EUAdb: A Resource for COVID-19 Test Development and Comparison

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases there is a need for increased world-wide SARS-CoV-2 testing capability that is both efficient and effective. Having open and easy access to detailed information about these tests, their sensitivity, the types of samples they use, etc. would be highly useful to ensure their reproducibility, to help clients compare and decide which tests would be best suited for their applications, and to avoid costs of reinventing similar or identical tests. Additionally, this resource would provide a means of comparing the many innovative diagnostic tools that are currently being developed in order to provide a foundation of technologies and methods for the rapid development and deployment of tests for future emerging diseases. Such a resource might thus help to avert the delays in testing and screening that was observed in the early stages of the pandemic and plausibly led to more COVID-19-related deaths than necessary. We aim to address these needs via a relational database containing standardized ontology and curated data about COVID-19 diagnostic tests that have been granted Emergency Use Authorizations (EUAs) by the FDA (US Food and Drug Administration). Simple queries of this actively growing database demonstrate considerable variation among these tests with respect to sensitivity (limits of detection, LoD), controls and targets used, criteria used for calling results, sample types, reagents and instruments, and quality and amount of information provided

Conservation Status of the Plains Spotted Skunk, Spilogale putorius interrupta, in Texas, with an Assessment of Genetic Variability in the Species

Robert C. Dowler, Department of Biology at Angelo State University is the corresponding author, robert dot dowler at angelo dot eduIn this report, we present results of research on the conservation status of the plains spotted skunk (Spilogale putorius interrupta) in Texas and an assessment of the genetic variability in populations throughout the range of the species. The conservation status portion of the study included (1) mapping the species’ potential habitat in Texas using maximum entropy modeling (Maxent) with historic museum specimen records, (2) field-based surveying of locations in 10 counties to determine occurrence of the plains spotted skunk, (3) seeking additional occurrence records in Texas through crowd sourcing and citizen scientist approaches (4) using all current (2001 – 2017) occurrences to produce a model of probable geographic distribution in Texas and (5) assessing anthropogenic changes in land use, which may threaten the species’ habitats, by mapping current and forecasted oil and gas development and urbanization within the species’ modeled range. The species distribution model, combined with the land-change assessment, was used to select sites in 10 representative counties for field-based surveys in the hopes of revealing patterns of current distribution. Field surveys were carried out using live traps, enclosed track plates, and camera traps. These methods documented detections of plains spotted skunks (n = 12) in 4 of the 10 sites sampled. All methods of detection were successful, but cameras and live traps out-performed track plates. Crowd-sourced approaches and citizen scientist camera trapping revealed an additional 82 occurrences in the state, 79 of which were since 2009. These recent records were used to produce a species distribution model that provides relative probability of occurrence for the plains spotted skunk in the state. Our land-change mapping revealed potential anthropogenic threats to habitats at 2 of the sites (Katy Prairie and Fort Hood), which also had robust populations of plains spotted skunks based on 25 and 51detections, respectively). For our genetic assessment, samples of tissue from three sources (i.e., field surveys, state agencies throughout the distribution of the eastern spotted skunk, and museum tissue collections) allowed a detailed assessment of the genetic variability in the species (S. putorius) using both microsatellite markers and cytochrome b gene sequence. Our analysis of 119 specimens was able to establish that genetic patterns were consistent with currently accepted taxonomy of the 3 recognized subspecies of S. putorius (S. p. putorius, S. p. ambarvalis, and S. p. interrupta). We also determined that there was no evidence for hybridization with the congener, S. gracilis (western spotted skunk), a species co-occurring with the eastern spotted skunk in parts of Texas. The differentiation between S. p. putorius and S. p. ambarvalis was less pronounced (FST = 0.178; cytochrome b sequence divergence = 1.2%) than between these subspecies and the plains spotted skunk (average FST = 0.278; cytochrome b sequence divergence = 2.9%). Overall, genetic variability (observed heterozygosity = 0.474) in the plains spotted skunk was lower than that seen in common carnivores (striped skunks, raccoons), but slightly higher than some endangered carnivores (black-footed ferret). The heterozygosity levels more closely resemble the levels found within the island spotted skunk (S. gracilis amphiala) from the Channel Islands of California and other vertebrates that have a “threatened” conservation status. Key findings of the study include: 1) the current geographic distribution of the plains spotted skunk in Texas is reduced relative to historic records; 2) the species distribution model based on recorded occurrences since 2001 suggests areas of the state that are in need of further survey efforts; 3) genetic variability of plains spotted skunks is lower than more common carnivores, but higher than some recognized endangered species; 4) the subspecies, S. p. interrupta is a distinct genetic subunit of the eastern spotted skunk; and 5) continued energy development and especially future urbanization in some parts of Texas may affect populations of the plains spotted skunk.Texas Comptroller of Public AccountsBureau of Economic Geolog

Locked out: liberating disabled people's lives and rights in Wales beyond COVID-19

This report originated from discussions at the Welsh Government’s Disability Equality Forum, Chaired by Deputy Minister and Chief Whip, Jane Hutt, MS. In the summer of 2020, having heard of the different ways that disabled people were being negatively affected by the pandemic, the Forum resolved to set up an evidence-based enquiry into disabled people’s experiences, in part to counter the significant under-reporting by central Government and the mainstream media. The decision to establish such an enquiry is significant. To our knowledge, it is the first of its kind to be published by a Government in the UK. This report is also unique in that it has been controlled and co-produced by a Steering Group of disabled people representing Disabled People’s Organisations (DPOs) and disability charities, supported by Welsh Government in terms of administrative support, supplementary research expertise and data analysis. The nominal ‘Chair’ (or co-ordinator) of the enquiry, was chosen by disabled members of the Disability Equality Forum and self-identifies as a disabled person. Dr Debbie Foster is Professor of Employment Relations and Diversity at Cardiff University’s Business School. She interpreted her role as one of co-ordinator of documentary evidence collated by Welsh Government and evidence voiced by members of the Steering Group, all of whom had lived experience of disability. Over 300 items of written evidence were considered, sifted, summarised then discussed, prioritised and supplemented, by the Steering Group, in what was an iterative process

Pulsed Doppler assessment of left ventricular diastolic filling in children with left ventricular outflow obstruction before and after balloon angioplasty

To assess left ventricular (LV) diastolic filling in children with pressure overload hypertrophy, 12 patients with LV outflow obstruction (7 with aortic valve stenosis and 5 with aortic coarctation) and 12 healthy, age-matched control subjects were examined. Each child underwent M-mode echocardiography and pulsed Doppler examination of the LV inflow. The patients with LV outflow obstruction had cardiac catheterization and balloon angioplasty. Their echo/Doppler examinations were performed in the catheterization laboratory before and immediately after balloon angioplasty. From the M-mode echocardiogram, the LV cavity dimensions and wall thicknesses, LV mass and shortening fraction were measured. The following measurements were made from the Doppler recording: peak velocities at rapid ventricular filling (peak E) and during atrial contraction (peak A), ratio of peak E to peak A velocities, total area under the Doppler curve, percent of the total Doppler area occurring in the first one-third of diastole (0.33 area fraction), percent of the total area occurring under the E wave (E area fraction), percent of the total area occurring under the A wave (A area fraction) and the ratio of E area to A area.Before balloon angioplasty, the patients with LV outflow obstruction had higher peak E velocity (1.06 +/- 0.18 vs 0.88 +/- 0.11 m/s, p < 0.01), higher peak A velocity (0.86 +/- 0.22 vs 0.47 +/- 0.08 m/s, p < 0.01) and lower E/A velocity ratio (1.29 +/- 0.27 vs 1.93 +/- 0.34, p < 0.01) than the normal subjects. In the patient group, 0.33 area fraction was significantly lower (0.38 +/- 0.07 vs 0.57 +/- 0.09, p < 0.01) and A area fraction was significantly higher (0.44 +/- 0.14 vs 0.23 +/- 0.07, p < 0.01) than in the normal subjects. Also, patients with LV outflow obstruction had greater LV wall thickness, smaller LV cavity dimensions and greater LV mass compared with normal subjects. In patients before and after balloon angioplasty, there was a significant decrease in LV outflow gradient (64 +/- 23 vs 33 +/- 22 mm Hg, p < 0.01), but there was no change in any echo/Doppler measurement. Thus, children with LV outflow obstruction have abnormal LV early diastolic relaxation with a shift in filling toward late diastole. Immediately after successful relief of the systolic pressure overload, diastolic filling patterns are unchanged, suggesting that hypertrophy rather than afterload mismatch is the primary determinant of the impaired relaxation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/28087/1/0000533.pd

Acute intestinal failure: international multicenter point-of-prevalence study

Background & aims: Intestinal failure (IF) is defined from a requirement or intravenous supplementation due to failing capacity to absorb nutrients and fluids. Acute IF is an acute, potentially reversible form of IF. We aimed to identify the prevalence, underlying causes and outcomes of acute IF. Methods: This point-of-prevalence study included all adult patients hospitalized in acute care hospitals and receiving parenteral nutrition (PN) on a study day. The reason for PN and the mechanism of IF (if present) were documented by local investigators and reviewed by an expert panel. Results: Twenty-three hospitals (19 university, 4 regional) with a total capacity of 16,356 acute care beds and 1237 intensive care unit (ICU) beds participated in this study. On the study day, 338 patients received PN (21 patients/1000 acute care beds) and 206 (13/1000) were categorized as acute IF. The categorization of reason for PN was revised in 64 cases (18.9% of total) in consensus between the expert panel and investigators. Hospital mortality of all study patients was 21.5%; the median hospital stay was 36 days. Patients with acute IF had a hospital mortality of 20.5% and median hospital stay of 38 days (P > 0.05 for both outcomes). Disordered gut motility (e.g. ileus) was the most common mechanism of acute IF, and 71.5% of patients with acute IF had undergone abdominal surgery. Duration of PN of ≥42 days was identified as being the best cut-off predicting hospital mortality within 90 days. PN ≥ 42 days, age, sepsis and ICU admission were independently associated with 90-day hospital mortality. Conclusions: Around 2% of adult patients in acute care hospitals received PN, 60% of them due to acute IF. High 90-day hospital mortality and long hospital stay were observed in patients receiving PN, whereas presence of acute IF did not additionally influence these outcomes. Duration of PN was associated with increased 90-day hospital mortality

Lassa Fever in Post-Conflict Sierra Leone

Background: Lassa fever (LF), an often-fatal hemorrhagic disease caused by Lassa virus (LASV), is a major public health threat in West Africa. When the violent civil conflict in Sierra Leone (1991 to 2002) ended, an international consortium assisted in restoration of the LF program at Kenema Government Hospital (KGH) in an area with the world's highest incidence of the disease. Methodology/Principal Findings Clinical and laboratory records of patients presenting to the KGH Lassa Ward in the post-conflict period were organized electronically. Recombinant antigen-based LF immunoassays were used to assess LASV antigenemia and LASV-specific antibodies in patients who met criteria for suspected LF. KGH has been reestablished as a center for LF treatment and research, with over 500 suspected cases now presenting yearly. Higher case fatality rates (CFRs) in LF patients were observed compared to studies conducted prior to the civil conflict. Different criteria for defining LF stages and differences in sensitivity of assays likely account for these differences. The highest incidence of LF in Sierra Leone was observed during the dry season. LF cases were observed in ten of Sierra Leone's thirteen districts, with numerous cases from outside the traditional endemic zone. Deaths in patients presenting with LASV antigenemia were skewed towards individuals less than 29 years of age. Women self-reporting as pregnant were significantly overrepresented among LASV antigenemic patients. The CFR of ribavirin-treated patients presenting early in acute infection was lower than in untreated subjects. Conclusions/Significance: Lassa fever remains a major public health threat in Sierra Leone. Outreach activities should expand because LF may be more widespread in Sierra Leone than previously recognized. Enhanced case finding to ensure rapid diagnosis and treatment is imperative to reduce mortality. Even with ribavirin treatment, there was a high rate of fatalities underscoring the need to develop more effective and/or supplemental treatments for LF

Identification and Characterization of Novel Mutations in the Human Gene Encoding the Catalytic Subunit Calpha of Protein Kinase A (PKA)

The genes PRKACA and PRKACB encode the principal catalytic (C) subunits of protein kinase A (PKA) Cα and Cβ, respectively. Cα is expressed in all eukaryotic tissues examined and studies of Cα knockout mice demonstrate a crucial role for Cα in normal physiology. We have sequenced exon 2 through 10 of PRKACA from the genome of 498 Norwegian donors and extracted information about PRKACA mutations from public databases. We identified four interesting nonsynonymous point mutations, Arg45Gln, Ser109Pro, Gly186Val, and Ser263Cys, in the Cα1 splice variant of the kinase. Cα variants harboring the different amino acid mutations were analyzed for kinase activity and regulatory (R) subunit binding. Whereas mutation of residues 45 and 263 did not alter catalytic activity or R subunit binding, mutation of Ser109 significantly reduced kinase activity while R subunit binding was unaltered. Mutation of Cα Gly186 completely abrogated kinase activity and PKA type I but not type II holoenzyme formation. Gly186 is located in the highly conserved DFG motif of Cα and mutation of this residue to Val was predicted to result in loss of binding of ATP and Mg2+, which may explain the kinetic inactivity. We hypothesize that individuals born with mutations of Ser109 or Gly186 may be faced with abnormal development and possibly severe disease

The cerebrospinal fluid proteome in HIV infection: change associated with disease severity

<p>Abstract</p> <p>Background</p> <p>Central nervous system (CNS) infection is a nearly universal feature of untreated systemic HIV infection with a clinical spectrum that ranges from chronic asymptomatic infection to severe cognitive and motor dysfunction. Analysis of cerebrospinal fluid (CSF) has played an important part in defining the character of this evolving infection and response to treatment. To further characterize CNS HIV infection and its effects, we applied advanced high-throughput proteomic methods to CSF to identify novel proteins and their changes with disease progression and treatment.</p> <p>Results</p> <p>After establishing an <it>accurate mass and time </it>(AMT) tag database containing 23,141 AMT tags for CSF peptides, we analyzed 91 CSF samples by LC-MS from 12 HIV-uninfected and 14 HIV-infected subjects studied in the context of initiation of antiretroviral therapy and correlated abundances of identified proteins a) within and between subjects, b) with all other proteins across the entire sample set, and c) with "external" CSF biomarkers of infection (HIV RNA), immune activation (neopterin) and neural injury (neurofilament light chain protein, NFL). We identified a mean of 2,333 +/- 328 (SD) peptides covering 307 +/-16 proteins in the 91 CSF sample set. Protein abundances differed both between and within subjects sampled at different time points and readily separated those with and without HIV infection. Proteins also showed inter-correlations across the sample set that were associated with biologically relevant dynamic processes. One-hundred and fifty proteins showed correlations with the external biomarkers. For example, using a threshold of cross correlation coefficient (Pearson's) ≤ -0.3 and ≥0.3 for potentially meaningful relationships, a total of 99 proteins correlated with CSF neopterin (43 negative and 56 positive correlations) and related principally to neuronal plasticity and survival and to innate immunity. Pathway analysis defined several networks connecting the identified proteins, including one with amyloid precursor protein as a central node.</p> <p>Conclusions</p> <p>Advanced CSF proteomic analysis enabled the identification of an array of novel protein changes across the spectrum of CNS HIV infection and disease. This initial analysis clearly demonstrated the value of contemporary state-of-the-art proteomic CSF analysis as a discovery tool in HIV infection with likely similar application to other neurological inflammatory and degenerative diseases.</p