New specimens of the basal ornithischian dinosaur Lesothosaurus diagnosticus Galton, 1978 from the Early Jurassic of South Africa

We describe new specimens of the basal ornithischian dinosaur Lesothosaurus diagnosticus Galton, 1978 collected from a bonebed in the Fouriesburg district of the Free State, South Africa. The material was collected from the upper Elliot Formation (Early Jurassic) and represents the remains of at least three individuals. These individuals are larger in body size than those already known in museum collections and offer additional information on cranial ontogeny in the taxon. Moreover, they are similar in size to the sympatric taxon Stormbergia dangershoeki. The discovery of three individuals at this locality might imply group-living behaviour in this early ornithischian.Palaeontologia africana 2016. ©2016 Paul M. Barrett, Richard J. Butler, Adam M. Yates, Matthew G. Baron&Jonah N. Choiniere. This is an open-access article published under the Creative Commons Attribution 4.0 Unported License (CC BY4.0). To view a copy of the license, please visit http://creativecommons.org/licenses/by/4.0/. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This item is permanently archived at: http://wiredspace.wits.ac.za/handle/10539/19886. The attached file is the published version of the article

Suspension and flow dynamics of the Allegro™ stirred tank reactor

Microcarrier suspension performance and ensemble-averaged flow fields at the just-suspended condition are studied in a scale-down mimic of the Allegro STR single-use bioreactor range (abbreviated A-STR) and compared to an equivalent standard cylindrical configuration (abbreviated S-STR). Four commercial microcarriers were assessed to determine the required impeller agitation rate and corresponding power input per unit volume to achieve suspension – Cytodex™ 1, Cytodex™ 3, Cytopore™ 1, and Hillex® II microcarriers. The A-STR operating in down-pumping mode (DP) achieved homogenous microcarrier suspension at considerably lower power input when compared to the other baffled configurations. For the A-STR (DP), the power input per unit volume demand was 67.8 % lower than the A-STR in up-pumping mode (UP), 77% lower than the S-STR (DP) and 66.8 % lower than the S-STR (UP). Flow structures investigated at the just-suspended condition, in the transitional regime, were in line with those previously presented in the turbulent regime at considerably higher Reynolds number. This indicates that the normalised flow structures presented in this work are representative of those in the commercial Allegro STR range, despite operating at significantly reduced scale and Reynolds number. Removal of baffles resulted in substantially reduced power input required to achieve homogenous suspension in all configurations – other than the A-STR (DP), which exhibited relatively similar performance to the corresponding baffled configuration. Considering adherent cell sensitivity and mixing implications, and based on the results found in this work, the baffled A-STR (DP) is recommended for achieving microcarrier suspension at the lowest specific power input

Contraceptive use, prevalence and predictors of pregnancy planning among female sex workers in Uganda: a cross sectional study

BACKGROUND: Unintended pregnancies are associated with negative consequences to both mother and baby. Female Sex Workers (FSWs) are at high risk of unintended/unplanned pregnancies. However, prevalence of pregnancy planning and its predictors among FSWs has not been comprehensively investigated. This study was designed to determine contraceptive use, the prevalence, and predictors of pregnancy planning among FSWs in Uganda. METHODS: In this cross-sectional study, 819 FSWs attending most at risk populations initiative (MARPI) clinics were recruited using systematic sampling and interviewed with a pretested questionnaire that included collection of data on pregnancy intention using the London Measure of Unplanned Pregnancy (LMUP). Data were analysed using STATA version 14.0. Multinomial logistic regression model was used to identify predictors of pregnancy planning, RESULTS: Of the 819 study participants, only 90 (11.0%) had planned pregnancies. Overall, 462 (56.4%) were hazardous alcohol users and 335 (40.9%) abused drugs; 172 (21.0%) had been raped in the last 2 years and 70 (40.7%) of these accessed emergency contraception post-rape. Dual contraception use (condom and other modern method) was 58.0%. Having a non-emotional partner as a man who impregnated the FSW compared to emotional partner was significantly associated with less planned relative to unplanned pregnancy, (aRR = 0.15 95%Cl =0.08, 0.30), so was lack of reported social support compared to support from friends, (aRR = 0.44; 95% CI = 0.22-0.87), keeping all factors constant in the model. Being raped (aRR = 0.51; 95% CI = 0.31-0.84) or abuse of substances (aRR = 0.65; 95% CI = 0.45-0.93) were significantly associated with lower ambivalence relative to unplanned pregnancy but not with planned relative to unplanned pregnancy. CONCLUSION: Compared to women in the general population, pregnancy planning was low among FSWs amidst modest use of dual contraceptive. There is an urgent need to promote dual contraception among FSWs to prevent unplanned pregnancies especially with non-emotional partners, drug users, and post-rape

Movement profiles of soccer substitutes

Modifying a soccer substitute’s pre-pitch-entry activities may represent an opportunity to maximise physical performance and minimise injury-risk following match-introduction. Using a professional team that has previously participated in substitute profiling research, this follow-up case study investigated the effects of a modified match-day protocol that included substitutes; 1) performing a new pre-match warm-up alongside members of the starting team (as opposed to a separate substitute-only warm-up), 2) participating in a staffled half-time rewarm-up (as opposed to player-led half-time activities), and 3) receiving ongoing education focusing on the efficacy of (re)warm-up activities. English Championship substitutes (n = 15) were monitored using Micro-electromechanical Systems during 13 matches incorporating the modified practices (35 observations). On an individual player basis, data were organised into bouts of warm-up activity (pre-pitch-entry) and five min epochs of match-play (post-pitch-entry). Linear mixed modelling assessed the influence of ‘bout’ and ‘epoch’, position, and scoreline. Substitutes performed 3±1 rewarm-up bouts�- player-1�match-1 between kick-off and pitch-entry, which were shorter (-17.2 to -27.1 min) and elicited less distance (-696 to -1257 m) than the pre-match warm-up (p�0.001). Compared with previous data, heightened absolute movement responses were observed during the pre-match and staff-led half-time (re)warm-ups, alongside greater relative distances covered during player-led activities performed between kick-off and pitch-entry. Whilst less distance (-10%) was covered during the second versus first five min period following matchintroduction, values remained higher than previously reported. Between pitch-entry and the end of the match, the scoreline improved and worsened following 26% and 11% of substitutions, respectively; a favourable record compared with existing observations. Acknowledging the likely contribution from external factors, this case study reports heightened movement profiles and improved match scorelines when pre-pitch-entry practices were modified. Practitioners should note the potential influence of match-day activities on the physical responses of soccer substitutes and, if deemed necessary, consider adapting their pre-pitch-entry routines accordingly

Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip

Genome-wide association studies are revolutionizing the search for the genes underlying human complex diseases. The main decisions to be made at the design stage of these studies are the choice of the commercial genotyping chip to be used and the numbers of case and control samples to be genotyped. The most common method of comparing different chips is using a measure of coverage, but this fails to properly account for the effects of sample size, the genetic model of the disease, and linkage disequilibrium between SNPs. In this paper, we argue that the statistical power to detect a causative variant should be the major criterion in study design. Because of the complicated pattern of linkage disequilibrium (LD) in the human genome, power cannot be calculated analytically and must instead be assessed by simulation. We describe in detail a method of simulating case-control samples at a set of linked SNPs that replicates the patterns of LD in human populations, and we used it to assess power for a comprehensive set of available genotyping chips. Our results allow us to compare the performance of the chips to detect variants with different effect sizes and allele frequencies, look at how power changes with sample size in different populations or when using multi-marker tags and genotype imputation approaches, and how performance compares to a hypothetical chip that contains every SNP in HapMap. A main conclusion of this study is that marked differences in genome coverage may not translate into appreciable differences in power and that, when taking budgetary considerations into account, the most powerful design may not always correspond to the chip with the highest coverage. We also show that genotype imputation can be used to boost the power of many chips up to the level obtained from a hypothetical “complete” chip containing all the SNPs in HapMap. Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated

Late Triassic dinosaur tracks from Penarth, south Wales

Evidence of Late Triassic large tetrapods from the UK is rare. Here, we describe a track-bearing surface located on the shoreline near Penarth, south Wales, United Kingdom. The total exposed surface is c. 50 m long and c. 2 m wide, and is split into northern and southern sections by a small fault. We interpret these impressions as tracks, rather than abiogenic sedimentary structures, because of the possession of marked displacement rims and their relationship to each other with regularly spaced impressions forming putative trackways. The impressions are large (up to c. 50 cm in length), but poorly preserved, and retain little information about track-maker anatomy. We discuss alternative, plausible, abiotic mechanisms that might have been responsible for the formation of these features, but reject them in favour of these impressions being tetrapod tracks. We propose that the site is an additional occurrence of the ichnotaxon Eosauropus, representing a sauropodomorph trackmaker, thereby adding a useful new datum to their sparse Late Triassic record in the UK. We also used historical photogrammetry to digitally map the extent of site erosion during 2009–2020. More than 1 m of the surface exposure has been lost over this 11-year period, and the few tracks present in both models show significant smoothing, breakage and loss of detail. These tracks are an important datapoint for Late Triassic palaeontology in the UK, even if they cannot be confidently assigned to a specific trackmaker. The documented loss of the bedding surface highlights the transient and vulnerable nature of our fossil resources, particularly in coastal settings, and the need to gather data as quickly and effectively as possible

Osteological and Soft-Tissue Evidence for Pneumatization in the Cervical Column of the Ostrich (Struthio camelus) and Observations on the Vertebral Columns of Non-Volant, Semi-Volant and Semi-Aquatic Birds

© 2015 Apostolaki et al. This is an open access article distributed under the terms of the Creative Commons Attribution License [4.0], which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing

<p>Abstract</p> <p>Background</p> <p>The use of haplotype-based association tests can improve the power of genome-wide association studies. Since the observed genotypes are unordered pairs of alleles, haplotype phase must be inferred. However, estimating haplotype phase is time consuming. When millions of single-nucleotide polymorphisms (SNPs) are analyzed in genome-wide association study, faster methods for haplotype estimation are required.</p> <p>Methods</p> <p>We developed a program package for parallel computation of haplotype estimation. Our program package, ParaHaplo 2.0, is intended for use in workstation clusters using the Intel Message Passing Interface (MPI). We compared the performance of our algorithm to that of the regular permutation test on both Japanese in Tokyo, Japan and Han Chinese in Beijing, China of the HapMap dataset.</p> <p>Results</p> <p>Parallel version of ParaHaplo 2.0 can estimate haplotypes 100 times faster than a non-parallel version of the ParaHaplo.</p> <p>Conclusion</p> <p>ParaHaplo 2.0 is an invaluable tool for conducting haplotype-based genome-wide association studies (GWAS). The need for fast haplotype estimation using parallel computing will become increasingly important as the data sizes of such projects continue to increase. The executable binaries and program sources of ParaHaplo are available at the following address: <url>http://en.sourceforge.jp/projects/parallelgwas/releases/</url></p