Search

Abstract In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22–1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.

Abstract The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Background: Acrylic bone cement is the most common method of fixation for primary total knee arthroplasty (TKA). Several studies have described good short-term outcomes; however, there have been reports of early failures due to tibial baseplate debonding at the implant-cement interface of The ATTUNE Knee System (DePuy Synthes, West Chester, PA). We examined the causes and rates of revision in patients who underwent TKA with this system to identify factors associated with this mode of early failure. Methods: A retrospective review of electronic health records between 2013 and 2018 identified all patients undergoing TKA with the ATTUNE Knee System with a minimum 2-year follow-up. Cause of revision, patient, implant, instrumentation, cement, and surgeon variables were collected. A descriptive analysis was used to identify characteristics of surgeon (fellowship-trained, surgical volume), implant (baseplate, bearing), and cement (brand, viscosity) that were associated with aseptic loosening. Results: A total of 668 patients representing 742 knees were identified. Eighteen (2.4%) required a revision surgery. Aseptic loosening was the leading cause of revision surgery (n = 10, 55.6%). All failures due to aseptic loosening involved debonding of the tibial implant-cement interface. A multivariate analysis identified low-volume surgeons (9.0%, P < .0001) and 1 specific brand of high-viscosity cement (14.3%, P < .0001) as risk factors for aseptic loosening. Conclusions: This study represents the largest nonregistry review of the original ATTUNE Knee System. Surgeon case volume and cement viscosity were factors associated with an increased rate of early failure due to tibial baseplate implant-cement interface debonding.

ABSTRACT Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes’ sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete,

ABSTRACT Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.

Category: Other; Hindfoot Introduction/Purpose: The internet is full of websites focused on different medical topics. With such a large accumulation of information, patients should be able to rely upon the internet as a reliable source for information on common medical conditions such as Achilles tendonitis. However, the question remains as to the accuracy, quality and readability of such online patient resources. Consumers themselves commonly evaluate online medical sites by trustworthiness, expertise, and objectivity. The purpose of this study was to investigate the top search-engine-generated online resources for Achilles tendonitis for their content and accuracy. Methods: The term 'Achilles tendonitis' was searched using the three most population search engines. The first 50 sites from each search were recorded. Duplicate sites were eliminated. Sites were categorized based on authorship type. Each website was independently evaluated by two reviewers. Quality was evaluated utilizing the DISCERN score and the Journal of the American Medical Association (JAMA) benchmark criteria. Accuracy was evaluated using a novel Achilles tendinosis-specific content rubric developed with a foot and ankle fellowship-trained orthopaedic surgeon and the AAOS OrthoInfo webpage, similar to previous studies. Readability was evaluated using the Flesch Kincaid grade level (FKGL) and Flesch Reading Ease (FRE) formulas. Higher FRE scores indicate better readability. FKGL was also compared against an 8th grade level, which represents the average US reading level. Results: The search resulted in 77 unique websites with 60 sites included for analysis. The average DISCERN score in our investigation is 42.1 which places it in the 'fair' category. Commercial websites were found to have higher DISCERN scores as compared to websites created by physicians or medical groups as well as academic websites. Our study found an average JAMA quality benchmark score of 2.2 out of 4. Our study found that on average, online patient resources on Achilles tendinosis was written at a 9th grade reading level with a FKGL score of 9.8. Academic websites were found to be written at a significantly lower reading level of 8.8. The average FRE score was 53.28 which translates to the 'fairly difficult' category. Utilizing our own content scoring system to assess the accuracy of online resources, the websites had an average accuracy of 11.5 points out of 20 possible points. Conclusion: The average online patient resource on Achilles tendinosis is too complex for the average patient, inaccurate, and is of low quality. This study found that the average website had low quality as measured by the DISCERN and JAMA benchmark scores. The average accuracy was also low as measured by our novel content specific score. The websites were also difficult to read as measured by the FRE and FKGL scores. More emphasis on improving the readability, quality, and accuracy of online patient resources on Achilles tendinosis should be undertaken in order to improve patient healthcare.

Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.

Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.

Abstract Spinosaurids are among the most distinctive and yet poorly-known of large-bodied theropod dinosaurs, a situation exacerbated by their mostly fragmentary fossil record and competing views regarding their palaeobiology. Here, we report two new Early Cretaceous spinosaurid specimens from the Wessex Formation (Barremian) of the Isle of Wight. Large-scale phylogenetic analyses using parsimony and Bayesian techniques recover the pair in a new clade within Baryonychinae that also includes the hypodigm of the African spinosaurid Suchomimus. Both specimens represent distinct and novel taxa, herein named Ceratosuchops inferodios gen. et sp. nov. and Riparovenator milnerae gen. et sp. nov. A palaeogeographic reconstruction suggests a European origin for Spinosauridae, with at least two dispersal events into Africa. These new finds provide welcome information on poorly sampled areas of spinosaurid anatomy, suggest that sympatry was present and potentially common in baryonychines and spinosaurids as a whole, and contribute to updated palaeobiogeographic reconstructions for the clade.

Cowpea is one of the major legumes cultivated in arid and semiarid regions of the world. Four soil-microbial samples (SS-1 through SS-4) collected from semiarid soils in Punjab, Pakistan were planted with cowpea (Vigna unguiculata) crops, which were grown under salinity stress to analyze bacterial composition in the rhizosphere and within nodules using cultivation-dependent and -independent methods. Two varieties, 603 and the salt-tolerant CB 46, were each inoculated with or without the four different native soil samples or grown in medium either N-deficient (−N) or supplemented with N (+N). Plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with SS-1- and SS-3 and grew comparably with the +N controls. Environmental DNA (eDNA) was isolated from SS-1 and SS-4, and, by 16S ribosomal RNA sequencing, the soil microbiomes consisted mainly of Actinobacteria, Firmicutes, Proteobacteria, and other nonproteobacterial genera. However, analysis of eDNA isolated from cowpea nodules established by the trap plants showed that the nodule microbiome consisted almost exclusively of proteobacterial sequences, particularly species of Bradyrhizobium. Bacteria were isolated from both soils and nodules, and 34 of the 51 isolates tested positive for plant-growth-promoting rhizobacteria traits in plate assays. Many could serve as future inocula for crops in arid soils. The discrepancy between the types of bacteria isolated by culturing bacteria isolated from surface-sterilized cowpea nodules (proteobacteria and nonproteobacteria) versus those detected by sequencing DNA isolated from the nodules (proteobacteria) from cowpea nodules (proteobacteria and nonproteobacteria) versus those detected in the nodule microbiome (proteobacteria) needs further study.

Category: Other; Hindfoot Introduction/Purpose: The internet is an inexpensive and convenient source for health information. However, without regulation, the quality and accuracy of the information is unknown. Tarsal coalition is a common cause of pediatric foot pain and disability. We hypothesized that the online patient information on tarsal coalition is of low accuracy, low quality, and of poor readability. Additionally, we hypothesized that sources found on the first search page were of higher quality, greater accuracy, and more readable. Methods: A cross-sectional review of the internet was performed using the term 'tarsal coalition' on the 3 most popular search engines. Unique sites were categorized based on authorship and search result order. Websites were evaluated using a novel content score based on the AAOS OrthoInfo site on tarsal coalition (max score: 20), JAMA Benchmark and DISCERN scores for quality, and Flesch-Kincaid Grade Level (FKGL) and Flesch Reading Ease (FRE) for readability. Results: A total of 47 unique websites were evaluated. They ranged from professional organization/society websites to websites for individual practices and professional blogs. The average content score was 13.1 (range: 4-20). The average DISCRN score was 34.2 (range: 19-57.5). We did find a positive correlation between the content score and DISCERN scores of the included resources (p=0.04). The average 11.4 (range 8.5-15.5). Only 2 of the websites (4%) were written at or below an 8th grade reading level, which has been documented as the average reading level of the general population in the United States. Websites that were authored by physicians had greater DISCRN and readability scores compared to academic and private practice websites (DISCERN 40.4 vs 32.3 (p=0.001) and 31.7 (p=0.01), respectively, FKGL 13.0 vs 10.4 (p=0.002) and 11.1 (p=0.03), respectively, FRE 31.5 vs 48.7 (p=0.0001) and 45.2 (p=0.025), respectively). Conclusion: Online patient resources on tarsal coalition are of low quality, inaccurate, and too complex for the average reader. Physician authored websites may serve as better resources compared to academic or private practice sites. Physicians should caution patients using the internet for information on tarsal coalition.

Category: Other Introduction/Purpose: The internet is a popular source of health information for patients. Professional organizations, such as the American Orthopaedic Foot & Ankle Society (AOFAS) and the American Academy of Orthopaedic Surgeons (AAOS) have created patient-directed websites containing high quality information. However, previous studies have demonstrated that these sites are often written at a level that is too complex for the average reader. We aimed to investigate the current landscape of the readability of these websites. Methods: Online patient resources on foot and ankle topics published by the AOFAS and AAOS were reviewed. Each page was analyzed using the Flesch Kincaid Grade Level (FKGL) and Flesch Reading Ease (FRE) formulas. Sites were noted if they were written at or below an 8th grade reading level, which corresponds to the average US reading level. An independent two-sample t- test or chi-square test, where appropriate, were used to compare resource characteristics between the two professional societies. Results: 162 total sites were reviewed, including 113 from the AOFAS and 49 from the AAOS. Overall, the mean FKGL was 9.4 (range, 6.7 - 15.3) and the mean FRE was 56.3 (range, 24.4 - 73.1). Websites written by the AAOS had significantly lower FKGL scores than sites written by the AOFAS (9.0 vs 9.5, p=0.01). 31.3% of all sites were written at or below an 8th grade reading level. Websites published by the AAOS had significantly more sites published at this level than sites published by the AOFAS (44.9% vs 25.7%, p=0.02). Conclusion: Online patient information on foot and ankle topics published by professional organizations are often written at a level that is too complex for the average reader. There was a statistical but not clinically significant difference between sites published by the AAOS and AOFAS. Professional organizations should continue to develop their online patient resources, with emphasis on increasing their readability.

An ethnopharmacological metanalysis was conducted with a large database available on antidiabetic activities of plant foods and medicines from the northern boreal forest, which are traditionally used by the indigenous Cree of James Bay, Quebec, Canada. The objective was to determine which bioassays are closely associated with the traditional knowledge of the Cree and which pharmacological metrics and phytochemical signals best define these plants and their groups. Data from 17 plant species, ethnobotanically ranked by syndromic importance value for treatment of 15 diabetic symptoms, was used along with 49 bioassay endpoints reported across numerous pharmacological studies and a metabolomics dataset. Standardized activities were separated into primary, secondary and safety categories and summed to produce a Pharmacological Importance Value (PIV) in each of the three categories for each species. To address the question of which pharmacological metrics and phytochemical signals best define the CEI anti-diabetes plants, multivariate analyses were undertaken to determine groupings of plant families and plant parts. The analysis identified Larix larcina as the highest PIV species in primary assays, Salix planifolia in secondary assays, and Kalmia angustifolia in safety assays, as well as a ranking of other less active species by PIV. Multivariate analysis showed that activity in safety PIV monitored mainly with cytochrome P450 inhibition patterns best reflected patterns of traditional medicine importance in Cree traditional knowledge, whereas potent primary bioactivities were seen in individual plants determined to be most important to the Cree for anti-diabetes purposes. In the secondary anti-diabetes assays, pharmacological variability was better described by plant biology, mostly in terms of the plant part used. Key signal in the metabolomics loadings plots for activity were phenolics especially quercetin derivatives. Traditional Indigenous knowledge in this analysis was shown to be able to guide the identification of plant pharmacological qualities in scientific terms.

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs data preprocessing, error correction, assembly, structural and functional annotation, and binning.

Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.

A laser-wire transverse electron beam size measurement system has been constructed and operated at the Accelerator Test Facility (ATF) extraction line at KEK. The construction of the system is described in detail along with the environment of the ATF related to the laser wire. A special set of electron beam optics was developed to generate an approximately 1 μm vertical focus at the laser-wire location. The results of our operation at the ATF extraction line are presented, where a minimum rms electron beam size of 4.8±0.3 μm was measured, and smaller electron beam sizes can be measured by developing the method further. The beam size at the laser-wire location was changed using quadrupoles and the resulting electron beam size measured, and vertical emittance extracted.