Featured
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Comment
| Open AccessImpression management in sex and gender neuroscience research reporting: the MAGIC guidelines
Here, the authors discuss guidelines to avoid miscommunication of findings in research into sex and gender-based differences in the brain.
- Gina Rippon
- , Katy Losse
- & Simon White
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Comment
| Open AccessChallenges and ways forward for sustainable weather and climate services in Africa
Sustainability of African weather and climate information can only be ensured by investing in improved scientific understanding, observational data, and model capability. These requirements must be underpinned by capacity development, knowledge management; and partnerships of co-production, communication and coordination.
- Benjamin Lamptey
- , Salah SAHABI ABED
- & Erik W. Kolstad
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Article
| Open AccessA framework for evaluating clinical artificial intelligence systems without ground-truth annotations
Estimating the performance of clinical AI systems on data in the wild is complicated by distribution shift and the absence of ground-truth annotations. Here, we introduce SUDO, a framework for more reliably evaluating AI systems on data in the wild.
- Dani Kiyasseh
- , Aaron Cohen
- & Nicholas Altieri
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Comment
| Open AccessThe bioethics of skeletal anatomy collections from India
Millions of skeletal remains from South Asia were exported in red markets (the underground economy of human tissues/organs) to educational institutions globally for over a century. It is time to recognize the personhood of the people who were systematically made into anatomical objects and acknowledge the scientific racism in creating and continuing to use them.
- Sabrina C. Agarwal
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Article
| Open AccessExtracting accurate materials data from research papers with conversational language models and prompt engineering
Efficient data extraction from research papers accelerates science and engineering. Here, the authors develop an automated approach which uses conversational large language models to achieve high precision and recall in extracting materials data.
- Maciej P. Polak
- & Dane Morgan
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Article
| Open AccessOpen-source microscope add-on for structured illumination microscopy
Researchers developed an open-hardware structured illumination microscopy add-on. This affordable upgrade provides super-resolution capabilities for normal optical microscopes. Detailed instructions enable easy reproduction to help democratize advanced microscopy.
- Mélanie T. M. Hannebelle
- , Esther Raeth
- & Georg E. Fantner
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Article
| Open AccessCases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA
Information on the occurrence of aneuploidies in prehistory human populations are rare. Here, from a large screen of ancient human genomes and osteological examination, the authors find genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome) in historic and prehistoric infants.
- Adam Benjamin Rohrlach
- , Maïté Rivollat
- & Kay Prüfer
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Article
| Open AccessStructured information extraction from scientific text with large language models
Extracting scientific data from published research is a complex task required specialised tools. Here the authors present a scheme based on large language models to automatise the retrieval of information from text in a flexible and accessible manner.
- John Dagdelen
- , Alexander Dunn
- & Anubhav Jain
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Article
| Open AccessDelayed increase in stone tool cutting-edge productivity at the Middle-Upper Paleolithic transition in southern Jordan
Lithic cutting-edge productivity is a way of quantifying prehistoric human technological evolution. Here, the authors examine the Middle-to-Upper Paleolithic transition across eight assemblages in the eastern Mediterranean, finding the transition to be later than expected and associated with bladelet technology development.
- Seiji Kadowaki
- , Joe Yuichiro Wakano
- & Sate Massadeh
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Article
| Open AccessOverlay databank unlocks data-driven analyses of biomolecules for all
In this work, the authors report NMR lipids Databank to promote decentralised sharing of biomolecular molecular dynamics (MD) simulation data with an overlay design. Programmatic access enables analyses of rare phenomena and advances the training of machine learning models.
- Anne M. Kiirikki
- , Hanne S. Antila
- & O. H. Samuli Ollila
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Comment
| Open AccessImplementing community-engaged pharmacogenomics in Indigenous communities
Innovative pharmacogenomic approaches (genetic variation related to medication response) are needed to reduce disease and disparities in Indigenous communities. We support community-based pharmacogenomics research, inclusive of Indigenous values and priorities, to improve the health and well-being of Indigenous peoples.
- Katrina G. Claw
- , Casey R. Dorr
- & Erica L. Woodahl
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Comment
| Open AccessA bumpy road ahead for genetic biocontainment
While the research community continues to develop novel proposals for intrinsic biocontainment of genetically engineered organisms, translation to real-world deployment faces several challenges.
- Dalton R. George
- , Mark Danciu
- & Emma K. Frow
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Article
| Open AccessA simulation-based analysis of the impact of rhetorical citations in science
Authors of scientific papers are generally discouraged from citing works that had no direct influence on their research. This paper uses simulations to show that such rhetorical citations may have underappreciated effects on the scientific community, such as deconcentrating attention away from already highly-cited papers.
- Honglin Bao
- & Misha Teplitskiy
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Comment
| Open AccessIntegrative and inclusive genomics to promote the use of underutilised crops
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
- Oluwaseyi Shorinola
- , Rose Marks
- & Mark A. Chapman
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Article
| Open Accessrworkflows: automating reproducible practices for the R community
Reproducibility is essential for the progress of research, yet achieving it remains elusive even in computational fields. Here, authors develop the rworkflows suite, making robust CI/CD workflows easy and freely accessible to all R package developers.
- Brian M. Schilder
- , Alan E. Murphy
- & Nathan G. Skene
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Article
| Open Accessvcfdist: accurately benchmarking phased small variant calls in human genomes
Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human genome sequencing. Here, the authors show that current approaches are biased towards certain variant representations and develop a new approach to ensure consistent and accurate benchmarking, regardless of the original variant representations.
- Tim Dunn
- & Satish Narayanasamy
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Comment
| Open AccessAccelerating African neuroscience to provide an equitable framework using perspectives from West and Southern Africa
Drawing on perspectives from West and Southern Africa, this Comment critically examines the current state of neuroscience progress in Africa, describing the unique landscape and ongoing challenges as embedded within wider socio-political realities. Distinct research opportunities in the African context are explored to include genetic and bio-diversity, multilingual and multicultural populations, life-course development, clinical neuroscience and neuropsychology, with applications to machine learning models, in light of complex post-colonial legacies that often impede research progress. Key determinants needed to accelerate African neuroscience are then discussed, as well as cautionary underpinnings that together create an equitable neuroscience framework.
- Sahba Besharati
- & Rufus Akinyemi
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Comment
| Open AccessOne Health approach at the heart of the French Committee for monitoring and anticipating health risks
Following the COVID-19 pandemic, the French government established a committee for monitoring and anticipating health risks. In this Comment, the authors describe the One Health approach taken by the committee, and outline its aims, composition, and initial actions.
- Thierry Lefrançois
- , Bruno Lina
- & Brigitte Autran
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Article
| Open AccessExtracting medicinal chemistry intuition via preference machine learning
Over their careers, medicinal chemists develop a gut feeling for what is a promising molecule. Here, the authors use machine learning models to learn this intuition and show that it can be successfully applied in several drug discovery scenarios.
- Oh-Hyeon Choung
- , Riccardo Vianello
- & José Jiménez-Luna
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Article
| Open AccesslesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation
Public proteomics data often lack essential metadata, limiting their potential. To address this, the authors developed lesSDRF, a tool to simplify the process of metadata annotation, thereby ensuring that data leave a lasting, impactful legacy well beyond their initial publication.
- Tine Claeys
- , Tim Van Den Bossche
- & Lennart Martens
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Article
| Open AccessSimulation of undiagnosed patients with novel genetic conditions
Rare Mendelian disorders pose a major diagnostic challenge, but evaluation of automated tools that aim to uncover causal genes tools is limited. Here, the authors present a computational pipeline that simulates realistic clinical datasets to address this deficit.
- Emily Alsentzer
- , Samuel G. Finlayson
- & Isaac S. Kohane
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Comment
| Open AccessExtending research impact by sharing maker information
The availability of maker resources such as 3D printers, makerspaces, and public repositories enable researchers to share information with research peers, educators, industry, and the general public. This broadens the impact of research and inspires its extension and application.
- Larry L. Howell
- & Terri Bateman
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Article
| Open AccessSugar-sweetened beverage intakes among adults between 1990 and 2018 in 185 countries
Recent estimates of sugar-sweetened beverages (SSBs) intake are generally unavailable. Here the authors show a global SSBs intake of 2.7 servings/week in 2018 in adults (range: 0.7 South Asia, 7.8 Latin America/Caribbean); intakes were higher among males, younger, more educated, and urban adults.
- Laura Lara-Castor
- , Renata Micha
- & Rubina Hakeem
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Review Article
| Open AccessThe promise of data science for health research in Africa
In this Review article, the authors discuss emerging efforts to build ethical governance frameworks for data science health research in Africa and the opportunities to advance these through investments by African governments and institutions, international funding organizations and collaborations for research and capacity development.
- Clement A. Adebamowo
- , Shawneequa Callier
- & Sally N. Adebamowo
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Comment
| Open AccessEngineered and natural gene drives: mechanistically the same, yet not same in kind
We propose the use of the terms natural gene drive (NGD) and engineered gene drive (EGD) arguing against James et al.
1 , who think both should be included within the term “gene drive”, based on their mechanistic similarities.- Raul F. Medina
- & Jennifer Kuzma
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Comment
| Open AccessZoonotic malaria requires new policy approaches to malaria elimination
WHO guidelines for classification of malaria elimination in a country require that the risk of human infection from zoonotic, as well as nonzoonotic, malaria parasites is negligible. In this Comment, the authors discuss the implications of this policy for countries, such as Malaysia, with no recent reported nonzoonotic cases but ongoing zoonotic transmission.
- Kimberly M. Fornace
- , Chris J. Drakeley
- & Kamruddin Ahmed
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Article
| Open AccessCD36 mediates SARS-CoV-2-envelope-protein-induced platelet activation and thrombosis
Aberrant coagulation and thrombosis are associated with severe SARS-CoV-2 infection. Here, the authors show that the E protein are associated with coagulation disorders in COVID-19 patients and could directly enhance platelet activation and thrombosis through a CD36/p38 MAPK/NF-kB signaling axis.
- Zihan Tang
- , Yanyan Xu
- & Tingting Liu
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Article
| Open AccessAn open resource combining multi-contrast MRI and microscopy in the macaque brain
Linking microscale cellular structures to macroscale features of the brain is required to fully understand its structure and function. Here, the authors present a resource which combines multi-contrast microscopy and MRI of a single whole macaque brain to facilitate multimodal analyses.
- Amy F. D. Howard
- , Istvan N. Huszar
- & Karla L. Miller
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Article
| Open AccessGender differences in the intention to study math increase with math performance
The authors show that there is a positive and linear relationship between the probability of intending to pursue math and math performance, and that this relationship is stronger among boys than among girls.
- Thomas Breda
- , Elyès Jouini
- & Clotilde Napp
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Article
| Open AccessDifferentially private knowledge transfer for federated learning
To ensure the privacy of processed data, federated learning approaches involve local differential privacy techniques which however require communicating a large amount of data that needs protection. The authors propose here a framework that uses selected small data to transfer knowledge in federated learning with privacy guarantees.
- Tao Qi
- , Fangzhao Wu
- & Xing Xie
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Article
| Open AccessUncertainty in non-CO2 greenhouse gas mitigation contributes to ambiguity in global climate policy feasibility
The potential for the mitigation of global non-CO2 greenhouse gases is highly uncertain. Harmsen et al. estimate this uncertainty and show that it has large implications for the feasibility of reaching the Paris Climate Agreement targets.
- Mathijs Harmsen
- , Charlotte Tabak
- & Detlef van Vuuren
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Comment
| Open AccessEthical considerations for researchers developing and testing minimal-risk devices
This comment explores ethical aspects in developing and testing minimal-risk devices, such as wearables and biomedical sensors. Authors outline the process of independent review, emphasizing the different levels of review depending on the research design and risk level. They also share examples of practical scenarios, highlighting key ethical considerations.
- Anna Wexler
- & Emily Largent
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Comment
| Open AccessMethod Reporting with Initials for Transparency (MeRIT) promotes more granularity and accountability for author contributions
Lack of information on authors’ contribution to specific aspects of a study hampers reproducibility and replicability. Here, the authors propose a new, easily implemented reporting system to clarify contributor roles in the Methods section of an article.
- Shinichi Nakagawa
- , Edward R. Ivimey-Cook
- & Malgorzata Lagisz
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Comment
| Open AccessA gene drive is a gene drive: the debate over lumping or splitting definitions
We address a controversy over use of the term “gene drive” to include both natural and synthetic genetic elements that promote their own transmission within a population, arguing that this broad definition is both practical and has advantages for risk analysis.
- Stephanie L. James
- , David A. O’Brochta
- & Omar S. Akbari
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Article
| Open AccessSurprising combinations of research contents and contexts are related to impact and emerge with scientific outsiders from distant disciplines
Here, using hypergraph modeling the authors show that surprising research (in terms of unexpected combinations of research contents and contexts) is associated with impact and arises from scientific outsiders solving problems in distant disciplines.
- Feng Shi
- & James Evans
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Perspective
| Open AccessToward sustainable space exploration: a roadmap for harnessing the power of microorganisms
Establishing sustainable approaches for human space exploration is key to achieve independency from terrestrial resources, as well as for ethical considerations. Here the authors highlight microbial biotechnologies that will support sustainable processes for space-based in situ resource utilization and loop-closure, and may be translatable to Earth applications.
- Rosa Santomartino
- , Nils J. H. Averesch
- & Luis Zea
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Article
| Open AccessRegional clozapine, ECT and lithium usage inversely associated with excess suicide rates in male adolescents
There are conflicting results on the effectiveness of pharmacologic interventions for suicide prevention in adolescence. Here, the authors show, in a retrospective registry study from Sweden during 2016–2020, that regional utilization rates of clozapine, electroconvulsive therapy and lithium in 15–19-year-olds were associated with lower excess suicide death rates in male adolescents
- Adrian E. Desai Boström
- , Peter Andersson
- & Jussi Jokinen
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Comment
| Open AccessResearch on scalable graphene faces a reproducibility gap
More than a decade after the first demonstration of large-scale graphene synthesis by chemical vapor deposition, the commercialization of graphene products is limited not only by price, but also by consistency, reproducibility, and predictability. Here, the author discusses the reproducibility issues in the field and proposes possible solutions to improve the reliability of published results.
- Peter Bøggild
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Article
| Open AccessA scoping review of the impacts of COVID-19 physical distancing measures on vulnerable population groups
Physical distancing measures introduced to control the spread of COVID-19 had socio-economic trade-offs that may have particularly impacted vulnerable population groups. Here, the authors perform a scoping review and summarise the impacts on different vulnerable groups described in 265 studies.
- Lili Li
- , Araz Taeihagh
- & Si Ying Tan
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Comment
| Open AccessCommunity voices: broadening participation in Science, Technology, Engineering, Mathematics, and Medicine among persons with disabilities
Disability has too often been peripheral to efforts to widen the STEMM pipeline, hampering research quality and innovation. Inspired by change in education delivery and research collaborations during the pandemic, we offer a structure for efforts to recruit and retain disabled scientists and practitioners.
- Siobhán M. Mattison
- , Logan Gin
- & Katherine Wander
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Comment
| Open AccessGreater genetic diversity is needed in human pluripotent stem cell models
While there are a growing number of human pluripotent stem cell repositories, genetic diversity remains limited in most collections and studies. Here, we discuss the importance of incorporating diverse ancestries in these models to improve equity and accelerate biological discovery.
- Sulagna Ghosh
- , Ralda Nehme
- & Lindy E. Barrett
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Article
| Open AccessGlobal disparities in SARS-CoV-2 genomic surveillance
In this study, the authors provide a global overview of SARS-CoV-2 genome sequencing, and estimate the proportion of cases sequenced and time to genome upload. They identify disparities and highlight the need to strengthen surveillance in lower and middle income countries.
- Anderson F. Brito
- , Elizaveta Semenova
- & Nuno R. Faria
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Perspective
| Open AccessThe history of sexual selection research provides insights as to why females are still understudied
While it is widely acknowledged that Darwin’s descriptions of females were gender-biased, gender bias in modern sexual selection research is less recognized. This Perspective highlights that sexual selection theory and research are still male-centered and suggest strategies for alleviating biases in this field and beyond.
- Malin Ah-King
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Article
| Open AccessFemale peer mentors early in college have lasting positive impacts on female engineering students that persist beyond graduation
The authors report findings from their study of female student participants interested in engineering at college entry who were randomly assigned to a female peer mentor, male mentor, or no mentor for their first year of college. The authors show that students assigned to a female peer mentor show benefits in psychological experiences in engineering, aspirations to pursue postgraduate engineering degrees, and emotional well-being, which persists up to one year after graduation.
- Deborah J. Wu
- , Kelsey C. Thiem
- & Nilanjana Dasgupta
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Article
| Open AccessEconomic interests cloud hazard reductions in the European regulation of substances of very high concern
The most important variable explaining the regulation of chemical substances of very high concern in the European REACH regulation is not how dangerous a chemical is but the fact that it is not produced nor imported into the European Economic Area.
- Jessica Coria
- , Erik Kristiansson
- & Mikael Gustavsson
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Article
| Open AccessUntangling the network effects of productivity and prominence among scientists
While inequalities in science are common, most efforts to understand them treat scientists as isolated individuals, ignoring the network effects of collaboration. Here, the authors develop models that untangle the network effects of productivity and prominence of individual scientists from their collaboration networks.
- Weihua Li
- , Sam Zhang
- & Aaron Clauset
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Comment
| Open AccessScience in the time of COVID-19: Reflections on the UK Events Research Programme
We reflect on the extent to which the UK Events Research Programme adhered to four principles of design and evaluation in assessing risk of transmission from attending such mass events as football matches and festivals, and lessons learned.
- Theresa M. Marteau
- , Michael J. Parker
- & W. John Edmunds
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Article
| Open AccessSystematic evidence and gap map of research linking food security and nutrition to mental health
There is a broad range of research available on the relationship between food security and mental health. Here the authors carry out a systematic mapping of evidence on food security and nutrition related to mental health and identifies trends in themes, setting, and study design over the 20 year period studied.
- Thalia M. Sparling
- , Megan Deeney
- & Suneetha Kadiyala
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Comment
| Open AccessCommunity voices: policy proposals to promote inclusion in academia through the lens of women in science
Diversity is a creative force that broadens views and enhances ideas; it increases productivity as well as the impact of our science, making our respective organisations more agile and timely. Equality of opportunity is a key to success for any research organisation. Here we argue that every research organisation, whether in academia or in industry, needs to have better inclusion policies to harness the benefits of diversity in research. Drawing from our personal experiences and perspectives as women in science, we share our suggestions on how to promote inclusion in academia and create a better research culture for all. Our shared experiences highlight the many hurdles women in science face on a daily basis. We stress that rules and regulations, as well as education for awareness, will play critical role in this much needed shift from a male-dominated scientific culture that dates from Victorian times to a modern focus on gender equality in science. The key ingredients of this new culture will be flexibility, transparency, fairness and thoughtfulness.
- Sarah A. Teichmann
- , Muzlifah Haniffa
- & Jasmin Fisher