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Every fifth published metagenome is not available to science

PLOS Biology (new articles) - Пт, 2020-04-03 23:00

by Ester M. Eckert, Andrea Di Cesare, Diego Fontaneto, Thomas U. Berendonk, Helmut Bürgmann, Eddie Cytryn, Despo Fatta-Kassinos, Andrea Franzetti, D. G. Joakim Larsson, Célia M. Manaia, Amy Pruden, Andrew C. Singer, Nikolina Udikovic-Kolic, Gianluca Corno

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.
Категорії: Biology, Journals

BigBrain 3D atlas of cortical layers: Cortical and laminar thickness gradients diverge in sensory and motor cortices

PLOS Biology (new articles) - Пт, 2020-04-03 23:00

by Konrad Wagstyl, Stéphanie Larocque, Guillem Cucurull, Claude Lepage, Joseph Paul Cohen, Sebastian Bludau, Nicola Palomero-Gallagher, Lindsay B. Lewis, Thomas Funck, Hannah Spitzer, Timo Dickscheid, Paul C. Fletcher, Adriana Romero, Karl Zilles, Katrin Amunts, Yoshua Bengio, Alan C. Evans

Histological atlases of the cerebral cortex, such as those made famous by Brodmann and von Economo, are invaluable for understanding human brain microstructure and its relationship with functional organization in the brain. However, these existing atlases are limited to small numbers of manually annotated samples from a single cerebral hemisphere, measured from 2D histological sections. We present the first whole-brain quantitative 3D laminar atlas of the human cerebral cortex. It was derived from a 3D histological atlas of the human brain at 20-micrometer isotropic resolution (BigBrain), using a convolutional neural network to segment, automatically, the cortical layers in both hemispheres. Our approach overcomes many of the historical challenges with measurement of histological thickness in 2D, and the resultant laminar atlas provides an unprecedented level of precision and detail. We utilized this BigBrain cortical atlas to test whether previously reported thickness gradients, as measured by MRI in sensory and motor processing cortices, were present in a histological atlas of cortical thickness and which cortical layers were contributing to these gradients. Cortical thickness increased across sensory processing hierarchies, primarily driven by layers III, V, and VI. In contrast, motor-frontal cortices showed the opposite pattern, with decreases in total and pyramidal layer thickness from motor to frontal association cortices. These findings illustrate how this laminar atlas will provide a link between single-neuron morphology, mesoscale cortical layering, macroscopic cortical thickness, and, ultimately, functional neuroanatomy.
Категорії: Biology, Journals

Neurophysiological evidence for crossmodal (face-name) person-identity representation in the human left ventral temporal cortex

PLOS Biology (new articles) - Пт, 2020-04-03 23:00

by Angélique Volfart, Jacques Jonas, Louis Maillard, Sophie Colnat-Coulbois, Bruno Rossion

Putting a name to a face is a highly common activity in our daily life that greatly enriches social interactions. Although this specific person–identity association becomes automatic with learning, it remains difficult and can easily be disrupted in normal circumstances or neurological conditions. To shed light on the neural basis of this important and yet poorly understood association between different input modalities in the human brain, we designed a crossmodal frequency-tagging paradigm coupled to brain activity recording via scalp and intracerebral electroencephalography. In Experiment 1, 12 participants were presented with variable pictures of faces and written names of a single famous identity at a 4-Hz frequency rate while performing an orthogonal task. Every 7 items, another famous identity appeared, either as a face or a name. Robust electrophysiological responses were found exactly at the frequency of identity change (i.e., 4 Hz / 7 = 0.571 Hz), suggesting a crossmodal neural response to person identity. In Experiment 2 with twenty participants, two control conditions with periodic changes of identity for faces or names only were added to estimate the contribution of unimodal neural activity to the putative crossmodal face-name responses. About 30% of the response occurring at the frequency of crossmodal identity change over the left occipito-temporal cortex could not be accounted for by the linear sum of unimodal responses. Finally, intracerebral recordings in the left ventral anterior temporal lobe (ATL) in 7 epileptic patients tested with this paradigm revealed a small number of “pure” crossmodal responses, i.e., with no response to changes of identity for faces or names only. Altogether, these observations provide evidence for integration of verbal and nonverbal person identity-specific information in the human brain, highlighting the contribution of the left ventral ATL in the automatic retrieval of face-name identity associations.
Категорії: Biology, Journals

Coronavirus latest: US hospitals come under increasing strain

Genetics - 3 hours 22 min ago
The latest coronavirus news updated every day including coronavirus cases, the latest news, features and interviews from New Scientist and essential information about the covid-19 pandemic
Категорії: Biology

Watch over 50 New Scientist Live talks for free on YouTube

Genetics - 3 hours 53 min ago
Add some science to your lockdown living routine, as we make more than 50 incredible talks from our flagship science festival New Scientist Live available for free on YouTube over the coming weeks.
Категорії: Biology

Coronavirus will play out very differently in world's poorest nations

Genetics - 5 hours 7 хв ago
Cases of covid-19 have been slow to appear in developing economies, but now they are ramping up. Slums and refugee camps could be particularly vulnerable
Категорії: Biology

Why we still don't know what the death rate is for covid-19

Genetics - 8 hours 56 хв ago
Despite data pouring in from many countries, estimates of how many of those infected with covid-19 die still vary widely
Категорії: Biology

The best science fiction TV shows to stream right now

Genetics - 9 hours 5 хв ago
From Chernobyl to Watchmen, this is the best sci-fi on Netflix, Amazon Prime Video and BBC iPlayer at the moment
Категорії: Biology

The best science fiction TV shows to stream right now

HIV and AIDS - 9 hours 5 хв ago
From Chernobyl to Watchmen, this is the best sci-fi on Netflix, Amazon Prime Video and BBC iPlayer at the moment
Категорії: Healthcare, Science and society

The best science fiction TV shows to stream right now

From Chernobyl to Watchmen, this is the best sci-fi on Netflix, Amazon Prime Video and BBC iPlayer at the moment
Категорії: Science and society

Supermassive stars may have formed by repeatedly eating their siblings

Genetics - 10 hours 52 min ago
Some black holes are way bigger than we can explain, and they may have come from supermassive stars that formed by devouring the other stars around them
Категорії: Biology

Supermassive stars may have formed by repeatedly eating their siblings

HIV and AIDS - 10 hours 52 min ago
Some black holes are way bigger than we can explain, and they may have come from supermassive stars that formed by devouring the other stars around them
Категорії: Healthcare, Science and society

Supermassive stars may have formed by repeatedly eating their siblings

Genetically modified organisms (GMO) - 10 hours 52 min ago
Some black holes are way bigger than we can explain, and they may have come from supermassive stars that formed by devouring the other stars around them
Категорії: Science and society

Thinking small: Next-generation sensor networks close the size gap in vertebrate biologging

PLOS Biology (new articles) - 23 hours 52 min ago

by Simon P. Ripperger, Gerald G. Carter, Rachel A. Page, Niklas Duda, Alexander Koelpin, Robert Weigel, Markus Hartmann, Thorsten Nowak, Jörn Thielecke, Michael Schadhauser, Jörg Robert, Sebastian Herbst, Klaus Meyer-Wegener, Peter Wägemann, Wolfgang Schröder-Preikschat, Björn Cassens, Rüdiger Kapitza, Falko Dressler, Frieder Mayer

Recent advances in animal tracking technology have ushered in a new era in biologging. However, the considerable size of many sophisticated biologging devices restricts their application to larger animals, whereas older techniques often still represent the state-of-the-art for studying small vertebrates. In industrial applications, low-power wireless sensor networks (WSNs) fulfill requirements similar to those needed to monitor animal behavior at high resolution and at low tag mass. We developed a wireless biologging network (WBN), which enables simultaneous direct proximity sensing, high-resolution tracking, and long-range remote data download at tag masses of 1 to 2 g. Deployments to study wild bats created social networks and flight trajectories of unprecedented quality. Our developments highlight the vast capabilities of WBNs and their potential to close an important gap in biologging: fully automated tracking and proximity sensing of small animals, even in closed habitats, at high spatial and temporal resolution.
Категорії: Biology, Journals

Coronavirus: China wildlife trade ban could become law within months

Genetically modified organisms (GMO) - Чт, 2020-04-02 19:15
China’s ban on eating and trading wildlife due to the coronavirus crisis could become law within the next three months, according to conservationists
Категорії: Science and society

Coronavirus: China wildlife trade ban could become law within months

Genetics - Чт, 2020-04-02 19:15
China’s ban on eating and trading wildlife due to the coronavirus crisis could become law within the next three months, according to conservationists
Категорії: Biology

Coronavirus: China wildlife trade ban could become law within months

HIV and AIDS - Чт, 2020-04-02 19:15
China’s ban on eating and trading wildlife due to the coronavirus crisis could become law within the next three months, according to conservationists
Категорії: Healthcare, Science and society

Hunt for George Clooney's face explains how stress affects decisions

Genetically modified organisms (GMO) - Чт, 2020-04-02 18:00
Being stressed changes the way we make decisions. An experiment that sees people hunt for George Clooney's face while experiencing electric shocks could help explain why
Категорії: Science and society

Hunt for George Clooney's face explains how stress affects decisions

Genetics - Чт, 2020-04-02 18:00
Being stressed changes the way we make decisions. An experiment that sees people hunt for George Clooney's face while experiencing electric shocks could help explain why
Категорії: Biology

Hunt for George Clooney's face explains how stress affects decisions

HIV and AIDS - Чт, 2020-04-02 18:00
Being stressed changes the way we make decisions. An experiment that sees people hunt for George Clooney's face while experiencing electric shocks could help explain why
Категорії: Healthcare, Science and society