Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6

Background <br/> The archaeology of North Africa remains enigmatic, with questions of population continuity versus discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as between the late Pleistocene and Holocene. <br/> Results Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of 39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for purifying selection and one with an internal calibration based on four approximate archaeological dates: the settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East. <br/> Conclusions <br/> A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around 20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this demographic event was to the west of North Africa. A comparison with U6's European sister clade, U5, revealed a stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the late Neolithic on the local population size of the southern Mediterranean coast

Excited Baryons from the FLIC Fermion Action

Masses of positive and negative parity excited nucleons and hyperons are calculated in quenched lattice QCD using an O(a^2) improved gluon action and a fat-link clover fermion action in which only the irrelevant operators are constructed with fat links. The results are in agreement with earlier N* simulations with improved actions, and exhibit a clear mass splitting between the nucleon and its parity partner, as well as a small mass splitting between the two low-lying J^P={1/2}^- N* states. Study of different Lambda interpolating fields suggests a similar splitting between the lowest two {1/2}^- Lambda* states, although the empirical mass suppression of the Lambda*(1405) is not seen.Comment: 3 pages, 3 figures, Lattice2002(QCD Spectrum and Quark Masses

Baryon resonances from a novel fat-link fermion action

We present first results for masses of positive and negative parity excited baryons in lattice QCD using an O(a^2) improved gluon action and a Fat Link Irrelevant Clover (FLIC) fermion action in which only the irrelevant operators are constructed with fat links. The results are in agreement with earlier calculations of N^* resonances using improved actions and exhibit a clear mass splitting between the nucleon and its chiral partner, even for the Wilson fermion action. The results also indicate a splitting between the lowest J^P = 1/2^- states for the two standard nucleon interpolating fields.Comment: 5 pages, 3 figures, talk given by W.Melnitchouk at LHP 2001 workshop, Cairns, Australi

Invasive Allele Spread under Preemptive Competition

We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.Comment: Computer Simulation Studies in Condensed Matter Physics XVIII, edited by D.P. Landau, S.P. Lewis, and H.-B. Schuttler, (Springer, Heidelberg, Berlin, in press

Roper Resonance and S_{11}(1535) from Lattice QCD

Using the constrained curve fitting method and overlap fermions with the lowest pion mass at $180 {\rm MeV}$, we observe that the masses of the first positive and negative parity excited states of the nucleon tend to cross over as the quark masses are taken to the chiral limit. Both results at the physical pion mass agree with the experimental values of the Roper resonance ($N^{1/2+}(1440)$) and $S_{11}$ ($N^{1/2-}(1535)$). This is seen for the first time in a lattice QCD calculation. These results are obtained on a quenched Iwasaki $16^3 \times 28$ lattice with $a = 0.2 {\rm fm}$. We also extract the ghost $\eta' N$ states (a quenched artifact) which are shown to decouple from the nucleon interpolation field above $m_{\pi} \sim 300 {\rm MeV}$. From the quark mass dependence of these states in the chiral region, we conclude that spontaneously broken chiral symmetry dictates the dynamics of light quarks in the nucleon.Comment: 10 pages, 5 figures, revised version to appear in PL

Spin-3/2 baryons in lattice QCD

Copyright © 2003. Elsevier. Printed in U.S.A. Submitted to Cornell University’s online archive www.arXiv.org in 2003 by James Zanotti. Post-print sourced from www.arxiv.org.We present first results for masses of spin-3/2 baryons in lattice QCD, using a novel fat-link clover fermion action in which only the irrelevant operators are constructed using fat links. In the isospin-1/2 sector, we observe, after appropriate spin and parity projection, a strong signal for the J^P=3/2^- state, and find good agreement between the 1/2^+ mass and earlier nucleon mass simulations with a spin-1/2 interpolating field. For the isospin-3/2 Delta states, clear mass splittings are observed between the various 1/2^+/- and 3/2^+/- channels, with the calculated level orderings in good agreement with those observed empirically.J.M. Zanotti, S. Choe, D.B. Leinweber, W. Melnitchouk, A.G. Williams, and J.B. Zhanghttp://www.elsevier.com/wps/find/journaldescription.cws_home/505717/description#descriptio

A Fragmented Parallel Stream: The Bass Lines of Eddie Gomez in the Bill Evans Trio

Eddie Gomez was the bassist in the Bill Evans Trio for eleven years. His contribution to the group’s sound was considerable, but while there has been some recognition of his virtuoso solos in the trio there has been little academic interest in his bass lines. This essay examines bass lines from the album Since We Met, recorded in 1974 by Evans, Gomez and drummer Marty Morell. Analysis of the bass accompaniments to the piano solos on “Since We Met” and “Time Remembered” reveals that they form a fragmented two-feel. A traditional two-feel employs two notes to emphasise the first and third beats in bar of 4/4 time. In Gomez’s bass lines these two notes are frequently replaced with short rhythmic motifs. These motifs occur in a variety of forms and at different metric displacements that alternately propel and retard the forward motion of the music. Additionally, Gomez uses a wide range of register and varied articulations to create a richly diverse bass line. The resulting effect has often been interpreted as interactive or conversational with the soloist. However there is very little interaction between the bass line and Evans’ solo. The bass line is a parallel stream to the solo that energises and colours the music

Women, men and coronary heart disease: a review of the qualitative literature

Aim. This paper presents a review of the qualitative literature which examines the experiences of patients with coronary heart disease. The paper also assesses whether the experiences of both female and male patients are reflected in the literature and summarizes key themes. Background. Understanding patients' experiences of their illness is important for coronary heart disease prevention and education. Qualitative methods are particularly suited to eliciting patients' detailed understandings and perceptions of illness. As much previous research has been 'gender neutral', this review pays particular attention to gender. Methods. Published papers from 60 qualitative studies were identified for the review through searches in MEDLINE, EMBASE, CINAHL, PREMEDLINE, PsychINFO, Social Sciences Citation Index and Web of Science using keywords related to coronary heart disease. Findings. Early qualitative studies of patients with coronary heart disease were conducted almost exclusively with men, and tended to generalize from 'male' experience to 'human' experience. By the late 1990s this pattern had changed, with the majority of studies including women and many being conducted with solely female samples. However, many studies that include both male and female coronary heart disease patients still do not have a specific gender focus. Key themes in the literature include interpreting symptoms and seeking help, belief about coronary 'candidates' and relationships with health professionals. The influence of social roles is important: many female patients have difficulties reconciling family responsibilities and medical advice, while male patients worry about being absent from work. Conclusions. There is a need for studies that compare the experiences of men and women. There is also an urgent need for work that takes masculinity and gender roles into account when exploring the experiences of men with coronary heart disease

Sex-biased expression of the TLR7 gene in severe COVID-19 patients: Insights from transcriptomics and epigenomics

This study received support from Instituto de Salud Carlos III (ISCIII): GePEM (PI16/01478/Cofinanciado FEDER; A.S.), DIAVIR (DTS19/00049/Cofinanciado FEDER, A.S.), Resvi-Omics (PI19/01039/Cofinanciado FEDER, A.S.), Agencia Gallega de Innovación (GAIN): Grupos con Potential de Crecimiento (IN607B 2020/08, A.S.); Agencia Gallega para la Gestión del Conocimiento en Salud (ACIS): BI-BACVIR (PRIS-3, A.S.), and CovidPhy (SA 304C, A.S.); ReSVinext (PI16/01569/Cofinanciado FEDER, F.M.T.), Enterogen (PI19/01090/Cofinanciado FEDER, F.M.T.) and consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CB21/06/00103; F.M.T.); GEN-COVID (IN845D 2020/23, F.M-T.) and Grupos de Referencia Competitiva (IIN607A2021/05, F.M-T). The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publicationThere is abundant epidemiological data indicating that the incidence of severe cases of coronavirus disease (COVID-19) is significantly higher in males than females worldwide. Moreover, genetic variation at the X-chromosome linked TLR7 gene has been associated with COVID-19 severity. It has been suggested that the sex-biased incidence of COVID-19 might be related to the fact that TLR7 escapes X-chromosome inactivation during early embryogenesis in females, thus encoding a doble dose of its gene product compared to males. We analyzed TLR7 expression in two acute phase cohorts of COVID-19 patients that used two different technological platforms, one of them in a multi-tissue context including saliva, nasal, and blood samples, and a third cohort that included different post-infection timepoints of long-COVID-19 patients. We additionally explored methylation patterns of TLR7 using epigenomic data from an independent cohort of COVID-19 patients stratified by severity and sex. In line with genome-wide association studies, we provide supportive evidence indicating that TLR7 has altered CpG methylation patterns and it is consistently downregulated in males compared to females in the most severe cases of COVID-19S

Impact of Salmonid alphavirus infection in diploid and triploid Atlantic salmon (Salmo salar L.) fry

With increasing interest in the use of triploid salmon in commercial aquaculture, gaining an understanding of how economically important pathogens affect triploid stocks is important. To compare the susceptibility of diploid and triploid Atlantic salmon (Salmo salar L.) to viral pathogens, fry were experimentally infected with Salmonid alphavirus sub-type 1 (SAV1), the aetiological agent of pancreas disease (PD) affecting Atlantic salmon aquaculture in Europe. Three groups of fry were exposed to the virus via different routes of infection: intraperitoneal injection (IP), bath immersion, or cohabitation (co-hab) and untreated fry were used as a control group. Mortalities commenced in the co-hab challenged diploid and triploid fish from 11 days post infection (dpi), and the experiment was terminated at 17 dpi. Both diploid and triploid IP challenged groups had similar levels of cumulative mortality at the end of the experimental period (41.1 % and 38.9 % respectively), and these were significantly higher (p < 0.01) than for the other challenge routes. A TaqMan-based quantitative PCR was used to assess SAV load in the heart, a main target organ of the virus, and also liver, which does not normally display any pathological changes during clinical infections, but exhibited severe degenerative lesions in the present study. The median viral RNA copy number was higher in diploid fish compared to triploid fish in both the heart and the liver of all three challenged groups. However, a significant statistical difference (p < 0.05) was only apparent in the liver of the co-hab groups. Diploid fry also displayed significantly higher levels of pancreatic and myocardial degeneration than triploids. This study showed that both diploid and triploid fry are susceptible to experimental SAV1 infection. The lower virus load seen in the triploids compared to the diploids may possibly be related to differences in cell metabolism between the two groups, however, further investigation is necessary to confirm this and also to assess the outcome of PD outbreaks in other developmental stages of the fish when maintained in commercial production systems