jMorp: Japanese Multi-Omics Reference Panel update report 2023.

Modern medicine is increasingly focused on personalized medicine, and multi-omics data is crucial in understanding biological phenomena and disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing disease risk and drug response. Therefore, multi-omics data from specific ethnic populations are essential for the effective implementation of personalized medicine. Various prospective cohort studies, such as the UK Biobank, All of Us and Lifelines, have been conducted worldwide. The Tohoku Medical Megabank project was initiated after the Great East Japan Earthquake in 2011. It collects biological specimens and conducts genome and omics analyses to build a basis for personalized medicine. Summary statistical data from these analyses are available in the jMorp web database (https://jmorp.megabank.tohoku.ac.jp), which provides a multidimensional approach to the diversity of the Japanese population. jMorp was launched in 2015 as a public database for plasma metabolome and proteome analyses and has been continuously updated. The current update will significantly expand the scale of the data (metabolome, genome, transcriptome, and metagenome). In addition, the user interface and backend server implementations were rewritten to improve the connectivity between the items stored in jMorp. This paper provides an overview of the new version of the jMorp.

The collapse of eastern Bering Sea snow crab.

The snow crab is an iconic species in the Bering Sea that supports an economically important fishery and undergoes extensive monitoring and management. Since 2018, more than 10 billion snow crab have disappeared from the eastern Bering Sea, and the population collapsed to historical lows in 2021. We link this collapse to a marine heatwave in the eastern Bering Sea during 2018 and 2019. Calculated caloric requirements, reduced spatial distribution, and observed body conditions suggest that starvation played a role in the collapse. The mortality event appears to be one of the largest reported losses of motile marine macrofauna to marine heatwaves globally.

High school science fair: School location trends in student participation and experience.

The findings reported in this paper are based on surveys of U.S. high school students who registered and managed their science and engineering fair (SEF) projects through the online Scienteer website over the three years 2019/20, 2020/21, and 2021/22. Almost 2500 students completed surveys after finishing all their SEF competitions. We added a new question in 2019/20 to our on-going surveys asking the students whether their high school location was urban, suburban, or rural. We learned that overall, 74% of students participating in SEFs indicated that they were from suburban schools. Unexpectedly, very few SEF participants, less than 4%, indicated that they were from rural schools, even though national data show that more than 20% of high school students attend rural schools. Consistent with previous findings, Asian and Hispanic students indicated more successful SEF outcomes than Black and White students. However, whereas Asian students had the highest percentage of SEF participants from suburban vs. urban schools- 81% vs. 18%, Hispanic students had the most balanced representation of participants from suburban vs. urban schools- 55% vs. 39%. Differences in students' SEF experiences based on gender and ethnicity showed the same patterns regardless of school location. In the few items where we observed statistically significant (probability < .05) differences based on school location, students from suburban schools were marginally favored by only a few percentage points compared to students from urban schools. In conclusion, based on our surveys results most students participating in SEFs come from suburban schools, but students participating in SEFs and coming from urban schools have equivalent SEF experiences, and very few students participating in SEFs come from rural schools.

Unmanned aerial vehicles (UAVs) with thermal infrared (TIR) sensors are effective for monitoring and counting threatened Vietnamese primates.

Monitoring the population size of threatened primate species with minimal disturbance is becoming an outstanding requirement for conservation and wildlife management. Drones with thermal infrared (TIR) and visible spectrum (RGB) imaging are increasingly used to survey arboreal primates, but ground-truthing is still required to assess the effectiveness of drone-based count estimates. Our pilot study aims to assess the ability of a drone with both TIR and RGB sensors to detect, count, and identify semi-wild population of four endangered species of langurs and gibbon in the Endangered Primate Rescue Center (EPRC) in northern Vietnam. We found that TIR imagery enabled higher detection rates compared to RGB imagery and obtained an accurate count with the TIR only after four drone flights. We could identify langurs species based on thermal signature at a flight height of 50 m from the ground level (max tree height = 15 m), via size and shape of the body. With TIR imagery, we were able to record inconspicuous behaviors such as foraging and play. While some individuals initially showed flight or avoidance behaviors when the drone was sighted, these behaviors decreased or were absent on following drone surveys. Our study suggests that monitoring and precisely counting langur and gibbon species populations could be successful with the use of thermal drones only.

On the genes, genealogies, and geographies of Quebec.

Population genetic models only provide coarse representations of real-world ancestry. We used a pedigree compiled from 4 million parish records and genotype data from 2276 French and 20,451 French Canadian individuals to finely model and trace French Canadian ancestry through space and time. The loss of ancestral French population structure and the appearance of spatial and regional structure highlights a wide range of population expansion models. Geographic features shaped migrations, and we find enrichments for migration, genetic, and genealogical relatedness patterns within river networks across regions of Quebec. Finally, we provide a freely accessible simulated whole-genome sequence dataset with spatiotemporal metadata for 1,426,749 individuals reflecting intricate French Canadian population structure. Such realistic population-scale simulations provide opportunities to investigate population genetics at an unprecedented resolution.

Evaluating the Influences of Health Expenditure, Energy Consumption, and Environmental Pollution on Life Expectancy in Asia.

This study examines the effects of health expenditure, energy consumption, CO2 emissions, population size, and income on health outcomes in 46 Asian nations between 1997 and 2019. Cross-sectional dependence (CSD) and slope heterogeneity (SH) tests are utilized due to the close linkages between Asian nations as a result of commerce, tourism, religion, and international agreements. The research uses unit root and cointegration tests of the second generation after validating CSD and SH issues. Due to the results of the CSD and SH tests, it is clear that conventional methods of estimation are inappropriate, so a new panel method, the inter autoregressive distributive lag (CS-ARDL) model, is used instead. In addition to CS-ARDL, the study's results were checked with a common correlated effects mean group (CCEMG) method and an augmented mean group (AMG) method. According to the CS-ARDL study, higher rates of energy use and healthcare spending lead to better health outcomes for Asian countries over the long run. CO2 emissions are shown to be harmful to human health, according to the study. The influence of a population's size on health outcomes is shown to be negative in the CS-ARDL and CCEMG, but favorable in the AMG. Only the AMG coefficient is significant. In most instances, the results of the AMG and CCEMG corroborate the results of the CS-ARDL. Among all the factors influencing life expectancy in Asian countries, healthcare spending is the most influential. Hence, to improve health outcomes, Asian countries need to take the required actions to boost health spending, energy consumption, and long-term economic growth. To achieve the best possible health outcomes, Asian countries should also reduce their CO2 emissions.

Meeting the ancestors.

DNA from a medieval German cemetery opens a window on the history of today's largest Jewish population.

Substitution mutational signatures in whole-genome-sequenced cancers in the UK population.

Whole-genome sequencing (WGS) permits comprehensive cancer genome analyses, revealing mutational signatures, imprints of DNA damage and repair processes that have arisen in each patient's cancer. We performed mutational signature analyses on 12,222 WGS tumor-normal matched pairs, from patients recruited via the UK National Health Service. We contrasted our results to two independent cancer WGS datasets, the International Cancer Genome Consortium (ICGC) and Hartwig Foundation, involving 18,640 WGS cancers in total. Our analyses add 40 single and 18 double substitution signatures to the current mutational signature tally. Critically, we show for each organ, that cancers have a limited number of 'common' signatures and a long tail of 'rare' signatures. We provide a practical solution for utilizing this concept of common versus rare signatures in future analyses.

A genetic probe into the ancient and medieval history of Southern Europe and West Asia.

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank.

Haplotype-based analyses have recently been leveraged to interrogate the fine-scale structure in specific geographic regions, notably in Europe, although an equivalent haplotype-based understanding across the whole of Europe with these tools is lacking. Furthermore, study of identity-by-descent (IBD) sharing in a large sample of haplotypes across Europe would allow a direct comparison between different demographic histories of different regions. The UK Biobank (UKBB) is a population-scale dataset of genotype and phenotype data collected from the United Kingdom, with established sampling of worldwide ancestries. The exact content of these non-UK ancestries is largely uncharacterized, where study could highlight valuable intracontinental ancestry references with deep phenotyping within the UKBB. In this context, we sought to investigate the sample of European ancestry captured in the UKBB. We studied the haplotypes of 5,500 UKBB individuals with a European birthplace; investigated the population structure and demographic history in Europe, showing in parallel the variety of footprints of demographic history in different genetic regions around Europe; and expand knowledge of the genetic landscape of the east and southeast of Europe. Providing an updated map of European genetics, we leverage IBD-segment sharing to explore the extent of population isolation and size across the continent. In addition to building and expanding upon previous knowledge in Europe, our results show the UKBB as a source of diverse ancestries beyond Britain. These worldwide ancestries sampled in the UKBB may complement and inform researchers interested in specific communities or regions not limited to Britain.

The enigmatic tropical alpine flora on the African sky islands is young, disturbed, and unsaturated.

Tropical alpine floras are renowned for high endemism, spectacular giant rosette plants testifying to convergent adaptation to harsh climates with nightly frosts, and recruitment dominated by long-distance dispersal from remote areas. In contrast to the larger, more recent (late Miocene onward) and contiguous expanses of tropical alpine habitat in South America, the tropical alpine flora in Africa is extremely fragmented across small patches on distant mountains of variable age (Oligocene onward). How this has affected the colonization and diversification history of the highly endemic but species-poor afroalpine flora is not well known. Here we infer phylogenetic relationships of ∼20% of its species using novel genome skimming data and published matrices and infer a timeframe for species origins in the afroalpine region using fossil-calibrated molecular clocks. Although some of the mountains are old, and although stem node ages may substantially predate colonization, most lineages appear to have colonized the afroalpine during the last 5 or 10 My. The accumulation of species increased exponentially toward the present. Taken together with recent reports of extremely low intrapopulation genetic diversity and recent intermountain population divergence, this points to a young, unsaturated, and dynamic island scenario. Habitat disturbance caused by the Pleistocene climate oscillations likely induced cycles of colonization, speciation, extinction, and recolonization. This study contributes to our understanding of differences in the histories of recruitment on different tropical sky islands and on oceanic islands, providing insight into the general processes shaping their remarkable floras.

The blood urea nitrogen/creatinine (BUN/cre) ratio was U-shaped associated with all-cause mortality in general population.

OBJECTIVES: This study aimed to explore the relationship between the blood urea nitrogen/creatinine (BUN/Cre) ratio and all-cause or cause-specific mortality in the general population. METHODS: Participants were enrolled from the National Health and Nutrition Examination Survey (NHANES) during 1999 to 2014. Baseline variables were acquired from questionnaires and examinations. Death status were ascertained from National Death Index records. Cox proportional hazards models with cubic spines were used to estimate hazard ratios (HRs) and 95% confidence interval (CI) of all-cause mortality, cardiovascular and cancer mortality. RESULTS: A total of 42038 participants were enrolled in the study with a median 8.13 years of follow-up. Older people and women tend to have a higher BUN/Cre ratio. After multivariable adjustment, BUN/Cre ratio between 11.43 and 14.64 was associated with the lowest all-cause mortality compared with the participants with the lowest quartile (HR 0.83 [0.76, 0.91]; p < 0.001). The highest quartile of BUN/Cre ratio was associated with the lowest risk of cancer mortality (HR 0.64 [0.53, 0.78]; p < 0.001). Restricted cubic splines showed BUN/Cre was nonlinearly associated with all-cause mortality and linearly associated with cancer mortality. CONCLUSIONS: This study confirmed a U-shape relationship between BUN/Cre ratio and all-cause mortality in the general population.

A population-based study of administrative data linkage to measure melanoma surgical and pathology quality.

BACKGROUND: Continuous quality improvement is important for cancer systems. However, collecting and compiling quality indicator data can be time-consuming and resource-intensive. Here we explore the utility and feasibility of linked routinely collected health data to capture key elements of quality of care for melanoma in a single-payer, universal health care setting. METHOD: This pilot study utilized a retrospective population-based cohort from a previously developed linked administrative data set, with a 65% random sample of all invasive cutaneous melanoma cases diagnosed 2007-2012 in the province of Ontario. Data from the Ontario Cancer Registry was utilized, supplemented with linked pathology report data from Cancer Care Ontario, and other linked administrative data describing health care utilization. Quality indicators identified through provincial guidelines and international consensus were evaluated for potential collection with administrative data and measured where possible. RESULTS: A total of 7,654 cases of melanoma were evaluated. Ten of 25 (40%) candidate quality indicators were feasible to be collected with the available administrative data. Many indicators (8/25) could not be measured due to unavailable clinical information (e.g. width of clinical margins). Insufficient pathology information (6/25) or health structure information (1/25) were less common reasons. Reporting of recommended variables in pathology reports varied from 65.2% (satellitosis) to 99.6% (body location). For stage IB-II or T1b-T4a melanoma patients where SLNB should be discussed, approximately two-thirds met with a surgeon experienced in SLNB. Of patients undergoing full lymph node dissection, 76.2% had adequate evaluation of the basin. CONCLUSIONS: We found that use of linked administrative data sources is feasible for measurement of melanoma quality in some cases. In those cases, findings suggest opportunities for quality improvement. Consultation with surgeons offering SLNB was limited, and pathology report completeness was sub-optimal, but was prior to routine synoptic reporting. However, to measure more quality indicators, text-based data sources will require alternative approaches to manual collection such as natural language processing or standardized collection. We recommend development of robust data platforms to support continuous re-evaluation of melanoma quality indicators, with the goal of optimizing quality of care for melanoma patients on an ongoing basis.