Kutsev Bengisu Ozyoruk, Sermet Can, Berkan Darbaz, Kayhan Başak, Derya Demir, Guliz Irem Gokceler, Gurdeniz Serin, Uguray Payam Hacisalihoglu, Emirhan Kurtuluş, Ming Y Lu, Tiffany Y Chen, Drew F K Williamson, Funda Yılmaz, Faisal Mahmood, Mehmet Turan <<<

Histological artefacts in cryosectioned tissue can hinder rapid diagnostic assessments during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality slides, but the process for obtaining them is laborious (typically lasting 12-48 h) and hence unsuitable for intra-operative use. Here we report the development and performance of a deep-learning model that improves the quality of cryosectioned whole-slide images by transforming them into the style of whole-slide FFPE tissue within minutes. The model consists of a generative adversarial network incorporating an attention mechanism that rectifies cryosection artefacts and a self-regularization constraint between the cryosectioned and FFPE images for the preservation of clinically relevant features. Transformed FFPE-style images of gliomas and of non-small-cell lung cancers from a dataset independent from that used to train the model improved the rates of accurate tumour subtyping by pathologists. <<<

Carlos Taboada, Jesse Delia, Maomao Chen, Chenshuo Ma, Xiaorui Peng, Xiaoyi Zhu, Laiming Jiang, Tri Vu, Qifa Zhou, Junjie Yao, Lauren O'Connell, Sönke Johnsen <<<

Transparency in animals is a complex form of camouflage involving mechanisms that reduce light scattering and absorption throughout the organism. In vertebrates, attaining transparency is difficult because their circulatory system is full of red blood cells (RBCs) that strongly attenuate light. Here, we document how glassfrogs overcome this challenge by concealing these cells from view. Using photoacoustic imaging to track RBCs in vivo, we show that resting glassfrogs increase transparency two- to threefold by removing ~89% of their RBCs from circulation and packing them within their liver. Vertebrate transparency thus requires both see-through tissues and active mechanisms that "clear" respiratory pigments from these tissues. Furthermore, glassfrogs' ability to regulate the location, density, and packing of RBCs without clotting offers insight in metabolic, hemodynamic, and blood-clot research. <<<

Natalie I Mazur, Jonne Terstappen, Ranju Baral, Azucena Bardají, Philippe Beutels, Ursula J Buchholz, Cheryl Cohen, James E Crowe, Clare L Cutland, Linda Eckert, Daniel Feikin, Tiffany Fitzpatrick, Youyi Fong, Barney S Graham, Terho Heikkinen, Deborah Higgins, Siddhivinayak Hirve, Keith P Klugman, Leyla Kragten-Tabatabaie, Philippe Lemey, Romina Libster, Yvette Löwensteyn, Asuncion Mejias, Flor M Munoz, Patrick K Munywoki, Lawrence Mwananyanda, Harish Nair, Marta C Nunes, Octavio Ramilo, Peter Richmond, Tracy J Ruckwardt, Charles Sande, Padmini Srikantiah, Naveen Thacker, Kody A Waldstein, Dan Weinberger, Joanne Wildenbeest, Dexter Wiseman, Heather J Zar, Maria Zambon, Louis Bont <<<

Respiratory syncytial virus is the second most common cause of infant mortality and a major cause of morbidity and mortality in older adults (aged >60 years). Efforts to develop a respiratory syncytial virus vaccine or immunoprophylaxis remain highly active. 33 respiratory syncytial virus prevention candidates are in clinical development using six different approaches: recombinant vector, subunit, particle-based, live attenuated, chimeric, and nucleic acid vaccines; and monoclonal antibodies. Nine candidates are in phase 3 clinical trials. Understanding the epitopes targeted by highly neutralising antibodies has resulted in a shift from empirical to rational and structure-based vaccine and monoclonal antibody design. An extended half-life monoclonal antibody for all infants is likely to be within 1 year of regulatory approval (from August, 2022) for high-income countries. Live-attenuated vaccines are in development for older infants (aged >6 months). Subunit vaccines are in late-stage trials for pregnant women to protect infants, whereas vector, subunit, and nucleic acid approaches are being developed for older adults. Urgent next steps include ensuring access and affordability of a respiratory syncytial virus vaccine globally. This review gives an overview of respiratory syncytial virus vaccines and monoclonal antibodies in clinical development highlighting different target populations, antigens, and trial results. <<<

The relationship between mental health and social media has received significant research and policy attention. However, there is little population representative data about who social media users are which limits understanding of confounding factors between mental health and social media. Here we profile users of Facebook, Twitter, Instagram, Snapchat and YouTube from the Avon Longitudinal Study of Parents and Children population cohort (N=4,083). We provide estimates of demographics and mental health and well-being outcomes by platform. We find that users of different platforms and frequencies are not homogeneous. User groups differ primarily by sex and YouTube users are the most likely to have poorer mental health outcomes. Instagram and Snapchat users tend to have higher well-being than the other social media sites considered. Relationships between use-frequency and well-being differ depending on the specific well-being construct measured. The reproducibility of future research may be improved by stratifying by sex and being specific about the well-being constructs used. <<<

Humans display astonishing skill in learning about the environment in which they operate. They assimilate a rich set of affordances and interrelations among different elements in particular contexts, and form flexible abstractions (i.e., concepts) that can be generalised and leveraged with ease. To capture these abilities, we present a deep hierarchical Active Inference model of goal-directed behaviour, and the accompanying belief update schemes implied by maximising model evidence. Using simulations, we elucidate the potential mechanisms that underlie and influence concept learning in a spatial foraging task. We show that the representations formed-as a result of foraging-reflect environmental structure in a way that is enhanced and nuanced by Bayesian model reduction, a special case of structure learning that typifies learning in the absence of new evidence. Synthetic agents learn associations and form concepts about environmental context and configuration as a result of inferential, parametric learning, and structure learning processes-three processes that can produce a diversity of beliefs and belief structures. Furthermore, the ensuing representations reflect symmetries for environments with identical configurations. <<<

8-Oxoguanine (8oxoG) in DNA is a major oxidized base that poses a severe threat to genome stability. To counteract the mutagenic effect generated by 8oxoG in DNA, cells have evolved 8oxoG DNA glycosylase (OGG) that can excise this oxidized base from DNA. Currently, OGG enzymes have been divided into three families: OGG1, OGG2 and AGOG (archaeal 8oxoG DNA glycosylase). Due to the limited reports, our understanding on AGOG enzymes remains incomplete. Herein, we present evidence that an AGOG from the hyperthermophilic euryarchaeon Ch5 (Tb-AGOG) excises 8oxoG from DNA at high temperature. The enzyme displays maximum efficiency at 75°C-95°C and at pH 9.0. As expected, Tb-AGOG is a bifunctional glycosylase that harbors glycosylase activity and AP (apurinic/apyrimidinic) lyase activity. Importantly, we reveal for the first time that residue D41 in Tb-AGOG is essential for 8oxoG excision and intermediate formation, but not essential for DNA binding or AP cleavage. Furthermore, residue E79 in Tb-AGOG is essential for 8oxoG excision and intermediate formation, and is partially involved in DNA binding and AP cleavage, which has not been described among the reported AGOG members to date. Overall, our work provides new insights into catalytic mechanism of AGOG enzymes. <<<

The immune system responds to cancer in two main ways. First, there are prewired responses involving myeloid cells, innate lymphocytes and innate-like adaptive lymphocytes that either reside in premalignant tissues or migrate directly to tumours, and second, there are antigen priming-dependent responses, in which adaptive lymphocytes are primed in secondary lymphoid organs before homing to tumours. Transforming growth factor-β (TGFβ) - one of the most potent and pleiotropic regulatory cytokines - controls almost every stage of the tumour-elicited immune response, from leukocyte development in primary lymphoid organs to their priming in secondary lymphoid organs and their effector functions in the tumour itself. The complexity of TGFβ-regulated immune cell circuitries, as well as the contextual roles of TGFβ signalling in cancer cells and tumour stromal cells, necessitates the use of rigorous experimental systems that closely recapitulate human cancer, such as autochthonous tumour models, to uncover the underlying immunobiology. The diverse functions of TGFβ in healthy tissues further complicate the search for effective and safe cancer therapeutics targeting the TGFβ pathway. Here we discuss the contextual complexity of TGFβ signalling in tumour-elicited immune responses and explain how understanding this may guide the development of mechanism-based cancer immunotherapy. <<<

Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. We demonstrate several use cases, including the clustering of all 54,118 NCBI RefSeq genomes in 33 CPU h; real-time database search using assembled or unassembled Illumina, Pacific Biosciences, and Oxford Nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition. Mash is freely released under a BSD license ( https://github.com/marbl/mash ). <<<

Importance: Childhood poverty has been associated with increased internalizing and externalizing problems in adolescence, a period of peak onset for psychiatric problems. The underlying neural mechanisms remain unclear because longitudinal studies of poverty, brain structure, and changes in psychiatric symptoms are lacking.Objective: To examine whether structural differences in cortical regions mediate the association between household poverty and change in psychiatric symptoms in early adolescence.Design, Setting, and Participants: This longitudinal cohort study used baseline and 1-year follow-up data from the Adolescent Brain Cognitive Development Study. Children aged 9 to 10 years in the US were enrolled between September 1, 2016, and October 15, 2018. Data analysis was performed from August 13, 2021, to September 30, 2022.Exposures: Household poverty as measured by income-to-needs ratio, which incorporates family income and adjusts for family size as a percentage of the federal poverty level.Main Outcomes and Measures: Mediators were children's cortical surface area, thickness, and volume, obtained using magnetic resonance imaging. Internalizing and externalizing problems at 1-year follow-up were outcomes measured by maternal report using the Child Behavior Checklist. Analyses were adjusted for baseline psychiatric problems and sociodemographic variables, including sex, race and ethnicity, parental educational level, and study site.Results: Of the 7569 children (mean [SD] age, 9.91 [0.62] years; 3970 boys [52.5%]) included in the analysis, 1042 children (13.8%) lived below the poverty threshold between 2016 and 2018. Poverty was associated with increased externalizing symptoms score at 1-year follow-up (b = 1.57; 95% CI, 1.14-1.99), even after adjustment for baseline externalizing symptoms (b = 0.35; 95% CI, 0.06-0.64). The longitudinal associations of poverty with increases in externalizing problems over time were mediated by reductions in surface area in multiple cortical regions that support executive functioning (middle frontal gyrus), decision-making (lateral orbitofrontal cortex), visual processing (fusiform gyrus), auditory processing (transverse temporal gyrus), and emotion and language processing (superior temporal gyrus).Conclusions and Relevance: The findings of this study suggest that childhood poverty is associated with increases in externalizing problems, but not internalizing problems, over time in early adolescence. This association is mediated by reductions in cortical surface area across numerous brain regions. These findings highlight potential neurobiological mechanisms underlying the link between poverty and the emergence of externalizing problems during early adolescence. <<<

Mark Schmitt, Fatih Ceteci, Jalaj Gupta, Marina Pesic, Tim W Böttger, Adele M Nicolas, Kilian B Kennel, Esther Engel, Matthias Schewe, Asude Callak Kirisözü, Valentina Petrocelli, Yasamin Dabiri, Julia Varga, Mallika Ramakrishnan, Madina Karimova, Andrea Ablasser, Toshiro Sato, Melek C Arkan, Frederic J de Sauvage, Florian R Greten <<<

Solid cancers exhibit a dynamic balance between cell death and proliferation ensuring continuous tumour maintenance and growth. Increasing evidence links enhanced cancer cell apoptosis to paracrine activation of cells in the tumour microenvironment initiating tissue repair programs that support tumour growth, yet the direct effects of dying cancer cells on neighbouring tumour epithelia and how this paracrine effect potentially contributes to therapy resistance are unclear. Here we demonstrate that chemotherapy-induced tumour cell death in patient-derived colorectal tumour organoids causes ATP release triggering P2X4 (also known as P2RX4) to mediate an mTOR-dependent pro-survival program in neighbouring cancer cells, which renders surviving tumour epithelia sensitive to mTOR inhibition. The induced mTOR addiction in persisting epithelial cells is due to elevated production of reactive oxygen species and subsequent increased DNA damage in response to the death of neighbouring cells. Accordingly, inhibition of the P2X4 receptor or direct mTOR blockade prevents induction of S6 phosphorylation and synergizes with chemotherapy to cause massive cell death induced by reactive oxygen species and marked tumour regression that is not seen when individually applied. Conversely, scavenging of reactive oxygen species prevents cancer cells from becoming reliant on mTOR activation. Collectively, our findings show that dying cancer cells establish a new dependency on anti-apoptotic programs in their surviving neighbours, thereby creating an opportunity for combination therapy in P2X4-expressing epithelial tumours. <<<

Braydon Meyer, Samuel Clifton, Warwick Locke, Phuc-Loi Luu, Qian Du, Dilys Lam, Nicola J Armstrong, Beena Kumar, Niantao Deng, Kate Harvey, Alex Swarbrick, Vinod Ganju, Susan J Clark, Ruth Pidsley, Clare Stirzaker <<<

Neoadjuvant chemotherapy (NAC) is used to treat triple-negative breast cancer (TNBC) prior to resection. Biomarkers that accurately predict a patient's response to NAC are needed to individualise therapy and avoid chemotoxicity from unnecessary chemotherapy. We performed whole-genome DNA methylation profiling on diagnostic TNBC biopsy samples from the Sequential Evaluation of Tumours Undergoing Preoperative (SETUP) NAC study. We found 9 significantly differentially methylated regions (DMRs) at diagnosis which were associated with response to NAC. We show that 4 of these DMRs are associated with TNBC overall survival (P < 0.05). Our results highlight the potential of DNA methylation biomarkers for predicting NAC response in TNBC. <<<

β-Galactosidases catalyze the hydrolysis of β(1-3) and β(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and transglycosylation. Here we report the crystallographic structures of Penicillium sp. β-galactosidase and its complex with galactose solved by the SIRAS quick cryo-soaking technique at 1.90 Å and 2.10 Å resolution, respectively. The amino acid sequence of this 120 kDa protein was first assigned putatively on the basis of inspection of the experimental electron density maps and then determined by nucleotide sequence analysis. Primary structure alignments reveal that Penicillium sp. β-galactosidase belongs to family 35 of glycosyl hydrolases (GHF-35). This model is the first 3D structure for a member of GHF-35. Five distinct domains which comprise the structure are assembled in a way previously unobserved for β-galactosidases. Superposition of this complex with other β-galactosidase complexes from several hydrolase families allowed the identification of residue Glu200 as the proton donor and residue Glu299 as the nucleophile involved in catalysis. Penicillium sp. β-galactosidase is a glycoprotein containing seven N-linked oligosaccharide chains and is the only structure of a glycosylated β-galactosidase described to date. <<<

Several lipogenic genes have been shown to have effects on lipid metabolism: stearoyl CoA desaturase 1 (SCD1) catalyzes the desaturation of several fatty acids (FA) in the cis-Delta(9) position in mammary glands of ruminant animals, diacylglycerol acyltransferase 1 (DGAT1) is a key enzyme in triacylglycerol synthesis in the mammary gland, and sterol regulatory element binding protein (SREBP-1) is a transcription factor that regulates expression levels of the SCD1 gene and other genes relevant to lipid and FA metabolism in adipose tissue and mammary gland. In this work, 351 Italian Brown cows were genotyped for polymorphisms in the SCD1, SREBP-1, and DGAT1 genes to reveal the allelic distribution in the population. Subsequently, effects on individual milk FA composition and on cis-9 unsaturated/saturated FA ratios, a proxy of mammary stearoyl CoA desaturase activity, were investigated. The genotypes of SCD1 (A293V) and DGAT1 (K232A) were determined by an approach based on the ligation detection reaction and a universal array, whereas the genotype of SREBP-1 (84-bp insertion-deletion) was revealed by PCR amplification of intron 5. The genotype analysis showed an unbalanced distribution of alleles within all genes, being the allele with higher gene frequency at 82, 84, and 98% for SCD1, SREBP-1, and DGAT1, respectively. Significant associations between SCD1 and DGAT1 polymorphisms and milk FA composition were found, whereas SREBP-1 polymorphism was not associated with milk FA composition. In particular, SCD1 showed significant association with C14:1 cis-9 and C14:1 cis-9/C14:0, which is considered the best proxy of the desaturation activity in mammary gland. The DGAT1 polymorphism had the strongest association with milk FA composition, which confirmed the key role of DGAT1 in lipid metabolism of mammary gland. However, the unbalanced distribution of alleles in all polymorphisms investigated suggested that the size of population should be increased to confirm the results of the present study. <<<

This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni-/multi-modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software. <<<

Episodic memory enables humans to encode and later vividly retrieve information about our rich experiences, yet the neural representations that support this mental capacity are poorly understood. Using a large fMRI dataset ( = 468) of face-name associative memory tasks and principal component analysis to examine neural representational dimensionality (RD), we found that the human brain maintained a high-dimensional representation of faces through hierarchical representation within and beyond the face-selective regions. Critically, greater RD was associated with better subsequent memory performance both within and across participants, and this association was specific to episodic memory but not general cognitive abilities. Furthermore, the frontoparietal activities could suppress the shared low-dimensional fluctuations and reduce the correlations of local neural responses, resulting in greater RD. RD was not associated with the degree of item-specific pattern similarity, and it made complementary contributions to episodic memory. These results provide a mechanistic understanding of the role of RD in supporting accurate episodic memory. <<<

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation; analyses timings and patterns of tumour evolution; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity; and evaluates a range of more-specialized features of cancer genomes. <<<

Longitudinal fetal brain atlas is a powerful tool for understanding and characterizing the complex process of fetus brain development. Existing fetus brain atlases are typically constructed by averaged brain images on discrete time points independently over time. Due to the differences in onto-genetic trends among samples at different time points, the resulting atlases suffer from temporal inconsistency, which may lead to estimating error of the brain developmental characteristic parameters along the timeline. To this end, we proposed a multi-stage deep-learning framework to tackle the time inconsistency issue as a 4D (3D brain volume + 1D age) image data denoising task. Using implicit neural representation, we construct a continuous and noise-free longitudinal fetus brain atlas as a function of the 4D spatial-temporal coordinate. Experimental results on two public fetal brain atlases (CRL and FBA-Chinese atlases) show that the proposed method can significantly improve the atlas temporal consistency while maintaining good fetus brain structure representation. In addition, the continuous longitudinal fetus brain atlases can also be extensively applied to generate finer 4D atlases in both spatial and temporal resolution. <<<

Predicting the future motion of road agents is a critical task in an autonomous driving pipeline. In this work, we address the problem of generating a set of scene-level, or joint, future trajectory predictions in multi-agent driving scenarios. To this end, we propose FJMP, a Factorized Joint Motion Prediction framework for multi-agent interactive driving scenarios. FJMP models the future scene interaction dynamics as a sparse directed interaction graph, where edges denote explicit interactions between agents. We then prune the graph into a directed acyclic graph (DAG) and decompose the joint prediction task into a sequence of marginal and conditional predictions according to the partial ordering of the DAG, where joint future trajectories are decoded using a directed acyclic graph neural network (DAGNN). We conduct experiments on the INTERACTION and Argoverse 2 datasets and demonstrate that FJMP produces more accurate and scene-consistent joint trajectory predictions than non-factorized approaches, especially on the most interactive and kinematically interesting agents. FJMP ranks 1st on the multi-agent test leaderboard of the INTERACTION dataset. <<<

Following a key developmental task of childhood-building a foundation of self-knowledge in the form of domain-specific self-concepts-adolescents begin to explore their emerging identities in ways that foster autonomy and connectedness. Neuroimaging studies of self-related processes demonstrate enhanced engagement of the ventromedial prefrontal cortex in adolescence, which may facilitate and reflect the development of identity by integrating the value of potential actions and choices. Drawing from neuroeconomic and social cognitive accounts, we propose that motivated behavior during adolescence can be modeled by a general value-based decision-making process centered around value accumulation in the ventromedial prefrontal cortex. This approach advances models of adolescent neurodevelopment that focus on reward sensitivity and cognitive control by considering more diverse value inputs, including contributions of developing self- and identity-related processes. It also considers adolescent decision making and behavior from adolescents' point of view rather than adults' perspectives on what adolescents should value or how they should behave. <<<

How could machines learn as efficiently as humans and animals? How could machines learn to reason and plan? How could machines learn representations of percepts and action plans at multiple levels of abstraction, enabling them to reason, predict, and plan at multiple time horizons? This position paper proposes an architecture and training paradigms with which to construct autonomous intelligent agents. It combines concepts such as configurable predictive world model, behavior driven through intrinsic motivation, and hierarchical joint embedding architectures trained with self-supervised learning. <<<