Robust canonical correlations: A comparative study.

Several approaches for robust canonical correlation analysis will be presented and discussed. A first method is based on the definition of canonical correlation analysis as looking for linear combinations of two sets of variables having maximal (robust) correlation. A second method is based on alternating robust regressions. These methods axe discussed in detail and compared with the more traditional approach to robust canonical correlation via covariance matrix estimates. A simulation study compares the performance of the different estimators under several kinds of sampling schemes. Robustness is studied as well by breakdown plots.

Regulation of transposable elements by DNA modifications

Wellcome Trust and the Royal Society (101225/Z/13/Z)People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement number 608765

Multiple gestation epidemiology--15 years survey

Between January of 1987 and December of 2001 were born 1243 twins related to 609 multiple pregnancies, in Maternidade Bissaya-Barreto. Data were grouped in periods of three years and several parameters were studied. The rate of multiple gestation has increased probably due to the contribution of the assisted conception techniques, and to the increase of the number of multiple fetal pregnancies (two or more) and to the increase of the mother age. These more frequent obstetric problems were preterm birth, gestational hypertension and abnormal sonographic data of fetal growth. The average age of delivery was 34 weeks and the birth weight has decreased. The most important factors for neonatal morbidity were hyaline membranous disease, intraventricular haemorrhage and the twin-twin transfusion syndrome. The neonatal mortality decreased in the last studied period

Hypercalcemic crisis associated with primary hyperparathyroidism during pregnancy

Primary hyperparathyroidism is a rare occurrence in pregnancy with significant risks to the mother and the foetus, witch is related to the level of serum calcium. A 41-year-old women, gravida 2, para 1, presented at 22 weeks gestation with nausea, vomiting and mild cognitive dysfunction associated with hypercalcemic crisis. The hypercalcemia was observed to be related to parathyroid hyperplasia that was surgically removed. Complete resolution of her symptomatology and hypercalcemia occurred postoperatively. The pregnancy was complicated with transient hypertension. A small for gestational age healthy male infant was delivered at term with no neonatal complications related with this pathology

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.EAR is a Herchel Smith Fellow. MB and HB are supported by the Centre for Trophoblast Research, MB is a Next Generation Research Fellow. MJB is supported by a BBSRC studentship. The WR lab is supported by BBSRC, MRC, the Wellcome Trust, EU EpiGeneSys and BLUEPRINT. The SB lab is supported by core funding from Cancer Research UK

SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells

Background Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role. It has been suggested that SETDB1 protects ERVs from TET-dependent DNA demethylation, but the relevance of this mechanism for ERV expression remains unclear. Moreover, previous studies have been performed in primed ESCs, which are not epigenetically or transcriptionally representative of preimplantation embryos. Results We use naïve ESCs to investigate the role of SETDB1 in ERV regulation and its relationship with TET-mediated DNA demethylation. Naïve ESCs show an increased dependency on SETDB1 for ERV silencing when compared to primed ESCs, including at the highly mutagenic intracisternal A particles (IAPs). We find that in the absence of SETDB1, TET2 activates IAP elements in a catalytic-dependent manner. Surprisingly, TET2 does not drive changes in DNA methylation levels at IAPs, suggesting that it regulates these retrotransposons indirectly. Instead, SETDB1 depletion leads to a TET2-dependent loss of H4R3me2s, which is indispensable for IAP silencing during epigenetic reprogramming. Conclusions Our results demonstrate a novel and unexpected role for SETDB1 in protecting IAPs from TET2-dependent histone arginine demethylation

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

BACKGROUND: Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. RESULTS: We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. CONCLUSIONS: We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.This work was supported by the Biotechnology and Biological Sciences Research Council (CASE studentship to N.O., BB/K010867/1 to W.R.), Wellcome Trust (095645/Z/11/Z to W.R.), EU EpiGeneSys (257082 to W.R.) and EU BLUEPRINT (282510 to W.R.); Babraham Institute/Cambridge European Trust scholarship to N.O.; M.R.B. is a Sir Henry Dale Fellow (101225/Z/ 13/Z), jointly funded by the Wellcome Trust and the Royal Society

COVID-19 and lockdown, as lived and felt by university students

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).In the last 2 years, the COVID-19 pandemic has spread all over the world, forcing the closure of universities, among other unusual measures in recent history. (1) Background: This work is based on the study HOUSE-ULisbon, a survey carried out during the second confinement (March-May 2021) in Portugal with the collaboration of all the Faculties of the University of Lisbon (UL). The present work aims to explore gender differences in how first-year college students experienced and felt COVID-19 and the second confinement. (2) Methods: A questionnaire was carried out. In total, 976 university students (19.66 years (SD = 4.033); Min = 17 and Max = 65) from the first year of the UL were included, of which 69.5% (n = 678) were female, and 30.5% were male (n = 298). SPSS v. 26 was used for quantitative data and MAXQDA 2020 for qualitative data. (3) Results: Overall, students reported various symptoms of physical and mental discomfort (especially females). Statistically significant differences were found in the problems that could arise from the pandemic, such as the prevalence of higher anxiety and worries by females, and online gaming by males. In coping strategies, differences were found in leisure and family relationships, with greater difficulty on the female side. Social interaction was perceived as difficult or very difficult by both genders. As strategies for future pandemics, they highlighted a concerted effort between the government and media in the transmission of messages to the population, facilitating information, knowledge and adoption of protective behaviors. (4) Conclusions: These results are important data for activating or maintaining resources and services for first-year university students, who in some university institutions were supported during the pandemic by psychological, material (e.g., computers, internet), and financial support measures, which are now diminished or extinct. The impacts on their lives will certainly not be extinguished post-pandemic, and health, education, and public policy measures should be prioritized for this group. These results are important data for activating resources and services for students, informing health and education professionals, and supporting public policies.Ana Cerqueira—Foundation for Science and Technology (FCT) PhD Grant (SFRH/BD/148403/2019); Fábio Botelho Guedes—Foundation for Science and Technology (FCT) PhD Grant (SFRH/BD/148299/2019).info:eu-repo/semantics/publishedVersio

Review of low-cost sensors for indoor air quality: Features and applications

Humans spend the majority of their time indoors, where they are potentially exposed to hazardous pollutants. Within this context, over the past few years, there has been an upsurge of low-cost sensors (LCS) for the measurement of indoor air pollutants, motivated both by recent technological advances and by increased awareness of indoor air quality (IAQ) and its potential negative health impacts. Although not meeting the performance requirements for reference regulatory-equivalent monitoring indoors, LCS can provide informative measurements, offering an opportunity for high-resolution monitoring, emission source identification, exposure mitigation and managing IAQ and energy efficiency, among others. This article discusses the strengths and limitations that LCS offer for applications in the field of IAQ monitoring; it provides an overview of existing sensor technologies and gives recommendations for different indoor applications, considering their performance in the complex indoor environment and discussing future trends