Exploring Neutral Hydrogen and Galaxy Evolution with the SKA

One of the key science drivers for the development of the SKA is to observe the neutral hydrogen, HI, in galaxies as a means to probe galaxy evolution across a range of environments over cosmic time. Over the past decade, much progress has been made in theoretical simulations and observations of HI in galaxies. However, recent HI surveys on both single dish radio telescopes and interferometers, while providing detailed information on global HI properties, the dark matter distribution in galaxies, as well as insight into the relationship between star formation and the interstellar medium, have been limited to the local universe. Ongoing and upcoming HI surveys on SKA pathfinder instruments will extend these measurements beyond the local universe to intermediate redshifts with long observing programmes. We present here an overview of the HI science which will be possible with the increased capabilities of the SKA and which will build upon the expected increase in knowledge of HI in and around galaxies obtained with the SKA pathfinder surveys. With the SKA1 the greatest improvement over our current measurements is the capability to image galaxies at reasonable linear resolution and good column density sensitivity to much higher redshifts (0.2 < z < 1.7). So one will not only be able to increase the number of detections to study the evolution of the HI mass function, but also have the sensitivity and resolution to study inflows and outflows to and from galaxies and the kinematics of the gas within and around galaxies as a function of environment and cosmic time out to previously unexplored depths. The increased sensitivity of SKA2 will allow us to image Milky Way-size galaxies out to redshifts of z=1 and will provide the data required for a comprehensive picture of the HI content of galaxies back to z~2 when the cosmic star formation rate density was at its peak.Comment: 25 pages, 5 figures, 3 tables. Contribution to the conference 'Advancing Astrophysics with the Square Kilometre Array', June 8-13, 2014, Giardini Naxos, Ital

Alzheimer’s Disease and Other Dementias Workgroup: Alzheimer’s Disease and Other Dementias Report and Recommendations

Rates of Alzheimer’s disease and other dementias are expected to increase greatly over the next decades. Many practices lack guidelines on how to increase quality of diagnosing, treating, and supporting people with dementia and their family members and other caregivers. This workgroup met from January to November 2017, aligned with and built off the Alzheimer’s State Plan, and organized recommendations with the following focus areas: Early detection and appropriate diagnosis Ongoing care and support or management including for family members and caregivers Advance care planning and palliative care Assessment and planning for need for increased support and/or higher levels of care Preparing for potential hospitalization Screening for delirium risk during hospitalization for all patients over 6

Automated CT and MRI Liver Segmentation and Biometry Using a Generalized Convolutional Neural Network.

PurposeTo assess feasibility of training a convolutional neural network (CNN) to automate liver segmentation across different imaging modalities and techniques used in clinical practice and apply this to enable automation of liver biometry.MethodsWe trained a 2D U-Net CNN for liver segmentation in two stages using 330 abdominal MRI and CT exams acquired at our institution. First, we trained the neural network with non-contrast multi-echo spoiled-gradient-echo (SGPR)images with 300 MRI exams to provide multiple signal-weightings. Then, we used transfer learning to generalize the CNN with additional images from 30 contrast-enhanced MRI and CT exams.We assessed the performance of the CNN using a distinct multi-institutional data set curated from multiple sources (n = 498 subjects). Segmentation accuracy was evaluated by computing Dice scores. Utilizing these segmentations, we computed liver volume from CT and T1-weighted (T1w) MRI exams, and estimated hepatic proton- density-fat-fraction (PDFF) from multi-echo T2*w MRI exams. We compared quantitative volumetry and PDFF estimates between automated and manual segmentation using Pearson correlation and Bland-Altman statistics.ResultsDice scores were 0.94 ± 0.06 for CT (n = 230), 0.95 ± 0.03 (n = 100) for T1w MR, and 0.92 ± 0.05 for T2*w MR (n = 169). Liver volume measured by manual and automated segmentation agreed closely for CT (95% limit-of-agreement (LoA) = [-298 mL, 180 mL]) and T1w MR (LoA = [-358 mL, 180 mL]). Hepatic PDFF measured by the two segmentations also agreed closely (LoA = [-0.62%, 0.80%]).ConclusionsUtilizing a transfer-learning strategy, we have demonstrated the feasibility of a CNN to be generalized to perform liver segmentations across different imaging techniques and modalities. With further refinement and validation, CNNs may have broad applicability for multimodal liver volumetry and hepatic tissue characterization

The impact of the new CHAMP and GRACE Earth gravity models on the measurement of the general relativistic Lense--Thirring effect with the LAGEOS and LAGEOS II satellites

Among the effects predicted by the General Theory of Relativity for the orbital motion of a test particle, the post-Newtonian gravitomagnetic Lense-Thirring effect is very interesting and, up to now, there is not yet an undisputable experimental direct test of it. To date, the data analysis of the orbits of the existing geodetic LAGEOS and LAGEOS II satellites has yielded a test of the Lense-Thirring effect with a claimed accuracy of 20%-30%. According to some scientists such estimates could be optimistic. Here we wish to discuss the improvements obtainable in this measurement, in terms of reliability of the evaluation of the systematic error and reduction of its magnitude, due to the new CHAMP and GRACE Earth gravity models.Comment: LaTex2e, 6 pages, no figures, no tables. Paper presented at 2nd CHAMP science meeting, Potsdam, 1-4 September 200

Artificial Intelligence

Contains research objectives and reports on eight research projects.Computation Center, M.I.T

The utility of diagnostic tests for immune-mediated hemolytic anemia

Background: A definitive diagnosis of immune‐mediated hemolytic anemia (IMHA) can be difficult to make. However, it is critical to differentiate IMHA from other causes of anemia due to the impact on prognosis and outcome for IMHA patients. Recently published American College of Veterinary Internal Medicine recommendations for the diagnosis of IMHA should be followed to concurrently confirm ongoing anemia, verify in vivo hemolysis, and detect anti‐erythrocyte antibodies. The reliability of immunologic IMHA tests varies depending on which test is used and how it is performed. Objectives: Our aims were to determine which tests are currently used in veterinary medicine to diagnose IMHA and review the utility of assays that have historically been used to diagnose IMHA. Methods: A short survey was designed to see which diagnostic tests for IMHA were currently being used by veterinary practices. The survey was distributed via listserves to veterinarians and veterinary technologists. A literature review was performed to report the utility of diagnostic tests for the diagnosis of IMHA. Results: Survey respondents indicated a variability in test protocols used to diagnose IMHA. Most respondents perform saline agglutination or Coombs’ tests to detect anti‐erythrocyte antibodies. Additional tests that can be used to support a diagnosis of IMHA are discussed in this review. Conclusions: A standardized diagnostic approach should be followed to differentiate IMHA from other causes of anemia. Test methodology can vary from one laboratory to another, and clinicians should be familiar with the procedures used by their laboratory

Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases.

PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the noncoding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity, and magnetic resonance image changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, probably missed owing to failure of alignment.ConclusionThese cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses

Acetate degradation at low pH by the moderately acidophilic sulfate reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov.

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2022.816605/full#supplementary-materialIn acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.This work was financed by ERC grants to AS (project 323009) and JS (project 694569), the research program TTW under project number 14797, which is financed by the Dutch Research Council (NWO) to IS-A, and a Gravitation grant (SIAM 024.002.002) of the Netherlands Ministry of Education, Culture and Science to AS and JS.info:eu-repo/semantics/publishedVersio

Using the past to constrain the future: how the palaeorecord can improve estimates of global warming

Climate sensitivity is defined as the change in global mean equilibrium temperature after a doubling of atmospheric CO2 concentration and provides a simple measure of global warming. An early estimate of climate sensitivity, 1.5-4.5{\deg}C, has changed little subsequently, including the latest assessment by the Intergovernmental Panel on Climate Change. The persistence of such large uncertainties in this simple measure casts doubt on our understanding of the mechanisms of climate change and our ability to predict the response of the climate system to future perturbations. This has motivated continued attempts to constrain the range with climate data, alone or in conjunction with models. The majority of studies use data from the instrumental period (post-1850) but recent work has made use of information about the large climate changes experienced in the geological past. In this review, we first outline approaches that estimate climate sensitivity using instrumental climate observations and then summarise attempts to use the record of climate change on geological timescales. We examine the limitations of these studies and suggest ways in which the power of the palaeoclimate record could be better used to reduce uncertainties in our predictions of climate sensitivity.Comment: The final, definitive version of this paper has been published in Progress in Physical Geography, 31(5), 2007 by SAGE Publications Ltd, All rights reserved. \c{opyright} 2007 Edwards, Crucifix and Harriso