Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.

Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity

Voice-selective prediction alterations in nonclinical voice hearers

Auditory verbal hallucinations (AVH) are a cardinal symptom of psychosis but also occur in 6-13% of the general population. Voice perception is thought to engage an internal forward model that generates predictions, preparing the auditory cortex for upcoming sensory feedback. Impaired processing of sensory feedback in vocalization seems to underlie the experience of AVH in psychosis, but whether this is the case in nonclinical voice hearers remains unclear. The current study used electroencephalography (EEG) to investigate whether and how hallucination predisposition (HP) modulates the internal forward model in response to self-initiated tones and self-voices. Participants varying in HP (based on the Launay-Slade Hallucination Scale) listened to self-generated and externally generated tones or self-voices. HP did not affect responses to self vs. externally generated tones. However, HP altered the processing of the self-generated voice: increased HP was associated with increased pre-stimulus alpha power and increased N1 response to the self-generated voice. HP did not affect the P2 response to voices. These findings confirm that both prediction and comparison of predicted and perceived feedback to a self-generated voice are altered in individuals with AVH predisposition. Specific alterations in the processing of self-generated vocalizations may establish a core feature of the psychosis continuum.The Authors gratefully acknowledge all the participants who collaborated in the study, and particularly Dr. Franziska Knolle for feedback on stimulus generation, Carla Barros for help with scripts for EEG time-frequency analysis, and Dr. Celia Moreira for her advice on mixed linear models. This work was supported by the Portuguese Science National Foundation (FCT; grant numbers PTDC/PSI-PCL/116626/2010, IF/00334/2012, PTDC/MHCPCN/0101/2014) awarded to APP

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype

<p>Abstract</p> <p>Background</p> <p>Osteoporosis is defined as the loss of bone mineral density that leads to bone fragility with aging. Population-based case-control studies have identified polymorphisms in many candidate genes that have been associated with bone mass maintenance or osteoporotic fracture. To investigate single nucleotide polymorphisms (SNPs) that are associated with osteoporosis, we examined the genetic variation among Koreans by analyzing 81 genes according to their function in bone formation and resorption during bone remodeling.</p> <p>Methods</p> <p>We resequenced all the exons, splice junctions and promoter regions of candidate osteoporosis genes using 24 unrelated Korean individuals. Using the common SNPs from our study and the HapMap database, a statistical analysis of deviation in heterozygosity depicted.</p> <p>Results</p> <p>We identified 942 variants, including 888 SNPs, 43 insertion/deletion polymorphisms, and 11 microsatellite markers. Of the SNPs, 557 (63%) had been previously identified and 331 (37%) were newly discovered in the Korean population. When compared SNPs in the Korean population with those in HapMap database, 1% (or less) of SNPs in the Japanese and Chinese subpopulations and 20% of those in Caucasian and African subpopulations were significantly differentiated from the Hardy-Weinberg expectations. In addition, an analysis of the genetic diversity showed that there were no significant differences among Korean, Han Chinese and Japanese populations, but African and Caucasian populations were significantly differentiated in selected genes. Nevertheless, in the detailed analysis of genetic properties, the LD and Haplotype block patterns among the five sub-populations were substantially different from one another.</p> <p>Conclusion</p> <p>Through the resequencing of 81 osteoporosis candidate genes, 118 unknown SNPs with a minor allele frequency (MAF) > 0.05 were discovered in the Korean population. In addition, using the common SNPs between our study and HapMap, an analysis of genetic diversity and deviation in heterozygosity was performed and the polymorphisms of the above genes among the five populations were substantially differentiated from one another. Further studies of osteoporosis could utilize the polymorphisms identified in our data since they may have important implications for the selection of highly informative SNPs for future association studies.</p

The Cultural Project : Formal Chronological Modelling of the Early and Middle Neolithic Sequence in Lower Alsace

Starting from questions about the nature of cultural diversity, this paper examines the pace and tempo of change and the relative importance of continuity and discontinuity. To unravel the cultural project of the past, we apply chronological modelling of radiocarbon dates within a Bayesian statistical framework, to interrogate the Neolithic cultural sequence in Lower Alsace, in the upper Rhine valley, in broad terms from the later sixth to the end of the fifth millennium cal BC. Detailed formal estimates are provided for the long succession of cultural groups, from the early Neolithic Linear Pottery culture (LBK) to the Bischheim Occidental du Rhin Supérieur (BORS) groups at the end of the Middle Neolithic, using seriation and typology of pottery as the starting point in modelling. The rate of ceramic change, as well as frequent shifts in the nature, location and density of settlements, are documented in detail, down to lifetime and generational timescales. This reveals a Neolithic world in Lower Alsace busy with comings and goings, tinkerings and adjustments, and relocations and realignments. A significant hiatus is identified between the end of the LBK and the start of the Hinkelstein group, in the early part of the fifth millennium cal BC. On the basis of modelling of existing dates for other parts of the Rhineland, this appears to be a wider phenomenon, and possible explanations are discussed; full reoccupation of the landscape is only seen in the Grossgartach phase. Radical shifts are also proposed at the end of the Middle Neolithic

The Spectacle of Crime, Digitized

International audienceOne of the most significant features of the television series CSI: Crime Scene Investigationis its central preoccupation – forensic evidence – and the profession practised by its major characters – forensic science. Scientific inscriptions consistently allow the crime scene investigators (CSIs) to determine 'evidence' and 'truths' that otherwise elude them. At the same time, the dazzling digital effects used to punctuate key moments in each episode inevitably reference scientific technologies and the knowledge about reality that these promise. The success of the CSIs in every episode is premised upon knowledge guaranteed by scientific inscriptions and is itself an inscription of ways of seeing human bodies and the social body, represented by police scientists working to ensure public safety – a healthy social body. And it is also about how bodies, individual and social, are constituted as information, made knowable and validated by scientific instruments and procedures used to produce evidence

Antiplatelet therapy with aspirin, clopidogrel, and dipyridamole versus clopidogrel alone or aspirin and dipyridamole in patients with acute cerebral ischaemia (TARDIS): a randomised, open-label, phase 3 superiority trial

Background: Intensive antiplatelet therapy with three agents might be more effective than guideline treatment for preventing recurrent events in patients with acute cerebral ischaemia. We aimed to compare the safety and efficacy of intensive antiplatelet therapy (combined aspirin, clopidogrel, and dipyridamole) with that of guideline-based antiplatelet therapy. Methods: We did an international, prospective, randomised, open-label, blinded-endpoint trial in adult participants with ischaemic stroke or transient ischaemic attack (TIA) within 48 h of onset. Participants were assigned in a 1:1 ratio using computer randomisation to receive loading doses and then 30 days of intensive antiplatelet therapy (combined aspirin 75 mg, clopidogrel 75 mg, and dipyridamole 200 mg twice daily) or guideline-based therapy (comprising either clopidogrel alone or combined aspirin and dipyridamole). Randomisation was stratified by country and index event, and minimised with prognostic baseline factors, medication use, time to randomisation, stroke-related factors, and thrombolysis. The ordinal primary outcome was the combined incidence and severity of any recurrent stroke (ischaemic or haemorrhagic; assessed using the modified Rankin Scale) or TIA within 90 days, as assessed by central telephone follow-up with masking to treatment assignment, and analysed by intention to treat. This trial is registered with the ISRCTN registry, number ISRCTN47823388. Findings: 3096 participants (1556 in the intensive antiplatelet therapy group, 1540 in the guideline antiplatelet therapy group) were recruited from 106 hospitals in four countries between April 7, 2009, and March 18, 2016. The trial was stopped early on the recommendation of the data monitoring committee. The incidence and severity of recurrent stroke or TIA did not differ between intensive and guideline therapy (93 [6%] participants vs 105 [7%]; adjusted common odds ratio [cOR] 0·90, 95% CI 0·67–1·20, p=0·47). By contrast, intensive antiplatelet therapy was associated with more, and more severe, bleeding (adjusted cOR 2·54, 95% CI 2·05–3·16, p<0·0001). Interpretation: Among patients with recent cerebral ischaemia, intensive antiplatelet therapy did not reduce the incidence and severity of recurrent stroke or TIA, but did significantly increase the risk of major bleeding. Triple antiplatelet therapy should not be used in routine clinical practice

iDAH Research Software Engineering (RSE) Steering Group working paper

This is the final version. Available from the iDAH Research Software Engineering (RSE) Steering Group via the DOI in this record. Our purpose was to convene a broad and representative group from the UK Research Software Engineering (RSE) community to discuss opportunities for and barriers to the development of Arts & Humanities (AH) RSE capability, with a specific focus on contributing to the AHRC Infrastructure for Digital Innovation and Curation in Arts and Humanities (iDAH) project and a wider remit to consider longer term strategic priorities and opportunities for alignment with UKRI and EU initiatives. The discussion was intended to be foundational, inclusive, and broad-ranging, involving a wide stakeholder group encouraged to engage in ‘blue-sky’ thinking over short, medium, and long-term time horizons. The analysis contained in this working paper should be read in that context, as a reflection of early stage discussions intended to provide a platform for future more focused activity. Additional discussion and analysis is needed to produce substantive actionable conclusions

Shear behavior of DFDP-1 borehole samples from the Alpine Fault, New Zealand, under a wide range of experimental conditions

The Alpine Fault is a major plate-boundary fault zone that poses a major seismic hazard in southern New Zealand. The initial stage of the Deep Fault Drilling Project has provided sample material from the major lithological constituents of the Alpine Fault from two pilot boreholes. We use laboratory shearing experiments to show that the friction coefficient µ of fault-related rocks and their precursors varies between 0.38 and 0.80 depending on the lithology, presence of pore fluid, effective normal stress, and temperature. Under conditions appropriate for several kilometers depth on the Alpine Fault (100 MPa, 160 °C, fluid-saturated), a gouge sample located very near to the principal slip zone exhibits µ = 0.67, which is high compared with other major fault zones targeted by scientific drilling, and suggests the capacity for large shear stresses at depth. A consistent observation is that every major lithological unit tested exhibits positive and negative values of friction velocity dependence. Critical nucleation patch lengths estimated using representative values of the friction velocity-dependent parameter a−b and the critical slip distance D c , combined with previously documented elastic properties of the wall rock, may be as low as ~3 m. This small value, consistent with a seismic moment M o = ~4 × 1010 for an M w = ~1 earthquake, suggests that events of this size or larger are expected to occur as ordinary earthquakes and that slow or transient slip events are unlikely in the approximate depth range of 3–7 km