Rheological Chaos in a Scalar Shear-Thickening Model

We study a simple scalar constitutive equation for a shear-thickening material at zero Reynolds number, in which the shear stress \sigma is driven at a constant shear rate \dot\gamma and relaxes by two parallel decay processes: a nonlinear decay at a nonmonotonic rate R(\sigma_1) and a linear decay at rate \lambda\sigma_2. Here \sigma_{1,2}(t) = \tau_{1,2}^{-1}\int_0^t\sigma(t')\exp[-(t-t')/\tau_{1,2}] {\rm d}t' are two retarded stresses. For suitable parameters, the steady state flow curve is monotonic but unstable; this arises when \tau_2>\tau_1 and 0>R'(\sigma)>-\lambda so that monotonicity is restored only through the strongly retarded term (which might model a slow evolution of material structure under stress). Within the unstable region we find a period-doubling sequence leading to chaos. Instability, but not chaos, persists even for the case \tau_1\to 0. A similar generic mechanism might also arise in shear thinning systems and in some banded flows.Comment: Reference added; typos corrected. To appear in PRE Rap. Com

State of the climate in 2013

In 2013, the vast majority of the monitored climate variables reported here maintained trends established in recent decades. ENSO was in a neutral state during the entire year, remaining mostly on the cool side of neutral with modest impacts on regional weather patterns around the world. This follows several years dominated by the effects of either La Niña or El Niño events. According to several independent analyses, 2013 was again among the 10 warmest years on record at the global scale, both at the Earths surface and through the troposphere. Some regions in the Southern Hemisphere had record or near-record high temperatures for the year. Australia observed its hottest year on record, while Argentina and New Zealand reported their second and third hottest years, respectively. In Antarctica, Amundsen-Scott South Pole Station reported its highest annual temperature since records began in 1957. At the opposite pole, the Arctic observed its seventh warmest year since records began in the early 20th century. At 20-m depth, record high temperatures were measured at some permafrost stations on the North Slope of Alaska and in the Brooks Range. In the Northern Hemisphere extratropics, anomalous meridional atmospheric circulation occurred throughout much of the year, leading to marked regional extremes of both temperature and precipitation. Cold temperature anomalies during winter across Eurasia were followed by warm spring temperature anomalies, which were linked to a new record low Eurasian snow cover extent in May. Minimum sea ice extent in the Arctic was the sixth lowest since satellite observations began in 1979. Including 2013, all seven lowest extents on record have occurred in the past seven years. Antarctica, on the other hand, had above-average sea ice extent throughout 2013, with 116 days of new daily high extent records, including a new daily maximum sea ice area of 19.57 million km2 reached on 1 October. ENSO-neutral conditions in the eastern central Pacific Ocean and a negative Pacific decadal oscillation pattern in the North Pacific had the largest impacts on the global sea surface temperature in 2013. The North Pacific reached a historic high temperature in 2013 and on balance the globally-averaged sea surface temperature was among the 10 highest on record. Overall, the salt content in nearsurface ocean waters increased while in intermediate waters it decreased. Global mean sea level continued to rise during 2013, on pace with a trend of 3.2 mm yr-1 over the past two decades. A portion of this trend (0.5 mm yr-1) has been attributed to natural variability associated with the Pacific decadal oscillation as well as to ongoing contributions from the melting of glaciers and ice sheets and ocean warming. Global tropical cyclone frequency during 2013 was slightly above average with a total of 94 storms, although the North Atlantic Basin had its quietest hurricane season since 1994. In the Western North Pacific Basin, Super Typhoon Haiyan, the deadliest tropical cyclone of 2013, had 1-minute sustained winds estimated to be 170 kt (87.5 m s-1) on 7 November, the highest wind speed ever assigned to a tropical cyclone. High storm surge was also associated with Haiyan as it made landfall over the central Philippines, an area where sea level is currently at historic highs, increasing by 200 mm since 1970. In the atmosphere, carbon dioxide, methane, and nitrous oxide all continued to increase in 2013. As in previous years, each of these major greenhouse gases once again reached historic high concentrations. In the Arctic, carbon dioxide and methane increased at the same rate as the global increase. These increases are likely due to export from lower latitudes rather than a consequence of increases in Arctic sources, such as thawing permafrost. At Mauna Loa, Hawaii, for the first time since measurements began in 1958, the daily average mixing ratio of carbon dioxide exceeded 400 ppm on 9 May. The state of these variables, along with dozens of others, and the 2013 climate conditions of regions around the world are discussed in further detail in this 24th edition of the State of the Climate series. © 2014, American Meteorological Society. All rights reserved

The United Kingdom and the Netherlands maternity care responses to COVID-19: A comparative study

BackgroundThe national health care response to coronavirus (COVID-19) has varied between countries. The United Kingdom (UK) and the Netherlands (NL) have comparable maternity and neonatal care systems, and experienced similar numbers of COVID-19 infections, but had different organisational responses to the pandemic. Understanding why and how similarities and differences occurred in these two contexts could inform optimal care in normal circumstances, and during future crises.AimTo compare the UK and Dutch COVID-19 maternity and neonatal care responses in three key domains: choice of birthplace, companionship, and families in vulnerable situations.MethodA multi-method study, including documentary analysis of national organisation policy and guidance on COVID-19, and interviews with national and regional stakeholders.FindingsBoth countries had an infection control focus, with less emphasis on the impact of restrictions, especially for families in vulnerable situations. Differences included care providers’ fear of contracting COVID-19; the extent to which community- and personalised care was embedded in the care system before the pandemic; and how far multidisciplinary collaboration and service-user involvement were prioritised.ConclusionWe recommend that countries should 1) make a systematic plan for crisis decision-making before a serious event occurs, and that this must include authentic service-user involvement, multidisciplinary collaboration, and protection of staff wellbeing 2) integrate women’s and families’ values into the maternity and neonatal care system, ensuring equitable inclusion of the most vulnerable and 3) strengthen community provision to ensure system wide resilience to future shocks from pandemics, or other unexpected large-scale events

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

NanoPipe—a web server for nanopore MinION sequencing data analysis

BACKGROUND: The fast-moving progress of the third-generation long-read sequencing technologies will soon bring the biological and medical sciences to a new era of research. Altogether, the technique and experimental procedures are becoming more straightforward and available to biologists from diverse fields, even without any profound experience in DNA sequencing. Thus, the introduction of the MinION device by Oxford Nanopore Technologies promises to “bring sequencing technology to the masses” and also allows quick and operative analysis in field studies. However, the convenience of this sequencing technology dramatically contrasts with the available analysis tools, which may significantly reduce enthusiasm of a “regular” user. To really bring the sequencing technology to every biologist, we need a set of user-friendly tools that can perform a powerful analysis in an automatic manner. FINDINGS: NanoPipe was developed in consideration of the specifics of the MinION sequencing technologies, providing accordingly adjusted alignment parameters. The range of the target species/sequences for the alignment is not limited, and the descriptive usage page of NanoPipe helps a user to succeed with NanoPipe analysis. The results contain alignment statistics, consensus sequence, polymorphisms data, and visualization of the alignment. Several test cases are used to demonstrate the efficiency of the tool. CONCLUSIONS: Freely available NanoPipe software allows effortless and reliable analysis of MinION sequencing data for experienced bioinformaticians, as well for wet-lab biologists with minimum bioinformatics knowledge. Moreover, for the latter group, we describe the basic algorithm necessary for MinION sequencing analysis from the first to last step

Early-life exposure to sibling modifies the relationship between CD14 polymorphisms and allergic sensitization

BACKGROUND:Markers of microbial exposure are thought to be associated with risk of allergic sensitization; however, the associations are inconsistent and may be related to gene-environment interactions. OBJECTIVE:To examine the relationship between polymorphisms in the CD14 gene and allergic sensitization and whether sibling exposure, as a marker of microbial exposure, modified this relationship. METHODS:We used data from the Tasmanian Longitudinal Health Study and the Melbourne Atopy Cohort Study. Two CD14 polymorphisms were genotyped. Allergic sensitization was defined by a positive response to a skin prick test. Sibling exposure was measured as cumulative exposure to siblings before age 6 months, 2 and 4 years. Logistic regression and multi-level mixed-effects logistic regression were used to examine the associations. Effect estimates across the cohorts were pooled using random-effects meta-analysis. RESULTS:CD14 SNPs were not individually associated with allergic sensitization in either cohort. In TAHS, cumulative sibling exposure before age 6 months, 2 and 4 years was each associated with a reduced risk of allergic sensitization at age 45 years. A similar effect was observed in MACS. Meta-analysis across the two cohorts showed consistent evidence of an interaction between cumulative sibling exposure before 6 months and the rs5744455-SNP (P = 0.001) but not with the rs2569190-SNP (P = 0.60). The pooled meta-analysis showed that the odds of sensitization with increasing cumulative exposure to sibling before 6 months of age was 20.9% smaller in those with the rs5744455-C-allele than the T-allele (OR = 0.83 vs 1.05, respectively). CONCLUSION AND CLINICAL RELEVANCE:Cumulative sibling exposure reduced the risk of sensitization from childhood to middle age in genetically susceptible individuals.Melisa Y. Z. Lau, Shyamali C. Dharmage, John A. Burgess, Aung K. Win, Adrian J. Lowe ... Christopher A. ... et al. (For the investigators of the TAHS and MACS

The genetic relationship between individual differences in social and nonsocial behaviours characteristic of autism

Two types of behaviours shown in children – those reflecting social impairment and nonsocial obsessive repetitive behaviours – are central to defining and diagnosing autism spectrum disorders (ASDs). Parent and teacher data on social and nonsocial behaviours were obtained from a community sample of >3000 7‐year‐old twin pairs. Social and nonsocial behaviours were only modestly correlated, and it was found that some individuals had extreme scores on either social or nonsocial scales but not both. Genetic model‐fitting showed that social and nonsocial behaviours are both highly heritable, but their genetic overlap is modest, with most of the genetic influence being specific to either social or nonsocial behaviours. Considering these behaviours separately might help clarify gene‐brain‐behaviour pathways in future research