excellent, whether operating as a standalone system or a hybrid PET/MRI.

Theory of Thomson scattering in inhomogeneous media.

Thomson scattering of laser light is one of the most fundamental diagnostics of plasma density, temperature and magnetic fields. It relies on the assumption that the properties in the probed volume are homogeneous and constant during the probing time. On the other hand, laboratory plasmas are seldom uniform and homogeneous on the temporal and spatial dimensions over which data is collected. This is particularly true for laser-produced high-energy-density matter, which often exhibits steep gradients in temperature, density and pressure, on a scale determined by the laser focus. Here, we discuss the modification of the cross section for Thomson scattering in fully-ionized media exhibiting steep spatial inhomogeneities and/or fast temporal fluctuations. We show that the predicted Thomson scattering spectra are greatly altered compared to the uniform case, and may lead to violations of detailed balance. Therefore, careful interpretation of the spectra is necessary for spatially or temporally inhomogeneous systems.

Quality Requirements for the early Fetal Ultrasound Assessment at 11-13+6 Weeks of Gestation (DEGUM Levels II and III).

The early fetal ultrasound assessment at 11 - 13(+6) weeks of gestation remains the cornerstone of care despite the progress in diagnosing fetal chromosomal defects using cell-free fetal DNA (cffDNA) from the maternal circulation. The measurement of nuchal translucency (NT) allows the risk calculation for the fetal trisomies 21, 18 and 13 but also gives information on those fetal chromosomal defects which are at present unable to be detected using cffDNA. Nuchal translucency is the only auditable parameter at 11 - 13(+6) weeks and gives thus information on the quality of the first trimester anomaly scan. In addition it gives indirect information on the risks for fetal defects and for cardiac anomalies. Also the chances for a healthy live baby can be estimated. As experience with first trimester anomaly scanning increases, and the resolution of the ultrasound equipment has increased substantially, more and more details of the fetal anatomy become accessible at the first trimester scan. Therefore fetal anatomical defects and complex anomalies have become amenable to examination in the first trimester. This guideline describes compulsory and optional parameters for investigation at the first trimester scan and outlines a structured method of examining a first trimester fetus at 11 - 13(+6) weeks of gestation.

Cranial and cerebral signs in the diagnosis of spina bifida between 18 and 22 weeks of gestation: a German multicentre study.

OBJECTIVE: The aim of this article is to study secondary cranial signs in fetuses with spina bifida in a precisely defined screening period between 18 + 0 and 22 + 0 weeks of gestation. METHOD: On the basis of retrospective analysis of 627 fetuses with spina bifida, the value of indirect cranial and cerebral markers was assessed by well-trained ultrasonographers in 13 different prenatal centres in accordance with the ISUOG (International Society of Ultrasound in Obstetrics and Gynecology) guidelines on fetal neurosonography. RESULTS: Open spina bifida was diagnosed in 98.9% of cases whereas 1.1% was closed spina bifida. Associated chromosomal abnormalities were found in 6.2%. The banana and lemon signs were evident in 97.1% and 88.6% of cases. Obliteration of the cisterna magna was seen in 96.7%. Cerebellar diameter, head circumference and biparietal diameter were below the 5th percentile in chromosomally normal fetuses in 72.5%, 69.7% and 52%, respectively. The width of the posterior horn of the lateral ventricle was above the 95th percentile in 57.7%. The secondary cranial and cerebral signs were dependent on fetal chromosome status and width of the posterior horn. Biparietal diameter was also dependent on the chromosome status with statistical significance p = 0.0068. Pregnancy was terminated in 89.6% of cases. CONCLUSION: In standard measuring planes, lemon sign, banana sign and an inability to image the cistern magna are very reliable indirect ultrasound markers of spina bifida. © 2014 John Wiley & Sons, Ltd.

Screening for chromosomal abnormalities by first trimester combined screening and noninvasive prenatal testing.

PURPOSE: To examine combined first trimester screening (FTS), noninvasive prenatal testing (NIPT) and a two-step policy that combines FTS and NIPT in screening for aneuploidy. MATERIALS AND METHODS: Retrospective study involving 21,052 pregnancies where FTS was performed at the Praxis Praenatal.de in Duesseldorf, Germany. In each case, the sum risk of trisomy 21, 18 and 13 was computed. We assumed that NIPT detects 99 %, 98 %, 90 % and 99 % of cases with trisomy 21, 18, 13 and sex chromosomal abnormalities and that the false-positive rate is 0.5 %. The following screening policies were examined: NIPT or FTS with sum risk cut-offs of 1 in 50 and 1 in 250 in all patients or a two-step-policy with FTS in all patients followed by NIPT in the intermediate sum risk group. For the intermediate risk group, sum risk cut-offs of 1 in 50 and 1 in 1000 and 1 in 150 and 1 in 500 were used. RESULTS: There were 127, 34, 13 and 15 pregnancies with trisomy 21, 18, 13 and sex chromosomal abnormalities. 23 fetuses had other chromosomal abnormalities with an increased risk for adverse outcome that are not detectable by NIPT. 20,840 pregnancies were classified as normal as ante- and postnatal examinations did not show any signs of clinically significant chromosomal abnormalities. FTS with a sum risk cut-off of 1 in 50 and 1 in 250 detects 81 % and 91 % for all aneuploidies. NIPT detects 88 % of the respective pregnancies. The 2-step approach with sum risk cut-offs of 1 in 50 and 1 in 1000 detects 94 % of all aneuploidies. With sum risk cut-offs of 1 in 150 and 1 in 500, the detection rate is 93 %. CONCLUSION: A 2-step policy with FTS for all patients and NIPT in the intermediate risk group results in the highest detection rate of all aneuploidies.

[Combined first trimester screening and cell-free fetal DNA - "next generation screening"]. / Kombiniertes Ersttrimesterscreening und zellfreie fetale DNA ­ "Next Generation Screening"

In the last decades, prenatal screening for aneuploidy has become increasingly effective. While first trimester combined screening is considered to be the current gold standard, the use of cell-free fetal DNA (cffDNA), which is also called noninvasive prenatal testing (NIPT), will result in a change of paradigm. Respective studies indicate that in screening for trisomy 21, the detection and false-positive rates are 99 % and 0.1 %, respectively. For trisomies 18 and 13, there is less evidence but recent studies report detection rates of 98 % and 86 %. Despite the excellent results in screening for trisomy 21, NIPT should not be considered as a diagnostic test. Due to the costs of NIPT, it is unlikely that NIPT will be applied in the near future in population-based screening for trisomy. In addition, the scope of the current approach in first trimester screening exceeds the screening for aneuploidy as it is possible to assess the risk for various pregnancy complications. Therefore, a combination of both NIPT and first trimester combined screening seems reasonable. Both examinations could be applied in a contingent model where the latter is offered to everyone and NIPT is restricted to women with an intermediate risk after first trimester combined screening. Such a policy would result in a detection rate of about 97 % for a false-positive rate of about 1 %. While NIPT currently focuses on screening for trisomy 21, 18, 13 and sex chromosomal abnormalities, the scope of NIPT will soon become broader. In this respect, some study groups have managed to examine the whole fetal genome within the course of the pregnancy. However, moral and ethical considerations need to be taken into account.

Fetal gastroschisis: a comparison of second vs. third-trimester bowel dilatation for predicting bowel atresia and neonatal outcomes.

PURPOSE: To compare various gestational ages and thresholds for diagnosing bowel dilatation in fetuses with gastroschisis and to evaluate the prognostic value of bowel dilatation for predicting postnatal bowel atresia and neonatal outcomes. MATERIALS AND METHODS: This was a retrospective observational study conducted from March 1997 to September 2009 that included 78 pregnancies with fetal gastroschisis. The predictive value of prenatal bowel dilatation for neonatal bowel atresia and postnatal complications was investigated in three subgroups: those with bowel dilatations ≥ 10 mm at a gestational age < 27 + 0 weeks, ≥ 10 mm at a gestational age < 30 + 0 weeks and ≥ 18 mm at a gestational age ≥ 30 weeks. RESULTS: Prenatally, 6 %, 81 % and 13 % of the bowel malformations were identified in the first, second and third trimesters, respectively. There were three stillbirths and three neonatal deaths, and the mean gestational age at delivery was 35.4 weeks (range 31 + 4 to 41 + 6). Bowel atresia was significantly correlated with prenatal bowel dilatation in all three subgroups. Bowel dilatations of ≥ 10 mm before 30 + 0 gestational weeks achieved the best performance in predicting bowel atresia, with a sensitivity of 89 % (8 / 9) and a specificity of 79 % (30 / 38). A prenatal bowel diameter ≥ 10 mm through 30 completed weeks was also the best predictor of a prolonged neonatal hospital stay ≥ 8 weeks (sensitivity = 61.1, 11 / 18, p = 0.002). CONCLUSION: Fetuses with isolated gastroschisis successfully underwent postnatal surgery in most cases (93.2 %), except for one termination, one intrauterine death and 3 cases of neonatal death. A fetal bowel dilatation > 10 mm before 30 + 0 weeks had the highest predictive value for postnatal bowel complications.

Comparison of systemic and mucosal vaccination: impact on intravenous and rectal SIV challenge.

Mucosal tissues are the primary route of transmission for most respiratory and sexually transmitted diseases, including human immunodeficiency virus. We aimed to generate strong mucosal immune responses to simian immunodeficiency virus (SIV) in rhesus macaques by targeting recombinant adenovirus serotype 5 (rAd5) to the lung. The immunogenicity and efficacy of aerosol (AE) vaccination was compared with intramuscular (IM) delivery in either an intravenous (IV) or intrarectal (IR) SIV(mac251) challenge model. Aerosolized rAd5 induced strong cellular responses in the lung and systemic humoral responses equivalent to IM. Strikingly, all immunization groups controlled acute viremia in the IV challenge model by 1-2 logs. By contrast, after IR challenge, only peak viremia was reduced by immunization, with no significant effect on SIV infection acquisition rate or mucosal CD4(+) T-cell preservation. Improved disease outcome was associated with pre-challenge cellular and humoral responses, while post-challenge T-cell responses were highly correlated with viremia control. The similar outcomes achieved by systemic and airway mucosal immunization support AE delivery as a safe, effective, and less invasive alternative to parenteral vaccination.

Sci-Fri AM: Imaging - 03: Temperature dependence of a SiPM detector for an MR compatible PET system.

Silicon photomultiplier (SiPM) detectors are rapidly becoming the detector of choice for research and development of new detectors for positron emission tomography (PET) due to their combination of high gain, fast timing, compact form factor and ability to function in a magnetic field. We are investigating using SiPM based detectors in a compact PET system designed to be inserted into a 7T animal MRI system and enable simultaneous PET/MRI imaging. In order to understand the level of thermal stability required for this PET system, we examined the stability of a prototype SiPM detector vs. temperature. A detector was constructed using a SensL SPMArray4 SiPM array coupled to a LYSO scintillator crystal array. The temperature of the detector was varied between 23 and 60°C in 5°C steps. At each temperature setting data were collected to characterize the detector flood histogram, photopeak amplitude and energy resolution at 511 keV, timing resolution and signal arrival time. While the flood image showed no noticeable changes with temperature, the 511 keV photopeak amplitude showed a linear decrease of 1.5%/°C and the energy resolution degraded by 0.08%/°C. The timing resolution degraded by 1.5 ns, from 3.5 ns to 5 ns when the temperature changed from 23 to 60°C. Over this temperature range there was a shift in the signal arrival time of approximately 3 ns. These results demonstrate that the detector can be operated over a wide range of temperature, giving a large degree of flexibility in choosing an operating temperature set-point for our PET system.

Sci-Fri AM: Imaging - 08: Comparison of single and dual layer detector blocks for pre-clinical MRI-PET.

Our group is developing a small animal PET scanner which would fit in a 7 Tesla MRI scanner to provide simultaneous PET and MR acquisitions and images. There is very little room for the PET detectors and we must use nonmagnetic materials. This presentation describes preliminary work with two PET detectors consisting of LYSO blocks each with two crystal layers: 49 1.67*1.67*6.0 mm on the bottom layer and 36 4.0 mm deep crystals on the top layer. These are mounted on SensL 4*4 arrays of silicon photo-multipliers whose outputs are multiplexed to provide three signals: Energy, X, Y. These detectors were mounted on translation stages and scanned past a 0.25 mm diameter 370 MBq Na-18 source embedded in tissue equivalent plastic. The results were compared with similar single layer crystal blocks with 10 mm deep crystals to assess the advantage of dual layer crystals to reduce radial blurring in a PET scanner with a diameter of only 64 mm. The ability to identify correctly each crystal is reported as its resolvability index, (RI), defined as the (crystal response FWHM)/(crystal's separation) in the crystal identification matrix. For the dual layer block RI =0.44, and for dual layer block RI=0.22. The coincidence response resolution for the single layer block varied from 1.23±0.05 mm at the centre of the scanner to 3.09±0.10 mm at 15.8 mm radius, while the dual layer block varied from 1.31±0.06 to 1.96±0.51 mm over the same range, confirming the Monte-Carlo simulations showing reduced radial blurring.

Assessment of Foetal DNA in Maternal Blood - A Useful Tool in the Hands of Prenatal Specialists.

Over the last few years, first trimester screening between 11+ and 13+ weeks of gestation has become one of the most important ultrasound examinations in pregnancy, as it allows physicians to predict several pregnancy complications including pre-eclampsia or pre-term birth. Screening for trisomies 21/18 and 13 using maternal and gestational age, foetal nuchal translucency, and maternal serum biochemistry was formerly the main reason for first trimester screening. However, today this is only one part of the overall examination. In the near future, the analysis of foetal DNA obtained from maternal blood will be used to supplement first trimester screening for aneuploidy or even replace current screening methods. In this review we show how prenatal medicine specialists can use foetal DNA analysis.