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Mission-driven nonprofit organizations sometimes struggle within a cycle of disempowerment resulting from oversaturation of data collection that is reactive to funder demands. In this article, we problematize Community Music School (CMS) data-collection and analysis efforts and discuss alternate approaches to learning about family and community desires and building community engagement. We first review literature on CMS goals, CMS engagement with communities, and the importance of student voice in educational research. Then, we briefly describe secondary analysis of a data subset from a previous study as context for critical discussion. Finally, drawing on literature from communications, urban planning, and school-family engagement, we make broader suggestions for how CMS can transform data collection practices into pathways for community engagement. We assert data quality and usefulness may improve when institutions seek input from community members who have not elected to participate and when CMS involve stakeholders in program design, goal setting, and measurement schemes from the outset. To that end, we describe three frameworks that could help CMS improve community engagement and make suggestions for future research.

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, numerous municipal wastewater treatment plants (WWTPs) participate in WW surveillance of infectious disease targets such as SARS-CoV-2 by qPCR and whole genome sequencing (WGS). The Greater Toronto Airports Authority (GTAA), operator of Toronto Pearson International Airport (Toronto Pearson), has been participating in WW surveillance since January 2022. As a major international airport in Canada and the largest national hub, this airport is an ideal location for tracking globally emerging SARS-CoV-2 variants of concern (VOCs). In this study, WW collected from Toronto Pearson’s two terminals and pooled aircraft sewage was processed for WGS using a tiled-amplicon approach targeting the SARS-CoV-2 virus genome. Data generated was analyzed to monitor trends of SARS-CoV-2 lineage frequencies. Initial detections of emerging lineages were compared between Toronto Pearson WW samples, municipal WW samples collected from the surrounding regions, and Ontario clinical data as published by Public Health Ontario. Results enabled the early detection of VOCs and individual mutations emerging in Ontario. On average, the emergence of novel lineages at the airport preceded clinical detections by 1–4 weeks, and up to 16 weeks in one case. This project illustrates the efficacy of WW surveillance at transitory transportation hubs and sets an example that could be applied to other viruses as part of a pandemic preparedness strategy and to provide monitoring on a mass scale.

This narrative inquiry aimed to re-story the experiences of Paulina, a blind music education major, as she navigated her degree program at a large university. While scholars have begun to document the experiences of students who are blind or visually impaired in both PK-12 settings and during student teaching, no known study has explored the experience of a blind preservice student during their music education coursework. Utilizing critical disability studies as a lens, this narrative inquiry utilized the three commonplaces of temporality, sociality, and place to highlight Paulina's experience. Data included interviews, memos from all three researchers, emails and texts, conversations at a research conference, and informal conversations. Paulina's story centered around three themes: sight is mandatory here; the hope, promise, and failure of support; and the emotional toll and physical consequences. Implications from this study may inform preservice preparation programs as well as offer insights regarding combating ableism in any musical space.

State governments have the purview to interpret federal special education policies as they see fit. Interpretations of these policies to music education rarely are addressed within state special education policy. The authors selected four states to analyze and compare state special education policies; Illinois, Michigan, Texas, and Virginia. Policies highlighted by the authors include funding, LRE, access to information, and professional development. The authors outline how these policies may apply to music education settings and what music educators can do to more fully support students with disabilities. Additionally, the authors offer policy and practice recommendations.

Abstract Wastewater surveillance of SARS-CoV-2 has emerged as a critical tool for tracking the spread of COVID-19. In addition to estimating the relative case numbers using quantitative PCR, SARS-CoV-2 genomic RNA can be extracted from wastewater and sequenced. There are many existing techniques for using the sequenced RNA to determine the relative abundance of known lineages in a sample. However, it is very challenging to predict novel lineages from wastewater data due to its mixed composition and unreliable genomic coverage. In this work, we present a novel technique based on non-negative matrix factorization which is able to reconstruct lineage definitions by analyzing data from across different samples. We test the method both on synthetic and real wastewater sequencing data. We show that the technique is able to determine major lineages such as Omicron and Delta as well as sub-lineages such as BA.5.2.1. We provide a method for determining emerging lineages in wastewater without the need for genomic data from clinical samples. This could be used for routine monitoring of SARS-CoV-2 as well as other emerging viral pathogens in wastewater. Additionally, it may be used to determine more full-genome sequences for viruses with fewer available genomes.

Fusarium oxysporum f. sp. fragariae (Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof race 2 is virulent on FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between a gene at the FW1 locus and an avirulence gene (AvrFW1) in Fof race 1. To identify a candidate AvrFW1, we compared genomes of 24 Fof race 1 and three Fof race 2 isolates. We found one candidate gene that was present in race 1, was absent in race 2, was highly expressed in planta, and was homologous to a known effector, secreted in xylem 6 (SIX6). We knocked out SIX6 in two Fof race 1 isolates by homologous recombination. All SIX6 knockout transformants (ΔSIX6) gained virulence on FW1/fw1 cultivars, whereas ectopic transformants and the wildtype isolates remained avirulent. ΔSIX6 isolates were quantitatively less virulent on FW1/fw1 cultivars Fronteras and San Andreas than fw1/fw1 cultivars. Seedlings from an FW1/fw1 × fw1/fw1 population were genotyped for FW1 and tested for susceptibility to a SIX6 knockout isolate. Results suggested that additional minor-effect quantitative resistance genes could be present at the FW1 locus. This work demonstrates that SIX6 acts as an avirulence factor interacting with a resistance gene at the FW1 locus. The identification of AvrFW1 enables surveillance for Fof race 2 and provides insight into the mechanisms of FW1-mediated resistance. [Graphic: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract The annual production of strawberry has increased by one million tonnes in the US and 8.4 million tonnes worldwide since 1960. Here we show that the US expansion was driven by genetic gains from Green Revolution breeding and production advances that increased yields by 2,755%. Using a California population with a century-long breeding history and phenotypes of hybrids observed in coastal California environments, we estimate that breeding has increased fruit yields by 2,974-6,636%, counts by 1,454-3,940%, weights by 228-504%, and firmness by 239-769%. Using genomic prediction approaches, we pinpoint the origin of the Green Revolution to the early 1950s and uncover significant increases in additive genetic variation caused by transgressive segregation and phenotypic diversification. Lastly, we show that the most consequential Green Revolution breeding breakthrough was the introduction of photoperiod-insensitive, PERPETUAL FLOWERING hybrids in the 1970s that doubled yields and drove the dramatic expansion of strawberry production in California.

Abstract Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.

The college admissions process (application, audition, acceptance) serves as a crucial milestone for many aspiring music educators. It also functions as a barrier to accessing the profession for historically marginalized students. In this article, we employ anti-racism as a lens to critically examine the admissions process as it exists in many music education programs. Incorporating this with Deleuze and Guattari's (1987) theorization of the state and the war machine, we consider ways to disrupt the seemingly iron-clad system of music education collegiate admissions and advocate for changes that benefit marginalized students and the music education profession.

IntroductionBone metastases are associated with increased morbidity and decreased quality of life in patients with solid tumors. Identifying patients at increased risk of bone metastases at diagnosis could lead to earlier interventions. We sought to retrospectively identify the incidence and predictive factors for bone metastases at initial diagnosis in a large population-based dataset.MethodsThe Surveillance, Epidemiology, and End Results (SEER) database was used to identify patients 18 years-old or older diagnosed with solid cancers from 2010 to 2019. Patients with hematologic malignancies and primary tumors of the bone were excluded. We calculated the incidence and predictive factors for bone metastases according to demographic and tumor characteristics.ResultsAmong 1,132,154 patients identified, 1,075,070 (95.0%) had known bone metastasis status and were eligible for the study. Bone metastases were detected in 55,903 patients (5.2% of those with known bone metastases status). Among patients with bone metastases, the most common primary tumors arose from lung (44.4%), prostate (19.3%), breast (12.3%), kidney (4.0%), and colon (2.2%). Bone metastases at presentation were most common in small cell lung cancer (25.2%), non-small cell lung cancer (18.0%), and esophageal adenocarcinoma (9.4%). In addition to stage classification, predictors for bone metastases included Gleason score (OR 95.7 (95% CI 73.1 – 125.4) for Grade Group 5 vs 1 and OR 42.6 (95% CI 32.3 – 55.9) for Group 4 vs 1) and PSA (OR 14.2 (95% CI 12.6 – 16.0) for PSA > 97 vs 0 – 9.9) for prostate cancer, HER2 and hormonal receptor (HR) status (OR 2.2 (95% CI 1.9 – 2.6) for HR+/HER2+ vs HR-/HER2-) for breast cancer, histology (OR 2.5 (95% CI 2.3 – 2.6) for adenocarcinoma vs squamous) for lung cancer, and rectal primary (OR 1.2 (95% 1.1 – 1.4) vs colon primary) and liver metastases (OR 8.6 (95% CI 7.3 – 10.0) vs no liver metastases) for colorectal tumors.ConclusionsBone metastases at presentation are commonly seen in solid tumors, particularly lung, prostate, breast, and kidney cancers. Clinical and pathologic factors are associated with a significantly increased risk for bone metastases.

Abstract Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × ananassa), has caused economic losses for nearly a century. This disease is caused by the soil‐borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW‐resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids (n=564) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids (n=386), genomic prediction accuracies of 0.47–0.48 were achieved and were predicted to explain 70%–75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations.

Acoustic recording tags provide fine-scale data linking acoustic signalling with individual behaviour; however, when an animal is in a group, it is challenging to tease apart calls of conspecifics and identify which individuals produce each call. This, in turn, prohibits a robust assessment of individual acoustic behaviour including call rates and silent periods, call bout production within and between individuals, and caller location. To overcome this challenge, we simultaneously instrumented small groups of humpback whales on a western North Atlantic feeding ground with sound and movement recording tags. This approach enabled a comparison of the relative amplitude of each call across individuals to infer caller identity for 97% of calls. We recorded variable call rates across individuals (mean = 23 calls/h) and groups (mean = 55 calls/h). Calls were produced throughout dives, and most calls were produced in bouts with short inter-call intervals of 2.2 s. Most calls received a likely response from a conspecific within 100 s. This caller identification (ID) method facilitates studying both individual- and group-level acoustic behaviour, yielding novel results about the nature of sequence production and vocal exchanges in humpback whale social calls. Future studies can expand on these caller ID methods for understanding intra-group communication across taxa.

Abstract High total organic sulfur (TOS) content (i.e., Type IIS kerogen) is well known to significantly influence kerogen transformation but the effect of TOS content on the evolution of organic porosity has only rarely and indirectly been investigated. This study demonstrates that organic porosity is generated at lower thermal maturity in mudstones containing Type IIS kerogen relative to those with Type II kerogen. To our knowledge this phenomenon has not been previously demonstrated. The implications are relevant for the characterization of organic-rich mudstones as cap rocks, hydrocarbon reservoirs, and disposal reservoirs for CO2 or nuclear waste because pore systems control storage volumes and matrix fluid flow. Five thermally immature core samples were selected from three organic-rich mudstone units with low to high TOS content: the late Devonian Duvernay Formation (Canada), middle late Miocene Onnagawa Formation (Japan), and early Jurassic Gordondale member of the Fernie Formation (Canada). Hydrous pyrolysis was used to artificially mature splits of the immature samples to four maturity stages, upon which petrophysical and organic geochemical properties were measured and compared to baseline immature samples. Most porosity growth in Type IIS samples occurred below 0.70% VRoeqv, but in Type II samples was broader and robust until 1.1% VRoeqv.

Abstract Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high‐density genetic marker platforms designed for strawberry. We developed mid‐density panels of molecular inversion probes (MIPs) to be deployed with the “DArTag” marker platform to provide a low‐cost, high‐throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype segregation, amplicon coverage, and their ability to produce subgenome‐specific amplicon alignments to the FaRR1 assembly and subsequent alignment‐based variant calls with strong concordance to DArT's alignment‐free, count‐based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K and 5K production panels for genotyping of large strawberry populations. We show that the 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low‐amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism in diverse F. × ananassa germplasm and UC Davis cultivars, with mean pairwise diversity (π) estimates of 0.40 and 0.32 and mean heterozygous genotype frequencies of 0.35 and 0.33, respectively.

Abstract Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the ‘FlyBi’ dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.

Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important Solanaceae crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruses in tomato plants. The development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detected ToBRFV in municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution of ToBRFV in WWI throughout Ontario, Canada. To aid in global ToBRFV surveillance efforts, we developed a tiled amplicon approach to sequence and track the evolution of ToBRFV genomes in municipal WWI. Our assay recovers 95.7% of the 6393 bp ToBRFV RefSeq genome, omitting the terminal 5′ and 3′ ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recovering ToBRFV genomes. Our ToBRFV assay was developed using existing ARTIC Network resources, including primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance of ToBRFV clades in samples.

‘UC Eclipse’, a photoperiod-insensitive cultivar of strawberry (Fragaria ×ananassa Duchesne), was developed and released by the University of California, Davis (UC Davis) College of Agriculture & Environmental Sciences for summer-plant production. The colloquial “summer-plant” designation has been adopted in California agriculture to distinguish summer- from autumn-planted production of day-neutral cultivars. The development of productive day-neutral cultivars has played a significant role in the evolution and expansion of strawberry production in California, starting with the release of an initial series of photoperiod-insensitive day-neutral cultivars in 1980 (‘Aptos’, ‘Brighton’, and ‘Hecker’) that effectively doubled the length of the harvest season, and complemented the seasonal production of photoperiod-sensitive short-day cultivars (Bringhurst and Voth 1980). The development of ‘Portola’, a “day-neutral” cultivar adapted for summer-plant production, 27 years later further widened the harvest season and greatly increased the supply of fresh strawberries in months of the year when production was historically more limited.

AbstractThe COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.

Abstract The development of strawberry (Fragaria × ananassa Duchesne ex Rozier) cultivars resistant to Phytophthora crown rot (PhCR), a devastating disease caused by the soil‐borne pathogen Phytophthora cactorum (Lebert & Cohn) J. Schröt., has been challenging partly because the resistance phenotypes are quantitative and only moderately heritable. To develop deeper insights into the genetics of resistance and build the foundation for applying genomic selection, a genetically diverse training population was screened for resistance to California isolates of the pathogen. Here we show that genetic gains in breeding for resistance to PhCR have been negligible (3% of the cultivars tested were highly resistant and none surpassed early 20th century cultivars). Narrow‐sense genomic heritability for PhCR resistance ranged from 0.41 to 0.75 among training population individuals. Using multivariate genome‐wide association studies (GWAS), we identified a large‐effect locus (predicted to be RPc2) that explained 43.6–51.6% of the genetic variance, was necessary but not sufficient for resistance, and was associated with calcium channel and other candidate genes with known plant defense functions. The addition of underutilized gene bank resources to our training population doubled additive genetic variance, increased the accuracy of genomic selection, and enabled the discovery of individuals carrying favorable alleles that are either rare or not present in modern cultivars. The incorporation of an RPc2‐associated single‐nucleotide polymorphism (SNP) as a fixed effect increased genomic prediction accuracy from 0.40 to 0.55. Finally, we show that parent selection using genomic‐estimated breeding values, genetic variances, and cross usefulness holds promise for enhancing resistance to PhCR in strawberry.

Introduction: The clinical course of patients who present to the emergency department (ED) with urinary retention is usually uneventful. In this case, we explore the life-threatening complications of urinary retention and bladder decompression. Case Report: We report the case of a 57-year-old man who presented to the ED with difficulty voiding. A urinary catheter was placed. The patient had severe post-obstructive diuresis. He developed hematuria and became hypotensive. After aggressive resuscitation, including blood products, the patient required operative intervention for hemorrhage control. Conclusion: Clinicians should be aware of and be able to manage the rare but life-threatening complications associated with urinary retention.

Enhanced weathering is a geoengineering strategy aiming to increase continental weathering rates, thereby increasing the delivery of atmospheric carbon (as HCO3-) to the oceans. Most enhanced weathering studies focus on the capacity of silicate rocks (e.g., basalt) and minerals (e.g., olivine, Mg2SiO4, or wollastonite CaSiO3) to remove atmospheric CO2. However, carbonate minerals (e.g., calcite, CaCO3) could provide an additional, rapid way to increase HCO3- export to the oceans. Recent studies suggest that 0.84 Gt C yr−1 could be removed from the atmosphere through the enhanced dissolution of calcite in soils, provided carbonic acid is the main dissolution agent. What is not clear is whether atmospheric CO2 dissolved in soils can be transported by rivers, which typically have lower [pCO2], to the oceans. This difference in calcite solubility between soils (where weathering occurs) and rivers (where HCO3- is transported) may lead to large amounts of secondary carbonate formation during transport, releasing the CO2 consumed through dissolution. Here, we present a modeling study comparing the estimated soil dissolution capacity (SDC) in 149 of Earth's largest river basins, to the potential transport capacity of carbon (PTCC) in corresponding rivers. We find the SDC can only be exported to the oceans, without secondary carbonate precipitation, if rivers are in disequilibrium with respect to calcite (i.e., SIc = 1). In this instance, 0.92 Gt C yr−1 may be sequestered above background weathering rates, which is ~20% of annual increases in atmospheric carbon. If rivers are at equilibrium with calcite (i.e., SIc = 0), approximately two-thirds of the carbon dissolved in soil waters are lost due to calcite precipitation in rivers, and just 0.26 Gt of additional atmospheric C yr−1 can be transported to the oceans. Overall, the efficacy of enhanced carbonate weathering is a function of the capacity rivers have for transporting the products from carbonate weathering to the oceans, rather than the dissolution capacity of soils. These findings have implications for the efficiency of enhancing silicate weathering for ocean alkalinity enhancement, as secondary carbonate precipitation during transport is not always considered.

Abstract Community‐engaged learning (CEL) integrates community service with structured learning to strengthen the knowledge and skills of future physicians while still in medical school. A national model forCEL during medical school does not currently exist. Emergency physicians have the opportunity to play a vital role in medical student education using CEL as a platform. This article elucidates the structure of a bystander cardiopulmonary resuscitation (B‐CPR) CEL program developed by emergency physicians that could serve as a national model for community engagement. As B‐CPR is a well‐known evidence‐based community intervention that can be taught by students and implemented by the community, it represents an ideal CEL that can also have a measurable impact on local B‐CPR rates. The development and structure of a B‐CPR CEL program, lessons learned, and impact on B‐CPR in a local area are reported.

AbstractMany important traits in plants, animals, and microbes are polygenic and challenging to improve through traditional marker-assisted selection. Genomic prediction addresses this by incorporating all genetic data in a mixed model framework. The primary method for predicting breeding values is genomic best linear unbiased prediction, which uses the realized genomic relationship or kinship matrix (K σ g 2 h g 2K σ g 2 h g 2ZKH K ASV σ g 2 h g 2

The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.

A catalog containing details of the highest-energy cosmic rays recorded through the detection of extensive air showers at the Pierre Auger Observatory is presented with the aim of opening the data to detailed examination. Descriptions of the 100 showers created by the highest-energy particles recorded between 2004 January 1 and 2020 December 31 are given for cosmic rays that have energies in the range 78–166 EeV. Details are also given on a further nine very energetic events that have been used in the calibration procedure adopted to determine the energy of each primary. A sky plot of the arrival directions of the most energetic particles is shown. No interpretations of the data are offered.

AbstractGray mold, a disease of strawberry (FragariaananassaBotrytis cinerea

The development of genome-informed methods for identifying quantitative trait loci (QTL) and studying the genetic basis of quantitative variation in natural and experimental populations has been driven by advances in high-throughput genotyping. For many complex traits, the underlying genetic variation is caused by the segregation of one or more 'large-effect' loci, in addition to an unknown number of loci with effects below the threshold of statistical detection. The large-effect loci segregating in populations are often necessary but not sufficient for predicting quantitative phenotypes. They are, nevertheless, important enough to warrant deeper study and direct modelling in genomic prediction problems. We explored the accuracy of statistical methods for estimating the fraction of marker-associated genetic variance (p) and heritability ([Formula: see text]) for large-effect loci underlying complex phenotypes. We found that commonly used statistical methods overestimate p and [Formula: see text]. The source of the upward bias was traced to inequalities between the expected values of variance components in the numerators and denominators of these parameters. Algebraic solutions for bias-correcting estimates of p and [Formula: see text] were found that only depend on the degrees of freedom and are constant for a given study design. We discovered that average semivariance methods, which have heretofore not been used in complex trait analyses, yielded unbiased estimates of p and [Formula: see text], in addition to best linear unbiased predictors of the additive and dominance effects of the underlying loci. The cryptic bias problem described here is unrelated to selection bias, although both cause the overestimation of p and [Formula: see text]. The solutions we described are predicted to more accurately describe the contributions of large-effect loci to the genetic variation underlying complex traits of medical, biological, and agricultural importance.

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

Cultivated strawberry has a compelling domestication history: the earliest cultivars originated in western Europe as spontaneous hybrids between non-sympatric wild species imported from the New World. The origin of those early hybrids went undiscovered for nearly a half century before conscious domestication began. Here, Pincot, Ledda, Feldmann et al

AbstractCharcoal rot caused by Macrophomina phaseolinaM. phaseolinaFragaria ×ananassaFaRMp1FaRMp2FaRMp3F.×ananassaF. virginianaF. chiloensis

Abstract Verticillium wilt, a soil‐borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a persistent challenge, in part because the genetics of resistance is complex. The heritability of resistance and genetic gains in breeding for resistance to this pathogen have not been well documented. To elucidate the genetics, assess long‐term genetic gains, and estimate the accuracy of genomic selection for resistance to Verticillium wilt, we analyzed a genetically diverse population of elite and exotic germplasm accessions (n = 984), including 245 cultivars developed since 1854. We observed a full range of phenotypes, from highly susceptible to highly resistant: 50% were classified as moderately to highly susceptible. Broad‐sense heritability estimates ranged from 0.70–0.76, whereas narrow‐sense genomic heritability estimates ranged from 0.33–0.45. We found that genetic gains in breeding for resistance to Verticillium wilt have been negative over the last 165 years (mean resistance has decreased over time). We identified several highly resistant accessions that might harbor favorable alleles that are either rare or non‐existent in modern populations. We did not observe the segregation of large‐effect loci. The accuracy of genomic predictions ranged from 0.38–0.53 among years and whole‐genome regression methods. We show that genomic selection has promise for increasing genetic gains and accelerating the development of resistant cultivars in strawberry by shortening selection cycles and enabling selection in early developmental stages without phenotyping.

Chemokines such as chemokine (C-C motif) ligand 2 (CCL2) play a role in several behaviors, including anxiety-like behavior, but whether neurons are an important source of CCL2 for behavior and how neuronal CCL2 may work to affect behavior are still debated. When a herpes simplex virus (HSV) vector was used to knockdown CCL2 mRNA in neurons of the central nucleus of the amygdala (CeA) in rats experiencing multiple withdrawals from low dose ethanol, anxiety-like behavior appeared in the social interaction task. To examine this finding further Fractalkine (CX3CL1), a chemokine that is often found to have an opposing function to CCL2 was measured in these rats. Both alcohol withdrawal and CCL2 knockdown increased the levels of the anti-inflammatory protein CX3CL1. The combination of alcohol withdrawal and CCL2 knockdown decreased CX3CL1 and may alter pro-inflammatory/anti-inflammatory balance, and thus highlights the potential importance of CCL2 and CCL2/CX3CL1 balance in anxiety. To find a mechanism by which neuronal chemokines like CCL2 could affect behavior, retrograde tracing with fluorescent nanobeads was done in two brain regions associated with anxiety the bed nucleus of the stria terminalis (BNST) and the ventral periaqueductal gray (VPAG). These studies identified CeA projection neurons to these brain regions that contain CCL2. To demonstrate that CCL2 can be transported via axons to downstream brain regions, the axonal transport blocker, colchicine, was given and 24 h later, the accumulation of CCL2 in CeA neuronal cell bodies was found. Finally, CCL2 in CeA neurons was localized to the synapse using confocal microscopy with enhanced resolution following deconvolution and electron microscopy, which along with the other evidence suggests that CCL2 may be transported down axons in CeA neurons and released from nerve terminals perhaps into brain regions like the BNST and VPAG to affect behaviors such as anxiety. These results suggest that neurons are an important target for chemokine research related to behavior.

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.

Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae, threatens strawberry (Fragaria × ananassa) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance. Here, we report the discovery of Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. The Fw1 locus was uncovered in a genome-wide association study of 565 historically and commercially important strawberry accessions genotyped with 14,408 SNP markers. Fourteen SNPs in linkage disequilibrium with Fw1 physically mapped to a 2.3 Mb segment on chromosome 2 in a diploid F. vesca reference genome. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid segregating populations. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested—broad-sense heritability was 0.96. Several disease resistance and defense-related gene homologs, including a small cluster of genes encoding nucleotide-binding leucine-rich-repeat proteins, were identified in the 0.7 Mb genomic segment predicted to harbor Fw1. DNA variants and candidate genes identified in the present study should facilitate the development of high-throughput genotyping assays for accurately predicting Fusarium wilt phenotypes and applying marker-assisted selection.

This work introduces two methods which extend the non-convex minimization problem arising in phaseless (NF) far-field (FF) transformations. With the new extensions, knowledge about phase differences between measurement points can be incorporated into the minimization problem. The additional information helps to avoid stationary points of the minimization cost functional which would otherwise compromise the result of the near-field far-field transformation. The methods are incorporated into the Fast Irregular Antenna Field Transformation Algorithm (FIAFTA), analyzed and compared. Their effectiveness is shown by transforming synthetic near-field data sets with partial knowledge of phase differences to the far-field.

Illegal hunters in Africa may be making rational decisions about the hunting activities they partake in. These decisions could be linked to their socioeconomic status and the livelihood opportunities available to them. In particular, poverty is widely considered the leading driver that causes a household's inhabitants to take up poaching in protected areas. Programs aiming to protect vulnerable wildlife populations by mitigating poaching have historically relied upon income-based poverty metrics in efforts to reduce regional poverty and incentivise local inhabitants to discontinue poaching activities. Because such data sets that deal with poachers directly are rare, assumptions about the role of poverty, and the extent of poverty, that drives poaching have been hard to test. This study uses a unique sample of 173 self-admitted poachers living in villages adjacent to Ruaha National Park in Tanzania to explore the influence of poverty on poaching. Results indicated high demographic and household economy heterogeneity among poaching households. Capability deprivation examined more subjective measures of poverty and revealed that poachers are strongly motivated by the need to improve their incomes, but are not necessarily the poorest of the poor.

Worldwide, 20–25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply chain due to rotting by fungal pathogens. Most postharvest pathogens exhibit necrotrophic or saprotrophic lifestyles, resulting in decomposition of the host tissues and loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit or remain quiescent until host conditions stimulate a successful infection. Previous research on infections of fruit has mainly been focused on the host’s genetic and physicochemical factors that inhibit or promote disease. Here, we investigated if fruit pathogens can modify their own infection strategies in response to the ripening stage of the host. To test this hypothesis, we profiled global gene expression of three fungal pathogens that display necrotrophic behavior—Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer—during interactions with unripe and ripe tomato fruit. We assembled and functionally annotated the transcriptomes of F. acuminatum and R. stolonifer as no genomic resources were available. Then, we conducted differential gene expression analysis to compare each pathogen during inoculations versus in vitro conditions. Through characterizing patterns of overrepresented pathogenicity and virulence functions (e.g., phytotoxin production, cell wall degradation, and proteolysis) among the differentially expressed genes, we were able to determine shared strategies among the three fungi during infections of compatible (ripe) and incompatible (unripe) fruit tissues. Though each pathogen’s strategy differed in the details, interactions with unripe fruit were commonly characterized by an emphasis on the degradation of cell wall components, particularly pectin, while colonization of ripe fruit featured more heavily redox processes, proteolysis, metabolism of simple sugars, and chitin biosynthesis. Furthermore, we determined that the three fungi were unable to infect fruit from the non-ripening (nor) tomato mutant, confirming that to cause disease, these pathogens require the host tissues to undergo specific ripening processes. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and the development of early detection tools and effective management strategies.