A pragmatic strategy for implementing spatially correlated observation errors in an operational system: an application to Doppler radial winds

Recent research has shown that high resolution observations, such as Doppler radar radial winds, exhibit spatial correlations. High resolution observations are routinely assimilated into convection permitting numerical weather prediction models assuming their errors are uncorrelated. To avoid violating this assumption observation density is severely reduced. To improve the quantity of observations used and the impact that they have on the forecast requires the introduction of full, correlated, error statistics. Some operational centres have introduced satellite inter-channel observation error correlations and obtained improved analysis’ accuracy and forecast skill scores. Here we present a strategy for implementing spatially correlated observation errors in an operational system. We then provide the first demonstration of the practical feasibility of incorporating spatially correlated Doppler radial wind error statistics in the Met Office numerical weather prediction system. Inclusion of correlated Doppler radial winds error statistics has little impact on the computation cost of the data assimilation system, even with a four-fold increase in the number of Doppler radial winds observations assimilated. Using the correlated observation error statistics with denser observations produces increments with shorter length scales than the control. Initial forecast trials show a neutral to positive impact on forecast skill overall, notably for quantitative precipitation forecasts. There is potential to improve forecast skill by optimising the use of Doppler radial winds and applying the technique to other observation types

Isolation, small population size, and management influence inbreeding and reduced genetic variation in K’gari dingoes

Small island populations are vulnerable to genetic decline via demographic and environmental stochasticity. In the absence of immigration, founder effects, inbreeding and genetic drift are likely to contribute to local extinction risk. Management actions may also have a greater impact on small, closed populations. The demographic and social characteristics of a species can, however, delay the impact of threats. K’gari, a ~ 1 660 km2 island off the Australian east coast and UNESCO World Heritage Site (Fraser Island 1842–2023), supports an isolated population of approximately 70–200 dingoes that represent an ideal opportunity to explore the small island paradigm. To examine temporal and spatial patterns of genetic diversity in this population we analysed single nucleotide polymorphism (SNP) genotype data (72 454 SNPS) for 112 K’gari dingoes collected over a 25-year period (1996 to 2020). Genetic diversity was lower in K’gari dingoes than mainland dingoes at the earliest time point in our study and declined significantly following a management cull in 2001. We did not find any spatial genetic patterns on the island, suggesting high levels of genetic connectivity between socially discrete packs. This connectivity, combined with the social structure and behaviour of dingoes, may act in concert to buffer the population from the impacts of genetic drift in the short term. Nevertheless, a general decline in genetic variation via inbreeding and drift has occurred over the past 20 years which we suggest should be considered in any future management planning for the population. Monitoring patterns of genetic variation, together with a clearer understanding of the social ecology of K’gari dingoes, will aid in the development of measurable genetic targets set over ecologically meaningful timelines, and help ensure continued survival of this culturally important population

The Grizzly, November 7, 1980

Reagan, Anderson Win In Campus Mock Election • Window Replacement To Start Soon • Weekend Crime Continues In New Men\u27s Dormitory • Bookstore Eyes Enlarged Facilities • Honorary Degrees Conferred At Founder\u27s Day • Library To Sponsor Open House • Breakdown For SAC Allocations Explored • Foreign Language Lunches Offered To Students • Another Viewpoint: I Object To War! • Students Do Their Stuff In Talent Show • Springsteen Unveils Interesting New Album • Party Brings Out Spirit On Halloween • Classics Club Underway • Why Carter Lost • UBEC Council Presents Three Faces Of Management • Soccer Finishes Season 7-7-1 • Breaks Carry Ursinus Past Lebanon Valley • Harriers Head Toward MACs • Field Hockey Enters Regional Competitionhttps://digitalcommons.ursinus.edu/grizzlynews/1046/thumbnail.jp

The Grizzly, November 14, 1980

Campus Life Committee Discusses Greek Societies • McDonald\u27s Opening Soon • Field Hockey Heading For Nationals • Frats Get Together for Clean-up • Ursinus News In Brief: Honors for Ursinus faculty member; College presents Rafferty art exhibit • Policy Unveiled for Gym • Elephant Man Seen As Statement On Human Behavior • Talented Student Performances • ProTheatre Opens • Aging Is Topic At College Forum • Coffeehouse Sings The Right Tune • En Garde, Ursinus! • Delta Pi Defeats Marines In Football • Disappointing Weekend For Volleyball • Harriers Take MAC Title • Demas, Rho To Meet In Hockey Finals • Grizzlies Win Behind Solid Offense Efforthttps://digitalcommons.ursinus.edu/grizzlynews/1047/thumbnail.jp

High-Resolution Melting Genotyping of Enterococcus faecium Based on Multilocus Sequence Typing Derived Single Nucleotide Polymorphisms

We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE) and an allele specific real-time PCR (AS kinetic PCR) SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs) in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 “melting types” (MelTs) and provides a Simpson's Index of Diversity (D) of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure

The Grizzly, September 19, 1980

Reagan, Anderson Leading Carter In Campus Poll • Wismer Lunch Off to Optimistic Start • Explosive Bomb Found At NMD • College Van Policy Drastically Revised • Campus Expands With Enrollment • Bad Conditions Haunt New Women\u27s Dorm • Kane Appointed As New Executive Assistant • Ursinus Still Packing Them In • Ursinus News In Brief: Myrin Hosts Davison Exhibit; Davies Promoted In Admissions • TG Annex Almost Complete • Evening School Expands Services • Freshmen Class & USGA Treasurer Elections Coming Soon • Ron Baltz and Jenny Perform • Ritter Center To Open October 4 • For The Musically Inclined • WRUC - On The Air? • Yes A Maybe • Alternatives To Typical Parties • The Rush Is On • Switchboard Under New Operation • Police Rally To Cut Down Thefts • 1978 Alumnus Selected To Receive Award • Freshmen Offer Good Stats And Great Figures • Pre-Medical Evaluation Committee Reorganized • Bomberger Tower Finally To Be Replaced • Booters Sloppy in Close Call Over Drew • Delta Pi, ZX Defend Title; Intramural Football Underway • MAC Title: Cross Country Goal • Lack of Offense Hurts in Loss to Alfred • Hockey Starts Strong at Penn State Tourneyhttps://digitalcommons.ursinus.edu/grizzlynews/1040/thumbnail.jp

The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis

Background: The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups—A and B—corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. Methods: We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. Findings: We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. Interpretation: A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital. Funding: Wellcome Trust.Peer Reviewe

Improvements in forecasting intense rainfall: results from the FRANC (forecasting rainfall exploiting new data assimilation techniques and novel observations of convection) project

The FRANC project (Forecasting Rainfall exploiting new data Assimilation techniques and Novel observations of Convection) has researched improvements in numerical weather prediction of convective rainfall via the reduction of initial condition uncertainty. This article provides an overview of the project’s achievements. We highlight new radar techniques: correcting for attenuation of the radar return; correction for beams that are over 90% blocked by trees or towers close to the radar; and direct assimilation of radar reflectivity and refractivity. We discuss the treatment of uncertainty in data assimilation: new methods for estimation of observation uncertainties with novel applications to Doppler radar winds, Atmospheric Motion Vectors, and satellite radiances; a new algorithm for implementation of spatially-correlated observation error statistics in operational data assimilation; and innovative treatment of moist processes in the background error covariance model. We present results indicating a link between the spatial predictability of convection and convective regimes, with potential to allow improved forecast interpretation. The research was carried out as a partnership between University researchers and the Met Office (UK). We discuss the benefits of this approach and the impact of our research, which has helped to improve operational forecasts for convective rainfall event

The ethical challenges of diversifying genomic data: a qualitative evidence synthesis

This article aims to explore the ethical issues arising from attempts to diversify genomic data and include individuals from underserved groups in studies exploring the relationship between genomics and health. We employed a qualitative synthesis design, combining data from three sources: 1) a rapid review of empirical articles published between 2000 and 2022 with a primary or secondary focus on diversifying genomic data, or the inclusion of underserved groups and ethical issues arising from this, 2) an expert workshop and 3) a narrative review. Using these three sources we found that ethical issues are interconnected across structural factors and research practices. Structural issues include failing to engage with the politics of knowledge production, existing inequities, and their effects on how harms and benefits of genomics are distributed. Issues related to research practices include a lack of reflexivity, exploitative dynamics and the failure to prioritise meaningful co-production. Ethical issues arise from both the structure and the practice of research, which can inhibit researcher and participant opportunities to diversify data in an ethical way. Diverse data are not ethical in and of themselves, and without being attentive to the social, historical and political contexts that shape the lives of potential participants, endeavours to diversify genomic data run the risk of worsening existing inequities. Efforts to construct more representative genomic datasets need to develop ethical approaches that are situated within wider attempts to make the enterprise of genomics more equitable

Citizen science can improve conservation science, natural resource management, and environmental protection

Citizen science has advanced science for hundreds of years, contributed to many peer-reviewed articles, and informed land management decisions and policies across the United States. Over the last 10 years, citizen science has grown immensely in the United States and many other countries. Here, we show how citizen science is a powerful tool for tackling many of the challenges faced in the field of conservation biology. We describe the two interwoven paths bywhich citizen science can improve conservation efforts, natural resource management, and environmental protection. The first path includes building scientific knowledge, while the other path involves informing policy and encouraging public action. We explore how citizen science is currently used and describe the investments needed to create a citizen science program. We find that: 1. Citizen science already contributes substantially to many domains of science, including conservation, natural resource, and environmental science. Citizen science informs natural resource management, environmental protection, and policymaking and fosters public input and engagement. 2. Many types of projects can benefit fromcitizen science, but one must be careful tomatch the needs for science and public involvement with the right type of citizen science project and the right method of public participation. 3. Citizen science is a rigorous process of scientific discovery, indistinguishable from conventional science apart from the participation of volunteers.When properly designed, carried out, and evaluated, citizen science can provide sound science, efficiently generate high-quality data, and help solve problems