The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

What’s in a (pseudo)name?: Ethical conundrums for the principles of anonymisation in social media research

Scholars from wide-ranging disciplines are turning to social media platforms as research sites, and as platforms expand their communicative possibilities, they create more spaces for users to enact a multitude of identities. Most platforms allow users to have ‘pseudonymous’ identities; that is, they can engage in practices intended to facilitate nonidentifiable content. But pseudonymity presents a series of unique challenges to the principles of anonymisation in qualitative research. This article explores the slippery nature of dealing with pseudonymous social media users’ personally identifiable data during research, framed around my responses to four questions I was asked when I applied for ethical approval to conduct research with pseudonymous fan communities on social media. The four questions concern: (Q1) changing notions of ‘public’ and ‘private’ forms of data; (Q2) identifying underage and therefore vulnerable participants online; (Q3) changes to the processes of obtaining informed consent from social media users; and (Q4) the risks social media research might bring to those conducting it. This article concludes by calling for qualitative researchers and Ethics Review Boards (ERBs) to engage with institutional ethics review across the duration of a project, or at the very least to advocate for ongoing consent as research progresses, especially for (but certainly not limited to) research involving pseudonymous social media users. The article aims to be useful to other researchers facing similar dilemmas. Indeed, given the popularity of pseudonymity on social media and the growing penetration of platforms across global demographics, a need for ethical discussions of this kind is surely set to increase

Combustion of a coal char particle in a stream of dry gas.

The burning rate, surface temperature, drag, and extinction conditions of a single char particle moving in a gas are computed numerically. The effects of the size and velocity of the particle and of the temperature and composition of the gas are examined in the framework of a simple model that includes O2 and CO2 heterogeneous reactions and, in some cases, a diffusion-controlled CO oxidation flame in the gas around the particle. In agreement with known results, the burning rate is found to increase with the velocity of the particle when the Reynolds number of the gas flow ceases to be small. The temperature of the particle increases with the temperature and oxygen mass fraction of the gas and is little affected by the size and velocity of the particle, except in the vicinity of extinction. The drag coefficient is a decreasing function of the particle size and velocity in the range of Reynolds numbers that has been analyzed. The presence of CO2 in the gas may have an important effect on the gasification of small particles

Naked mole-rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles.

The naked mole-rat Heterocephalus glaber is a eusocial mammal exhibiting extreme longevity (37-year lifespan), extraordinary resistance to hypoxia and absence of cardiovascular disease. To identify the mechanisms behind these exceptional traits, metabolomics and RNAseq of cardiac tissue from naked mole-rats was compared to other African mole-rat genera (Cape, Cape dune, Common, Natal, Mahali, Highveld and Damaraland mole-rats) and evolutionarily divergent mammals (Hottentot golden mole and C57/BL6 mouse). We identify metabolic and genetic adaptations unique to naked mole-rats including elevated glycogen, thus enabling glycolytic ATP generation during cardiac ischemia. Elevated normoxic expression of HIF-1α is observed while downstream hypoxia responsive-genes are down-regulated, suggesting adaptation to low oxygen environments. Naked mole-rat hearts show reduced succinate levels during ischemia compared to C57/BL6 mouse and negligible tissue damage following ischemia-reperfusion injury. These evolutionary traits reflect adaptation to a unique hypoxic and eusocial lifestyle that collectively may contribute to their longevity and health span

Seroepidemiology of Human Enterovirus 71, Singapore

Human enterovirus 71 has caused outbreaks in many parts of the world, especially Southeast Asia, with some fatal cases. The epidemiology of this viral infection is not well understood. We conducted a serologic survey in Singapore children, and the results indicate that infection occurs largely in preschool settings

The transglutaminase type 2 and pyruvate kinase isoenzyme M2 interplay in autophagy regulation

Autophagy is a self-degradative physiological process by which the cell removes worn-out or damaged components. Constant at basal level it may become highly active in response to cellular stress. The type 2 transglutaminase (TG2), which accumulates under stressful cell conditions, plays an important role in the regulation of autophagy and cells lacking this enzyme display impaired autophagy/mitophagy and a consequent shift their metabolism to glycolysis. To further define the molecular partners of TG2 involved in these cellular processes, we analysed the TG2 interactome under normal and starved conditions discovering that TG2 interacts with various proteins belonging to different functional categories. Herein we show that TG2 interacts with pyruvate kinase M2 (PKM2), a rate limiting enzyme of glycolysis which is responsible for maintaining a glycolytic phenotype in malignant cells and displays non metabolic functions, including transcriptional co-activation and protein kinase activity. Interestingly, the ablation of PKM2 led to the decrease of intracellular TG2's transamidating activity paralleled by an increase of its tyrosine phosphorylation. Along with this, a significant decrease of ULK1 and Beclin1 was also recorded, thus suggesting a block in the upstream regulation of autophagosome formation. These data suggest that the PKM2/TG2 interplay plays an important role in the regulation of autophagy in particular under cellular stressful conditions such as those displayed by cancer cells

Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian Brain

SummaryPrecise control of gene expression plays fundamental roles in brain development, but the roles of chromatin regulators in neuronal connectivity have remained poorly understood. We report that depletion of the NuRD complex by in vivo RNAi and conditional knockout of the core NuRD subunit Chd4 profoundly impairs the establishment of granule neuron parallel fiber/Purkinje cell synapses in the rodent cerebellar cortex in vivo. By interfacing genome-wide sequencing of transcripts and ChIP-seq analyses, we uncover a network of repressed genes and distinct histone modifications at target gene promoters that are developmentally regulated by the NuRD complex in the cerebellum in vivo. Finally, in a targeted in vivo RNAi screen of NuRD target genes, we identify a program of NuRD-repressed genes that operate as critical regulators of presynaptic differentiation in the cerebellar cortex. Our findings define NuRD-dependent promoter decommissioning as a developmentally regulated programming mechanism that drives synaptic connectivity in the mammalian brain

Modular thermal Hall effect measurement setup for fast-turnaround screening of materials over wide temperature range using capacitive thermometry

We demonstrate a simple and easy-to-build probe designed to be loaded into a widely available Quantum Design Physical Properties Measurement System (PPMS) cryostat, with a detachable shielded sample puck section and robust heat sinking of three pairs of coaxial cables. It can be in principle used with any low-temperature cryostat. Our modular puck design has a radiation shield for thermal isolation and protection of the delicate sample space while handling and allows any variety of experimental setup benefiting from shielded coaxial wiring to be constructed on a selection of sample pucks. Pucks can be quickly and easily switched, and the system makes use of the simple yet extremely stable temperature and magnetic field control of the easy-to-use PPMS system. We focus on a setup designed for measurements of the thermal Hall effect and show that this system can yield unprecedented resolution over a wide temperature range and with rapid sample mounting or changing—allowing a large collection of potential samples to be screened for this novel physics. Our design aims to make these sensitive but challenging measurements quick, reliable, cheap, and accessible, through the use of a standard, widespread base cryostat and a system of modular removable sample stage pucks to allow quick turnaround and screening of a large number of candidate samples for potential new thermal Hall physics

Sensor Network Architectures for Monitoring Underwater Pipelines

This paper develops and compares different sensor network architecture designs that can be used for monitoring underwater pipeline infrastructures. These architectures are underwater wired sensor networks, underwater acoustic wireless sensor networks, RF (Radio Frequency) wireless sensor networks, integrated wired/acoustic wireless sensor networks, and integrated wired/RF wireless sensor networks. The paper also discusses the reliability challenges and enhancement approaches for these network architectures. The reliability evaluation, characteristics, advantages, and disadvantages among these architectures are discussed and compared. Three reliability factors are used for the discussion and comparison: the network connectivity, the continuity of power supply for the network, and the physical network security. In addition, the paper also develops and evaluates a hierarchical sensor network framework for underwater pipeline monitoring

Refined saddle-point preconditioners for discretized Stokes problems

This paper is concerned with the implementation of efficient solution algorithms for elliptic problems with constraints. We establish theory which shows that including a simple scaling within well-established block diagonal preconditioners for Stokes problems can result in significantly faster convergence when applying the preconditioned MINRES method. The codes used in the numerical studies are available online