Nuclear and mitochondrial genome assemblies for the endangered wood-decaying fungus Somion occarium.

Somion occarium is a wood-decaying bracket fungus belonging to an order known to be rich in useful chemical compounds. Despite its widespread distribution, S. occarium has been assessed as endangered on at least one national Red List, presumably due to loss of old-growth forest habitat.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A.

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion.

We present a reference genome assembly from an individual male Violet Carpenter Bee (Xylocopa violacea, Linnaeus 1758). The assembly is 1.02 gigabases in span.

Evolution with recombination as Gibbs sampling.

This work presents a population genetic model of evolution, which includes haploid selection, mutation, recombination, and drift. The mutation-selection equilibrium can be expressed exactly in closed form for arbitrary fitness functions without resorting to diffusion approximations. Tractability is achieved by generating new offspring using n-parent rather than 2-parent recombination.

Prediction as a basis for skilled reading: insights from modern language models.

Reading is not an inborn human capability, and yet, English-speaking adults read with impressive speed. This study considered how predictions of upcoming words impact on this skilled behaviour. We used a powerful language model (GPT-2) to derive predictions of upcoming words in text passages.

An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.

We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. Following the optimization of a logistics pipeline that involved shipping isolates as thermolysates in ambient conditions, the project assembled a diverse collection of 10,419 isolates from low- and middle-income countries.

What is semantic diversity and why does it facilitate visual word recognition?

Previous research has speculated that semantic diversity and lexical ambiguity may be closely related constructs. Our research sought to test this claim in respect of the semantic diversity measure proposed by Hoffman et al. (2013).

Rapid Creation of an Online Discussion Space (r/nipah) During a Serious Disease Outbreak: Observational Study.

Background: During health emergencies, the people within affected communities ask many questions at a time when professional medics and health agencies are overstretched and struggling to cope. Our previous research has shown that, during the 2014-2015 West Africa Ebola crisis, volunteer-moderated online discussion forums were able to provide peer-to-peer reliable, trustworthy, and well-managed information. We speculated that with the right mix of epistemic and experiential knowledge, such a discussion forum could be set up rapidly during a future serious disease outbreak.

Realtime Tracking of Passengers on the London Underground Transport by Matching Smartphone Accelerometer Footprints.

Passengers travelling on the London underground tubes currently have no means of knowing their whereabouts between stations. The challenge for providing such service is that the London underground tunnels have no GPS, Wi-Fi, Bluetooth, or any kind of terrestrial signals to leverage. This paper presents a novel yet practical idea to track passengers in realtime using the smartphone accelerometer and a training database of the entire London underground network.

Health Advice from Internet Discussion Forums: How Bad Is Dangerous?

Background: Concerns over online health information-seeking behavior point to the potential harm incorrect, incomplete, or biased information may cause. However, systematic reviews of health information have found few examples of documented harm that can be directly attributed to poor quality information found online.

Objective: The aim of this study was to improve our understanding of the quality and quality characteristics of information found in online discussion forum websites so that their likely value as a peer-to-peer health information-sharing platform could be assessed.

International employees' concerns during serious disease outbreaks and the potential impact on business continuity: Lessons identified from the 2014-15 West African Ebola outbreak.

This paper presents the findings of research carried out into the information-seeking behaviour, and information requirements of a small sample of international workers stationed in West Africa during the Zaire Ebola virus outbreak of 2014-15. The research study under which these results were obtained was part of exploratory research for a PhD focused on the use, and potential uses, of social media platforms during serious disease outbreaks that might be used to inform policy planning for public health and emergency response interventions. Thus, the findings from this study may provide valuable insights to business continuity managers and emergency planners in making future decisions about information exchange and crisis decision-making during future serious disease outbreaks.

Pioneering government-sponsored drug repositioning collaborations: progress and learning.

A new model for translational research and drug repositioning has recently been established based on three-way partnerships between public funders, the pharmaceutical industry and academic investigators. Through two pioneering initiatives - one involving the Medical Research Council in the United Kingdom and one involving the National Center for Advancing Translational Sciences of the National Institutes of Health in the United States - new investigations of highly characterized investigational compounds have been funded and are leading to the exploration of known mechanisms in new disease areas. This model has been extended beyond these first two initiatives.

Immune Tolerance Maintained by Cooperative Interactions between T Cells and Antigen Presenting Cells Shapes a Diverse TCR Repertoire.

The T cell population in an individual needs to avoid harmful activation by self peptides while maintaining the ability to respond to an unknown set of foreign peptides. This property is acquired by a combination of thymic and extra-thymic mechanisms. We extend current models for the development of self/non-self discrimination to consider the acquisition of self-tolerance as an emergent system level property of the overall T cell receptor repertoire.

Acquire: an open-source comprehensive cancer biobanking system.

Motivation: The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research.

Results: To support the complex data management needs and workflows of several such biobanks, we developed Acquire.

Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense Az39, Successfully Applied in Agriculture.

We present the complete genome sequence of Azospirillum brasilense Az39, isolated from wheat roots in the central region of Argentina and used as inoculant in extensive and intensive agriculture during the last four decades. The genome consists of 7.39 Mb, distributed in six replicons: one chromosome, three chromids, and two plasmids.

Nitric oxide inhibition of alcohol dehydrogenase in fresh-cut apples ( Malus domestica Borkh).

The effects of nitric oxide (NO) and nitrite treatment on alcohol dehydrogenase activity and the shelf life of apple tissue were investigated. Fresh-cut apple slices were stored for 2 days at 6 °C in 0.25-1% NO (v/v, balance N2) or 100% N2 atmospheres.

Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes.

Several apple cultivars are susceptible to CO2 injury, a physiological disorder that can be expressed either externally or internally, and which can cause major losses of fruit during controlled atmosphere (CA) storage. Disorder development can also be enhanced using SmartFresh™ technology, based on the inhibition of ethylene perception by 1-methylcyclopropene (1-MCP). Injury development is associated with less mature fruit with lower ethylene production, but the aetiology of the disorder is poorly understood.

The spread of awareness and its impact on epidemic outbreaks.

When a disease breaks out in a human population, changes in behavior in response to the outbreak can alter the progression of the infectious agent. In particular, people aware of a disease in their proximity can take measures to reduce their susceptibility. Even if no centralized information is provided about the presence of a disease, such awareness can arise through first-hand observation and word of mouth.

Ethylene and alpha-farnesene metabolism in green and red skin of three apple cultivars in response to 1-methylcyclopropene (1-MCP) treatment.

Relationships among alpha-farnesene synthesis and oxidation, ethylene production and perception, antioxidative enzyme activities, and superficial scald development in fruit of three commercial apple cultivars were investigated at the biochemical and gene transcriptional levels. Scald-susceptible Cortland and Law Rome and scald-resistant Idared apples were untreated or treated with the ethylene action inhibitor 1-methylcyclopropene (1-MCP) and stored for up to 25 weeks at 0.5 degrees C.

A reevaluation of the key factors that influence tomato fruit softening and integrity.

The softening of fleshy fruits, such as tomato (Solanum lycopersicum), during ripening is generally reported to result principally from disassembly of the primary cell wall and middle lamella. However, unsuccessful attempts to prolong fruit firmness by suppressing the expression of a range of wall-modifying proteins in transgenic tomato fruits do not support such a simple model. 'Delayed Fruit Deterioration' (DFD) is a previously unreported tomato cultivar that provides a unique opportunity to assess the contribution of wall metabolism to fruit firmness, since DFD fruits exhibit minimal softening but undergo otherwise normal ripening, unlike all known nonsoftening tomato mutants reported to date.

The use of 1-methylcyclopropene (1-MCP) on fruits and vegetables.

The recent availability of the inhibitor of ethylene perception, 1-methylcyclopropene (1-MCP), has resulted in an explosion of research on its effects on fruits and vegetables, both as a tool to further investigate the role of ethylene in ripening and senescence, and as a commercial technology to improve maintenance of product quality. The commercialization of 1-MCP was followed by rapid adoption by many apple industries around the world, and strengths and weaknesses of the new technology have been identified. However, use of 1-MCP remains limited for other products, and therefore it is still necessary to speculate on its commercial potential for most fruits and vegetables.

Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community.

The nuclear receptor signaling (NRS) field has generated a substantial body of information on nuclear receptors, their ligands and coregulators, with the ultimate goal of constructing coherent models of the biological and clinical significance of these molecules. As a component of the Nuclear Receptor Signaling Atlas (NURSA)--the development of a functional atlas of nuclear receptor biology--the NURSA Bioinformatics Resource is developing a strategy to organize and integrate legacy and future information on these molecules in a single web-based resource (www.nursa.

Disabling musculoskeletal pain and its relation to somatization: a community-based postal survey.

Background: Somatization (a tendency to report distress from somatic symptoms) is a little studied, but potentially important, confounder and effect modifier in occupational studies of musculoskeletal disease.

Aims: To assess the role of somatization as a risk factor for disabling regional pain.

Methods: A questionnaire was mailed to 4998 subjects of working age.

Factors affecting feasibility and acceptability of a practice-based educational intervention to support evidence-based prescribing: a qualitative study.

Background: Inappropriate and costly GP prescribing is a major problem facing Primary Care Trusts. Educational outreach into practices, alongside other measures, such as audit and feedback, have the potential to enable GP prescribing to become more evidence based. High GP prescribing costs are associated with GPs who see drug company representatives; tend to end consultations with prescriptions; and 'try out' new drugs on an 'ad hoc basis' and use this as evidence of the drug's effect.