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Provides information on how humans see color including sensitivity of the eye, spatial effects, and temporal effects, and relative to the characteristics of the human eye explains how color is measured. (GS)

Funder: National Institute of Health (NIH) DP2-GM123495, DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individuals. We show that the human genome���s replication program is broadly encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs) ��� sequence determinants of replication initiation. rtQTLs function individually, or in combinations of proximal and distal regulators, and are enriched at sites of histone H3 trimethylation of lysines 4, 9, and 36 together with histone hyperacetylation. H3 trimethylation marks are individually repressive yet synergistically associate with early replication. We identify pluripotency-related transcription factors and boundary elements as positive and negative regulators of replication timing, respectively. Taken together, human replication timing is controlled by a multi-layered mechanism with dozens of effectors working combinatorially and following principles analogous to transcription regulation.

BackgroundEnvironmental water samples are increasingly recognised as an important reservoir of antimicrobial resistance (AMR) genes. Polymerase chain reaction (PCR) and next generation sequencing (NGS) offer a potentially inclusive surveillance platform for a wide range of AMR genes. However, molecular methods are dependent upon the extraction of DNA of high yield and quality. Current options for DNA extraction from complex environmental matrices for downstream molecular applications are either expensive or low yielding. We present here a novel magnetic bead-based DNA extraction method, for the detection of antimicrobial resistance genes (ARGs) from river water in Malawi, named MagnaExtract. MethodsMagnaExtract involves initial filtration of 250ml freshwater, followed by an overnight incubation of the filter in 15ml buffered peptone water (BPW), common procedure in microbiology laboratories. 200{micro}l is then taken for a boil (95{degrees}C) and spin step and mixed with magnetic beads to bind DNA. Following washes with ethanol, the DNA is eluted in nuclease-free water. To determine the effectiveness of this method, 98 freshwater samples were collected from two rivers in Southern Malawi, and DNA was isolated using the MagnaExtract method, two commercial Qiagen (Germany) kits; PowerWater and DNeasy Blood and tissue, alongside a boil and spin of BPW, and a boil and spin from bacterial isolate grown on agar media. All samples were screened with a high-resolution melt (HRM) PCR panel previously validated for the detection of third generation cephalosporin and carbapenem ARGs. We compared the DNA yield obtained using all extraction methods, as well as the identification of each ARG. ResultsDNA yield using MagnaExtract was statistically greater than both boil and spin methods and DNeasy Blood & Tissue (Qiagen, Germany). DNA yield was slightly lower than using PowerWater (Qiagen) but the difference was not statistically significant. MagnaExtract was the only method to identify ARGs in all 98 water samples compared with PowerWater (n=82), DNeasy (n=95) boilate of BPW (n=75) and boilate of bacterial isolate (n=87). The most commonly detected ARG was OXA-48 (n=93). In addition, we found overnight incubation in non-selective enrichment broth (BPW) to promote the growth of bacteria harbouring extended spectrum beta lactamase (ESBL) genes and reduction in the detection of carbapenemase genes. ConclusionThe MagnaExtract approach offers a simple, affordable, high yielding DNA extraction method for the detection of ARGs isolated from river water samples.

Introduction The Ayurvedic theory of Tri-Dosha offers a unique framework for understanding human differences in health and disease. The Doshas could be readily applied in clinical studies to control for such differences the same way sex, age, height and weight are routinely used except that clinical evaluation is required and methods vary. No open-source questionnaire has been shown to be reliable for self-assessment. Therefore, we undertook this study to develop a reliable Dosha self-assessment questionnaire with characteristics suitable for use in clinical research. Methods A review of published questionnaires and translations of classic Ayurvedic texts along with an analysis of item-total correlations and ANOVAs by Dosha for 735 responses to a 37-item ipsative questionnaire from an Ayurveda products company served as the basis for generating 108 Dosha-specific test items featuring a 7-point Likert scale. We used item-total and inter-item correlations from a convenience sample of 176 individuals to identify the best performing items. We then solicited repeat responses to the resultant 39-item questionnaire (13 for each Dosha) from these and other website visitors and calculated test-retest reliability as the intraclass correlation coefficient for absolute agreement (ICC 2,1) for each Dosha. Results The final questionnaire gives normally distributed results. Among 76 self-selected adults, the test-retest reliabilities for Vata, Pitta and Kapha Dosha scores are all above 0.8. Conclusions This study demonstrates that it is possible to quantify the three Doshas with adequate reliability for most clinical studies.

A link between diet and avian intestinal anatomy is generally assumed. We collated the length of intestinal sections and body mass of 390 bird species and tested relationships with diet, climate and locomotion. There was a strong phylogenetic signal in all datasets. The total and small intestine scaled more-than-geometrically (95%CI of the scaling exponent > 0.33). The traditional dietary classification (faunivore, omnivore and herbivore) had no significant effect on total intestine (TI) length. Significant dietary proxies included %folivory, %frugi-nectarivory and categories (frugi-nectarivory, granivory, folivory, omnivory, insectivory and vertivory). Individual intestinal sections were affected by different dietary proxies. The best model indicates that higher consumption of fruit and nectar, drier habitats, and a high degree of flightedness are linked to shorter TI length. Notably, the length of the avian intestine depends on other biological factors as much as on diet. Given the weak dietary signal in our datasets, the diet intestinal length relationships lend themselves to narratives of flexibility (morphology is not destiny) rather than of distinct adaptations that facilitate using one character (intestine length) as proxy for another (diet). Birds have TIs of about 85% that of similar-sized mammals, corroborating systematic differences in intestinal macroanatomy between vertebrate clades.

This study investigates and ranks the critical capacity building challenges (CBC) impacting the Tanzanian public–private partnerships (PPPs) projects. The strength of interactions between CBC is established, with practical solution proposals offered and benchmarked with previous studies. A total of 8 CBC were identified from a scoping review. Data was then collected from 81 PPP practitioners, and subjected to descriptive and inferential statistics. The results demonstrated a disparity of ranking of the 8 CBC among those with and without PPP experience, with the most highly ranked 4 CBC identified as ‘limited local people with experience’, ‘lack of resources’; ‘lack of successful PPP projects’, and ‘lack of permanent PPP trainers’. The least ranked was ‘lack of political will for promoting PPPs’. Strong and positive correlation between ‘inadequate qualifications’ and ‘lack of hands-on training’ was established. Suggested solutions were broadly classified in the following four categories: (1) Training and education; (2) Benchmarking and lessons learnt; (3) Knowledge transfer and experience sharing; and (4) Institutional reforms; and supportive enabling environments. The results of this study foster better understanding of the facets of capacity building, provides PPP stakeholders with solutions for mitigating and addressing the challenges during the PPP project lifecycle. Refereed/Peer-reviewed

RATIONALE Additional biomarkers are needed to guide initiation of treatment for Mycobacterium avium pulmonary disease (Mav-PD). Time to positive sputum culture detection (TTP) may offer potential prognostic and monitoring value. OBJECTIVE To determine whether TTP is associated with infection severity and early treatment response in Mav-PD? METHODS We undertook a retrospective cohort study of patients with ≥2 sputum cultures positive for M. avium, an 'index' sputum M. avium isolate during 2015-2019, a CT scan within 6 months, and no treatment for ≥6 months prior to index sputum. TTP was estimated from the date of laboratory receipt of the specimen to the date of culture positivity confirmation. TTP was tested for association with markers of infection severity (Mav-PD, bronchiectasis, cavitary disease, treatment initiation by 3 and 6 months, AFB smear) and treatment response using Mann-Whitney U, Spearman's Correlation Coefficient, and Wilcoxon signed-rank tests. We explored a threshold TTP that could identify significant M. avium disease. RESULTS We included 125 patients with mean (SD) age 68.5 (12.5) years and 65% fulfilled disease criteria. Median TTP was 12 days (IQR 10-15; range 6-44). TTP and AFB smear grade were negatively correlated (ρ -0.58, p

Digestive functions of the colon depend on sensory-motor reflexes in the enteric nervous system (ENS), initiated by intrinsic primary afferent neurons (IPANs). IPAN terminals project to the mucosal layer of the colon, allowing communication with epithelial cells comprising the colon lining. The chemical nature and functional significance of this epithelial-neural communication in regard to secretion and colon motility are of high interest. Colon epithelial cells can produce and release neuroactive substances such as ATP and 5-hydroxytryptamine (5-HT), which can activate receptors on adjacent nerve fibers, including IPAN subtypes. In this study, we examined if stimulation of epithelial cells alone is sufficient to activate neural circuits that control colon motility. Optogenetics and calcium imaging were used in ex vivo preparations of the mouse colon to selectively stimulate the colon epithelium, measure changes in motility, and record activity of neurons within the myenteric plexus. Light-mediated activation of epithelial cells lining the distal, but not proximal, colon caused local contractions and increased the rate of colonic migrating motor complexes. Epithelial-evoked local contractions in the distal colon were reduced by both ATP and 5-HT receptor antagonists. Our findings indicate that colon epithelial cells likely use purinergic and serotonergic signaling to initiate activity in myenteric neurons, produce local contractions, and facilitate large-scale coordination of ENS activity responsible for whole colon motility patterns. NEW & NOTEWORTHY Using an all-optical approach to measure real-time cell-to-cell communication responsible for colon functions, we show that selective optogenetic stimulation of distal colon epithelium produced activity in myenteric neurons, as measured with red genetically encoded calcium indicators. The epithelial-induced neural response led to local contractions, mediated by both purinergic and serotonergic signaling, and facilitated colonic motor complexes that propagate from proximal to distal colon.

Background and aim Metabolic syndrome (MetS) is a complex disease of physiological imbalances interrelated to abnormal metabolic conditions, such as abdominal obesity, type II diabetes, dyslipidemia and hypertension. In the present pilot study, we investigated the nutraceutical bitter melon (Momordica charantia L) -intake induced transcriptome and metabolome changes and the converging metabolic signaling networks underpinning its inhibitory effects against MetS-associated risk factors. Experimental procedure Metabolic effects of lyophilized bitter melon juice (BMJ) extract (oral gavage 200 mg/kg/body weight-daily for 40 days) intake were evaluated in diet-induced obese C57BL/6J male mice [fed-high fat diet (HFD), 60 kcal% fat]. Changes in a) serum levels of biochemical parameters, b) gene expression in the hepatic transcriptome (microarray analysis using Affymetrix Mouse Exon 1.0 ST arrays), and c) metabolite abundance levels in lipid-phase plasma [liquid chromatography mass spectrometry (LC-MS)-based metabolomics] after BMJ intervention were assessed. Results and conclusion BMJ-mediated changes showed a positive trend towards enhanced glucose homeostasis, vitamin D metabolism and suppression of glycerophospholipid metabolism. In the liver, nuclear peroxisome proliferator-activated receptor (PPAR) and circadian rhythm signaling, as well as bile acid biosynthesis and glycogen metabolism targets were modulated by BMJ (p

There is increasing interest in growing European origin apple cultivars for the production of hard cider in Canada; however, little is known about their winter hardiness. Eleven promising cider cultivars were evaluated for cold hardiness over two consecutive winters and compared with the winter tender cultivar ‘Golden Delicious’. Sections of the current season’s dormant shoots were frozen in a series of test temperatures ranging from −20 °C to −40 °C in a programmable freezer. Xylem tissue browning ratings were used to assess injury after thawing. The temperature of incipient damage (TID), the warmest temperature at which 1-yr-old shoot segments begin to show injury, was obtained from tissue browning curves using non-linear regression. TID varied significantly among cultivars and between sampling years. Overall, the cultivars could be classified according to relative winter hardiness as follows: Ashmead’s Kernel, Bramley’s Seedling (very tender)

Pest density – plant damage relationships are essential guides for decision-making in integrated pest management. In this article, we established pest density – leaf damage relationships for the beech leaf-mining weevil, Orchestes fagi L. (formerly Rhynchaenus fagi, Coleoptera: Curculionidae), in its invasive range of Nova Scotia, Canada. Outbreaks of O. fagi cause tree-wide leaf necrosis in American beech (Fagus grandifolia Ehrh.), which can eventually result in tree mortality. In 2014 and 2016, we collected weekly samples in stands with American beech and assessed leaves for densities during different life stages (eggs, larvae, and pupae), population proxy measures (adult feeding damage, egg slits, and larval galleries), and percent necrosis. In general, feeding damage and leaf necrosis plateaued soon after the end of budburst, but before the larval mine expanded. This strongly suggested that leaf necrosis may be linked to damage caused by adults or by mine initiation rather than that caused by larval mine expansion and gallery development. The density of O. fagi per leaf for life stages and population proxies all significantly explained ∼42%–81% of the variation in end-of-season percent leaf necrosis. Results from this study provide a variety of relationships that could be used in both short- and long-term monitoring efforts for O. fagi.

Spatial stock assessment models are recognised as increasingly important for estimation of stock status and a sustainable exploitation rate. The inclusion of movement between spatial units within a model is difficult because the data requirements are high. However, for populations with low levels of spatial exchange it is possible to reduce the data requirements by distributing information on biological parameters between neighbouring units, or units with shared environmental conditions. This can allow spatial modelling to be applied even in data-limited situations. We develop this approach here through application to orange roughy (Hoplostethus atlanticus) subpopulations inhabiting neighbouring seamounts in the South Pacific. Despite limited data for each seamount, we were able to simultaneously fit multiple, localised, process-based models of the depletion dynamics. This was achieved by sharing information on the unexploited population size via known environmental covariates, with the relationship estimated in a hierarchical and integrated manner during the model fit. Cross-validation demonstrated that this approach can compensate for a lack of seamount-specific abundance data and improve ability of the model to estimate localised depletions.

Uterine fibroids disproportionately impact Black women. Evidence suggests Black women have earlier onset and higher cumulative risk. This risk disparity may be due an imbalance of risk alleles in one parental geographic ancestry subgroup relative to others. We investigated ancestry proportions for the 1000 Genomes phase 3 populations clustered into six geographic groups for association with fibroid traits in Black women (n = 583 cases, 797 controls) and White women (n = 1195 cases, 1164 controls). Global ancestry proportions were estimated using ADMIXTURE. Dichotomous (fibroids status and multiple fibroid status) and continuous outcomes (volume and largest dimension) were modeled for association with ancestry proportions using logistic and linear regression adjusting for age. Effect estimates are reported per 10% increase in genetically inferred ancestry proportion. Among Black women, West African (WAFR) ancestry was associated with fibroid risk, East African ancestry was associated with risk of multiple fibroids, Northern European (NEUR) ancestry was protective for multiple fibroids, Southern European ancestry was protective for fibroids and multiple fibroids, and South Asian (SAS) ancestry was positively associated with volume and largest dimension. In White women, NEUR ancestry was protective for fibroids, SAS ancestry was associated with fibroid risk, and WAFR ancestry was positively associated with volume and largest dimension. These results suggest that a proportion of fibroid risk and fibroid trait racial disparities are due to genetic differences between geographic groups. Further investigation at the local ancestry and single variant levels may yield novel insights into disease architecture and genetic mechanisms underlying ethnic disparities in fibroid risk.

Forestry plantations have been established globally to meet timber demands, often leading to the conversion of natural to artificial forests. Forestry plantations may support natural elements of forest biodiversity, but understanding their role in the maintenance of biodiversity is a crucial question. We performed a meta-analysis of 48 studies to determine how forestry plantations relative to natural forests influence the species richness and abundance of three important coleopteran groups (i.e., ground beetles, rove beetles, and dung beetles), given their essential role in ecosystem functioning. We assessed whether beetle responses depended on taxonomic group, geographical location, native or exotic character of the planted tree species, and associated management characteristics (i.e., composition, size, age, and connectivity of the plantations). We found that forestry plantations negatively affected coleopteran species richness and abundance compared to natural forests. The negative impact was most severe in plantations with exotic tree species and located in tropical biomes. Species richness and abundance of beetles significantly increased with plantation age in native plantations but decreased in exotic ones. Also, small plantations close to native forest had higher beetle species richness and abundance than ones located far away from native forest. Stopping the conversion of natural forests to plantations, promoting the use of native tree species, and lengthening rotations are critical for allowing biodiversity recovery in forestry plantations, combined with a robust conservation strategy to protect threatened biodiversity and ecosystem functioning., Hungarian Basic Research Fund, Remedinal, Natural Environment Research Council, Ministerio de Ciencia e Innovación

The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.

As Arctic ecosystems become increasingly vulnerable to climate- and human-induced stressors, effective marine management will rely on the characterization of fish movements. Over a six-year study period, the movements of 65 Greenland sharks (Somniosus microcephalus) (41 males, 24 females; mean LT = 2.48 ± 0.50 m) were monitored using static acoustic telemetry. Shark presence in a typical deep-water fjord was restricted to the summer open-water period. Residency duration varied based on age class (juvenile, n = 17; subadult, n = 48); however, activity space size and extent were comparable. A quarter of tagged sharks (n = 16) returned to the system in subsequent years after tagging, with individuals redetected for a maximum of 4 years. Movements between coastal and offshore waters occurred primarily via a deep-water channel with sharks detected along the channel banks. These multiyear data depict how a potentially vulnerable Arctic predator utilizes a deep-water fjord in the context of the regional development of community inshore and offshore commercial fisheries.

Sown wildflower areas are increasingly recommended as an agri-environmental intervention measure, but evidence for their success is limited to particular insect groups or hampered by the challenges of establishing seed mixes and maintaining flower abundance over time. We conducted a replicated experiment to establish wildflower areas to support insect pollinators in apple orchards. Over three years, and across 23 commercial UK orchards with and without sown wildflowers, we conducted 828 transect surveys across various non-crop habitats. We found that the abundance of flower-visiting solitary bees, bumblebees, honeybees, and beetles was increased in sown wildflower areas, compared with existing non-crop habitats in control orchards, from the second year following floral establishment. Abundance of hoverflies and other non-syrphid flies was increased in wildflower areas from the first year. Beyond the effect of wildflower areas, solitary bee abundance was also positively related to levels of floral cover in other local habitats within orchards, but neither local nor wider landscape-scale context affected abundance of other studied insect taxa within study orchards. There was a change in plant community composition on the sown wildflower areas between years, and in patterns of flowering within and between years, showing a succession from unsown weedy species towards a dominance of sown species over time. We discuss how the successful establishment of sown wildflower areas and delivery of benefits for different insect taxa relies on appropriate and reactive management practices as a key component of any such agri-environment scheme.

Aquatic vegetation provides many services for aquatic habitats and fish communities. The federally listed fountain darter Etheostoma fonticola, found only in spring systems of the San Marcos and Comal rivers in central Texas, is reported to associate with vegetation for feeding, reproduction, and refuge. Descriptions of associations with vegetation range from preferred to exclusive, whereas other studies describe fountain darters found outside of vegetation. The purposes of this study were to quantify fountain darter occurrences and abundances among vegetated habitats using the concept of obligate and facultative habitat use. Wadeable and non-wadeable habitats among multiple reaches of the San Marcos and Comal rivers were sampled with seines and SCUBA diving methods in the spring and fall from 2014 to 2019. Fountain darters were often associated with aquatic vegetation but demonstrated both obligate and facultative tendencies. Fountain darters occurred in vegetation more than expected among wadeable and non-wadeable habitats in the majority of reaches within the San Marcos and Comal rivers. Among vegetation taxa, they were positively associated with bryophytes and negatively associated with Texas wild rice, but associations with other vegetation taxa varied by river and were possibly influenced by other variables. Current vegetation management in both rivers includes the removal of non-native species and restoration of native vegetation, so understanding the patterns of fountain darter associations with vegetation can guide future management and restoration efforts of these spring systems.

Tropical forest degradation affects host-parasite interactions, determining the probability of animals acquiring an infection. The activation of an immune response to fight off infections requires energy and other resources such as antioxidants which may be redirected from growth and reproduction. A key question is how selective logging—the most common form of tropical forest degradation—impacts the prevalence of avian haemosporidian infection and its correlated physiological responses (nutritional and oxidative status markers). We investigated the prevalence of Plasmodium, Haemoproteus, and Leucocytozoon parasites in 14 understorey bird species in lowland, logged and unlogged, old-growth forests of Borneo. Prevalences of infections were similar between selectively logged and unlogged forests. To explore nutritional and oxidative status effects of haemosporidian infections, we examined associations between infections and plasma proteins, plasma triglycerides, and multiple blood-based markers of oxidative status, testing for an impact of selective logging on those markers. Birds infected with Plasmodium showed higher levels of plasma proteins and non-enzymatic antioxidant capacity, and lower levels of plasma triglycerides and glutathione, compared with haemosporidian-free individuals. Conversely, birds infected with Haemoproteus showed no changes in nutritional or physiological markers compared with uninfected individuals. These results indicate higher metabolic and physiological costs of controlling Plasmodium infection, compared with Haemoproteus, possibly due to higher pathogenicity of Plasmodium. Selectively logged forests had no effect on the responses of birds to infection, suggesting that the environmental conditions of degraded forests do not appear to induce any appreciable physiological demands in parasitised birds.

Building the Tree of Life is an ongoing activity of scientists around the world, one that combines information from both the genotype and phenotype of organisms. I review recent trends in this effort and describe a number of models, including the multispecies coalescent model, as a means to achieve this end.

Nearly two years since the start of the SARS-CoV-2 pandemic, which has caused over 5 million deaths, the world continues to be on high COVID-19 alert. The World Health Organization (WHO), in collaboration with national authorities, public health institutions and scientists have been closely monitoring and assessing the evolution of SARS-CoV-2 since January 2020 (WHO 2021a; WHO 2021b). The emergence of specific SARS-CoV-2 variants were characterised as Variant of Interest (VOI) and Variant of Concern (VOC), to prioritise global monitoring and research, and to inform the ongoing global response to the COVID-19 pandemic. The WHO and its international sequencing networks continuously monitor SARS-CoV-2 mutations and inform countries about any changes that may be needed to respond to the variant, and prevent its spread where feasible. Multiple variants of the virus have emerged and become dominant in many countries since January 2021, with the Alpha, Beta, Gamma and Delta variants being the most prominent to date. (Table 1).

Background & Aims Colonic motor patterns have been described by a number of different groups, but the neural connectivity and ganglion architecture supporting patterned motor activity have not been elucidated. Our goals were to describe quantitatively, by region, the structural architecture of the mouse enteric nervous system and use functional calcium imaging, pharmacology, and electrical stimulation to show regional underpinnings of different motor patterns. Methods Excised colon segments from mice expressing the calcium indicator GCaMP6f or GCaMP6s were used to examine spontaneous and evoked (pharmacologic or electrical) changes in GCaMP-mediated fluorescence and coupled with assessment of colonic motor activity, immunohistochemistry, and confocal imaging. Three-dimensional image reconstruction and statistical methods were used to describe quantitatively mouse colon myenteric ganglion structure, neural and vascular network patterning, and neural connectivity. Results In intact colon, regionally specific myenteric ganglion size, architecture, and neural circuit connectivity patterns along with neurotransmitter-receptor expression underlie colonic motor patterns that define functional differences along the colon. Region-specific effects on spontaneous, evoked, and chemically induced neural activity contribute to regional motor patterns, as does intraganglionic functional connectivity. We provide direct evidence of neural circuit structural and functional regional differences that have only been inferred in previous investigations. We include regional comparisons between quantitative measures in mouse and human colon that represent an important advance in showing the usefulness and relevance of the mouse system for translation to the human colon. Conclusions There are several neural mechanisms dependent on myenteric ganglion architecture and functional connectivity that underlie neurogenic control of patterned motor function in the mouse colon., Graphical abstract

In the first results from an ongoing global cancer screening data repository, screening program organization was better overall in Europe compared to other continents; however, there were substantial gaps in implementation across both high- and low-resource settings. The CanScreen5 project is a global cancer screening data repository that aims to report the status and performance of breast, cervical and colorectal cancer screening programs using a harmonized set of criteria and indicators. Data collected mainly from the Ministry of Health in each country underwent quality validation and ultimately became publicly available through a Web-based portal. Until September 2022, 84 participating countries reported data for breast (n = 57), cervical (n = 75) or colorectal (n = 51) cancer screening programs in the repository. Substantial heterogeneity was observed regarding program organization and performance. Reported screening coverage ranged from 1.7% (Bangladesh) to 85.5% (England, United Kingdom) for breast cancer, from 2.1% (Cote d'Ivoire) to 86.3% (Sweden) for cervical cancer, and from 0.6% (Hungary) to 64.5% (the Netherlands) for colorectal cancer screening programs. Large variability was observed regarding compliance to further assessment of screening programs and detection rates reported for precancers and cancers. A concern is lack of data to estimate performance indicators across the screening continuum. This underscores the need for programs to incorporate quality assurance protocols supported by robust information systems. Program organization requires improvement in resource-limited settings, where screening is likely to be resource-stratified and tailored to country-specific situations.

Identification of pollen vectors is a fundamental objective of pollination biology. The foraging and social behavior of these pollinators has profound effects on plant mating, making quantification of their behavior critical for understanding the ecological and evolutionary consequences of different pollinators for the plants they visit. However, accurate quantification of visitation may be problematic, especially for shy animals and/or when the temporal and spatial scale of observation desired is large. Sophisticated heat‐ and movement‐triggered motion‐sensor cameras (“camera trapping”) provide new, underutilized tools to address these challenges. However, to date, there has been no rigorous evaluation of the sampling considerations needed for using camera trapping in pollination research.We measured the effectiveness of camera trapping for identifying vertebrate visitors and quantifying their visitation rates and foraging behavior on Banksia menziesii (Proteaceae). Multiple still cameras (Reconyx HC 500) and a video camera (Little Acorn LTL5210A) were deployed.From 2,753 recorded visits by vertebrates, we identified five species of nectarivorous honeyeater (Meliphagidae) and the honey possum (Tarsipedidae), with significant variation in the species composition of visitors among inflorescences. Species of floral visitor showed significant variation in their time of peak activity, duration of visits, and numbers of flowers probed per visit. Where multiple cameras were deployed on individual inflorescences, effectiveness of individual still cameras varied from 15% to 86% of all recorded visits. Methodological issues and solutions, and the future uses of camera traps in pollination biology, are discussed. Conclusions and wider implications: Motion‐triggered cameras are promising tools for the quantification of vertebrate visitation and some aspects of behavior on flowers. However, researchers need to be mindful of the variation in effectiveness of individual camera traps in detecting animals. Pollinator studies using camera traps are in their infancy, and the full potential of this developing technology is yet to be realized.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences., We thank them for their permission to publish. A.R., S.K., B.P.W. and A.M.P. were supported by the Intramural Research Program of the NHGRI, NIH (1ZIAHG200398). A.R. was also supported by the Korea Health Technology R&D Project through KHIDI, funded by the Ministry of Health & Welfare, Republic of Korea (HI17C2098). S.A.M., I.B. and R.D. were supported by Wellcome Trust grant WT207492; W.C., M. Smith, Z.N., Y.S., J.C., S. Pelan, J.T., A.T., J.W. and Kerstin Howe by WT206194; L.H., F.M., Kevin Howe and P. Flicek by WT108749/Z/15/Z, WT218328/B/19/Z and the European Molecular Biology Laboratory. O.F. and E.D.J. were supported by Howard Hughes Medical Institute and Rockefeller University start-up funds for this project. J.D. and H.A.L. were supported by the Robert and Rosabel Osborne Endowment. M.U.-S. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (750747). F.T.-N., J. Hoffman, P. Masterson and K.C. were supported by the Intramural Research Program of the NLM, NIH. C.L., B.J.K., J. Kim and H.K. were supported by the Marine Biotechnology Program of KIMST, funded by the Ministry of Ocean and Fisheries, Republic of Korea (20180430). M.C. was supported by Sloan Research Fellowship (FG-2020-12932). S.C.V. was funded by a Max Planck Research Group award from the Max Planck Society, and a Human Frontiers Science Program (HFSP) Research grant (RGP0058/2016). T.M.L., W.E.J. and the Canada lynx genome were funded by the Maine Department of Inland Fisheries & Wildlife (F11AF01099), including when W.E.J. held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research (WRAIR). C.B. was supported by the NSF (1457541 and 1456612). D.B. was funded by The University of Queensland (HFSP - RGP0030/2015). D.I. was supported by Science Exchange Inc. (Palo Alto, CA). H.W.D. was supported by NSF grants (OPP-0132032 ICEFISH 2004 Cruise, PLR-1444167 and OPP-1955368) and the Marine Science Center at Northeastern University (416). G.J.P.N. and the thorny skate genome were funded by Lenfest Ocean Program (30884). M.P. was funded by the German Federal Ministry of Education and Research (01IS18026C). M. Malinsky was supported by an EMBO fellowship (ALTF 456-2016). The following authors’ contributions were supported by the NIH: S. Selvaraj (R44HG008118); C.V.M., S.R.F., P.V.L. (R21 DC014432/DC/NIDCD); K.D.M. (R01GM130691); H.C. (5U41HG002371-19); M.D. (U41HG007234); and B.P. (R01HG010485). D.G. was supported by the National Key Research and Development Program of China (2017YFC1201201, 2018YFC0910504 and 2017YFC0907503). F.O.A. was supported by Al-Gannas Qatari Society and The Cultural Village Foundation-Katara, Doha, State of Qatar and Monash University Malaysia. C.T. was supported by The Rockefeller University. M. Hiller was supported by the LOEWE-Centre for Translational Biodiversity Genomics (TBG) funded by the Hessen State Ministry of Higher Education, Research and the Arts (HMWK). H.C. was supported by the NHGRI (5U41HG002371-19). R.H.S.K. was funded by the Max Planck Society with computational resources at the bwUniCluster and BinAC funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg, Germany (bwHPC-C5). B.V. was supported by the Biomedical Research Council of A*STAR, Singapore. T.M.-B. was funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (864203), MINECO/FEDER, UE (BFU2017-86471-P), Unidad de Excelencia María de Maeztu, AEI (CEX2018-000792-M), a Howard Hughes International Early Career award, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). E.C.T. was supported by the European Research Council (ERC-2012-StG311000) and an Irish Research Council Laureate Award. M.T.P.G. was supported by an ERC Consolidator Award 681396-Extinction Genomics, and a Danish National Research Foundation Center Grant (DNRF143). T.W. was supported by the NSF (1458652). J. M. Graves was supported by the Australian Research Council (CEO561477). E.W.M. was partially supported by the German Federal Ministry of Education and Research (01IS18026C). Complementary sequencing support for the Anna’s hummingbird and several genomes was provided by Pacific Biosciences, Bionano Genomics, Dovetail Genomics, Arima Genomics, Phase Genomics, 10X Genomics, NRGene, Oxford Nanopore Technologies, Illumina, and DNAnexus. All other sequencing and assembly were conducted at the Rockefeller University, Sanger Institute, and Max Planck Institute Dresden genome labs. Part of this work used the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov). We acknowledge funding from the Wellcome Trust (108749/Z/15/Z) and the European Molecular Biology Laboratory., With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M).