Diagnostic Setup Research Articles

AltAFplotter: a web app for reliable UPD detection in NGS diagnostics

BackgroundThe detection of uniparental disomies (the inheritance of both chromosome homologues from a single parent, UPDs) is not part of most standard or commercial NGS-pipelines in human genetics and thus a common gap in NGS diagnostics. To address this we developed a tool for UPD-detection based on panel or exome data which is easy to use and publicly available.ResultsThe app is freely available at https://altafplotter.uni-leipzig.de/ and implemented in Python, using the Streamlit framework for data science web apps. It utilizes bcftools and tabix for processing vcf files. The source code is available at https://github.com/HUGLeipzig/altafplotter and can be used to host your own instance of the tool.ConclusionWe believe the app to be a great benefit for research and diagnostic labs, which struggle identifying and interpreting UPDs in their NGS diagnostic setup. The information provided allows a quick interpretation of the results and thus is suitable for usage in a high throughput manner by clinicians and biologists.

Comparison of Full-Field Digital Mammography with Synthesized Mammography from Tomosynthesis in a Diagnostic population: Prospective Study

Abstract Background Synthesized mammography (SM) refers to two-dimensional (2D) images derived from the digital breast tomosynthesis (DBT) data. It can reduce the radiation dose and scan duration when compared with conventional full-field digital mammography (FFDM) plus tomosynthesis. Purpose To compare the diagnostic performance of 2D FFDM with synthetic mammograms obtained from DBT in a diagnostic population. Materials and Methods A total of 1,468 mammograms with both FFDM and SM + DBT images were obtained and analyzed over 2 years, after obtaining approval from the institute ethics committee. The images were reported and compared as per the 2013 American College of Radiology Breast Imaging Reporting and Data System (BI-RADS) lexicon in terms of breast density, morphological features of mass, calcifications, and presence of asymmetry or architectural distortion followed by the BI-RADS category. The agreement between the two modalities was studied using the Kappa value, and the radiation exposure dose was recorded in both groups. Results FFDM and SM + DBT showed strong agreement for breast density, mass characteristics, and detection of calcifications (kappa > 0.8). Downstaging of breast density and mass density were seen by SM + DBT without any statistically significant difference. The nipple–areola complex visualization was poor in SM (50.34 vs. 76.29% in FFDM), and there were SM-specific artifacts mainly related to the reconstruction algorithm. The radiation dose was higher with SM. Conclusion FFDM has comparable performance to SM + DBT in diagnostic setup. The latter may be particularly helpful in patients with dense breasts.

First spectroscopic study of HFRC plasma

An advanced spectral diagnostic system was developed to measure the electron temperature (T e), electron density (N e), and ion temperature (T i) of the Huazhong University of Science and Technology field-reversed configuration plasma. The system consists of an optic fiber spectrometer with a wide spectral band and a 670 mm focal length high throughout Czerny–Turner monochromator equipped with both a 3600 g mm−1 grating and a 2400 g mm−1 grating to measure the line spectrum. Accompanying these components is an electron-multiplying charge-coupled device camera to capture spectral data. The relative intensity of the optical fiber spectrometer was calibrated using a standard luminance source, and the wavelength calibration of the spectrometer was accomplished using a Hg/Ar lamp. This diagnostic setup was configured to measure electron density based on the Stark effect of Hγ (n = 5 → n = 2; 434.04 nm). Doppler broadening of an O III (2s22p(2P0)3p → 2s22p(2P0)3s; 375.988 nm) emission line was measured and analyzed to obtain the ion temperature, and electron temperatures were estimated from the relative strength of Hβ (n = 4 → n = 2; 486.14 nm) (Dβ) and Hγ (Dγ) spectral lines when the electron density was obtained from Stark effect measurements. The initial experimental results indicate that the highest electron temperature of the formation region was approximately 8 eV, the electron density of the colliding-and-merging region was approaching 1020 m−3, and the ion temperature reached about 40 eV.

Validation of a novel NGS based BCR::ABL1 kinase domain mutation detection assay in Indian cohort

The efficacy and treatment outcome of a CML patient are heavily dependent on BCR::ABL1 kinase domain (KD) mutation status. Next-generation sequencing technology is a bright alternative to the previously used sanger sequencing method due to its global presence in diagnostic setups, massive parallel sequencing ability, and far better sensitivity. In the present study, we have demonstrated a new protocol for kinase domain mutation analysis using the next-generation sequencing (NGS) method using the ion torrent sequencing platform. This protocol uses RNA as the starting material, followed by nested PCR to amplify the fusion transcript, which is subsequently used as a template for NGS. Initial validation and comparison of this assay with the sanger sequencing (SS) method yielded 95.23% agreement. CML samples (n = 121) with a failure to TKI response were subjected to this newly developed NGS-based assay to detect KD mutations, from which samples were found to have mutations with a sensitivity ranging from 2.32 to 93.41%. A total of 34.71% of samples (n = 42) were found to be positive for one or more KD mutations, whereas 65.29% of samples (n = 81) were found to be negative. Nine samples out of 42 positive samples, i.e., 21.42%, were found to have compound mutations. This is one of the first studies from India, which includes more than 160 samples and is analyzed by the NGS approach for KD mutation analysis.

A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer.

Most clinical diagnostic and genomic research setups focus almost exclusively on coding regions and essential splice sites, thereby overlooking other non-coding variants. As a result, intronic variants that can promote mis-splicing events across a range of diseases, including cancer, are yet to be systematically investigated. Such investigations would require both genomic and transcriptomic data, but there currently exist very few datasets that satisfy these requirements. We address this by developing a single-nucleus full-length RNA-sequencing approach that allows for the detection of potentially pathogenic intronic variants. We exemplify the potency of our approach by applying pancreatic cancer tumor and tumor-derived specimens and linking intronic variants to splicing dysregulation. We specifically find that prominent intron retention and pseudo-exon activation events are shared by the tumors and affect genes encoding key transcriptional regulators. Our work paves the way for the assessment and exploitation of intronic mutations as powerful prognostic markers and potential therapeutic targets in cancer.

Spatially resolved TALIF investigation of atomic oxygen in the effluent of a CO2 microwave discharge

A diagnostic setup for one-dimensionally spatially resolved two-photon absorption laser-induced fluorescence (TALIF) detection of ground state oxygen atoms ( 2p43P2,1,0 ) is developed. The goal of this study is to investigate the evolution of temperatures and absolute number densities of oxygen atoms along the effluent of a low-pressure CO2 microwave discharge in order to gain insights into some of the mechanisms governing the post-discharge regime. The plasma source is operated at conditions of 600 W– 1200 W of absorbed power with flow rates of 74 sccm and 370 sccm pure CO2 at pressures between 1.2 mbar and 5 mbar with specific energy inputs up to 111.9 eV/molecule. These operating conditions exhibit high CO2 conversions (up to 90%) at low energy efficiencies (2%–7.4%), due to direct electron impact dissociation driving the conversion process resulting in splitting of CO2 into CO and metastable oxygen atoms. The TALIF measurements yield spatially resolved translational temperatures between 1000 K– 1600 K for most operating conditions and axial positions along the effluent. Reference measurements with xenon 6p′[3/2]2 are used for absolute number density calibration. The resulting axially resolved number density profiles of ground state atomic oxygen increase along the effluent, even at considerable distances of several centimeters from the active discharge, before they reach a maximum between 5×1020 m−3 and 2.2×1021 m−3 depending on the condition, and decrease after that. This behavior indicates the potential significance of quenching of metastable oxygen atoms within the post-discharge regime of the investigated CO2 discharges. The measured spatially resolved number density evolutions are qualitatively consistent with quenching via wall collisions being the dominant deactivation mechanism, underlining the importance of particle-wall interactions.

An overview of the evolution of the modeling of reflectometry diagnostics in fusion plasmas using finite-difference time-domain codes

Microwave reflectometry, having its origins in ionosphere probing techniques to evaluate electronic density, has become one of the most important diagnostics for the same quantity in fusion plasmas. Reflectometry will play a major role in next-generation machines, in particular in DEMO, where it is expected to provide plasma positioning, shaping, and tracking data. The ability to have an ever-increasing comprehensive description of reflectometry is particularly important since it allows us to assess the measuring capabilities of existing experimental systems and to predict the performance of new diagnostic concepts based on probing waves. Furthermore, wave propagation in a thermonuclear plasma with fluctuating electronic densities is far from straightforward and the need for a numerical full-wave treatment becomes fundamental. We will present the reader with the fundamentals of this technique and introduce the usage and evolution of FDTD in reflectometry, using as an example, the synthetic diagnostics setup that uses the family of REFMUL* codes, which is employed in the assessment of the performance of several reflectometry systems in different fusion machines.

Evaluation of digital and manual orthodontic diagnostic setups in non-extraction cases using ABO model grading system: an in-vitro study

BackgroundTo evaluate the outcome quality of manual and digital orthodontic diagnostic setups in non-extraction cases according to the American Board of Orthodontics model grading system and to calculate the laboratory time needed for orthodontic diagnostic setup construction.MethodsThe sample consisted of 60 pretreatment models of non-extraction orthodontic cases with age ranges of 18–30. The study models were duplicated and scanned with 3Shape R-750 scanner. Digital and manual diagnostic setups were constructed according to their respective treatment plans. Digital diagnostic setups were 3D printed and then both manual and digital setups were assessed using the modified American Board of Orthodontics Cast Radiograph evaluation score (ABO CRE), which includes alignment, marginal ridge, buccolingual inclination, occlusal contacts, occlusal relationships, interproximal contacts, and overjet. The laboratory time needed for orthodontic setups was measured in minutes.ResultsThe total ABO CRE score of the digital diagnostic setup group (5.93 ± 2.74) was significantly lower than that of the manual diagnostic setup group (13.08 ± 3.25). The manual diagnostic setup had significantly larger scores in marginal ridge, overjet, overbite, buccolingual inclination, occlusal relationship, and total scores (P < 0.01). However, the digital diagnostic setup had a statistically larger occlusal contacts score than the manual diagnostic setup (P < 0.01). There was no significant difference between the alignment and the interproximal contacts scores in either group. The manual diagnostic setup needed significantly longer laboratory time (187.8 ± 14.22) than the digital setup (93.08 ± 12.65) (P < 0.01). Comparison between broken teeth was performed by using the chi-square test which found no significant difference between different tooth types.ConclusionsDigital diagnostic setup is a reliable tool for orthodontic diagnostic setup construction providing excellent quality setup models. Manual diagnostic setup is time consuming with a technique-sensitive laboratory procedure.

Diagnostic weight functions in constants-of-motion phase-space

The fast-ion phase-space distribution function in axisymmetric tokamak plasmas is completely described by the three constants of motion: energy, magnetic moment and toroidal canonical angular momentum. In this work, the observable regions of constants-of-motion phase-space, given a diagnostic setup, are identified and explained using projected velocities of the fast ions along the diagnostic lines-of-sight as a proxy for several fast-ion diagnostics, such as fast-ion Dα spectroscopy, collective Thomson scattering, neutron emission spectroscopy and gamma-ray spectroscopy. The observable region in constants-of-motion space is given by a position condition and a velocity condition, and the diagnostic sensitivity is given by a gyro-orbit and a drift-orbit weighting. As a practical example, 3D orbit weight functions quantifying the diagnostic sensitivity to each point in phase-space are computed and investigated for the future COMPASS-Upgrade and MAST-Upgrade tokamaks.

Thermal Stabilization of a Bacterial Zn(II)-Dependent Phospholipase C through Consensus Sequence Design.

Proteins' extraordinary performance in recognition and catalysis has led to their use in a range of applications. However, proteins obtained from natural sources are oftentimes not suitable for direct use in industrial or diagnostic setups. Natural proteins, evolved to optimally perform a task in physiological conditions, usually lack the stability required to be used in harsher conditions. Therefore, the alteration of the stability of proteins is commonly pursued in protein engineering studies. Here, we achieved a substantial thermal stabilization of a bacterial Zn(II)-dependent phospholipase C by consensus sequence design. We retrieved and analyzed sequenced homologues from different sources, selecting a subset of examples for expression and characterization. A non-natural consensus sequence showed the highest stability and activity among those tested. Comparison of the stability parameters of this stabilized mutant and other natural variants bearing similar mutations allows us to pinpoint the sites most likely to be responsible for the enhancement. Point mutations in these sites alter the unfolding process of the consensus sequence. We show that the stabilized version of the protein retains full activity even in harsh oil degumming conditions, making it suitable for industrial applications.

A Retrospective Observational Study to Assess the Quality Management System in a Molecular Diagnostic Laboratory of a COVID-19 Dedicated Hospital in Delhi, India

Introduction: A molecular diagnostic laboratory is the cornerstone of Coronavirus Disease-2019 (COVID-19) disease diagnosis, as the patient’s treatment and management protocol depend on molecular results. Therefore, the laboratory conducting these tests must adhere to quality management process to increase the accuracy and validity of the generated reports. Rajiv Gandhi Super Speciality Hospital established its molecular diagnostic set-up at the beginning of the pandemic. Hence, this study aims to generate quality management data to help improve weak points. Aim: To assess the quality management system for COVID-19 diagnosis. Materials and Methods: This retrospective observational study was conducted at Rajiv Gandhi Super Speciality Hospital in Delhi, India. A total of 14,561 samples were collected over six months, from February 2021 to July 2021. Data from all samples received during this period for COVID-19 ReverseTranscriptase Polymerase Chain Reaction (RT-PCR) testing were included. Data were retrospectively collected from the electronic Laboratory Information Management System (LIMS). Quality variables were analysed over six months from July to December 2021 and classified into preanalytical, analytical, and postanalytical variables. Quality Indicators (QIs) were selected from a common model of QIs set by the International Federation of Clinical Chemistry and Laboratory Medicine. The results were presented in percentages, and descriptive statistics were analysed using Statistical Package for Social Sciences (SPSS) software. Results: During the six-month study period, the molecular laboratory received 14,561 samples. Among the preanalytical variables, sample leakage was the most common cause of sample rejection (134 samples, 0.92%), followed by the non generation of Specimen Referral Form (SRF) identification (76 samples, 0.52%), and non compliance with triple packaging (44 samples, 0.3%). Other preanalytical aspects assessed included incomplete patient identification (17 samples, 0.11%), insufficient sample quantity (12 samples, 0.08%), missing forms/samples (7 samples, 0.04%), samples in the wrong vials/ empty Viral Transport Media (VTM) tubes (5 samples, 0.03%), and incomplete LIMS entry (2 samples, 0.01%). Internal Quality Control (QC) was not obtained in 55 samples (0.37%), and two incidents of cross-contamination resulted in false-positive results. Among the postanalytical factors, 11 samples (0.07%) could not be dispatched within the stipulated time frame. Conclusion: The assessment of the quality management system revealed some areas for improvement, emphasising the importance of adhering to QC processes for the smooth operation of diagnostic laboratories, especially those involved in critical reporting. The assessment of QIs helped monitor laboratory parameters effectively.

Photon Diagnostics for the High-Gain THz FEL at PITZ

Research and development of an accelerator-based THz source prototype for pump-probe experiments at the European XFEL are ongoing at the Photo Injector Test Facility at DESY in Zeuthen (PITZ). Proof-of-principle experiments have been performed to generate a high-gain THz Free-electron Laser (FEL) based on the Self-Amplified Spontaneous Emission scheme. The FEL radiation pulses with a central wavelength of about 100 μm (3 THz) and single pulse energy of several tens μm can be generated. In this paper, we present and discuss the photon diagnostic setup for the THz FEL together with examples of diagnostic results, including pulse energy and an FEL gain curve. The upgraded photon diagnostic setup, capable of measuring pulse energy, transverse distribution, and spectral distribution, is expected to be operational in the spring of 2023.

Danish Prostate Cancer Consortium Study 1 (DPCC-1) protocol: Multicentre prospective validation of the urine-based three-microRNA biomarker model uCaP

IntroductionThe primary objective of the Danish Prostate Cancer Consortium Study 1 (DPCC-1) is to provide validation for a novel urine-based microRNA biomarker, called uCaP, for a diagnosis of prostate cancer.Methods...

Integration and first operation of the Gotthard-II detector at European XFEL

Gotthard-II (G-II) is a 1-D silicon microstrip hybrid detector developed by the Paul Scherrer Institut within the framework of a collaboration agreement with the European XFEL. The ASIC features a dynamic gain switching architecture, in order to cope with the luminosity of European XFEL, and a 12-bit analog-to-digital converter with a sampling/conversion rate of more than 18 MS/s as well as a Static random-access memory, making it capable of matching the European XFEL pulse train structure, thus acquiring up to 2700 images at 4.5 MHz per burst. The sensor’s strip pitch can be either of 50 μm or 25 μm , for a total of 1280 or 2560 output channels per detector, respectively, with a spectral sensitivity that allows either X-ray detection (optimized in the 5–20 keV range) or visible light detection. Its exceptionally good compliance with the European XFEL beam conditions will make G-II the most widely employed detector across the facility, with a total of 29 modules of different flavors that will be installed in scientific instruments and beam diagnostic setups. Although the detector will be predominantly used for spectroscopic measurements it will have a variety of other applications, including X-ray diffraction/emission/absorption experiments, relative pulse arrival time monitoring (of fundamental importance for pump–probe experiments), spectral diagnostics, and beam quality monitoring, with the possibility for the detector itself to generate a veto patterns for the large area MHz framerate pixel detectors employed at the scientific instruments, such as AGIPD, LPD and DSSC. In this paper, an overview of G-II detector technology and its usage at the European XFEL will be presented; the focus will then move on towards the process of detector integration in the European XFEL control system, data acquisition, and data correction infrastructure, highlighting its challenges. Finally, an overview of the first results obtained at scientific instruments will be given.

The influence of patient positioning and immobilization equipment on MR image quality and image registration in radiation therapy.

MRI is preferred for brain tumor assessment, while CT is used for radiotherapy simulation. This study evaluated immobilization equipment's impact on CT-MRI registration accuracy and MR image quality in RT setup. We included CT and MR images from 11 patients with high-grade glioma, all of whom were immobilized with a thermoplastic mask and headrest. T1- and T2-weighted MR images were acquired using an MR head coil in a diagnostic setup (DS) and a body matrix coil in RT setup. To assess MR image quality, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were considered in some dedicated regions of interest. We also evaluated the impact of immobilization equipment on CT-MRI rigid registration using line profile and external contour methods. The CNR and SNR reduction was in the RT setup of imaging. This was more evident in T1-weighted images than in T2-weighted ones. The SNR decreased by 14.91% and 12.09%, while CNR decreased by 25.12% and 20.15% in T1- and T2-weighted images, respectively. The immobilization equipment in the RT setup decreased the mean error in rigid registration by 1.02mm. The external contour method yielded Dice similarity coefficients (DSC) of 0.84 and 0.92 for CT-DS MRI and CT-RT MRI registration, respectively. The image quality reduction in the RT setup was due to the imaged region's anatomy and its position relative to the applied coil. Furthermore, optimizing the pulse sequence is crucial for MR imaging in RT applications. Although the use of immobilization equipment may decrease the image quality in the RT setup, it does not affect organ delineation, and the image quality is still satisfactory for this purpose. Also, the use of immobilization equipment in the RT setup has increased registration accuracy.

Diagnostic setup procedure simplified : a case report

Diagnostic setup procedure simplified : a case report

An exploratory study for the perception and attitude of internship program by students of speech and hearing

Background: The attitude and opinion of internship experience as reported by students can be a useful data for effective monitoring of any academic program. Such methods are common practice worldwide, e.g., ASHA publishes survey reports annually. The present project was aimed at evaluating the perception and attitude of students of the internship program of speech and hearing sciences at the graduate level of DrSRCISH. Methods: The data was from 75 intern students posted at different rehabilitation, diagnostic and school setups. The study used a self-administered questionnaire in digital form (Google form) which had 22 questions in multiple choice or true/false statements. The questionnaire had three sections-demographic, experiences of the internship, and shortcomings in the internship. Results: Completed forms were received from the 31 out of 75 subjects. The forms were available for internees for a period of one month. Return rate was 41%. Current internship is able to provide diversity of internship training. Institution, special schools and Hospitals were the highest choices with 23%. The results support the principles of internship as formulated by RCI and ASHA. i.e. internship is necessary for clinical training programs. Supervision received, infrastructure, case load and working hours received favourable rating. The least favourite part of internship postings was logistics or travel concerns. Conclusions: The results of the data depict the effectiveness of the internship program on the professional - personal growth and skills of the students of speech and hearing sciences. Multidisciplinary working atmosphere, learning new skills were the strength of the program.

Free-electron laser temporal diagnostic beamline FL21 at FLASH.

A beamline for temporal diagnostics of extreme ultraviolet (XUV) femtosecond pulses at the free-electron laser in Hamburg (FLASH) at DESY was designed, built and put into operation. The intense ultra-short XUV pulses of FLASH fluctuate from pulse to pulse due to the underlying FEL operating principle and demand single-shot diagnostics. To cope with this, the new beamline is equipped with a terahertz field-driven streaking setup that enables the determination of single pulse duration and arrival time. The parameters of the beamline and the diagnostic setup as well as some first experimental results will be presented. In addition, concepts for parasitic operation are investigated.

Quality assurance and temporal stability of a 1.5 T MRI scanner for MR-guided Photon and Particle Therapy

PurposeTo describe performance measurements, adaptations and time stability over 20 months of a diagnostic MR scanner for integration into MR-guided photon and particle radiotherapy. Material and methodsFor realization of MR-guided photon and particle therapy (MRgRT/MRgPT), a 1.5 T MR scanner was installed at the Heidelberg Ion Beam Therapy Center. To integrate MRI into the treatment process, a flat tabletop and dedicated coil holders for flex coils were used, which prevent deformation of the patient external contour and allow for the use of immobilization tools for reproducible positioning. The signal-to-noise ratio (SNR) was compared for the diagnostic and therapy-specific setup using the flat couch top and flexible coils for the a) head & neck and b) abdominal region as well as for different bandwidths and clinical pulse sequences. Additionally, a quality assurance (QA) protocol with monthly measurements of the ACR phantom and measurement of geometric distortions for a large field-of-view (FOV) was implemented to assess the imaging quality parameters of the device over the course of 20 months. ResultsThe SNR measurements showed a decreased SNR for the RT-specific as compared to the diagnostic setup of (a) 26% to 34% and (b) 11% to 33%. No significant bandwidth dependency for this ratio was found. The longitudinal assessment of the image quality parameters with the ACR and distortion phantom confirmed the long-term stability of the MRI device. ConclusionA diagnostic MRI was commissioned for use in MR-guided particle therapy. Using a radiotherapy specific setup, a high geometric accuracy and signal homogeneity was obtained after some adaptions and the measured parameters were shown to be stable over a period of 20 months.

Phase-space tomography in magnetically confined plasmas

In this paper, a tomography approach aiming at reconstructing a phase-space structure is proposed. For the phase-space resolved diagnostic system, a signal must be decomposed in real-space, velocity-space, and time; therefore, it is challenging to obtain a sufficiently high signal intensity in a single detector bin. To overcome this difficulty, three different sets of data having different integration directions in real-space, velocity-space, and time are simultaneously used, and a reconstruction of the original structure in the phase-space is attempted by a tomographic manner. The proposed method is demonstrated using a synthetic dataset in the actual diagnostic setup in the Large Helical Device. Time evolution of a phase-space perturbation induced by the Landau damping, which is caused by energetic particle-driven magnetohydrodynamic bursts, is successfully reconstructed by this method. Robustness against realistic diagnostic noise is also presented.