In resource-limited settings, patients are often first presented to clinical settings when seriously ill and access to proper clinical microbial diagnostics is often very limited or non-existing. On ...February 16th, 2022 we were on a field trip to test a completely field-deployable metagenomics sequencing set-up, that includes DNA purification, sequencing, and bioinformatics analyses using bioinformatics tools installed on a laptop for water samples, just outside Moshi, Tanzania. On our way to the test site, we were contacted by the nearby Machame hospital regarding a child seriously ill with diarrhea and not responding to treatment. Within the same day, we conducted an onsite metagenomics examination of a fecal sample from the child, and Campylobacter jejuni was identified as the causative agent. The treatment was subsequently changed, with almost immediate improvement, and the child was discharged on February 21st.
Abstract
For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance matrix from a set of sequencing reads. ...Importantly, the program is able to handle a separate mix of both short reads from the Illumina sequencing platforms and long reads from Oxford Nanopore Technologies’ (ONT) platforms as input. MINTyper performs automated reference identification, alignment, alignment trimming, optional methylation masking, and pairwise distance calculations. With this approach, we could rapidly and accurately cluster a set of DNA sequenced isolates, with a known epidemiological relationship to confirm the clustering. Functions were built to allow for both high-accuracy methylation-aware base-called MinION reads (hac_m Q10) and fast generated lower-quality reads (fast Q8) to be used, also in combination with Illumina data. With fast Q8 reads a higher number of base pairs were excluded from the calculated distance matrix, compared with the high-accuracy methylation-aware Q10 base-calling of ONT data. Nonetheless, when using different qualities of ONT data with corresponding input parameters, the clustering of isolates were nearly identical.
The overall dimensions of the ATLAS experiment and its harsh environment, due to radiation and magnetic field, represent new challenges for the implementation of the detector control system (DCS). It ...supervises all hardware of the ATLAS detector, monitors the infrastructure of the experiment, and provides information exchange with the LHC accelerator. The system must allow for the operation of the different ATLAS subdetectors in stand-alone mode, as required for calibration and debugging, as well as the coherent and integrated operation of all subdetectors for physics datataking. For this reason, the detector control system is logically arranged to map the hierarchical organization of the ATLAS detector. Special requirements are placed onto the ATLAS detector control system because of the large number of distributed I/O channels and of the inaccessibility of the equipment during operation. Standardization is a crucial issue for the design and implementation of the control system because of the large variety of equipment and the high number of different groups involved working all around the world. The functions of the two main components of the DCS, namely the distributed back-end software system, which will be based on a commercial SCADA package, and the subdetector's front-end systems, with extensive use of the CAN fieldbus, are explained. The standard readout chain of the DCS, which comprises both back-end software and general-purpose front-end equipment, is described and its performance is discussed.
Background
The diagnosis of appendicitis is difficult and resource consuming. New inflammatory markers have been proposed for the diagnosis of appendicitis, but their utility in combination with ...traditional diagnostic variables has not been tested. Our objective is to explore the potential of new inflammatory markers for improving the diagnosis of appendicitis.
Methods
The diagnostic properties of the six most promising out of 21 new inflammatory markers (interleukin IL-6, chemokine ligand CXCL-8, chemokine C–C motif ligand CCL-2, serum amyloid A SAA, matrix metalloproteinase MMP-9, and myeloperoxidase MPO) were compared with traditional diagnostic variables included in the Appendicitis Inflammatory Response (AIR) score (right iliac fossa pain, vomiting, rebound tenderness, guarding, white blood cell WBC count, proportion neutrophils, C-reactive protein and body temperature) in 432 patients with suspected appendicitis by uni- and multivariable regression models.
Results
Of the new inflammatory variables, SAA, MPO, and MMP9 were the strongest discriminators for all appendicitis (receiver operating characteristics ROC 0.71) and SAA was the strongest discriminator for advanced appendicitis (ROC 0.80) compared with defence or rebound tenderness, which were the strongest traditional discriminators for all appendicitis (ROC 0.84) and the WBC count for advanced appendicitis (ROC 0.89). CCL2 was the strongest independent discriminator beside the AIR score variables in a multivariable model. The AIR score had an ROC area of 0.91 and could correctly classify 58.3 % of the patients, with an accuracy of 92.9 %. This was not improved by inclusion of the new inflammatory markers.
Conclusion
The conventional diagnostic variables for appendicitis, as combined in the AIR score, is an efficient screening instrument for classifying patients as low-, indeterminate-, or high-risk for appendicitis. The addition of the new inflammatory variables did not improve diagnostic performance further.
Improved accuracy in the modeled gate capacitance of GaAs metal-semiconductor field-effect transistors (MESFET's) is obtained in SPICE using conservation of charge in an implanted layer. The gate ...junction creates a natural partition between mobile and fixed channel charges. Relating the gate charge to the channel current creates gate capacitances dependent upon the channel current derivatives linking the small-signal model to the large-signal equations. Results are illustrated using a depletion-mode MESFET.
Abstract Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in ...metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this paper, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads. NanoMGT excels in its ability to accurately identify mutations amidst high error rates, ensuring the reliable detection of multiple strain-specific marker genes. Our tool implements a novel scoring system that rewards mutations co-occurring across different reads and penalizes densely grouped, likely erroneous variants, thereby achieving a good balance between sensitivity and precision. A comparative evaluation of NanoMGT using a simulated multi-strain sample of seven bacterial species demonstrated superior performance relative to existing tools and the advantages of using a threshold-based filtering approach to calling minority variants in Oxford Nanopore Technologies’ sequencing data. NanoMGT’s potential as a post-binning tool in metagenomic pipelines is particularly notable, enabling researchers to more accurately determine specific alleles and understand strain diversity in microbial communities. Our findings have significant implications for clinical diagnostics, environmental microbiology, and the broader field of genomics. The findings offer a reliable and efficient approach to marker gene typing in complex metagenomic samples.
BackgroundThe purpose of this study was to report the radiographic results and complications of magnetically controlled growing rod (MCGR) treatment in patients with early-onset scoliosis (EOS). ...MethodsPatient records and radiographs from a consecutive series of patients treated with MCGR for EOS at two Swedish institutions were reviewed retrospectively. Radiographic analysis included Cobb angle, T1-T12 height, T1-S1 height, thoracic kyphosis, and lung height. Subgroup analyses were performed on primary versus conversion cases and single versus dual rods using one-way analysis of variance (ANOVA) and independent samples t-test. ResultsFifty-two cases treated with MCGR (24 single rods, 28 dual rods) were included from local surgical records into this cohort study, 32 primary and 20 converted from other growth friendly surgical treatment. Mean age at MCGR implantation was 7.4 (2.0-14.6) years old in the primary group and 9.3 (5.0-16.1) years old in the converted group. Mean follow-up time was 3.7 (2.0-7.6) years. Mean (standard deviation; SD) Cobb angle of the major curve changed from 62° (17°) preoperatively to 42° (16°) postoperatively to 46° (18°) at final follow-up (P<0.001). Mean (SD) overall thoracic kyphosis changed from 41° (19°) preoperatively to 32° (14°) postoperatively to 39° (17°) at final follow-up (P=0.018). Mean T1-T12 height was 177 mm (34 mm) preoperatively, 183 mm (35 mm) immediate postoperative and 199 mm (35 mm) at final follow-up (P=0.047). The mean T1-T12 height increased significantly in the primary group but not in the converted group. The number of surgeries was 114 (78 planned, 36 unplanned). The rate of unplanned surgeries did not differ significantly between single and dual rods. The total number of complications was 70 of which 38 were implant related. The overall mean complication rate was 1.4 (0-4). There were no significant differences in complication rates between subgroups. ConclusionsMCGR treatment enabled and maintained correction of spinal deformity while allowing spinal growth. There were no significant differences in complication rates or unplanned surgeries between the groups treated with single or dual rods.
Possible applications of the sigma delta digitizer in particle physics
Nuclear instruments and methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment/Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
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