Parallel String Sample Sort

We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations.Comment: 34 pages, 7 figures and 12 table

Determining the effects of cattle grazing treatments on Yosemite toads (Anaxyrus [=Bufo] canorus) in montane meadows.

Amphibians are experiencing a precipitous global decline, and population stability on public lands with multiple uses is a key concern for managers. In the Sierra Nevada Mountains (California, USA), managers have specifically identified livestock grazing as an activity that may negatively affect Yosemite toads due to the potential overlap of grazing with toad habitat. Grazing exclusion from Yosemite toad breeding and rearing areas and/or entire meadows have been proposed as possible management actions to alleviate the possible impact of cattle on this species. The primary objective of this study was to determine if different fencing treatments affect Yosemite toad populations. We specifically examined the effect of three fencing treatments on Yosemite toad breeding pool occupancy, tadpoles, and young of the year (YOY). Our hypothesis was that over the course of treatment implementation (2006 through 2010), Yosemite toad breeding pool occupancy and early life stage densities would increase within two fencing treatments relative to actively grazed meadows due to beneficial changes to habitat quality in the absence of grazing. Our results did not support our hypothesis, and showed no benefit to Yosemite toad presence or early life stages in fenced or partially fenced meadows compared to standard USDA Forest Service grazing levels. We found substantial Yosemite toad variation by both meadow and year. This variation was influenced by meadow wetness, with water table depth significant in both the tadpole and YOY models

Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae

Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceace metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate, and the reduction of arsenate, selenate and elemental sulfur. Numerous membrane-bound multi-heme c type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humics and syntrophic partners

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names “Candidatus Methanoperedens manganicus” and “Candidatus Methanoperedens manganireducens” for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment

British trade unions and the academics: the case of Unionlearn

Unionlearn and union learning representatives were developed by the British TUC to match workers with education and training opportunities, strengthen the economy, foster market inclusion and facilitate social mobility. Their contribution to union revitalisation was emphasised. This article questions whether, with unions confronting global crisis, this is a necessary initiative. It stemmed from TUC failure to achieve policy goals, institutional needs, consequent acceptance of a lesser role, and the availability of state finance. Claims by academics that it provides influence over state policy and contributes to revitalisation remain inadequately evidenced. Union resurgence is not immanent. The way forward is through adversarial grassroots organising and socialist education, not through retooling capital, improving members’ marketability and partnership with a hostile state

A fundamental rule: determining the importance of flow prior to polymer crystallization

A continuum-level model for non-isothermal polymer crystallization following a complex flow is presented, along with a fundamental rule that may be employed to determine if the flow will influence the ensuing crystallization dynamics. This rule is based on two dimensionless parameters: the (Rouse) Weissenberg number, and an inverse Deborah number de�ned by the ratio between the time taken to cool to the melting point versus the stretch relaxation time, which determines the time available for flow-enhanced crystallization. Moreover, we show how the time to reach the melting point can be derived semi-analytically and expressed in terms of the processing conditions in the case of pipe flow - ubiquitous in polymer processing. Whilst the full numerical model is required to quantitatively predict induction times and spherulite-size distributions, the proposed fundamental rule may be used practically to ensure, or eliminate, flow-enhanced structures by controlling the processing conditions or material properties. We discuss how ow-enhanced structures may be revealed only after post-processing annealing, and finally examine previous works that have successfully applied the model to extrusion-based three-dimensional (3D) printing

A Comprehensive Resource for Induced Pluripotent Stem Cells from Patients with Primary Tauopathies.

Primary tauopathies are characterized neuropathologically by inclusions containing abnormal forms of the microtubule-associated protein tau (MAPT) and clinically by diverse neuropsychiatric, cognitive, and motor impairments. Autosomal dominant mutations in the MAPT gene cause heterogeneous forms of frontotemporal lobar degeneration with tauopathy (FTLD-Tau). Common and rare variants in the MAPT gene increase the risk for sporadic FTLD-Tau, including progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD). We generated a collection of fibroblasts from 140 MAPT mutation/risk variant carriers, PSP, CBD, and cognitively normal controls; 31 induced pluripotent stem cell (iPSC) lines from MAPT mutation carriers, non-carrier family members, and autopsy-confirmed PSP patients; 33 genome engineered iPSCs that were corrected or mutagenized; and forebrain neural progenitor cells (NPCs). Here, we present a resource of fibroblasts, iPSCs, and NPCs with comprehensive clinical histories that can be accessed by the scientific community for disease modeling and development of novel therapeutics for tauopathies

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience

Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont

High-solids black liquor firing in pulp and paper industry kraft recovery boilers: Phase 1 -- Final report. Volume 2: Project technical results

This project is a multiple-phase effort to develop technologies to improve high-solids black liquor firing in pulp mill recovery boilers. The principal means to this end is to construct and operate a pilot-scale recovery furnace simulator (RFS) in which these technologies can be tested. The Phase 1 objectives are to prepare a preliminary design for the RFS, delineate a project concept for evaluating candidate technologies, establish industrial partners, and report the results. Phase 1 addressed the objectives with seven tasks: Develop a preliminary design of the RFS; estimate the detailed design and construction costs of the RFS and the balance of the project; identify interested parties in the paper industry and key suppliers; plan the Phase 2 and Phase 3 tests to characterize the RFS; evaluate the economic justification for high-solids firing deployment in the industry; evaluate high-solids black liquor property data to support the RFS design; manage the project and reporting results, which included planning the future program direction

Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice

The authors would like to thank undergraduate student Aleksandra Kowalczuk (University of Aberdeen) for assisting in experiments and Dr. Emma K. Lees (School of Health Sciences, Liverpool Hope University, Liverpool, UK) for invaluable discussions concerning the regulation of FGF21. We thank Dr. Calum Sutherland and Dr. Amy Cameron (both Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Scotland, UK) for technical support and expertise in performing hepatocyte studies. Fenretinide was a generous gift of T. Martin (Johnson & Johnson, New Brunswick, NJ) and U. Thumeer (Cilag AG, Schaffhausen, Switzerland), for use completely without restriction or obligation. Quantitative-PCR was carried out using the qPCR Core Facility (Institute of Medical Sciences, University of Aberdeen). RNA-sequencing was carried out at the University of Aberdeen Centre for Genome Enabled Biology and Medicine. Pancreas histology was performed by Dr Linda Davidson (Department of Histology, Aberdeen Royal Infirmary, NHS Grampian, Foresterhill Health Campus, Aberdeen, UK). This study was supported by the British Heart Foundation Intermediate Basic Research Fellowship FS/09/026 to N. Mody, RCUK fellowship to MD, EFSD/Lilly Programme Grant to MD and N. Mody, Tenovus Scotland grants G10/04 and G14/14 to N. Mody, University of Aberdeen Centre for Genome Enabled Biology and Medicine (CGEBM) PhD studentship to N. Morrice and Biotechnology and Biological Sciences Research Council studentship to GDM.Peer reviewedPublisher PD