Ultrasensitive ctDNA detection for preoperative disease stratification in early-stage lung adenocarcinoma.

Circulating tumor DNA (ctDNA) detection can predict clinical risk in early-stage tumors. However, clinical applications are constrained by the sensitivity of clinically validated ctDNA detection approaches. NeXT Personal is a whole-genome-based, tumor-informed platform that has been analytically validated for ultrasensitive ctDNA detection at 1-3 ppm of ctDNA with 99.

Towards Preanalytical Best Practices for Liquid Biopsy Studies: A BLOODPAC Landscape Analysis.

BLOODPAC is a public-private consortium that develops best practices, coordinates clinical and translational research, and manages the BLOODPAC Data Commons to broadly support the liquid biopsy community and accelerate regulatory review to aid patient accessibility. BLOODPAC previously recommended 11 preanalytical minimal technical data elements (MTDEs) for BLOODPAC-sponsored studies and data submitted to BLOODPAC Data Commons. The current landscape analysis evaluates the overlap of the BLOODPAC MTDEs with current best practices, guidelines, and standards documents related to clinical and research liquid biopsy applications.

Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay.

We describe the analytical validation of NeXT Personal, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA.

A guide for social science journal editors on easing into open science.

Journal editors have a large amount of power to advance open science in their respective fields by incentivising and mandating open policies and practices at their journals. The Data PASS Journal Editors Discussion Interface (JEDI, an online community for social science journal editors: www.dpjedi.

Development of matrix-specific standards for LA-ICP-MS zinc analysis in sand flathead (Platycephalus bassensis).

The use of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to analyse soft tissues is limited because of the lack of suitable certified reference materials resulting in difficulties with calibration. In this study, several laboratory-prepared thin agarose sections were tested as matrix-specific standards. Our results showed 1 mm thin agarose sections were suitable as calibration standards for LA-ICP-MS Zn analyses in fish muscle, especially when the signal intensity of Zn was normalised to C.

Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay.

We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment.

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t.

Cardiovascular waveforms - can we extract more from routine signals?

Cardiovascular waveforms such as blood pressure, ECG and photoplethysmography (PPG), are routinely acquired by specialised monitoring devices. Such devices include bedside monitors, wearables and radiotelemetry which sample at very high fidelity, yet most of this numerical data is disregarded and focus tends to reside on single point averages such as the maxima, minima, amplitude, rate and intervals. Whilst, these measures are undoubtedly of value, we may be missing important information by simplifying the complex waveform signal in this way.

Detecting paroxysmal atrial fibrillation from normal sinus rhythm in equine athletes using Symmetric Projection Attractor Reconstruction and machine learning.

Background: Atrial fibrillation (AF) is a common cardiac arrhythmia in both human and equine populations. It is associated with adverse outcomes in humans and decreased athletic performance in both populations. Paroxysmal atrial fibrillation (PAF) presents with intermittent, self-terminating AF episodes, and is difficult to diagnose once sinus rhythm resumes.

Symmetric projection attractor reconstruction: Embedding in higher dimensions.

Symmetric Projection Attractor Reconstruction (SPAR) provides an intuitive visualization and simple quantification of the morphology and variability of approximately periodic signals. The original method takes a three-dimensional delay coordinate embedding of a signal and subsequently projects this phase space reconstruction to a two-dimensional image with threefold symmetry, providing a bounded visualization of the waveform. We present an extension of the original work to apply delay coordinate embedding in any dimension N≥3 while still deriving a two-dimensional output with some rotational symmetry property that provides a meaningful visualization of the higher dimensional attractor.

The use of image analysis techniques for the study of muscle melanisation in sand flathead (Platycephalus bassensis).

Muscle melanisation in sand flathead is visible as black spots in the normally white flesh of fish. It is widespread in Tasmania, including at the Tamar Estuary, with increasing frequency of reporting by recreational fishers. The phenomenon is more prevalent in areas impacted by heavy metal pollution and has been linked to heavy metal accumulation.

Symmetric Projection Attractor Reconstruction: Sex Differences in the ECG.

The electrocardiogram (ECG) is a key tool in patient management. Automated ECG analysis supports clinical decision-making, but traditional fiducial point identification discards much of the time-series data that captures the morphology of the whole waveform. Our Symmetric Projection Attractor Reconstruction (SPAR) method uses all the available data to provide a new visualization and quantification of the morphology and variability of any approximately periodic signal.

Role of the Electron-Dipole Interaction in Photodetachment Angular Distributions.

The importance of including long-range electron-molecule interactions in treatments of photodetachment and/or photoionization is demonstrated. A combined experimental and computational study of CN detachment is presented in which near threshold anisotropy parameters (β) are measured via photoelectron imaging. Calculated β values, based on an EOM-IP-CCSD/aug-cc-pVTZ Dyson orbital, are obtained using free-particle and point dipole models.

Dataset construction challenges for digital forensics.

As the digital forensic field develops, taking steps towards ensuring a level of reliability in the processes implemented by its practitioners, emphasis on the need for effective testing has increased. In order to test, test datasets are required, but creating these is not a straightforward task. A poorly constructed and documented test dataset undermines any testing which has taken place using it, eroding the reliability of any subsequent test results.

Symmetric Projection Attractor Reconstruction analysis of murine electrocardiograms: Retrospective prediction of Scn5a genetic mutation attributable to Brugada syndrome.

Background: Life-threatening arrhythmias resulting from genetic mutations are often missed in current electrocardiogram (ECG) analysis. We combined a new method for ECG analysis that uses all the waveform data with machine learning to improve detection of such mutations from short ECG signals in a mouse model.

Objective: We sought to detect consequences of Na channel deficiencies known to compromise action potential conduction in comparisons of Scn5a mutant and wild-type mice using short ECG signals, examining novel and standard features derived from lead I and II ECG recordings by machine learning algorithms.

Retracing migration pattern in reproductive and non-reproductive female kutum Rutilus frisii, in south Caspian Sea, using otolith microchemistry.

Because trace elements of otoliths are considered a natural marker capable of recognizing the chemical composition of ambient water and fish migration history, these elements could be potentially used to analyse the movement of reproductive (R) and non-reproductive (NR) mature-sized fish. Supposedly, it is not essential for NR individuals to migrate to rivers for spawning because they do not have developed gonads. To investigate the potential differences in migration history between female R and NR kutum, Rutilus frisii, in the southwest waters of the Caspian Sea, the ratios of Sr, Ba, Mg, Na, K and P to Ca in otoliths (from the core to the edge) were examined using laser ablation-inductively coupled plasma-mass spectrometry.

The endemic and endangered Maugean Skate () exhibits short-term severe hypoxia tolerance.

The endangered and range-restricted Maugean skate () is subjected to large environmental variability coupled with anthropogenic stressors in its endemic habitat, Macquarie Harbour, Tasmania. However, little is known about the basic biology/physiology of this skate, or how it may respond to future environmental challenges predicted from climate change and/or increases in human activities such as aquaculture. These skate live at a preferred depth of 5-15 m where the dissolved oxygen (DO) levels are moderate (~55% air saturation), but can be found in areas of the Harbour where DO can range from 100% saturation to anoxia.

Home range, site fidelity and synchronous migrations of three co-occurring, morphologically distinct estuarine fish species.

Determining the movement behaviours of animals is essential for understanding population dynamics. This is fundamental for developing effective spatial management strategies and in assessing the response of species to anthropogenic disturbance. This study uses a Bayesian state-space model applied to acoustic transmitter data to describe the temporal and spatial movement patterns of three estuarine fish species commonly targeted by recreational anglers in southeast Australia: Black Bream (Acanthopagrus butcheri), Sand Flathead (Platycephalus bassensis), and Brown Trout (Salmo trutta).

Muscle melanisation of southern sand flathead (Platycephalus bassensis) in the Tamar Estuary, Tasmania, Australia.

Tasmanian recreational fishers have reported the presence of dark pigmentations in the usually white fillets of southern sand flathead (Platycephalus bassensis), a phenomenon known as muscle melanisation. Based on histology, it is suggested that eumelanin and pheomelanin are involved in the occurrence of the phenomenon. A gross melanisation scoring system was validated through a comparison with an image analysis technique, that quantified the percentage surface area of the fillets affected by muscle melanisation.

Muscle melanisation in sand flathead (Platycephalus bassensis) and links to elevated zinc levels.

Melanisation of muscle, observed as black pigmentation of the normally white flesh, has been reported in sand flathead from Tasmania and investigated in this study. There was a significant difference in the presence of melanised muscle in sand flathead from two sites within the Tamar Estuary (northern Tasmania), with higher proportion of sand flathead from Deceitful Cove with this condition. Presence of melanisation was not related to length or weight of the fish.

Pre-diagnosis physical activity habits are associated with age of diagnosis in Parkinson's disease.

Introduction: Studies suggest that exercise may be neuroprotective when implemented before the clinical presentation of Parkinson's disease (PD). Levels of brain-derived neurotrophic factor (BDNF), theorized to play a role in neuroprotection, are affected by its genotype and exercise. Here we explore this previously unstudied interaction on age at diagnosis and severity of symptoms.

Spectroscopy of temporary anion states: Renner-Teller coupling and electronic autodetachment in copper difluoride anion.

Photoelectron angular distributions determined in small energy increments between 3.522 and 3.650 eV reveal distinctly different detachment mechanisms within the CuF(X Σ) → linear CuF(X Σ) + e band.