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  • High-throughput transcriptomics has revolutionised the field of transcriptome research by offering a cost-effective and powerful screening tool. Standard bulk RNA sequencing (RNA-Seq) enables characterisation of the average expression profiles for individual samples and facilitates identification of the molecular functions associated with genes differentially expressed across conditions. RNA-Seq can also be applied to disentangle splicing variants and discover novel transcripts, thus contributing to a comprehensive understanding of the transcriptome landscape. A closely related technique, single-cell RNA-Seq, has enabled the study of cell-type-specific gene expressions in hundreds to thousands of cells, aiding the exploration of cell heterogeneity. Nowadays, bulk RNA-Seq and single-cell RNA-Seq serve as complementary tools to advance and accelerate the development of transcriptome-based resources. This Collection illustrates how the current global research community makes use of these techniques to address a broad range of questions in life sciences. It demonstrates the usefulness and popularity of high-throughput transcriptomics and presents the best practices and potential issues for the benefit of future end-users.

    • Nunzio D’Agostino
    • Wenli Li
    • Dapeng Wang
    Editorial Open Access
  • Recent advances in genome editing technologies have redefined our ability to probe and precisely edit the human genome and epigenome in vitro and in vivo. More specifically, RNA-guided CRISPR/Cas systems have revolutionized the field due to their simplicity in design and adaptability across biological systems. This Collection highlights results in CRISPR/Cas technology that increase the efficiency of precision genome editing, and allow genetic manipulation in model systems traditionally intractable to site-directed gene modification.

    • Maura McGrail
    • Tetsushi Sakuma
    • Leonidas Bleris
    Editorial Open Access
  • The tumor microenvironment (TME) comprises of components that exist within the immediate vicinity of tumor cells, including fibroblasts, immune cells, the extracellular matrix, and more. Significant advances have been made in recent years in our understanding of the components of TME and their mutual interactions. Part of the focus of this research has been on epigenetic events, which are increasingly being recognized for their importance in gene regulation and cancer progression. The Collection represents the gradual growth in our understanding of the overall process of how cancer progresses, along with the factors that play a decisive role in this progression. It features studies conducted on models representing many different cancers, and includes mechanistic reports conducted using appropriate in vitro models, studies that analyzed human cancer patients-derived specimens, clinical trials and, additionally, studies involving bioinformatics, metabolomics, chemical libraries screening, next-generation sequencing, and single-cell analysis approaches.

    • Aamir Ahmad
    Editorial Open Access
  • Membrane transporters are an important group of proteins in physiology and disease. Their functions make them common drug targets, but their location in the lipid bilayers poses a tremendous challenge to researchers. The current stage of development of structural biology, in addition to new research tools, has largely facilitated the acquisition of knowledge about transporters and mechanisms. This Collection presents recent studies, covering bioenergetics, structure and functional characterization of various transporters, lipids-protein interactions, and novel research tool development.

    • Lan Guan
    Editorial Open Access
  • Optical coherence tomography (OCT) is a three-dimensional optical imaging technique, frequently (but not exclusively) used for retinal imaging, that was first reported in the early 1990s. Since this time the technological development of OCT has been strongly influenced by its potential as a medical imaging technique. The first clinical prototype for use in ophthalmology was completed in 1994, paving the way for the first commercially available ophthalmic OCT system to be released to the market in 1996. Since then, OCT has become a mainstay of ophthalmology. OCT is also widely used in research, in an array of biomedical applications, and increasingly in industrial settings. Although there is still much activity in advancing OCT technology, there has been an increased emphasis in applying OCT to translational research. One direction of this research is in the development of quantitative and computational techniques to aid in the retrieval of clinically useful information from OCT images. This Collection brings together original research articles, which exploit realistic mathematical models of OCT image formation and machine learning approaches to obtain insight not otherwise available from raw OCT images. This includes research for measuring clinically relevant parameters such as retinal nerve fibre layer thickness, fractional flow reserve, and corneal biomechanics, and for performing feature identification and image process tasks.

    • Peter Munro
    Editorial Open Access
  • The COVID-19 pandemic has encouraged scientists and the general population to think more than ever before about how we interact with microbes in our indoor spaces. Research investigating transmission of SARS-CoV-2 has advanced our knowledge significantly in the last two years. However, indoor and built environment microbiomes are extremely complex polymicrobial systems. We have barely scratched the surface in our understanding of the microbial inhabitants of our indoor and urban spaces. The Microbes in the Built Environment Collection showcases recent research in this important topic around the globe.

    • Lena Ciric
    Editorial Open Access
  • Taphonomical analysis allows us to understand the processes that underlie site formation, as well as provide insights into the modification and composition of studied fossil materials. Taphonomy has become crucial to many scientific fields, providing conceptual advances through a renewal of models, protocols, and paradigms. In these studies, trans-disciplinary approaches (geology, palaeontology, biology, ecology, archaeology) have been developed using a wide array of methodologies. In addition, experimental work on modern assemblages, focusing on specific geological and biological processes (‘actualism’), are used to make referential data and proxies. This Collection contributes to the field’s methodological development, while gathering research articles investigating Quaternary period bone assemblages, with special interest in the Pleistocene.

    • Ruth Blasco
    Editorial Open Access
  • Advances in cognitive neuroscience and neurotechnology have increased our understanding of the neurobiological mechanisms underlying cognitive processes. This Collection brings together research in animal behaviour and cognition, with studies investigating their physiology, neural mechanisms, and genetic bases, in order to provide insight into the function and evolution of neurocognitive systems.

    • Elisa Frasnelli
    Editorial Open Access
  • Scientific Reports launched in June 2011 with an inclusive ethos, and a mission to publish high-quality research without selecting papers based on perceived impact or significance. We reflect on our first 10 years, and thank our authors, reviewers and Editorial Board Members for their contributions to the success of the journal.

    Editorial Open Access
  • The impaired brain is often difficult to restore, owing to our limited knowledge of the complex nervous system. Accumulating knowledge in systems neuroscience, combined with the development of innovative technologies, may enable brain restoration in patients with nervous system disorders that are currently untreatable. The Neuroprosthetics in Systems Neuroscience and Medicine Collection provides a platform for interdisciplinary research in neuroprosthetics.

    • Kenji Kansaku
    Editorial Open Access
  • Mountains cover about a quarter of the world’s land surface, and directly support a significant proportion of the world’s population living within mountainous regions. Mountains provide water, timber and non-timber forest products, mineral resources, and many other food, fiber, and fuel products. Mountains also provide diverse ecosystems, in terms of both species and genetics, due to the topographic complexity in mountains increasing isolation and promoting speciation. Managing mountain regions for the sustainable delivery of critical goods and services requires an increasingly detailed understanding of mountain surface processes and regulation. The aim of this Guest Edited Collection is to provide a platform for interdisciplinary studies of mountain surface processes, and their responses to climate change and human activities.

    • Xuyang Lu
    Editorial Open Access
  • We are a story telling species. We make sense of the world by looking for order and patterns. So we often see a signal—and build explanatory edifice around it—where there is just noise; and we often see noise where there may well be a signal. This habit of shaping reality into an easy to follow narrative affects even one of the most structured and systematic human activities: science. One of two things tends to happen next. We either ignore the evidence that does not fit our story, or we bend and mould it until it does.

    Editorial Open Access
  • Sperm are unique cells, produced through the complex and precisely orchestrated process of spermatogenesis, in which there are a number of checkpoints in place to guarantee delivery of a high-quality and high-fidelity DNA product. On the other hand, reproductive pressure in males means that to produce more is, in very general terms, to perform better. Balancing quantity and quality in sperm production is thus a delicate process, subject to specific cellular and molecular control mechanisms, and sensitive to environmental conditions, that can impact fertility and offspring health. This Collection is focused on these aspects of sperm biology, as well as their impact on reproductive performance and male infertility.

    • Ricardo P. Bertolla
    Editorial Open Access
  • There have been increasingly lively discussions about many published scientific results failing validation by independent studies. This so-called reproducibility crisis has led to particularly strong criticism of methodological weaknesses in animal research. Inappropriate statistical methods, poor experimental design, and extreme standardization in trial design are some contributing factors to the problem. The purpose of this Collection is to present original methodologies to improve the status quo and additionally to report meta-research about the reproducibility of published animal research.

    • Florian Frommlet
    Editorial Open Access
  • Agriculture must overcome several challenges in order to increase—or even maintain—production, while also reducing negative environmental impact. Nanotechnology, fundamentally through the development of smart delivery systems and nanocarriers, can contribute to engineering more efficient and less contaminant agrochemicals. This Collection presents recent related works, covering nanodevices that improve crop protection against pests and diseases, nanoformulations for enhancing plant nutrition, and nanomaterials strengthening the general crop performance.

    • Alejandro Pérez-de-Luque
    Editorial Open Access
  • Detecting clinically relevant diagnostic biomarkers, suitable for point-of-care detection, may facilitate rapid treatment and prevention of disease. However, medical diagnosis for which there are limited quantities of testable tissue or fluid, require point-of-care technologies with superior sensitivity and specificity. The purpose of this Editorial is to provide an overview of the Collection’s content, comprising original research into fluidics-based diagnostic platforms—specifically those made of paper or other low-cost materials, that can suitably operate with tiny sample volumes from mL to nL. In particular, we will focus on the clinical applications of such research, with potential uses in a number of fields including combating the COVID-19 pandemic for instance.

    • Chao-Min Cheng
    Editorial Open Access
  • 3D bioprinting has emerged as a promising new approach for fabricating complex biological constructs in the field of tissue engineering and regenerative medicine. It aims to alleviate the hurdles of conventional tissue engineering methods by precise and controlled layer-by-layer assembly of biomaterials in a desired 3D pattern. The 3D bioprinting of cells, tissues, and organs Collection at Scientific Reports brings together a myriad of studies portraying the capabilities of different bioprinting modalities. This Collection amalgamates research aimed at 3D bioprinting organs for fulfilling demands of organ shortage, cell patterning for better tissue fabrication, and building better disease models.

    • Madhuri Dey
    • Ibrahim T. Ozbolat
    Editorial Open Access
  • Neuromorphic systems are currently experiencing a rapid upswing due to the fact that today's CMOS (complementary metal oxide silicon) based technologies are increasingly approaching their limits. In particular, for the area of machine learning, energy consumption of today's electronics is an important limitation, that also contributes toward the ever-increasing impact of digitalization on our climate. Thus, in order to better meet the special requirements of unconventional computing, new physical substrates for bio-inspired computing schemes are extensively exploited. The aim of this Guest Edited Collection is to provide a platform for interdisciplinary research along three main lines: memristive materials and devices, emulation of cellular learning (neurons and synapses), and unconventional computing and network schemes.

    • Martin Ziegler
    Editorial Open Access
  • Extracellular vesicles (EVs) represent a new paradigm, both in cell biology and medicine; specifically, the idea that functional content itself may be delivered directly to cells. EVs are cell-derived membranous structures that work as intercellular communicators exerting their function by transporting their cargo that includes nucleic acids, proteins and lipids. EVs play an essential role in normal physiology, but also in pathological communication, for instance, in cancer, EVs are thought to deliver oncogenic molecules (such as proteins, peptides, RNAs…) to neighboring cells, enhancing propagation of neoplastic cells. Not surprisingly, EV research has become common-place in every field of biomedicine, being explored as diagnostics and therapeutics.

    This Collection gathers original Articles that investigate the application of extracellular vesicles on diagnostics and therapeutics, and that report advances in the knowledge of EV biology and the methodological tools for their study.

    • Joana Maria Ramis
    Editorial Open Access
  • Radioisotopes can be produced artificially from stable nuclei through the interaction with particles or highly energetic photons. In combination with modern detection and counting techniques, radioisotopes and radiochemical methods uniquely contribute to the health sciences. This Collection showcases salient aspects of medical radioisotope science ranging from the production, recovery and purification of radioisotopes to the methods used to attach them to biomolecules. The Collection also presents studies that highlight the importance of radiochemistry in the assessment of environmental radioactivity.

    • Michael E. Fassbender
    Editorial Open Access