We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy ...without sacrificing scalability.
Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the "CAT" approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100-1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory.
FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
The medical market is a continuing success story for the application of shape memory alloy products. Increasing life expectancy and advances in surgical procedures mean that the medical market will ...remain an area of great opportunity for commercial applications.
This paper will consider just why the shape memory effect holds so many opportunities for medical devices and will review a selection of current applications. Interventional radiology in particular has benefited from the unique properties of superelastic nitinol and this will be reviewed in detail.
As well as considering the benefits of shape memory alloys in medical devices this paper will also consider the factors that impinge on the associated risk analysis of using nitinol in medical applications.
As online data collection services such as Amazon’s Mechanical Turk (MTurk) gain popularity, the quality and representativeness of such data sources have gained research attention. To date, the ...majority of existing studies have compared MTurk workers with undergraduate samples, localized community samples, or other Internet-based samples, and thus, there remains little known about the personality and mental health constructs of MTurk workers relative to a national representative sample. The present study addresses these limitations and broadens the scope of existing research through the use of the Personality Assessment Inventory, a multiscale, self-report questionnaire which provides information regarding data validity and personality and psychopathology features standardized against a national U.S. census–matched normative sample. Results indicate that MTurk workers generally provide high-quality data and are reasonably representative of the general population across most psychological dimensions assessed. However, several distinguishing features of MTurk workers emerged that were consistent with prior findings of such individuals, primarily involving somewhat higher negative affect and lower social engagement.
To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon ...sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind's predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.
Aims/hypothesis Evidence that the beta cells of human patients with type 1 diabetes can be infected with enterovirus is accumulating, but it remains unclear whether such infections occur at high ...frequency and are important in the disease process. We have now assessed the prevalence of enteroviral capsid protein vp1 (vp1) staining in a large cohort of autopsy pancreases of recent-onset type 1 diabetic patients and a range of controls. Methods Serial sections of paraffin-embedded pancreatic autopsy samples from 72 recent-onset type 1 diabetes patients and up to 161 controls were immunostained for insulin, glucagon, vp1, double-stranded RNA activated protein kinase R (PKR) and MHC class I. Results vp1-immunopositive cells were detected in multiple islets of 44 out of 72 young recent-onset type 1 diabetic patients, compared with a total of only three islets in three out of 50 neonatal and paediatric normal controls. vp1 staining was restricted to insulin-containing beta cells. Among the control pancreases, vp1 immunopositivity was also observed in some islets from ten out of 25 type 2 diabetic patients. A strong correlation was established between islet cell vp1 positivity and PKR production in insulin-containing islets of both type 1 and type 2 diabetic patients, consistent with a persistent viral infection of the islets. Conclusions/interpretation Immunoreactive vp1 is commonly found in the islets of recent-onset type 1 diabetes patients, but only rarely in normal paediatric controls. vp1 immunostaining was also observed in some islets of type 2 diabetes patients, suggesting that the phenomenon is not restricted to type 1 diabetes patients.
Policing under disability law Morgan, Jamelia N
Stanford law review,
06/2021, Letnik:
73, Številka:
6
Journal Article
Recenzirano
In recent years, there has been increased attention to the problem of police violence against disabled people. Disabled people are overrepresented in police killings and, in a number of cities, ...police use-of-force incidents. Further, though police violence dominates the discussion of policing, disabled people also disproportionately experience more ordinary forms of policing that can lead to police violence. For example, disabled people, particularly those with untreated psychiatric disabilities, are vulnerable to policing even in medical facilities-the very places they seek to access care. Many are also arrested pursuant to aggressive enforcement policies aimed at removing so-called unwanted persons or regulating those labeled disruptive or disorderly. Though they pose no risk of physical harm, some are arrested and taken to jail, at times simply because they have no place else to go.
This Article centers disability theory as a lens for understanding the problems of policing and police violence as they impact disabled people. In doing so, the Article examines how federal disability law addresses these ongoing problems. Disabled plaintiffs have alleged disability discrimination and challenged policing and police violence under both Title II of the Americans with Disabilities Act (ADA) and the Rehabilitation Act of 1973, another federal disability law and the precursor to the ADA. The Supreme Court has yet to decide whether Title II of the ADA applies to arrests, and federal appellate courts are split on whether and to what extent Title II's antidiscrimination provisions apply to street encounters and arrests. Although the Court granted certiorari to a case presenting the question, 'City and County of San Francisco v. Sheehan', it subsequently dismissed that question as improvidently granted. There is no telling when the question will reach the Supreme Court again, but before it does, it is important to develop a theory not just of liability but also of disability under Title II that is consistent with the text, history, and animating goals of the ADA.
Courts are already adopting a theory of disability that informs how they decide policing cases under Title II: the medical model of disability. However, that theory is inconsistent with that reflected by the ADA and the ADA Amendments of 2008, and it leads courts to pay insufficient attention to disability as a social construction. I examine cases showing how the ADA-contrary to its celebrated goals of access and social inclusion-has been interpreted to exclude a class of individuals from civil rights protection and from the entitlement to an accommodation by law enforcement. Ultimately, I show how the medical model of disability in policing cases serves to limit the broad scope of protections available under the ADA that could otherwise be used to push back against such disability based subordination.
Adopting and incorporating a social model of disability-that is, viewing disability as a social construction-requires a reexamination of extant legal standards regarding causation, intentional discrimination, disparate impact, and deference to law enforcement under the ADA. As I argue, the social model of disability is not only more consistent with the animating goals of the ADA but also more attuned to the social meanings at play that work to expose disabled people to policing and police violence. By centering a social model of disability in cases challenging disability-based discrimination under federal disability laws-and by incorporating disability law into ongoing public activism, discourse, and policymaking on policing-we can better identify and redress the harms stemming from the policing of disability along with the long-standing social problem of police violence.
Though scholars have identified the expanding scope of First Amendment speech doctrine, little attention has been paid to the theoretical transformation happening inside the doctrine that has ...accompanied its outward creep. Taking up this overlooked perspective, this Article uncovers a new speech theory: the libertarian tradition. This new tradition both is generative of the doctrine's expansion and risks undermining the First Amendment's theoretical foundations. This Article excavates the libertarian tradition through an analysis of Supreme Court cases that, beginning in the 1970s, consistently expanded speech protections by striking down limits on commercial speech and corporate political spending. The Court justified this expansion with the rationale of vindicating listeners' rights in the free flow of information—the corporate benefit was incidental. But by narrowly conceptualizing listeners as individuals whose interests are aligned with corporate speech interests, the Court ended up instrumentalizing listeners' rights in the service of corporate speech rights. This is the libertarian tradition. Today, the tradition has abandoned listeners' rights altogether, directly embracing corporate speech rights. This pure iteration of the libertarian tradition facilitates First Amendment doctrine's more aggressive expansion to increasingly diverse and dissonant types of corporate "speech"—for instance, data transmission and potentially fraudulent claims. The libertarian tradition represents a radical departure from, and threat to, the two longstanding speech theories: the republican and liberal traditions. First, by reconceptualizing listeners as individuals whose interests are vindicated through deregulation, the libertarian tradition draws from and is hostile to the republican tradition, which emphasizes the rights of the public, figured as listeners. Second, because the libertarian tradition focuses on vindicating corporate speech rights, it strips away the hallmarks of individual autonomy central to the liberal tradition, leaving only a naked speech right against the state, which this article names "thin autonomy." If the two traditions have value, then the libertarian tradition is problematic. This insight cuts against the widespread belief that to protect speech we must be willing to countenance nearly any application of the right, even—and perhaps especially—if it goes against our most deeply held beliefs. That view is a myth; the speech right must have limits.
To determine the relative importance of a wide variety of personality and psychopathology variables in influencing patients' adherence to psychotherapy treatment.
Two classification trees were ...trained to predict patients' (1) treatment utilization (i.e., their likelihood of missing a given appointment) and (2) termination status (i.e., their likelihood of dropping out of therapy prematurely). Each tree was then validated in an external dataset to examine performance accuracy.
Patients' social detachment was most influential in predicting their treatment utilization, followed by affective instability and activity/energy levels. Patients' interpersonal warmth was most influential in predicting their termination status, followed by levels of disordered thought and resentment. The overall accuracy rating for the tree for termination status was 71.4%, while the tree for treatment utilization had a 38.7% accuracy rating.
Classification trees are a practical tool for clinicians to determine patients at risk of premature termination. More research is needed to develop trees that predict treatment utilization with high accuracy across different types of patients and settings.
The immunopathology of type 1 diabetes (T1D) has proved difficult to study in man because of the limited availability of appropriate samples, but we now report a detailed study charting the evolution ...of insulitis in human T1D. Pancreas samples removed post-mortem from 29 patients (mean age 11·7 years) with recent-onset T1D were analysed by immunohistochemistry. The cell types constituting the inflammatory infiltrate within islets (insulitis) were determined in parallel with islet insulin content. CD8⁺ cytotoxic T cells were the most abundant population during insulitis. Macrophages (CD68⁺) were also present during both early and later insulitis, although in fewer numbers. CD20⁺ cells were present in only small numbers in early insulitis but were recruited to islets as beta cell death progressed. CD138⁺ plasma cells were infrequent at all stages of insulitis. CD4⁺ cells were present in the islet infiltrate in all patients but were less abundant than CD8⁺ or CD68⁺ cells. Forkhead box protein P3⁺ regulatory T cells were detected in the islets of only a single patient. Natural killer cells were detected rarely, even in heavily inflamed islets. The results suggest a defined sequence of immune cell recruitment in human T1D. They imply that both CD8⁺ cytotoxic cells and macrophages may contribute to beta cell death during early insulitis. CD20⁺ cells are recruited in greatest numbers during late insulitis, suggesting an increasing role for these cells as insulitis develops. Natural killer cells and forkhead box protein P3⁺ T cells do not appear to be required for beta cell death.
Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence ...of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.
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