Clades and clans: a comparison study of two evolutionary models

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1<k<\kappa(n)$, and lower if $\kappa(n)<k<n$. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.Comment: 21page

DREAMS-START (Dementia RElAted Manual for Sleep; STrAtegies for RelaTives) for people with dementia and sleep disturbances: a single-blind feasibility and acceptability randomized controlled trial

BACKGROUND: 40% of people with dementia have disturbed sleep but there are currently no known effective treatments. Studies of sleep hygiene and light therapy have not been powered to indicate feasibility and acceptability and have shown 40-50% retention. We tested the feasibility and acceptability of a six-session manualized evidence-based non-pharmacological therapy; Dementia RElAted Manual for Sleep; STrAtegies for RelaTives (DREAMS-START) for sleep disturbance in people with dementia. / METHODS: We conducted a parallel, two-armed, single-blind randomized trial and randomized 2:1 to intervention: Treatment as Usual. Eligible participants had dementia and sleep disturbances (scoring ≥4 on one Sleep Disorders Inventory item) and a family carer and were recruited from two London memory services and Join Dementia Research. Participants wore an actiwatch for two weeks pre-randomization. Trained, clinically supervised psychology graduates delivered DREAMS-START to carers randomized to intervention; covering Understanding sleep and dementia; Making a plan (incorporating actiwatch information, light exposure using a light box); Daytime activity and routine; Difficult night-time behaviors; Taking care of your own (carer's) sleep; and What works? Strategies for the future. Carers kept their manual, light box, and relaxation recordings post-intervention. Outcome assessment was masked to allocation. The co-primary outcomes were feasibility (≥50% eligible people consenting to the study) and acceptability (≥75% of intervention group attending ≥4 intervention sessions). / RESULTS: In total, 63out of 95 (66%; 95% CI: 56-76%) eligible referrals consented between 04/08/2016 and 24/03/2017; 62 (65%; 95% CI: 55-75%) were randomized, and 37 out of 42 (88%; 95% CI: 75-96%) adhered to the intervention. / CONCLUSIONS: DREAM-START for sleep disorders in dementia is feasible and acceptable

The pseudogap: friend or foe of high Tc?

Although nineteen years have passed since the discovery of high temperature superconductivity, there is still no consensus on its physical origin. This is in large part because of a lack of understanding of the state of matter out of which the superconductivity arises. In optimally and underdoped materials, this state exhibits a pseudogap at temperatures large compared to the superconducting transition temperature. Although discovered only three years after the pioneering work of Bednorz and Muller, the physical origin of this pseudogap behavior and whether it constitutes a distinct phase of matter is still shrouded in mystery. In the summer of 2004, a band of physicists gathered for five weeks at the Aspen Center for Physics to discuss the pseudogap. In this perspective, we would like to summarize some of the results presented there and discuss its importance in the context of strongly correlated electron systems.Comment: expanded version, 20 pages, 11 figures, to be published, Advances in Physic

What are the living conditions and health status of those who don't report their migration status? a population-based study in Chile

BACKGROUND: Undocumented immigrants are likely to be missing from population databases, making it impossible to identify an accurate sampling frame in migration research. No population-based data has been collected in Chile regarding the living conditions and health status of undocumented immigrants. However, the CASEN survey (Caracterizacion Socio- Economica Nacional) asked about migration status in Chile for the first time in 2006 and provides an opportunity to set the base for future analysis of available migration data. We explored the living conditions and health of self-reported immigrants and respondents who preferred not to report their migration status in this survey. METHODS: Cross-sectional secondary analysis of CASEN survey in Chile in 2006. Outcomes: any disability, illness/accident, hospitalization/surgery, cancer/chronic condition (all binary variables); and the number of medical/emergency attentions received (count variables). Covariates: Demographics (age, sex, marital status, urban/rural, ethnicity), socioeconomic status (education level, employment status and household income), and material standard of living (overcrowding, sanitation, housing quality). Weighted regression models were estimated for each health outcome, crude and adjusted by sets of covariates, in STATA 10.0. RESULTS: About 1% of the total sample reported being immigrants and 0.7% preferred not to report their migration status (Migration Status - Missing Values; MS-MV). The MS-MV lived in more deprived conditions and reported a higher rate of health problems than immigrants. Some gender differences were observed by health status among immigrants and the MS-MV but they were not statistically significant. Regressions indicated that age, sex, SES and material factors consistently affected MS-MVs’ chance of presenting poor health and these patterns were different to those found among immigrants. Great heterogeneity in both the MS-MV and the immigrants, as indicated by wide confidence intervals, prevented the identification of other significantly associated covariates. CONCLUSION: This is the first study to look at the living conditions and health of those that preferred not to respond their migration status in Chile. Respondents that do not report their migration status are vulnerable to poor health and may represent undocumented immigrants. Surveys that fail to identify these people are likely to misrepresent the experiences of immigrants and further quantitative and qualitative research is urgently required

HIV Traffics through a Specialized, Surface-Accessible Intracellular Compartment during trans-Infection of T Cells by Mature Dendritic Cells

In vitro, dendritic cells (DCs) bind and transfer intact, infectious HIV to CD4 T cells without first becoming infected, a process known as trans-infection. trans-infection is accomplished by recruitment of HIV and its receptors to the site of DC–T cell contact and transfer of virions at a structure known as the infectious synapse. In this study, we used fluorescent microscopy to track individual HIV particles trafficking in DCs during virus uptake and trans-infection. Mature DCs rapidly concentrated HIV into an apparently intracellular compartment that lacked markers characteristic of early endosomes, lysosomes, or antigen-processing vesicles. Live cell microscopy demonstrated that the HIV-containing compartment was rapidly polarized toward the infectious synapse after contact with a T cell; however, the bulk of the concentrated virus remained in the DCs after T cell engagement. Individual virions were observed emerging from the compartment and fusing with the T cell membrane at the infectious synapse. The compartmentalized HIV, although engulfed by the cytoplasm, was fully accessible to HIV envelope-specific inhibitors and other membrane-impermeable probes that were delivered to the cell surface. These results demonstrate that HIV resides in an invaginated domain within DCs that is both contiguous with the plasma membrane and distinct from endocytic vesicles. We conclude that HIV virions are routed through this specialized compartment, which allows individual particles to be delivered to T cells during trans-infection

The impact of a minimal smoking cessation intervention for pregnant women and their partners on perinatal smoking behaviour in primary health care: A real-life controlled study

<p>Abstract</p> <p>Background</p> <p>There is a demand for strategies to promote smoking cessation in high-risk populations like smoking pregnant women and their partners. The objectives of this study were to investigate parental smoking behaviour during pregnancy after introduction of a prenatal, structured, multi-disciplinary smoking cessation programme in primary care, and to compare smoking behaviour among pregnant women in the city of Trondheim with Bergen and Norway.</p> <p>Methods</p> <p>Sequential birth cohorts were established to evaluate the intervention programme from September 2000 to December 2004 in primary care as a part of the Prevention of Allergy among Children in Trondheim study (PACT). The primary outcome variables were self reported smoking behaviour at inclusion and six weeks postnatal. Data from the Medical Birth Registry of Norway (MBR) were used to describe smoking cessation during pregnancy in Trondheim, Bergen and Norway 1999–2004.</p> <p>Results</p> <p>Maternal smoking prevalence at inclusion during pregnancy were 5% (CI 95% 4–6) in the intervention cohort compared to 7% (CI 95% 6–9), p = 0.03, in the control cohort. Of the pre-pregnancy maternal smokers 25% (CI 95% 20–31) and 32% (CI 95% 26–38), p = 0.17, were still smoking at inclusion in the intervention and control cohorts, respectively. Six weeks postnatal 72% (CI 95% 59–83) and 68% (CI 95% 57–77), p = 0.34 of the maternal smokers at inclusion still smoked. No significant difference in paternal smoking between the cohorts was found after the intervention period. Data from the MBR showed a significantly higher proportion of women who stopped smoking during pregnancy in Trondheim than in Bergen in 2003 and 2004, p = 0.03 and < 0.001, respectively.</p> <p>Conclusion</p> <p>No impact on parental smoking behaviour between the cohorts was observed after the smoking intervention programme. Of the women who stopped smoking during pregnancy most of them stopped smoking before the intervention. However, we observed a significantly higher quitting rate in Trondheim than in Bergen in 2003 and 2004 which may have been facilitated by the supplemental attention on smoking behaviour the PACT study initiated.</p

Impact of social ties on self reported health in France: Is everyone affected equally?

<p>Abstract</p> <p>Aim</p> <p>To examine the association of social ties and income with self reported health, in order to investigate if social ties have a greater impact on the health of people on low incomes compared to those financially better off.</p> <p>Methods</p> <p>A nationally representative cross-sectional study of 5205 French adults using data from questionnaires which asked about health, income and relationships with family and friends etc.</p> <p>Results</p> <p>Less than good self-rated health (SRH) is twice as frequently reported by people in the lowest income group than those in the highest income group. People with low incomes are also more likely to have felt alone on the previous day, received no phone call during the last week, have no friends, not be a member of a club, and to live alone. Socially isolated people report lower SRH. Likelihood ratio tests for interaction vs. main effect models were statistically significant for 2 of the measures of social ties, borderline for 2 others and non-significant for one. For 4 of the 5 indicators of social ties, larger odd ratios show that social isolation is more strongly associated with less than good SRH among people on low incomes compared to those with a higher income.</p> <p>Conclusion</p> <p>Social isolation is associated with 'less than good' self-rated health. This effect appears to be more important for people on a low income.</p

Genome Sequence Analysis of Dengue Virus 1 Isolated in Key West, Florida

Dengue virus (DENV) is transmitted to humans through the bite of mosquitoes. In November 2010, a dengue outbreak was reported in Monroe County in southern Florida (FL), including greater than 20 confirmed human cases. The virus collected from the human cases was verified as DENV serotype 1 (DENV-1) and one isolate was provided for sequence analysis. RNA was extracted from the DENV-1 isolate and was used in reverse transcription polymerase chain reaction (RT-PCR) to amplify PCR fragments to sequence. Nucleic acid primers were designed to generate overlapping PCR fragments that covered the entire genome. The DENV-1 isolate found in Key West (KW), FL was sequenced for whole genome characterization. Sequence assembly, Genbank searches, and recombination analyses were performed to verify the identity of the genome sequences and to determine percent similarity to known DENV-1 sequences. We show that the KW DENV-1 strain is 99% identical to Nicaraguan and Mexican DENV-1 strains. Phylogenetic and recombination analyses suggest that the DENV-1 isolated in KW originated from Nicaragua (NI) and the KW strain may circulate in KW. Also, recombination analysis results detected recombination events in the KW strain compared to DENV-1 strains from Puerto Rico. We evaluate the relative growth of KW strain of DENV-1 compared to other dengue viruses to determine whether the underlying genetics of the strain is associated with a replicative advantage, an important consideration since local transmission of DENV may result because domestic tourism can spread DENVs

Early changes in Orthopteran assemblages after grassland restoration : a comparison of space-for-time substitution versus repeated-measures monitoring

Grasslands harbour significant biodiversity and their restoration is a common intervention in biodiversity conservation. However, we know very little on how grassland restoration influences arthropod groups. Here we compared orthopteran assemblages in croplands, natural grasslands and one to four-year-old grasslands restored in a large-scale restoration on former croplands in Hortobágy National Park (E-Hungary). Sampling was done by standardized sweep-netting both in a repeated measures design and space-for-time substitution (chronosequence) design. General linear models with repeated measures from five years showed that species richness, abundance and Shannon diversity of orthopterans decreased in the year following restoration but increased afterwards. By the fourth year, species richness almost doubled and abundance increased almost ten-fold in restored grasslands compared to croplands. Multivariate analyses showed that species composition in the first two years did not progress much but by the third and fourth year there was partial overlap with natural grasslands. Local restoration conditions (last crop, seed mixture) and landscape configuration (proportion of natural grasslands < 1 km away) did not influence the above patterns in either the repeated measures or the chronosequence design, whereas time since restoration affected almost all community variables. Our results suggest that generalist ubiquitous species appeared in restored grasslands first and the more sensitive species colonized the restored fields gradually in later years. The qualitative and quantitative properties of the orthopteran assemblages in restored fields did not yet reach those of natural grasslands, therefore, our study suggests that the full regeneration of the orthopteran assemblages takes more than four years