Patients avoided important care during the early weeks of the coronavirus pandemic: diverticulitis patients were more likely to present with an abscess on CT

PURPOSE: To evaluate the frequency with which patients with an urgent health concern, specifically diverticulitis, avoided appropriate medical care during the early weeks of the coronavirus pandemic of 2020 and to study the consequences of the resultant delay in care, the incidence of an associated abscess. METHODS: This study was institutional review board approved. Reports for CT studies with findings of newly diagnosed diverticulitis within Henry Ford Health System during the early weeks of the coronavirus pandemic of 2020 were reviewed and compared with the same time period in 2019. Total cases of diverticulitis on CT were compared, as well as the prevalence of an associated abscess. A chi-squared analysis was performed to determine the statistical significance of the percentage of patients presenting with an abscess in each year. RESULTS: During the early weeks of the coronavirus pandemic, 120 patients were identified with CT findings of newly diagnosed diverticulitis with 11.7% of those patients (14 patients) presenting with an associated abscess. During the same time period in 2019, many more CT studies with newly diagnosed diverticulitis were obtained (339), and, compared to 2020, less than half the percentage of those patients had an associated abscess (4.4% or 15 patients). CONCLUSION: Patients with urgent health concerns avoided appropriate and necessary care during the early weeks of the coronavirus pandemic. While non-COVID-19 emergency visits were diminished, patients who did present with diverticulitis were more likely to present with greater disease severity as manifested by an associated abscess. Patients must be encouraged to seek care when appropriate and need reassurance that hospitals and their emergency departments are safe to visit. Furthermore, emergency physicians and radiologists in particular should be vigilant during times when emergency volumes are low, such as a future surge in coronavirus patients, other pandemics, snow storms, and holidays as the patients who do present for care are more likely to present at later stages and with serious complications

Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA

BACKGROUND: RNA editing is the process whereby an RNA sequence is modified from the sequence of the corresponding DNA template. In the mitochondria of land plants, some cytidines are converted to uridines before translation. Despite substantial study, the molecular biological mechanism by which C-to-U RNA editing proceeds remains relatively obscure, although several experimental studies have implicated a role for cis-recognition. A highly non-random distribution of nucleotides is observed in the immediate vicinity of edited sites (within 20 nucleotides 5' and 3'), but no precise consensus motif has been identified. RESULTS: Data for analysis were derived from the the complete mitochondrial genomes of Arabidopsis thaliana, Brassica napus, and Oryza sativa; additionally, a combined data set of observations across all three genomes was generated. We selected datasets based on the 20 nucleotides 5' and the 20 nucleotides 3' of edited sites and an equivalently sized and appropriately constructed null-set of non-edited sites. We used tree-based statistical methods and random forests to generate models of C-to-U RNA editing based on the nucleotides surrounding the edited/non-edited sites and on the estimated folding energies of those regions. Tree-based statistical methods based on primary sequence data surrounding edited/non-edited sites and estimates of free energy of folding yield models with optimistic re-substitution-based estimates of ~0.71 accuracy, ~0.64 sensitivity, and ~0.88 specificity. Random forest analysis yielded better models and more exact performance estimates with ~0.74 accuracy, ~0.72 sensitivity, and ~0.81 specificity for the combined observations. CONCLUSIONS: Simple models do moderately well in predicting which cytidines will be edited to uridines, and provide the first quantitative predictive models for RNA edited sites in plant mitochondria. Our analysis shows that the identity of the nucleotide -1 to the edited C and the estimated free energy of folding for a 41 nt region surrounding the edited C are the most important variables that distinguish most edited from non-edited sites. However, the results suggest that primary sequence data and simple free energy of folding calculations alone are insufficient to make highly accurate predictions

Chemical rule-based filtering of MS/MS spectra

Abstract Motivation: Identification of proteins by mass spectrometry–based proteomics requires automated interpretation of peptide tandem mass spectrometry spectra. The effectiveness of peptide identification can be greatly improved by filtering out extraneous noise peaks before the subsequent database searching steps. Results: Here we present a novel chemical rule-based filtering algorithm, termed CRF, which makes use of the predictable patterns (rules) of collision-induced peptide fragmentation. The algorithm selects peak pairs that obey the common fragmentation rules within plausible limits of mass tolerance as well as peak intensity and produces spectra that can be subsequently submitted to any search engine. CRF increases the positive predictive value and decreases the number of random matches and thus improves performance by 15–20% in terms of peptide annotation using search engines, such as X!Tandem. Importantly, the algorithm also achieves data compression rates of ∼75%. Availability: The MATLAB source code and a web server are available at http://hydrax.icgeb.trieste.it/CRFilter/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Role of the HCF-1 Basic Region in Sustaining Cell Proliferation

BACKGROUND: The human herpes simplex virus-associated host cell factor 1 (HCF-1) is a conserved human transcriptional co-regulator that links positive and negative histone modifying activities with sequence-specific DNA-binding transcription factors. It is synthesized as a 2035 amino acid precursor that is cleaved to generate an amino- (HCF-1(N)) terminal subunit, which promotes G1-to-S phase progression, and a carboxy- (HCF-1(C)) terminal subunit, which controls multiple aspects of cell division during M phase. The HCF-1(N) subunit contains a Kelch domain that tethers HCF-1 to sequence-specific DNA-binding transcription factors, and a poorly characterized so called "Basic" region (owing to a high ratio of basic vs. acidic amino acids) that is required for cell proliferation and has been shown to associate with the Sin3 histone deacetylase (HDAC) component. Here we studied the role of the Basic region in cell proliferation and G1-to-S phase transition assays. METHODOLOGY/PRINCIPAL FINDINGS: Surprisingly, much like the transcriptional activation domains of sequence-specific DNA-binding transcription factors, there is no unique sequence within the Basic region required for promoting cell proliferation or G1-to-S phase transition. Indeed, the ability to promote these activities is size dependent such that the shorter the Basic region segment the less activity observed. We find, however, that the Basic region requirements for promoting cell proliferation in a temperature-sensitive tsBN67 cell assay are more stringent than for G1-to-S phase progression in an HCF-1 siRNA-depletion HeLa-cell assay. Thus, either half of the Basic region alone can support G1-to-S phase progression but not cell proliferation effectively in these assays. Nevertheless, the Basic region displays considerable structural plasticity because each half is able to promote cell proliferation when duplicated in tandem. Consistent with a potential role in promoting cell-cycle progression, the Sin3a HDAC component can associate independently with either half of the Basic region fused to the HCF-1 Kelch domain. CONCLUSIONS/SIGNIFICANCE: While conserved, the HCF-1 Basic region displays striking structural flexibility for controlling cell proliferation

The potential impact of Ocean Thermal Energy Conversion (OTEC) on fisheries

The commercial development of ocean thermal energy conversion (OTEC) operations will involve some environmental perturbations for which there is no precedent experience. The pumping of very large volumes of warm surface water and cold deep water and its subsequent discharge will result in the impingement, entrainment, and redistribution of biota. Additional stresses to biota will be caused by biocide usage and temperature depressions. However, the artificial upwelling of nutrients associated with the pumping of cold deep water, and the artificial reef created by an OTEC plant may have positive effects on the local environment. Although more detailed information is needed to assess the net effect of an OTEC operation on fisheries, certain assumptions and calculations are made supporting the conclusion that the potential risk to fisheries is not significant enough to deter the early development of IDEe. It will be necessary to monitor a commercial-scale plant in order to remove many of the remaining uncertainties. (PDF file contains 39 pages.

In search of flavour-nutrient learning:A study of the Samburu pastoralists of North-Central Kenya

Much of our dietary behaviour is learned. In particular, one suggestion is that ‘flavour-nutrient learning’ (F-NL) influences both choice and intake of food. F-NL occurs when an association forms between the orosensory properties of a food and its postingestive effects. Unfortunately, this process has been difficult to evaluate because F-NL is rarely observed in controlled studies of adult humans. One possibility is that we are disposed to F-NL. However, learning is compromised by exposure to a complex Western diet that includes a wide range of energy-dense foods. To test this idea we explored evidence for F-NL in a sample of semi-nomadic pastoralists who eat a very limited diet, and who are lean and food stressed. Our Samburu participants (N = 68) consumed a sensory-matched portion (400 g) of either a novel low (0.72 kcal/g) or higher (1.57 kcal/g) energy-dense semi-solid food on two training days, and an intermediate version on day 3. Before and after each meal we measured appetite and assessed expected satiation and liking for the test food. We found no evidence of F-NL. Nevertheless, self-reported measures were very consistent and, as anticipated, expected satiation increased as the test food became familiar (expectedsatiation drift). Surprisingly,we observed insensitivity to the effects of test-meal energy density on measures of post-meal appetite. To explore this further we repeated a single training day using participants (N = 52) from the UK. Unlike in the Samburu, the higher energy-dense meal caused greater suppression of appetite. These observations expose interesting cross-cultural differences in sensitivity to the energy content of food. More generally, our work illustrates how measures can be translated to assess different populations, highlighting the potential for further comparisons of this kind

Near Infrared Spectra and Intrinsic Luminosities of Candidate Type II Quasars at 2 < z < 3.4

We present JHK near-infrared (NIR) spectroscopy of 25 candidate Type II quasars selected from the Sloan Digital Sky Survey, using Triplespec on the Apache Point Observatory 3.5m telescope, FIRE at the Magellan/Baade 6.5m telescope, and GNIRS on Gemini. At redshifts of 2 < z < 3.4, our NIR spectra probe the rest-frame optical region of these targets, which were initially selected to have strong lines of CIV and Ly alpha, with FWHM<2000 km/s from the SDSS pipeline. We use the [OIII]5007 line shape as a model for the narrow line region emission, and find that \halpha\ consistently requires a broad component with FWHMs ranging from 1000 to 7500 km/s. Interestingly, the CIV lines also require broad bases, but with considerably narrower widths of 1000 to 4500 km/s. Estimating the extinction using the Balmer decrement and also the relationship in lower-z quasars between rest equivalent width and luminosity in the [OIII] line, we find typical A_V values of 0-2 mag, which naturally explain the attenuated CIV lines relative to Halpha. We propose that our targets are moderately obscured quasars. We also describe one unusual object with three distinct velocity peaks in its [OIII] spectrum.Comment: Accepted for publication in ApJ, 18 pages, 14 figure

Characterization of the HIV-1 RNA associated proteome identifies Matrin 3 as a nuclear cofactor of Rev function

<p>Abstract</p> <p>Background</p> <p>Central to the fully competent replication cycle of the human immunodeficiency virus type 1 (HIV-1) is the nuclear export of unspliced and partially spliced RNAs mediated by the Rev posttranscriptional activator and the Rev response element (RRE).</p> <p>Results</p> <p>Here, we introduce a novel method to explore the proteome associated with the nuclear HIV-1 RNAs. At the core of the method is the generation of cell lines harboring an integrated provirus carrying RNA binding sites for the MS2 bacteriophage protein. Flag-tagged MS2 is then used for affinity purification of the viral RNA. By this approach we found that the viral RNA is associated with the host nuclear matrix component MATR3 (Matrin 3) and that its modulation affected Rev activity. Knockdown of MATR3 suppressed Rev/RRE function in the export of unspliced HIV-1 RNAs. However, MATR3 was able to associate with Rev only through the presence of RRE-containing viral RNA.</p> <p>Conclusions</p> <p>In this work, we exploited a novel proteomic method to identify MATR3 as a cellular cofactor of Rev activity. MATR3 binds viral RNA and is required for the Rev/RRE mediated nuclear export of unspliced HIV-1 RNAs.</p

Visualization and functional analysis of a maxi-K channel (mSlo) fused to green fluorescent protein (GFP)

We have constructed a fusion protein between (mSlo) (a recombinant, high conductance, calcium-activated potassium channel or Maxi-K), and GFP (green flourescent protein). This construct represents a tag to not only monitor channel expression, but to locate the protein in living cells. The GFP was fused in frame to the carboxy-terminus of the (mSlo) core protein (mSlo-GFP fusion protein). Expression of this fusion protein in COS-7 cells resulted in robust fluorescence localized near the cell membrane. Fluorescing cells that were patch clamped exhibited whole cell currents with a direction consistent with potassium currents. Conversely, non-fluorescing cells showed no significant whole cell currents. Excised inside out patches revealed single channel currents and calculated conductances in the range of those expected for the maxi-K. The mSlo and mSlo-GFP channels reconstituted into lipid bilayers bound wild-type, recombinant CTX with high affinity and displayed a half-blocking concentration (KD) of 7.4 and 7.6 nM, respectively (at +30 mV in 150 mM equimolar KCl). This resulted in single channel evaluation of the functional inhibition of CTX on these clones. As newly constructed GFP chimeras emerge for the study of physiological processes in living organisms, this work provides another area of insight illuminated by GFP

The z=5 Quasar Luminosity Function from SDSS Stripe 82

We present a measurement of the Type I quasar luminosity function at z=5 using a large sample of spectroscopically confirmed quasars selected from optical imaging data. We measure the bright end (M_1450<-26) with Sloan Digital Sky Survey (SDSS) data covering ~6000 deg^2, then extend to lower luminosities (M_1450<-24) with newly discovered, faint z~5 quasars selected from 235 deg^2 of deep, coadded imaging in the SDSS Stripe 82 region (the celestial equator in the Southern Galactic Cap). The faint sample includes 14 quasars with spectra obtained as ancillary science targets in the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), and 59 quasars observed at the MMT and Magellan telescopes. We construct a well-defined sample of 4.7<z<5.1 quasars that is highly complete, with 73 spectroscopic identifications out of 92 candidates. Our color selection method is also highly efficient: of the 73 spectra obtained, 71 are high redshift quasars. These observations reach below the break in the luminosity function (M_1450* ~ -27). The bright end slope is steep (beta <~ -4), with a constraint of beta < -3.1 at 95% confidence. The break luminosity appears to evolve strongly at high redshift, providing an explanation for the flattening of the bright end slope reported previously. We find a factor of ~2 greater decrease in the number density of luminous quasars (M_1450<-26) from z=5 to z=6 than from z=4 to z=5, suggesting a more rapid decline in quasar activity at high redshift than found in previous surveys. Our model for the quasar luminosity function predicts that quasars generate ~30% of the ionizing photons required to keep the universe ionized at z=5.Comment: 29 pages, 22 figures, ApJ accepted (updated to published version