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Female aging: when translational models don’t translate
Abstract For many pathologies associated with aging, female patients present with higher morbidity and more frequent adverse events from treatments compared to male patients. While preclinical models are the foundation of our mechanistic understanding of age-related diseases, the most common models fail to recapitulate archetypical female aging trajectories. For example, while over 70% of the…
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Vitamin B12 boosts cellular reprogramming
“There is currently a lot of interest in cellular reprogramming, yet we still know very little about the mechanisms of in vivo reprogramming, its metabolic requirements and how to control it. We thought that by studying the microbiota — a community of microorganisms that is in metabolic equilibrium with its host — during in vivo…
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Bugs as features (part 1): concepts and foundations for the compositional data analysis of the microbiome–gut–brain axis
Abstract There has been a growing acknowledgment of the involvement of the gut microbiome—the collection of microorganisms that reside in our gut—in regulating our mood and behavior. This phenomenon is referred to as the microbiome–gut–brain axis. Although our techniques to measure the presence and abundance of these microorganisms have been steadily improving, the analysis of…
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Hypoblast from human pluripotent stem cells regulates epiblast development
Abstract Recently, several studies using cultures of human embryos together with single-cell RNA-seq (scRNA-seq) analyses have revealed differences between humans and mice, necessitating the study of human embryos 1-8. Despite the importance of human embryology, ethical and legal restrictions have limited post-implantation stage studies. Thus, recent efforts have focused on developing in vitro self-organising models…
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Guest edited collection: fungal evolution and diversity
There are 5 million fungal species. However, the discovery and classification of fungi are in high flux. Modern concepts indicate that the three kingdoms of “fungi” are Chromista, Fungi and Protozoa. Strong support for the wrong phylogeny can occur without correct analytical methods. In the current Collection we envisaged fungi representing extremely diverse and ancient…
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Quantifying spatial under-reporting disparities in resident crowdsourcing
Abstract Modern city governance relies heavily on crowdsourcing to identify problems such as downed trees and power lines. A major concern is that residents do not report problems at the same rates, with heterogeneous reporting delays directly translating to downstream disparities in how quickly incidents can be addressed. Here we develop a method to identify…
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Revisiting the use of structural similarity index in Hi-C
arising from S. Galan et al. Nature Genetics https://doi.org/10.1038/s41588-020-00712-y (2020) This is a preview of subscription content, access via your institution Access options Access through your institution Change institution Buy or subscribe /* style specs start */ style{display:none!important}.LiveAreaSection-193358632 *{align-content:stretch;align-items:stretch;align-self:auto;animation-delay:0s;animation-direction:normal;animation-duration:0s;animation-fill-mode:none;animation-iteration-count:1;animation-name:none;animation-play-state:running;animation-timing-function:ease;azimuth:center;backface-visibility:visible;background-attachment:scroll;background-blend-mode:normal;background-clip:borderBox;background-color:transparent;background-image:none;background-origin:paddingBox;background-position:0 0;background-repeat:repeat;background-size:auto 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It is time to talk openly about menopause in academia
During the COVID-19 lockdown period, while working from home and sitting through endless Zoom meetings, we decided to add a late afternoon walk with our dogs to our calendars, while talking to each other over the phone. The menopause transition had begun for both of us, and we needed to create a space that we…
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Risk factors for 5-year complications after midurethral sling surgery for stress urinary incontinence: a retrospective cohort study from Taiwan
Abstract Midurethral sling surgery is the current gold standard worldwide for stress urinary incontinence (SUI) surgery, with over 90% of surgeons worldwide using the midurethral sling for SUI between 2008 and 2018. However, concerns surround mesh-related adverse events associated with the midurethral sling. The decision to use the midurethral sling for surgical treatment has become…
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Reverse metabolomics for the discovery of chemical structures from humans
Abstract Determining structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here, we present reverse metabolomics as a discovery strategy, where MS/MS spectra are acquired from newly synthesized compounds and searched for in public metabolomics data to uncover phenotypic associations. To demonstrate the concept, we broadly synthesized and explored multiple classes…