Folding and unfolding phylogenetic trees and networks

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks

Examination of Impulsivity and Contemplation Differences in Incarcerated Opiate Users versus Other Substance Users

Opiate addiction is widespread across the country and yet it is a treatable disease. Incarcerated men and women were screened upon commitment to a jail in Rhode Island about their substance use history. Of the 432 individuals screened, 430 survey responses were used in this study. Opiate users accounted for 23% (97) of the total with 77% (333) noting they use other substances. All study participants voluntarily admitted to using opiates or other substances at the time of informed consent. Two hundred and thirty-one (231) or 53% plan to stop using drugs after release from incarceration. The unadjusted total impulsivity score for opiate users revealed a mean of 38.21 (8.0 s.d.) as compared to a score of 33.83 (8.7 s.d.) for other substance users. The goal of this study is to compare opiate users to other substance users as it relates to the character trait of impulsivity using Barratt\u27s Impulsivity Scale as well as whether they contemplate remaining drug-free post-release through the use of the In-Prison Drug Contemplation Ladder

Real-time detection of TDP1 activity using a fluorophore-quencher coupled DNA-biosensor

Real-time detection of enzyme activities may present the easiest and most reliable way of obtaining quantitative analyses in biological samples. We present a new DNA-biosensor capable of detecting the activity of the potential anticancer drug target tyrosyl-DNA phosphodiesterase 1 (TDP1) in a very simple, high throughput, and real-time format. The biosensor is specific for Tdp1 even in complex biological samples, such as human cell extracts, and may consequently find future use in fundamental studies as well as a cancer predictive tool allowing fast analyses of diagnostic cell samples such as biopsies. TDP1 removes covalent 3'DNA adducts in DNA single-strand break repair. This enzymatic activity forms the basis of the design of the TDP1-biosensor, which consists of a short hairpin-forming oligonucleotide having a 5'fluorophore and a 3'quencher brought in close proximity by the secondary structure of the biosensor. The specific action of TDP1 removes the quencher, thereby enabling optical detection of the fluorophore. Since the enzymatic action of TDP1 is the only "signal amplification" the increase in fluorescence may easily be followed in real-time and allows quantitative analyses of TDP1 activity in pure enzyme fractions as well as in crude cell extracts. In the present study we demonstrate the specificity of the biosensor, its ability to quantitatively detect up- or down-regulated TDP1 activity, and that it may be used for measuring and for analyzing the mechanism of TDP1 inhibition

The International Bathymetric Chart of the Arctic Ocean (IBCAO) Version 3.0

[1] The International Bathymetric Chart of the Arctic Ocean (IBCAO) released its first gridded bathymetric compilation in 1999. The IBCAO bathymetric portrayals have since supported a wide range of Arctic science activities, for example, by providing constraint for ocean circulation models and the means to define and formulate hypotheses about the geologic origin of Arctic undersea features. IBCAO Version 3.0 represents the largest improvement since 1999 taking advantage of new data sets collected by the circum-Arctic nations, opportunistic data collected from fishing vessels, data acquired from US Navy submarines and from research ships of various nations. Built using an improved gridding algorithm, this new grid is on a 500 meter spacing, revealing much greater details of the Arctic seafloor than IBCAO Version 1.0 (2.5 km) and Version 2.0 (2.0 km). The area covered by multibeam surveys has increased from ∼6% in Version 2.0 to ∼11% in Version 3.0

Fertility, Living Arrangements, Care and Mobility

There are four main interconnecting themes around which the contributions in this book are based. This introductory chapter aims to establish the broad context for the chapters that follow by discussing each of the themes. It does so by setting these themes within the overarching demographic challenge of the twenty-first century – demographic ageing. Each chapter is introduced in the context of the specific theme to which it primarily relates and there is a summary of the data sets used by the contributors to illustrate the wide range of cross-sectional and longitudinal data analysed

Amplifying Women's Voices in Menopause Research: The Importance of Inclusive Perspectives

Menopause, a significant life transition for half the global population, intersects biological, cultural and social dimensions. Despite its universal occurrence, menopause research has historically been dominated by biomedical perspectives, often neglecting women's voices and diverse experiences. This article highlights the importance of including women's perspectives in menopause research to ensure relevance, accuracy and equity. It explores cultural variations in menopause experiences, the impact of socioeconomic status and the often-overlooked emotional and psychological dimensions. This article advocates for participatory approaches, emphasising that women's involvement enhances research design, implementation and policy development. Evidence-based interventions that are tailored to the individual can better address the diverse needs of menopausal women. The discussion extends to addressing health disparities, calling for inclusive research and policies to ensure equitable access to care. Ultimately, empowering women through co-designed research and inclusive policies can transform the menopause journey into an enriching life phase, promoting resilience and inclusivity across communities. This paradigm shift in menopause research and policy highlights the need for diversity, collaboration and evidence-based approaches to improve health outcomes and quality of life for all women. PATIENT OR PUBLIC CONTRIBUTION: This article has been informed by a menopause service user group who discuss their experiences of menopause. The group was formed because of initial qualitative research and now meet on a regular basis to co-design and co-produce activities that inform ongoing research for the menopause taskforce.fals

Nuclear localization of the CK2a-subunit correlates with poor prognosis in clear cell renal cell carcinoma

Protein kinase CK2a, one of the two catalytic isoforms of the protein kinase CK2 has been shown to contribute to tumor development, tumor proliferation and suppression of apoptosis in various malignancies. We conducted this study to investigate CK2 expression in different subtypes of Renal Cell Carcinoma (RCC) and in the benign oncocytoma. qRT-PCR, immunohistochemistry and Western blot analyses revealed that CK2a expression was significantly increased at the mRNA and protein levels in clear cell RCC (ccRCC). Also the kinase activity of CK2 was significantly increased in ccRCC compared to normal renal cortex. Nuclear protein expression of CK2a correlated in univariate analysis with poor Progression Free Survival (HR = 8.11, p = 0.016). Functional analyses (cell proliferation assay) revealed an inhibitory effect of Caki-2 cell growth following CK2 inhibition with CX-4945. Our results suggest that CK2a promotes migration and invasion of ccRCC and therefore could serve as a novel prognostic biomarker and molecular therapeutic target in this type of cancer

Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex

Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.UE FWF; P22260UE: Y66

Exploring digital interventions to facilitate coping and discomfort for nurses experiencing the menopause in the workplace: An international qualitative study.

INTRODUCTION: The global nursing workforce is predominantly female, with a large proportion working in the 45-55 age group. Menopause is a transition for all women, and; therefore needs recognition as it can impact work performance and consequently staff turnover. BACKGROUND: Women will go through the menopause, but not all women are affected. The menopause transition presents a range of signs and symptoms both physical and psychological which can impact the quality of life and individuals' work/life balance. The nursing workforce is predominantly women that will work through the menopause transition. OBJECTIVES: The study explored perspectives on digital health interventions as strategies to support menopausal women and to understand the requirements for designing health interventions for support in the workplace. DESIGN: A qualitative explorative design. SETTINGS: Nurses working in a range of clinical settings in England, Finland, Denmark, New Zealand, Australia and USA. METHODS: Nurses (n = 48) participated in focus groups from six different countries from February 2020-June 2022 during the pandemic from a range of acute, primary care and education settings. Nurses were invited to participate to share their experiences. Thematic analysis was used. RESULTS: All participants were able to describe the physical symptoms of menopause, with some cultural and possible hemisphere differences; more noticeable was the psychological burden of menopause and fatigue that is not always recognized. Four themes were identified: Managing symptoms in the workplace; Recognition in the workplace; Menopause interventions; and Expectation versus the invisible reality. These themes revealed information that can be translated for implementation into digital health interventions. CONCLUSIONS: Managers of nursing female staff in the menopausal age range need greater awareness, and menopause education should involve everyone. Finally, our results demonstrate design attributes suitable for inclusion in digital health strategies that are aligned with likely alleviation of some of the discomforts of menopause. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution.fals