The Lucy Thermal Emission Spectrometer (L'TES) Instrument

The Lucy Thermal Emission Spectrometer (L'TES) will provide remote measurements of the thermophysical properties of the Trojan asteroids studied by the Lucy mission. L'TES is build-to-print hardware copy of the OTES instrument flown on OSIRIS-REx. It is a Fourier Transform spectrometer covering the spectral range 5.71-100 μm (1750-100 cm-1) with spectral sampling intervals of 8.64, 17.3, and 34.6 cm-1 and a 7.3-mrad field of view. The L'TES telescope is a 15.2-cm diameter Cassegrain telescope that feeds a flat-plate Michelson moving mirror mounted on a linear voice-coil motor assembly to a single uncooled deuterated l-alanine doped triglycine sulfate (DLATGS) pyroelectric detector. A significant firmware change from OTES is the ability to acquire interferograms of different length and spectral resolution with acquisition times of 0.5, 1, and 2 seconds. A single ∼0.851 μm laser diode is used in a metrology interferometer to provide precise moving mirror control and IR sampling at 772 Hz. The beamsplitter is a 38-mm diameter, 1-mm thick chemical vapor deposited diamond with an antireflection microstructure to minimize surface reflection. An internal calibration cone blackbody target, together with observations of space, provides radiometric calibration. The radiometric precision in a single spectrum is ≤2.2 × 10-8 W cm-2 sr-1 /cm-1 between 300 and 1350 cm-1. The absolute temperature error is <2 K for scene temperatures >75 K. The overall L'TES envelope size is 37.6 × 29.0 × 30.4 cm, and the mass is 6.47 kg. The power consumption is 12.6 W average. L'TES was developed by Arizona State University with AZ Space Technologies developing the electronics. L'TES was integrated, tested, and radiometrically calibrated on the Arizona State University campus in Tempe, AZ. Initial data from space have verified the instrument's radiometric and spatial performance.

Calculating variant penetrance from family history of disease and average family size in population-scale data

BACKGROUND

Genetic penetrance is the probability of a phenotype when harbouring a particular pathogenic variant. Accurate penetrance estimates are important across biomedical fields including genetic counselling, disease research, and gene therapy. However, existing approaches for penetrance estimation require, for instance, large family pedigrees or availability of large databases of people affected and not affected by a disease.

METHODS

We present a method for penetrance estimation in autosomal dominant phenotypes. It examines the distribution of a variant among people affected (cases) and unaffected (controls) by a phenotype within population-scale data and can be operated using cases only by considering family disease history. It is validated through simulation studies and candidate variant-disease case studies.

RESULTS

Our method yields penetrance estimates which align with those obtained via existing approaches in the Parkinson's disease LRRK2 gene and pulmonary arterial hypertension BMPR2 gene case studies. In the amyotrophic lateral sclerosis case studies, examining penetrance for variants in the SOD1 and C9orf72 genes, we make novel penetrance estimates which correspond closely to understanding of the disease.

CONCLUSIONS

The present approach broadens the spectrum of traits for which reliable penetrance estimates can be obtained. It has substantial utility for facilitating the characterisation of disease risks associated with rare variants with an autosomal dominant inheritance pattern. The yielded estimates avoid any kinship-specific effects and can circumvent ascertainment biases common when sampling rare variants among control populations.

Micro-dose, macro-impact: Leveraging psychedelics in frontline healthcare workers during the COVID-19 pandemic

Background and aims

The COVID-19 pandemic exacerbated pre-existing high-levels of physician stress and burnout1. In order to help treat frontline colleagues who were diagnosed with acute stress disorder, we chose a non-psychedelic, ketamine micro-dose treatment strategy for symptom management.

Methods

We provided care virtually, and all patients were prescribed sublingual ketamine once daily. Each patient was evaluated using the NIH-PROMIS CAT assessments for stress, depression, anxiety, and PTSD via a remote, HIPAA compliant patient self-reporting platform. Progress was tracked and assessed against a baseline value obtained prior to the start of treatment. Patient progress was evaluated at a 4–6-week interval. Patients did not report any significant side effects to the treatment regimen.

Results

100% (25/25) of patients experienced improved anxiety, 92% (23/25) experienced improved stress, 96% (24/25) experienced improved PTSD, and 91% (20/22) experienced improved depression.

Conclusions

While we cannot draw definitive conclusions from the association demonstrated by this data, we believe these results demonstrate that further research into the efficacy of daily, short-term ketamine micro-doses for treatment of acute stress disorder is warranted.

RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data

Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training. Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.

The SOD1-mediated ALS phenotype shows a decoupling between age of symptom onset and disease duration

Superoxide dismutase (SOD1) gene variants may cause amyotrophic lateral sclerosis, some of which are associated with a distinct phenotype. Most studies assess limited variants or sample sizes. In this international, retrospective observational study, we compare phenotypic and demographic characteristics between people with SOD1-ALS and people with ALS and no recorded SOD1 variant. We investigate which variants are associated with age at symptom onset and time from onset to death or censoring using Cox proportional-hazards regression. The SOD1-ALS dataset reports age of onset for 1122 and disease duration for 883 people; the comparator population includes 10,214 and 9010 people respectively. Eight variants are associated with younger age of onset and distinct survival trajectories; a further eight associated with younger onset only and one with distinct survival only. Here we show that onset and survival are decoupled in SOD1-ALS. Future research should characterise rarer variants and molecular mechanisms causing the observed variability.

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans. Currently, a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and datasets. These included 50 human short-read whole-genome sequencing samples, matching long and short-read sequencing data, and simulated short-read NGS data. Our results highlight a great performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. However, specialized tools designed to detect exclusively human endogenous retroviruses consistently outperformed generalist tools that detect a wider range of transposable elements. We suggest that, if sufficient computing resources are available, using multiple HERV detection tools to obtain a consensus set of insertion loci may be ideal. Furthermore, given that the false positive discovery rate of the tools varied between 8% and 55% across tools and datasets, we recommend the wet lab validation of predicted insertions if DNA samples are available.

A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex

There is increasing evidence that endogenous retroviruses (ERVs) play a significant role in central nervous system diseases, including amyotrophic lateral sclerosis (ALS). Studies of ALS have consistently identified retroviral enzyme reverse transcriptase activity in patients. Evidence indicates that ERVs are the cause of reverse transcriptase activity in ALS, but it is currently unclear whether this is due to a specific ERV locus or a family of ERVs. We employed a combination of bioinformatic methods to identify whether specific ERVs or ERV families are associated with ALS. Using the largest post-mortem RNA-sequence datasets available we selectively identified ERVs that closely resembled full-length proviruses. In the discovery dataset there was one ERV locus (HML6_3p21.31c) that showed significant increased expression in post-mortem motor cortex tissue after multiple-testing correction. Using six replication post-mortem datasets we found HML6_3p21.31c was consistently upregulated in ALS in motor cortex and cerebellum tissue. In addition, HML6_3p21.31c showed significant co-expression with cytokine binding and genes involved in EBV, HTLV-1 and HIV type-1 infections. There were no significant differences in ERV family expression between ALS and controls. Our results support the hypothesis that specific ERV loci are involved in ALS pathology.

Multimodal approach in radioguided surgery in a case of multiple paraganglioma

The case involves a 34-year-old woman who underwent surgical removal of a retroperitoneal paraganglioma adjacent to the left kidney's lower pole, previously visualized by CT and MRI. The ¹²³I-MIBG scan was positive for this lesion and, in addition, another uptake was observed located caudally at the level of L5 and of smaller size and less intensity. The second lesion was not considered for surgical removal, due to its lack of morphological definition. One week after surgical intervention, the patient presented difficult-to-control high blood pressure. A second ¹²³I-MIBG scan was performed. The previously described second image was more intense in this study, and surgery was planned to remove it. A combination of techniques including freehand-SPECT and a portable hybrid gamma camera (with optical camera) were used pre-operatively to identify the location of the lesion. The combination of intra-operative laparoscopic gamma probe and portable hybrid gamma camera enabled the tumor to be located, excised, and its complete removal to be monitored. The histopathology analysis confirmed a second paraganglioma.

Hybrid-fusion SPECT/CT systems in parathyroid adenoma: Technological improvements and added clinical diagnostic value

Nuclear medicine traditionally employs planar and single photon emission computed tomography (SPECT) imaging techniques to depict the biodistribution of radiotracers for the diagnostic investigation of a range of disorders of endocrine gland function. The usefulness of combining functional information with anatomy derived from computed tomography (CT), magnetic resonance imaging (MRI), and high resolution ultrasound (US), has long been appreciated, either using visual side-by-side correlation, or software-based co-registration. The emergence of hybrid SPECT/CT camera technology now allows the simultaneous acquisition of combined multi-modality imaging, with seamless fusion of 3D volume datasets. Thus, it is not surprising that there is growing literature describing the many advantages that contemporary SPECT/CT technology brings to radionuclide investigation of endocrine disorders, showing potential advantages for the pre-operative locating of the parathyroid adenoma using a minimally invasive surgical approach, especially in the presence of ectopic glands and in multiglandular disease. In conclusion, hybrid SPECT/CT imaging has become an essential tool to ensure the most accurate diagnostic in the management of patients with hyperparathyroidism.

Radioguided surgery and the GOSTT concept: From pre-operative image and intraoperative navigation to image-assisted excision

Radio-guided surgery has been developed for application in those disease scheduled for surgical management, particularly in areas of complex anatomy. This is based on the use of pre-operative scintigraphic planar, tomographic and fused SPECT/CT images, and the possibility of 3D reconstruction for the subsequent intraoperative locating of active lesions using handheld devices (detection probes, gamma cameras, etc.). New tracers and technologies have also been incorporated into these surgical procedures. The combination of visual and acoustic signals during the intraoperative procedure has become possible with new portable imaging modalities. In daily practice, the images offered by these techniques and devices combine perioperative nuclear medicine imaging with the superior resolution of additional optical guidance in the operating room. In many ways they provide real-time images, allowing accurate guidance during surgery, a reduction in the time required for tissue location and an anatomical environment for surgical recognition. All these approaches have been included in the concept known as (radio) Guided intraOperative Scintigraphic Tumour Targeting (GOSTT). This article offers a general view of different nuclear medicine and allied technologies used for several GOSTT procedures, and illustrates the crossing of technological frontiers in radio-guided surgery.