The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Very Cold Gas and Dark Matter

We have recently proposed a new candidate for baryonic dark matter: very cold molecular gas, in near-isothermal equilibrium with the cosmic background radiation at 2.73 K. The cold gas, of quasi-primordial abundances, is condensed in a fractal structure, resembling the hierarchical structure of the detected interstellar medium. We present some perspectives of detecting this very cold gas, either directly or indirectly. The H$_2$ molecule has an "ultrafine" structure, due to the interaction between the rotation-induced magnetic moment and the nuclear spins. But the lines fall in the km domain, and are very weak. The best opportunity might be the UV absorption of H$_2$ in front of quasars. The unexpected cold dust component, revealed by the COBE/FIRAS submillimetric results, could also be due to this very cold H$_2$ gas, through collision-induced radiation, or solid H$_2$ grains or snowflakes. The $\gamma$-ray distribution, much more radially extended than the supernovae at the origin of cosmic rays acceleration, also points towards and extended gas distribution.Comment: 16 pages, Latex pages, crckapb macro, 3 postscript figures, uuencoded compressed tar file. To be published in the proceeedings of the "Dust-Morphology" conference, Johannesburg, 22-26 January, 1996, D. Block (ed.), (Kluwer Dordrecht

Research interrupted: The impact of the COVID-19 pandemic on multiple sclerosis research in the field of rehabilitation and quality of life

Background The COVID-19 pandemic has likely had a negative impact on rehabilitation and quality of life (QoL) research in multiple sclerosis (MS). Method We explored perceived barriers to research among 87 researchers, representing 18 countries, both prior to and since COVID-19. Results A Wilcoxon signed-rank test found that significantly more researchers reported experiencing barriers to research since the onset of the pandemic compared to pre-COVID-19 (p &lt; .001), with 78% of respondents reporting at least some barriers since COVID-19. The most commonly-cited barriers related to participant access (n = 38) and interruptions/delays to projects (n = 19). Although no gender differences were found in the number of barriers reported, female respondents were more likely to cite time or competing demands as barriers to research. Females were also more likely to perceive being negatively impacted by the pandemic compared to other genders (p = .007). Conclusions Implications for the future landscape of rehabilitation research in MS are discussed. </jats:sec

Constraints on perception of information from obstacles during foot clearance in people with chronic stroke

The aim of this study was to examine effects of different types of task constraints on coupling of perception and action in people with chronic stroke when crossing obstacles during a walking task. Ten participants with hemiplegic chronic stroke volunteered to walk over a static obstacle under two distinct task constraints: simple and dual task. Under simple task constraints, without specific instructions, participants walked at their preferred speed and crossed over an obstacle. Under dual task constraints the same individuals were required to subtract numbers whilst walking. Under both distinct task constraints, we examined emergent values of foot distance when clearing a static obstacle in both affected and unaffected legs, measured by a 3D motion tracking system. Principal Component Analysis was used to quantify task performance and discriminant analysis was used to compare gait performance between task constraints. Results suggested that patients, regardless of affected body side, demonstrated differences in perception of distance information from the obstacle, which constrained gait differences in initial swing, mid-swing and crossing phases. Further, dual task constraints, rather than hemiplegic body side, was a significant discriminator in patients' perceptions of distance and height information to the obstacle. These findings suggested how performance of additional cognitive tasks might constrain perception of information from an obstacle in people with chronic stroke during different phases of obstacle crossing, and thus may impair their adaptive ability to successfully manoeuvre around objects

Probabilistic Daily ILI Syndromic Surveillance with a Spatio-Temporal Bayesian Hierarchical Model

BACKGROUND: For daily syndromic surveillance to be effective, an efficient and sensible algorithm would be expected to detect aberrations in influenza illness, and alert public health workers prior to any impending epidemic. This detection or alert surely contains uncertainty, and thus should be evaluated with a proper probabilistic measure. However, traditional monitoring mechanisms simply provide a binary alert, failing to adequately address this uncertainty. METHODS AND FINDINGS: Based on the Bayesian posterior probability of influenza-like illness (ILI) visits, the intensity of outbreak can be directly assessed. The numbers of daily emergency room ILI visits at five community hospitals in Taipei City during 2006-2007 were collected and fitted with a Bayesian hierarchical model containing meteorological factors such as temperature and vapor pressure, spatial interaction with conditional autoregressive structure, weekend and holiday effects, seasonality factors, and previous ILI visits. The proposed algorithm recommends an alert for action if the posterior probability is larger than 70%. External data from January to February of 2008 were retained for validation. The decision rule detects successfully the peak in the validation period. When comparing the posterior probability evaluation with the modified Cusum method, results show that the proposed method is able to detect the signals 1-2 days prior to the rise of ILI visits. CONCLUSIONS: This Bayesian hierarchical model not only constitutes a dynamic surveillance system but also constructs a stochastic evaluation of the need to call for alert. The monitoring mechanism provides earlier detection as well as a complementary tool for current surveillance programs

The Impact of Voluntary Counselling and Testing Services on Sexual Behaviour Change and HIV Incidence: Observations from a Cohort Study in Rural Tanzania.

It is widely assumed that voluntary counselling and testing (VCT) services contribute to HIV prevention by motivating clients to reduce sexual risk-taking. However, findings from sub-Saharan Africa have been mixed, particularly among HIV-negative persons. We explored associations between VCT use and changes in sexual risk behaviours and HIV incidence using data from a community HIV cohort study in northwest Tanzania. Data on VCT use, sexual behaviour and HIV status were available from three HIV serological surveillance rounds undertaken in 2003-4 (Sero4), 2006-7 (Sero5) and 2010 (Sero6). We used multinomial logistic regression to assess changes in sexual risk behaviours between rounds, and Poisson regression to estimate HIV incidence. The analyses included 3,613 participants attending Sero4 and Sero5 (3,474 HIV-negative and 139 HIV-positive at earlier round) and 2,998 attending Sero5 and Sero6 (2,858 HIV-negative and 140 HIV-positive at earlier round). Among HIV-negative individuals VCT use was associated with reductions in the number of sexual partners in the last year (aRR Seros 4-5: 1.42, 95% CI 1.07-1.88; aRR Seros 5-6: 1.68, 95% CI 1.25-2.26) and in the likelihood of having a non-cohabiting partner in the last year (aRR Seros 4-5: 1.57, 95% CI 1.10-2.25; aRR Seros 5-6: 1.48, 95% CI 1.07-2.04) or a high-risk partner in the last year (aRR Seros 5-6 1.57, 95% CI 1.06-2.31). However, VCT was also associated with stopping using condoms with non-cohabiting partners between Seros 4-5 (aRR 4.88, 95% CI 1.39-17.16). There were no statistically significant associations between VCT use and changes in HIV incidence, nor changes in sexual behaviour among HIV-positive individuals, possibly due to small sample sizes. We found moderate associations between VCT use and reductions in some sexual risk behaviours among HIV-negative participants, but no impacts among HIV-positive individuals in the context of low overall VCT uptake. Furthermore, there were no significant changes in HIV incidence associated with VCT use, although declining background incidence and small sample sizes may have prevented us from detecting this. The impact of VCT services will ultimately depend upon rates of uptake, with further research required to better understand processes of behaviour change following VCT use

Induced abortion, pregnancy loss and intimate partner violence in Tanzania: a population based study

BACKGROUND: Violence by an intimate partner is increasingly recognized as an important public and reproductive health issue. The aim of this study is to investigate the extent to which physical and/or sexual intimate partner violence is associated with induced abortion and pregnancy loss from other causes and to compare this with other, more commonly recognized explanatory factors. METHODS: This study analyzes the data of the Tanzania section of the WHO Multi-Country Study on Women's Health and Domestic Violence, a large population-based cross-sectional survey of women of reproductive age in Dar es Salaam and Mbeya, Tanzania, conducted from 2001 to 2002. All women who answered positively to at least one of the questions about specific acts of physical or sexual violence committed by a partner towards her at any point in her life were considered to have experienced intimate partner violence. Associations between self reported induced abortion and pregnancy loss with intimate partner violence were analysed using multiple regression models. RESULTS: Lifetime physical and/or sexual intimate partner violence was reported by 41% and 56% of ever partnered, ever pregnant women in Dar es Salaam and Mbeya respectively. Among the ever pregnant, ever partnered women, 23% experienced involuntary pregnancy loss, while 7% reported induced abortion. Even after adjusting for other explanatory factors, women who experienced intimate partner violence were 1.6 (95%CI: 1.06,1.60) times more likely to report an pregnancy loss and 1.9 (95%CI: 1.30,2.89) times more likely to report an induced abortion. Intimate partner violence had a stronger influence on induced abortion and pregnancy loss than women's age, socio-economic status, and number of live born children. CONCLUSIONS: Intimate partner violence is likely to be an important influence on levels of induced abortion and pregnancy loss in Tanzania. Preventing intimate partner violence may therefore be beneficial for maternal health and pregnancy outcomes

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201

A case study of new assessment and training of unilateral spatial neglect in stroke patients: effect of visual image transformation and visual stimulation by using a head mounted display system (HMD)

<p>Abstract</p> <p>Background</p> <p>Unilateral spatial neglect (USN) is most damaging to an older stroke patient who also has a lower performance in their activities of daily living or those elderly who are still working. The purpose of this study was to understand more accurately pathology of USN using a new HMD system.</p> <p>Methods</p> <p>Two stroke patients (Subject A and B) participated in this study after gaining their informed consent and they all had Left USN as determined by clinical tests. Assessments of USN were performed by using the common clinical test (the line cancellation test) and six special tests by using HMD system in the object-centered coordinates (OC) condition and the egocentric coordinates (EC) condition. OC condition focused the test sheet only by a CCD. EC condition was that CCD can always follow the subject's movement. Moreover, the study focused on the effect of the reduced image condition of real image and the arrows.</p> <p>Results</p> <p>In Patient A who performed the common test and special tests of OC and EC conditions, the results showed that for the line cancellation test under the common condition, both of the percentage of the correct answers at the right and left sides in the test sheet was 100 percent. However, in the OC condition, the percentage of the correct answers at the left side in the test sheet was 44 percent and the right side was 94 percent. In the EC condition, the left side was 61 percent and the right side was 67 percent. In Patient B, according to the result of the use of reduced image condition and the arrows condition by HMD system, these line cancellation scores more increased than the score of the common test.</p> <p>Conclusions</p> <p>The results showed that the assessment of USN using an HMD system may clarify the left neglect area which cannot be easily observed in the clinical evaluation for USN. HMD may be able to produce an artificially versatile environment as compared to the common clinical evaluation and treatment.</p