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Vocal production learning (vocal learning) is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

It is still debated whether arterial elasticity provides prognostic information for cardiovascular risk beyond blood pressure measurements in a healthy population. To investigate the association between arterial elasticity obtained by radial artery pulse wave analysis and risk for cardiovascular diseases (CVD) in men and women. In 2002-2005, 2362 individuals (men=1186, 50.2%) not taking antihypertensive medication were included. C2 (small artery elasticity) was measured using the HDI/Pulse Wave CR2000. Data on acute myocardial infarction or stroke, fatal or non-fatal, was obtained between 2002-2019. Cox- regression was used to investigate associations between C2 and future CVD, adjusting for confounding factors such as age, sex, systolic blood pressure, heart rate, HOMA-IR (Homeostatic Model Assessment for Insulin Resistance), LDL- cholesterol, CRP (C-Reactive Protein), alcohol consumption, smoking and physical activity. At baseline, the mean age of 46 ± 10.6 years and over the follow-up period, we observed 108 events 70 events in men [event rate: 5.9%], 38 in women [event rate: 3.2%]. In the fully adjusted model, and for each quartile decrease in C2, there was a significant increase in the risk for incident CVD by 36%. (HR = 1.36, 95% CI: 1.01-1.82, p = 0.041). The results were accentuated for all men (HR = 1.74, 95% CI: 1.21-2.50, p = 0.003) and women over the age of 50 years (HR = 1.70, 95% CI: 0.69-4.20). We showed a strong and independent association between C2 and CVD in men. In women after menopause, similar tendencies and effect sizes were observed.

Leptomeninges, consisting of the pia mater and arachnoid, form a connective tissue investment and barrier enclosure of the brain. The exact nature of leptomeningeal cells has long been debated. In this study, we identify five molecularly distinct fibroblast-like transcriptomes in cerebral leptomeninges; link them to anatomically distinct cell types of the pia, inner arachnoid, outer arachnoid barrier, and dural border layer; and contrast them to a sixth fibroblast-like transcriptome present in the choroid plexus and median eminence. Newly identified transcriptional markers enabled molecular characterization of cell types responsible for adherence of arachnoid layers to one another and for the arachnoid barrier. These markers also proved useful in identifying the molecular features of leptomeningeal development, injury, and repair that were preserved or changed after traumatic brain injury. Together, the findings highlight the value of identifying fibroblast transcriptional subsets and their cellular locations toward advancing the understanding of leptomeningeal physiology and pathology.

Abstract Background A complex inheritance has been suggested in families with colorectal-, gastric- and prostate cancer. Therefore, we conducted a genome-wide association study (GWAS) in colorectal cancer patients, who’s relatives had prostate-, and/or gastric cancer. Methods The GWAS analysis consisted of 685 cases of colorectal cancer and 4780 healthy controls from Sweden. A sliding window haplotype analysis was conducted using a logistic regression model. Thereafter, we performed sequencing to find candidate variants, finally to be tested in a nested case–control study. Results Candidate loci/genes on ten chromosomal regions were suggested with odds ratios between 1.71–3.62 and p-values

Abstract In tissue characterization and cancer diagnostics, multimodal imaging has emerged as a powerful technique. Thanks to computational advances, large datasets can be exploited to discover patterns in pathologies and improve diagnosis. However, this requires efficient and scalable image retrieval methods. Cross-modality image retrieval is particularly challenging, since images of similar (or even the same) content captured by different modalities might share few common structures. We propose a new application-independent content-based image retrieval (CBIR) system for reverse (sub-)image search across modalities, which combines deep learning to generate representations (embedding the different modalities in a common space) with robust feature extraction and bag-of-words models for efficient and reliable retrieval. We illustrate its advantages through a replacement study, exploring a number of feature extractors and learned representations, as well as through comparison to recent (cross-modality) CBIR methods. For the task of (sub-)image retrieval on a (publicly available) dataset of brightfield and second harmonic generation microscopy images, the results show that our approach is superior to all tested alternatives. We discuss the shortcomings of the compared methods and observe the importance of equivariance and invariance properties of the learned representations and feature extractors in the CBIR pipeline. Code is available at: https://github.com/MIDA-group/CrossModal_ImgRetrieval .

Abstract Background The Nova Scotia Duck Tolling Retriever (NSDTR) has previously been highlighted as a breed at risk for developing immune mediated diseases and cancer. The immune response is of great importance for the development of neoplastic disease and a dysregulated immune response may predispose to cancer. Two of the commonly seen immune mediated diseases in NSDTRs are immune mediated rheumatic disease (IMRD), which bears similarities to systemic lupus erythematosus (SLE) affecting humans, and steroid-responsive meningitis-arteritis (SRMA), which is a non-infectious inflammation of the meninges and the leptomeningeal vessels. The aim of this survey study was to investigate the lifetime prevalence of immune mediated diseases and tumors among Swedish NSDTRs based on owners’ information. The study design was cross-sectional. A questionnaire was sent to 4102 persons who owned or had previously owned a NSDTR. The questions concerned information about the dog and its overall health status as well as specific diseases. Results The response rate was 30%, including 935 live NSDTRs, corresponding to approximately 20% of the current population registered in Sweden (n = 4564), and 177 dead dogs. The surveyed dogs were spread over different ages and sex and corresponded to the typical demographic profile of the general dog population. Of the 935 individuals that were alive, 28 dogs (3%) were reported as previously diagnosed with IMRD and 33 dogs (3.5%) were reported as previously diagnosed with SRMA, one dog was reported to have been diagnosed with both SRMA and IMRD. There were 129 dogs (14%) reported to have or have had a neoplasia of some kind. For the dead dogs (n = 177), almost 40% of the owners reported neoplasia as the main reason for death/euthanasia. Conclusion This study reports an estimated lifetime prevalence of IMRD and SRMA, in the studied population of Swedish NSDTRs, of 3.0 and 3.5% respectively. In this study, 14% of the living dogs (n = 935) were reported to have a neoplasia of some kind and almost 40% of the deceased dogs (n = 177) were euthanized due to neoplasia or suspicion of it.

Burn mass casualty event occurrences are rare but will place significant burdens on any burn unit or healthcare system. Effective disaster preparedness plays a significant role in mitigating the aftermath of a burn mass casualty. The aim of this study was to assess the resource requirements during the initial two weeks of a burn mass casualty event. Eight patients in a burn mass casualty event were simulated using the Emergo Train System®. These simulated patients were matched with real historical patients treated in our burn centre, and their resource requirements were analysed. An average of eight staff is required to care for a patient per day along with almost 75 h of operating time (excluding anaesthesia and turnover time). A substantial quantity of consumables was used in the first two weeks. This study has demonstrated the substantial material consumption and staff requirements in the first two weeks of management in a burn mass casualty event. Such findings will offer valuable insight for disaster preparedness planning and resource management strategies.

Abstract Plasmonic materials convert light into hot carriers and heat to mediate catalytic transformation. The participation of hot carriers (photocatalysis) remains a subject of vigorous debate, often argued on the basis that carriers have ultrashort lifetime incompatible with drive photochemical processes. This study utilises plasmon hot electrons directly in the photoelectrocatalytic reduction of CO2 to CO via a Ppasmonic nanohybrid. Through the deliberate construction of a plasmonic nanohybrid system comprising NiO/Au/ReI(phen-NH 2 )(CO)3Cl (phen-NH 2 = 1,10-Phenanthrolin-5-amine) that is unstable above 580 K; it was possible to demonstrate hot electrons are the main culprit in CO2 reduction. The engagement of hot electrons in the catalytic process is derived from many approaches that cover the processes in real-time, from ultrafast charge generation and separation to catalysis occurring on the minute scale. Unbiased in situ FTIR spectroscopy confirmed the stepwise reduction of the catalytic system. This, coupled with the low thermal stability of the ReI(phen-NH 2 )(CO)3Cl complex, explicitly establishes plasmonic hot carriers as the primary contributors to the process. Therefore, mediating catalytic reactions by plasmon hot carriers is feasible and holds promise for further exploration. Plasmonic nanohybrid systems can leverage plasmon’s unique photophysics and capabilities because they expedite the carrier’s lifetime.

Background & Aims: Transforming growth factor β (TGF-β) plays an oncogenic role in advanced cancer by promoting cell proliferation, metastasis and immunosuppression. PMEPA1 (prostate transmembrane protein androgen induced 1) has been shown to promote TGF-β oncogenic effects in other tumour types. Thus, we aimed to explore the role of PMEPA1 in hepatocellular carcinoma (HCC). Methods: We analysed 1,097 tumours from patients with HCC, including discovery (n = 228) and validation (n = 361) cohorts with genomic and clinicopathological data. PMEPA1 levels were assessed by qPCR (n = 228), gene expression data (n = 869) and at the single-cell level (n = 54). Genetically engineered mouse models overexpressing MYC+PMEPA1 compared to MYC were generated and molecular analyses were performed on the HCCs obtained. Results: PMEPA1 was overexpressed in 18% of HCC samples (fold-change >2; n = 201/1,097), a feature associated with TGF-β signalling activation (p

Kuormatraktoreiden käytön aiheuttamat juuristovauriot ja urapainumat ovat todennäköinen riski suometsien puunkorjuussa. Suometsien puunkorjuussa oleellista on soveltuvan korjuukaluston valinta. Työtapaan kuuluu yleensä havutuksen käyttö ajourien vahvistamisessa. Erilliset maaperän vahvistamisratkaisut, kuten erityyppiset ajosillat ja kumimatot, ovat jääneet lähinnä kokeiluasteelle. Projektissa kehitettiin puutavara-autolla ja kuormatraktorilla käsiteltävät ja siirrettävät CLT-levyt (cross laminated timber). CLT-levyjä käytettäisiin kuormatraktorin kokoojaurien ja varastopaikkojen vahvistamiseen heikosti kantavilla turvemailla. CLT-levyjen rakenneratkaisuiden lisäksi tutkittiin puutavara-auton ja kuormatraktorin soveltuvuutta, ajanmenekkiä ja kustannuksia CLT-levyjen käsittelyssä ja siirroissa. Logistiikkakustannusten määritys perustui levyjen käsittelyn työaikatutkimuksella määritettyyn ajanmenekkiin sekä kuljetuskapasiteetin osalta levyjen laskennalliseen mitoitukseen. Kokonaispainoltaan 76 000 kg:n puutavara-auton laskennallinen kuljetuskapasiteetti oli 54 CLT-levyä, joista pystyttäisiin rakentamaan nimellispituudeltaan 108 metrin pituinen ajoura. Kuorma täyttäisi puutavara-auton tilavuuskapasiteetin, mutta kantavuudesta jäisi käyttämättä noin 16 000 kg. Kenttäkokeiden kokemusten ja aikatutkimuksen tulosten perusteella levyjen kuormaus (kuormaussykli noin 40 s/levy) ja kuorman purkaminen (kuormaussykli noin 35 s/levy) puutavara-autolla ja kuormatraktorilla oli kohtalaisen sujuvaa ja ajanmenekkien hajonta pientä. Sen sijaan varsinkin levyjen asennus ajouralle oli aikaa vievää (kuormaussykli noin 100 s/levy). Työn sujuvuuteen vaikuttivat merkittävästi muun muassa kuormatraktorin tyyppi, näkyvyys ja levyjen tartuntaratkaisut. Kun levyjen kaukokuljetusmatka korjuukohteelle oli noin 50 kilometriä, oli levyjen edestakaisen autokuljetuksen kokonaiskustannus vetoauton kuormalla (18 levyä) yli 500 euroa ja täysperävaunukuormalla (54 levyä) alle 800 euroa. Kuljetuskustannus kasvoi jyrkästi kuljetusmatkan suhteen, ja toisaalta muiden kuljetusten ketjuttaminen ja tyhjänä ajon korvaaminen muilla kuljetuksilla vaikuttivat oleellisesti kustannusten tasoon. Levyjen metsäkuljetuksen ja asennuksen yksikkökustannukset olivat pienimmillään 8–9 €/levy ja kasvoivat noin 1 €/levy kun metsäkuljetusmatka kasvoi sadalla metrillä. Levyjen määrän vaikutus yksikkökustannukseen oli vähäinen. Levyjen käytöllä voitaisiin saavuttaa puunkorjuussa suoria kustannussäästöjä tilanteissa, joissa puutavaran metsäkuljetusmatkaa voitaisiin lyhentää merkittävästi ja kuljetettava puutavara­määrä olisi suurehko, vähintään 500–1000 kuutiometriä. Tilanteissa, joissa korjuulohkon sijainti on heikosti kantavan maapohjan takana, voitaisiin levyjen käytöllä mahdollistaa korjuun ajoittaminen sulan maan ajalle.

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.