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  • Article
    Wu D, Jospin G, Eisen JA.
    PLoS One. 2013;8(10):e77033.
    With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as "marker" genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for "all bacteria and archaea", 114 for "all bacteria (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.
    Digital Access Access Options
  • Article
    van Dijk CE, van Gils AL, van Zijl MD, Koullali B, van der Weide MC, van den Akker ES, ... Show More Hermsen BJ, van Baal WM, Visser H, van Drongelen J, Vollebregt KC, Muller M, van der Made FW, Gordijn SJ, de Mooij YM, Oudijk MA, de Boer MA, Mol BW, Kazemier BM, Pajkrt E, Quadruple P Research Group.
    BMJ. 2024 03 12;384:e077033.
    OBJECTIVE: To compare the effectiveness of cervical pessary and vaginal progesterone in the prevention of adverse perinatal outcomes and preterm birth in pregnant women of singletons with no prior spontaneous preterm birth at less than 34 weeks' gestation and who have a short cervix of 35 mm or less.
    DESIGN: Open label, multicentre, randomised, controlled trial.
    SETTING: 20 hospitals and five obstetric ultrasound practices in the Netherlands.
    PARTICIPANTS: Women with a healthy singleton pregnancy and an asymptomatic short cervix of 35 mm or less between 18 and 22 weeks' gestation were eligible. Exclusion criteria were prior spontaneous preterm birth at less than 34 weeks, a cerclage in situ, maternal age of younger than 18 years, major congenital abnormalities, prior participation in this trial, vaginal blood loss, contractions, cervical length of less than 2 mm or cervical dilatation of 3 cm or more. Sample size was set at 628 participants.
    INTERVENTIONS: 1:1 randomisation to an Arabin cervical pessary or vaginal progesterone 200 mg daily up to 36 weeks' of gestation or earlier in case of ruptured membranes, signs of infection, or preterm labour besides routine obstetric care.
    MAIN OUTCOME MEASURES: Primary outcome was a composite adverse perinatal outcome. Secondary outcomes were rates of (spontaneous) preterm birth at less than 28, 32, 34, and 37 weeks. A predefined subgroup analysis was planned for cervical length of 25 mm or less.
    RESULTS: From 1 July 2014 to 31 March 2022, 635 participants were randomly assigned to pessary (n=315) or to progesterone (n=320). 612 were included in the intention to treat analysis. The composite adverse perinatal outcome occurred in 19 (6%) of 303 participants with a pessary versus 17 (6%) of 309 in the progesterone group (crude relative risk 1.1 (95% confidence interval (CI) 0.60 to 2.2)). The rates of spontaneous preterm birth were not significantly different between groups. In the subgroup of cervical length of 25 mm or less, spontaneous preterm birth at less than 28 weeks occurred more often after pessary than after progesterone (10/62 (16%) v 3/69 (4%), relative risk 3.7 (95% CI 1.1 to 12.9)) and adverse perinatal outcomes seemed more frequent in the pessary group (15/62 (24%) v 8/69 (12%), relative risk 2.1 (0.95 to 4.6)).
    CONCLUSIONS: In women with a singleton pregnancy with no prior spontaneous preterm birth at less than 34 weeks' gestation and with a midtrimester short cervix of 35 mm or less, pessary is not better than vaginal progesterone. In the subgroup of a cervical length of 25 mm or less, a pessary seemed less effective in preventing adverse outcomes. Overall, for women with single baby pregnancies, a short cervix, and no prior spontaneous preterm birth less than 34 weeks' gestation, superiority of a cervical pessary compared with vaginal progesterone to prevent preterm birth and consecutive adverse outcomes could not be proven.
    TRIAL REGISTRATION: International Clinical Trial Registry Platform (ICTRP, EUCTR2013-002884-24-NL).
    Digital Access Access Options
  • Book
    by Morteza Mahmoudi.
    Summary: Targets of bullying are often the most vulnerable members of the scientific workforce -- they may be low-paid graduate students or postdocs, living in a foreign country, navigating a foreign language and culture, and whose immigration status is tied directly to their employment. They may also have young families, be living paycheck-to-paycheck, and have health insurance and other benefits that depend on a contract position that can be revoked with little to no notice or cause. Finally, targets on the low end of a power differential are not likely to be supported by their institutions, particularly institutions that rely on the big grant earnings brought in by senior "bullies." The main focus of this book is to provide a brief guide regarding the cause and solution to academic bullying.

    Contents:
    Foreword
    Chapter 1: You Are a Target, Not a Victim
    Chapter 2: A Sample Target Story
    Chapter 3: Causes of Abusive Supervision: The Case of Bullying in Academic Science
    Chapter 4: Targets’ Responses to Abusive Supervision
    Chapter 5: Mobbing in Academia
    Chapter 6: What to Expect After Speaking Up?
    Chapter 7: Possible Solutions to Academic Bullying in Higher Education
    Chapter 8: Epilogue
    Index.
    Digital Access TandFonline 2021