The vertebrate genome annotation (Vega) database

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome. In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega

Exploration of hyperfine interaction between constituent quarks via eta productions

In this work, the different exchange freedom, one gluon, one pion or Goldstone boson, in constituent quark model is investigated, which is responsible to the hyperfine interaction between constituent quarks, via the combined analysis of the eta production processes, $\pi^{-}p\rightarrow\eta n$ and $\gamma p\rightarrow\eta p$. With the Goldstone-boson exchange, as well as the one-gluon or one-pion exchange, both the spectrum and observables, such as, the differential cross section and polarized beam asymmetry, are fitted to the suggested values of Particle Data Group and the experimental data. The first two types of exchange freedoms give acceptable description of the spectrum and observables while the one pion exchange can not describe the observables and spectrum simultaneously, so can be excluded. The experimental data for the two processes considered here strongly support the mixing angles for two lowest S11 sates and D13 states as about -30 and 6 degree respectively.Comment: 7 pages, 4 figures, 4 table

Geographically touring the eastern bloc: British geography, travel cultures and the Cold War

This paper considers the role of travel in the generation of geographical knowledge of the eastern bloc by British geographers. Based on oral history and surveys of published work, the paper examines the roles of three kinds of travel experience: individual private travels, tours via state tourist agencies, and tours by academic delegations. Examples are drawn from across the eastern bloc, including the USSR, Poland, Romania, East Germany and Albania. The relationship between travel and publication is addressed, notably within textbooks, and in the Geographical Magazine. The study argues for the extension of accounts of cultures of geographical travel, and seeks to supplement the existing historiography of Cold War geography

A unitary model for meson-nucleon scattering

In an effective Lagrangian model employing the K-matrix approximation we extract nucleon resonance parameters. To this end we analyze simultaneously all available data for reactions involving the final states $\pi N$, $\pi\pi N$, $\eta N$ and $K \Lambda$ in the energy range $m_N + m_{\pi} \le \sqrt s \le 1.9$ GeV. The background contributions are generated consistently from the relevant Feynman amplitudes, thus significantly reducing the number of free parameters.Comment: Revised version. 60 pages, 17 figures. Two figures and a short discussion (\pi N \to \eta N, K \Lambda amplitudes) added, typos and minor errors in the citations correcte

NIST--Los Alamos racetrack microtron status

The NIST-Los Alamos Racetrack Microtron (RTM) is designed to deliver a low-emittance electron beam of up to 0.5 mA cw over an energy range of 17 MeV to 185 MeV. Fed by a 5 MeV injector, the RTM contains two 180/degree/ end magnets that recirculate the beam up to 15 times through a 12 MeV RF linac. The linac, which operates in a standing-wave mode at 2380 MHz, has been tested to nearly full RF power. At present, the injector has undergone beam tests, and the beam transport system is complete through the 12 MeV linac. A temporary beam line has been installed at the exit of one end magnet to measure the beam energy, energy spread, and emittance after one pass through the accelerator. Preliminary results indicate that the accelerated beam energy spread and emittance are within design goals. 4 refs., 7 figs

The Effect of Authigenic Clays on Fault Zone Permeability

From Wiley via Jisc Publications RouterHistory: received 2021-06-21, rev-recd 2021-09-27, accepted 2021-09-30, pub-print 2021-10, pub-electronic 2021-10-15Article version: VoRPublication status: PublishedFunder: Leverhulme Trust; Id: http://dx.doi.org/10.13039/501100000275; Grant(s): ECF‐2020‐560Funder: Natural Environment Research Council (NERC); Id: http://dx.doi.org/10.13039/501100000270; Grant(s): NE/N003063/1Abstract: Clays are understood to form the majority of fluid‐flow barriers in faulted reservoirs and numerous fault gouge and fault seal studies have quantified the volumes of smeared and abraded clays create fluid‐flow barriers along fault surfaces. However, clay‐related permeability adjacent to the fault surface, including in the fault damage zone, has largely been neglected. Previous studies have shown the morphology and distribution of unfaulted authigenic clays, and not just clay volume, exert a significant control on the magnitude of permeability. However, fault‐related studies have neither characterized deformed authigenic clays nor addressed their influence on fluid‐flow. In this study laboratory permeabilities of faulted, authigenic clay bearing sandstones sampled from the Otway basin (Australia) and the Orcadian basin (UK) present trends which; (a) do not correspond to expected patterns of fluid‐flow in faulted clay‐bearing sandstones and, (b) cannot be explained using published models of permeability related to changing clay volume. Microscopic analysis shows that faulting has disaggregated authigenic clays and, similarly to framework grain deformation, comminuted and sheared clay grains. However, instead of impeding fluid‐flow, analysis of pore networks (using mercury injection porosimetry) showed that faulting of authigenic clays has increased pore connectivity, contributing to increased magnitude of permeability and development of permeability anisotropy. Contrary to published results of faulting and fluid‐flow in impure sandstones, our results show that fault related processes involving the formation of clays in the fault zone can increase permeability and reduce the capillary threshold pressures of fault rocks relative to the unfaulted host rock

Replication of the association between variants in WFS1 and risk of type 2 diabetes in European populations

Aims/hypothesis: Mutations at the Wolframin encoding gene, WFS1, cause Wolfram syndrome, a rare neurological condition. Associations between single nucleotide polymorphisms (SNPs) at WFS1 and type 2 diabetes have recently been reported. In the present study, we sought to replicate those associations in a northern Swedish case-control study for type 2 diabetes. We also meta-analyzed published and previously unpublished data from Sweden, Finland and France to obtain updated summary effect estimates. Methods: Four WFS1 SNPs (rs10010131, rs6446482, rs752854, rs734312 [R611H]) were genotyped in a type 2 diabetes case-control study (N=1,296/1,412) of Swedish adults. Logistic regression was used to assess the association between each WFS1 SNP and type 2 diabetes, following adjustment for age, sex, and body mass index. We then performed a meta-analysis of 11 studies of type 2 diabetes, comprising up to 14,139 cases and 16,109 controls, to obtain a summary effect estimate for the WFS1 variants. Results: In the northern Swedish study, the minor allele at rs752854 was associated with reduced type 2 diabetes risk (OR=0.85; 95% CI=0.75-0.96; p=0.010). Borderline statistical associations were observed for the remaining SNPs. The meta-analysis of the four independent replication studies for SNP rs10010131, or its proxy variants, showed evidence for statistical association (OR=0.87; 95% CI=0.82-0.93; p=4.5×10−5). In an updated meta-analysis of all 11 studies, comprising 14,139 cases and 16,109 controls, strong evidence for statistical association was also observed (OR=0.89; 95% CI=0.86-0.92; p=4.9×10−11). Conclusion: In this study of WFS1 gene variants and type 2 diabetes risk, we have replicated the previously reported associations between SNPs at this locus and risk of type 2 diabetes

SARS-CoV-2 positivity in offspring and timing of mother-to-child transmission: living systematic review and meta-analysis

OBJECTIVES: To assess the rates of SARS-CoV-2 positivity in babies born to mothers with SARS-CoV-2 infection, the timing of mother-to-child transmission and perinatal outcomes, and factors associated with SARS-CoV-2 status in offspring. DESIGN: Living systematic review and meta-analysis. DATA SOURCES: Major databases between 1 December 2019 and 3 August 2021. STUDY SELECTION: Cohort studies of pregnant and recently pregnant women (including after abortion or miscarriage) who sought hospital care for any reason and had a diagnosis of SARS-CoV-2 infection, and also provided data on offspring SARS-CoV-2 status and risk factors for positivity. Case series and case reports were also included to assess the timing and likelihood of mother-to-child transmission in SARS-CoV-2 positive babies. DATA EXTRACTION: Two reviewers independently extracted data and assessed study quality. A random effects model was used to synthesise data for rates, with associations reported using odds ratios and 95% confidence intervals. Narrative syntheses were performed when meta-analysis was inappropriate. The World Health Organization classification was used to categorise the timing of mother-to-child transmission (in utero, intrapartum, early postnatal). RESULTS: 472 studies (206 cohort studies, 266 case series and case reports; 28 952 mothers, 18 237 babies) were included. Overall, 1.8% (95% confidence interval 1.2% to 2.5%; 140 studies) of the 14 271 babies born to mothers with SARS-CoV-2 infection tested positive for the virus with reverse transcriptase polymerase chain reaction (RT-PCR). Of the 592 SARS-CoV-2 positive babies with data on the timing of exposure and type and timing of tests, 14 had confirmed mother-to-child transmission: seven in utero (448 assessed), two intrapartum (18 assessed), and five during the early postnatal period (70 assessed). Of the 800 SARS-CoV-2 positive babies with outcome data, 20 were stillbirths, 23 were neonatal deaths, and eight were early pregnancy losses; 749 babies were alive at the end of follow-up. Severe maternal covid-19 (odds ratio 2.4, 95% confidence interval 1.3 to 4.4), maternal death (14.1, 4.1 to 48.0), maternal admission to an intensive care unit (3.5, 1.7 to 6.9), and maternal postnatal infection (5.0, 1.2 to 20.1) were associated with SARS-CoV-2 positivity in offspring. Positivity rates using RT-PCR varied between regions, ranging from 0.1% (95% confidence interval 0.0% to 0.3%) in studies from North America to 5.7% (3.2% to 8.7%) in studies from Latin America and the Caribbean. CONCLUSION: SARS-CoV-2 positivity rates were found to be low in babies born to mothers with SARS-CoV-2 infection. Evidence suggests confirmed vertical transmission of SARS-CoV-2, although this is likely to be rare. Severity of maternal covid-19 appears to be associated with SARS-CoV-2 positivity in offspring. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42020178076. READERS' NOTE: This article is a living systematic review that will be updated to reflect emerging evidence. Updates may occur for up to two years from the date of original publication

P-wave excited baryons from pion- and photo-induced hyperon production

We report evidence for $N(1710)P_{11}$, $N(1875)P_{11}$, $N(1900)P_{13}$, $\Delta(1600)P_{33}$, $\Delta(1910)P_{31}$, and $\Delta(1920)P_{33}$, and find indications that $N(1900)P_{13}$ might have a companion state at 1970\,MeV. The controversial $\Delta(1750)P_{31}$ is not seen. The evidence is derived from a study of data on pion- and photo-induced hyperon production, but other data are included as well. Most of the resonances reported here were found in the Karlsruhe-Helsinki (KH84) and the Carnegie-Mellon (CM) analyses but were challenged recently by the Data Analysis Center at GWU. Our analysis is constrained by the energy independent $\pi N$ scattering amplitudes from either KH84 or GWU. The two $\pi N$ amplitudes from KH84 or GWU, respectively, lead to slightly different $\pi N$ branching ratios of contributing resonances but the debated resonances are required in both series of fits.Comment: 22 pages, 28 figures. Some additional sets of data are adde

Spectroscopy of Kr 70 and isospin symmetry in the T=1 fpg shell nuclei SPECTROSCOPY of Kr 70 and ISOSPIN SYMMETRY ... D. M. DEBENHAM et al.

The recoil-β tagging technique has been used in conjunction with the Ca40(S32,2n) reaction at a beam energy of 88 MeV to identify transitions associated with the decay of the 2+ and, tentatively, 4+ states in the nucleus Kr70. These data are used, along with previously published data, to examine the triplet energy differences (TED) for the mass 70 isobars. The experimental TED values are compared with shell model calculations, performed with the JUN45 interaction in the fpg model space, that include a J=0 isospin nonconserving (INC) interaction with an isotensor strength of 100 keV. The agreement is found to be very good up to spin 4 and supports the expectation for analog states that all three nuclei have the same oblate shape at low-spin. The A=70 results are compared with the experimental and shell model predicted TED and mirror energy differences (MED) for the mass 66 and 74 systems. The comparisons clearly demonstrate the importance of the isotensor INC interaction in replicating the TED data in this region. Issues related to the observed MED values and their interpretation within the shell model are discussed