1,072 results on '"Nguyen, Oanh"'
Search Results
2. Roots of random trigonometric polynomials with general dependent coefficients
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Angst, Jürgen, Nguyen, Oanh, and Poly, Guillaume
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Mathematics - Probability ,26C10 - Abstract
We consider random trigonometric polynomials with general dependent coefficients. We show that under mild hypotheses on the structure of dependence, the asymptotics as the degree goes to infinity of the expected number of real zeros coincides with the independent case. To the best of our knowledge, this universality result is the first obtained in a non-Gaussian dependent context. Our proof highlights the robustness of real zeros, even in the presence of dependencies. These findings bring the behavior of random polynomials closer to real-world models, where dependencies between coefficients are common., Comment: 29 pages
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- 2024
3. A genome assembly of the American black bear, Ursus americanus, from California
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Supple, Megan A, Escalona, Merly, Adkins, Jillian, Buchalski, Michael R, Alexandre, Nicolas, Sahasrabudhe, Ruta M, Nguyen, Oanh, Sacco, Samuel, Fairbairn, Colin, Beraut, Eric, Seligmann, William, Green, Richard E, Meredith, Erin, and Shapiro, Beth
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Biological Sciences ,Ecology ,Genetics ,Biotechnology ,Human Genome ,Ursidae ,Animals ,California ,Genome ,Genomics ,California Conservation Genomics Project ,CCGP ,Conservation Genomics ,wildlife management ,Evolutionary Biology ,Evolutionary biology - Abstract
The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.
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- 2024
4. A draft reference genome assembly of California Pipevine, Aristolochia californica Torr.
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Chaturvedi, Samridhi, Escalona, Merly, Marimuthu, Mohan PA, Nguyen, Oanh, Chumchim, Noravit, Fairbairn, Colin W, Seligmann, William, Miller, Courtney, Shaffer, H Bradley, and Whiteman, Noah K
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Biological Sciences ,Bioinformatics and Computational Biology ,Ecology ,Genetics ,Biotechnology ,Human Genome ,California ,Aristolochia ,Animals ,Genomics ,Molecular Sequence Annotation ,angiosperm ,California Conservation Genomics Project ,genomics ,Evolutionary Biology ,Evolutionary biology - Abstract
The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.
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- 2024
5. Disparities in Use of Novel Diabetes Medications by Insurance: A Nationally Representative Cohort Study
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Bepo, Lurit, Nguyen, Oanh K, and Makam, Anil N
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Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Health Disparities ,Diabetes ,Women's Health ,Minority Health ,Health Services ,Clinical Research ,Behavioral and Social Science ,Metabolic and endocrine ,Good Health and Well Being ,Clinical Sciences ,General & Internal Medicine ,Clinical sciences ,Health services and systems ,Public health - Abstract
BackgroundMinority racial and ethnic populations have the highest prevalence of type 2 diabetes mellitus but lower use of sodium-glucose co-transporter-2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP1ra), novel medications that reduce morbidity and mortality. Observed disparities may be due to differences in insurance coverage, which have variable cost-sharing, prior authorization, and formulary restrictions that influence medication access.ObjectiveTo assess whether racial/ethnic differences in SGLT2i and GLP1ra use differ by payer.DesignCross-sectional analysis of 2018 and 2019 Medical Expenditure Panel Survey data.ParticipantsAdults ≥ 18 years old with diabetes.Main measuresWe defined insurance as private, Medicare, or Medicaid using ≥ 7 months of coverage in the calendar year. We defined race/ethnicity as White (non-Hispanic) vs non-White (including Hispanic). The primary outcome was use of ≥ 1 SGLT2i or GLP1ra medication. We used multivariable logistic regression to assess the interaction between payer and race/ethnicity adjusted for cardiovascular, socioeconomic, and healthcare access factors.Key resultsWe included 4997 adults, representing 24.8 million US adults annually with diabetes (mean age 63.6 years, 48.8% female, 38.8% non-White; 33.5% private insurance, 56.8% Medicare, 9.8% Medicaid). In our fully adjusted model, White individuals with private insurance had significantly more medication use versus non-White individuals (16.1% vs 8.3%, p
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- 2024
6. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)
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Tsai, Whitney LE, Escalona, Merly, Garrett, Kimball L, Terrill, Ryan S, Sahasrabudhe, Ruta, Nguyen, Oanh, Beraut, Eric, Seligmann, William, Fairbairn, Colin W, Harrigan, Ryan J, McCormack, John E, Alfaro, Michael E, Smith, Thomas B, and Bay, Rachael A
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Biological Sciences ,Ecology ,Genetics ,Animals ,Songbirds ,Genome ,Female ,California ,Gene Flow ,California Conservation Genomics Project ,Parulidae ,Evolutionary Biology ,Evolutionary biology - Abstract
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
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- 2024
7. The application of Sentinel-2 satellite imagery to construct a model to estimate the concentration of Chlorophyll-a in surface water in the Hinh River basin, Vietnam
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Ngo, Dung Trung, Nguyen, Khanh Quoc, Nguyen, Hoi Dang, Nguyen, Chinh Thi, Nguyen, Oanh Thi Kim, Tran, Nhan Thi, Nguyen, Binh Thi Thanh, and Pham, Hai Hong
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- 2024
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8. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery
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Benham, Phred M, Cicero, Carla, Escalona, Merly, Beraut, Eric, Fairbairn, Colin, Marimuthu, Mohan PA, Nguyen, Oanh, Sahasrabudhe, Ruta, King, Benjamin L, Thomas, W Kelley, Kovach, Adrienne I, Nachman, Michael W, and Bowie, Rauri CK
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Animals ,DNA Transposable Elements ,Sparrows ,Sequence Analysis ,DNA ,Passerellidae ,transposable elements ,genome size ,California Conservation Genomics Project ,C-value ,Biochemistry and Cell Biology ,Evolutionary Biology ,Developmental Biology ,Biochemistry and cell biology ,Evolutionary biology - Abstract
Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.
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- 2024
9. A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris
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Kozak, Krzysztof M, Escalona, Merly, Chumchim, Noravit, Fairbairn, Colin, Marimuthu, Mohan PA, Nguyen, Oanh, Sahasrabudhe, Ruta, Seligmann, William, Conroy, Chris, Patton, James L, Bowie, Rauri CK, and Nachman, Michael W
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Biological Sciences ,Ecology ,Genetics ,Human Genome ,Life on Land ,Animals ,Mice ,Genome ,Chromosomes ,Genomics ,North America ,California Conservation Genomics Project ,comparative genomics ,conservation genetics ,Heteromyidae ,Perognathus ,repetitive elements ,Evolutionary Biology ,Evolutionary biology - Abstract
The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.
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- 2024
10. A genome assembly of the Yuma myotis bat, Myotis yumanensis
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Curti, Joseph N, Fraser, Devaughn, Escalona, Merly, Fairbairn, Colin W, Sacco, Samuel, Sahasrabudhe, Ruta, Nguyen, Oanh, Seligmann, William, Sudmant, Peter H, Toffelmier, Erin, Vazquez, Juan Manuel, Wayne, Robert, Shaffer, H Bradley, and Buchalski, Michael R
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Animals ,Chiroptera ,North America ,Genome ,Genomics ,Biological Evolution ,California Conservation Genomics Project ,CCGP ,chiroptera ,long-read assembly ,Myotis yumanensis ,reference genome ,Evolutionary Biology ,Evolutionary biology - Abstract
The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of 12 bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these 12 species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project. The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb, and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high-quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.
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- 2024
11. Concentration inequalities for the number of real zeros of Kac polynomials
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Can, Van Hao and Nguyen, Oanh
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Mathematics - Probability - Abstract
We study concentration inequalities for the number of real roots of the classical Kac polynomials $$f_{n} (x) = \sum_{i=0}^n \xi_i x^i$$ where $\xi_i$ are independent random variables with mean 0, variance 1, and uniformly bounded $(2+\ep_0)$-moments. We establish polynomial tail bounds, which are optimal, for the bulk of roots. For the whole real line, we establish sub-optimal tail bounds., Comment: more references added
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- 2023
12. The organisational impact of agility: a systematic literature review
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Nguyen, Tien, Le, Cat Vi, Nguyen, Minh, Nguyen, Gam, Lien, Tran Thi Hong, and Nguyen, Oanh
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- 2024
- Full Text
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13. Hole radii for the Kac polynomials and derivatives
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Nguyen, Hoi H. and Nguyen, Oanh
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Mathematics - Probability - Abstract
The Kac polynomial $$f_n(x) = \sum_{i=0}^{n} \xi_i x^i$$ with independent coefficients of variance 1 is one of the most studied models of random polynomials. It is well-known that the empirical measure of the roots converges to the uniform measure on the unit disk. On the other hand, at any point on the unit disk, there is a hole in which there are no roots, with high probability. In a beautiful work \cite{michelen2020real}, Michelen showed that the holes at $\pm 1$ are of order $1/n$. We show that in fact, all the hole radii are of the same order. The same phenomenon is established for the derivatives of the Kac polynomial as well., Comment: 23 pages, 4 figures
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- 2023
14. Provision of digital devices and internet connectivity to improve synchronous telemedicine access in the U.S.: a systematic scoping review.
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Bell, Joshua, Gottlieb, Laura, Lyles, Courtney, Nguyen, Oanh, Ackerman, Sara, and De Marchis, Emilia
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access ,health equity ,healthcare utilization ,scoping review ,telemedicine - Abstract
INTRODUCTION: The COVID-19 pandemic led to a dramatic increase in telemedicine use for direct patient care. Inequities in device/internet access can limit the extent to which patients can engage with telemedicine care and exacerbate health disparities. In this review, we examined existing literature on interventions designed to improve patient telemedicine access by providing digital devices including tablets, smartphones, and computers and/or internet connectivity. METHODS: In this systematic scoping review, we searched four databases for peer-reviewed studies published 1/1/2000-10/19/2021 that described healthcare interventions that provided patients with devices and/or internet connectivity and reported outcomes related to telemedicine access and/or usage. Data extraction elements included: study population, setting, intervention design, details on device/connectivity provision, and outcomes evaluated. RESULTS: Twelve articles reflecting seven unique interventions met inclusion criteria. Ten articles examined telemedicine utilization (83%) and reported improved patient show rates/utilization. Seven articles examined patient satisfaction with the interventions (58%) and reported positive experiences. Fewer articles examined health outcomes (17%; 2/12) though these also demonstrated positive results. Across included studies, study quality was low. There were no controlled trials, and the most rigorously designed studies (n = 4) involved pre/post-intervention assessments. DISCUSSION: Findings from this review indicate that providing material technology supports to patients can facilitate telemedicine access, is acceptable to patients and clinicians, and can contribute to improved health outcomes. The low number and quality of existing studies limits the strength of this evidence. Future research should explore interventions that can increase equitable access to telemedicine services. SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=183442, identifier, PROSPERO: CRD42020183442.
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- 2024
15. The impacts of cancer treatment on lifestyle habits and mental health in Vietnamese women: an exploratory qualitative study
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Nguyen, Huyen Thi Hoa, Nguyen, Oanh Thi Kieu, Tran, Tran Ngoc, Nguyen, Anh Chau, Liamputtong, Pranee, and Bui, Linh Khanh
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- 2024
- Full Text
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16. Techniques for restoring optimal spinal biomechanics to alleviate symptoms in Bertolotti syndrome: illustrative case.
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Brown, Nolan, Pennington, Zach, Shahin, Hania, Nguyen, Oanh, and Pham, Martin
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Bertolotti syndrome ,anomaly ,low-back pain ,lumbar spine ,lumbosacral transitional vertebrae ,sacrum ,spine surgery - Abstract
BACKGROUND: Lumbosacral transitional vertebrae (LSTVs) are congenital anomalies that occur in the spinal segments of L5-S1. These vertebrae result from sacralization of the lowermost lumbar segment or lumbarization of the uppermost sacral segment. When the lowest lumbar vertebra fuses or forms a false joint with the sacrum (pseudoarticulation), it can cause pain and manifest clinically as Bertolotti syndrome. OBSERVATIONS: A 36-year-old female presented with severe right-sided low-back pain. Computed tomography was unremarkable except for a right-sided Castellvi type IIA LSTV. The pain proved refractory to physical therapy and lumbar epidural spinal injections, but targeted steroid and bupivacaine injection of the pseudoarticulation led to 2 weeks of complete pain relief. She subsequently underwent minimally invasive resection of the pseudoarticulation, with immediate improvement in her low-back pain. The patient continued to be pain free at the 3-year follow-up. LESSONS: LSTVs alter the biomechanics of the lumbosacral spine, which can lead to medically refractory mechanical pain requiring surgical intervention. Select patients with Bertolotti syndrome can benefit from operative management, including resection, fusion, or decompression of the pathologic joint.
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- 2023
17. Endoscopic Anterior Lumbar Interbody Fusion: Systematic Review and Meta-Analysis.
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Brown, Nolan, Pennington, Zach, Kuo, Cathleen, Lopez, Alexander, Picton, Bryce, Solomon, Sean, Nguyen, Oanh, Yang, Chenyi, Tantry, Evelyne, Shahin, Hania, Gendreau, Julian, Albano, Stephen, Oh, Michael, and Pham, Martin
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Anterior lumbar interbody fusion ,Endoscopy ,Interbody fusion ,Laparoscopy ,Lumbar spine ,Meurosurgery ,Spine surgery - Abstract
Laparoscopic anterior lumbar interbody fusion (L-ALIF), which employs laparoscopic cameras to facilitate a less invasive approach, originally gained traction during the 1990s but has subsequently fallen out of favor. As the envelope for endoscopic approaches continues to be pushed, a recurrence of interest in laparoscopic and/or endoscopic anterior approaches seems possible. Therefore, evaluating the current evidence base in regard to this approach is of much clinical relevance. To this end, a systematic literature search was performed according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines using the following keywords: (laparoscopic OR endoscopic) AND (anterior AND lumbar). Out of the 441 articles retrieved, 22 were selected for quantitative analysis. The primary outcome of interest was the radiographic fusion rate. The secondary outcome was the incidence of perioperative complications. Meta-analysis was performed using RStudios metafor package. Of the 1,079 included patients (mean age, 41.8±2.9 years), 481 were males (44.6%). The most common indication for L-ALIF surgery was degenerative disk disease (reported by 18 studies, 81.8%). The mean follow-up duration was 18.8±11.2 months (range, 6-43 months). The pooled fusion rate was 78.9% (95% confidence interval [CI], 68.9-90.4). Complications occurred in 19.2% (95% CI, 13.4-27.4) of L-ALIF cases. Additionally, 7.2% (95% CI, 4.6-11.4) of patients required conversion from L-ALIF to open surgery. Although L-ALIF does not appear to be supported by studies available in the literature, it is important to consider the context from which these results have been obtained. Even if these results are taken at face value, the failure of endoscopy to have a role in the ALIF approach does not mean that it should not be incorporated in posterior approaches.
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- 2023
18. De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica
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DeRaad, Devon A, Escalona, Merly, Benham, Phred M, Marimuthu, Mohan PA, Sahasrabudhe, Ruta M, Nguyen, Oanh, Chumchim, Noravit, Beraut, Eric, Fairbairn, Colin W, Seligmann, William, Bowie, Rauri CK, Cicero, Carla, McCormack, John E, and Wayne, Robert K
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Animals ,Female ,Phylogeny ,Genome ,Passeriformes ,Chromosomes ,California ,\California Conservation Genomics Project ,CCGP ,long-read sequencing ,N50 ,Omni-C ,PacBio ,California Conservation Genomics Project ,Evolutionary Biology ,Evolutionary biology - Abstract
We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.
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- 2023
19. A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex
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Westeen, Erin P, Escalona, Merly, Holding, Matthew L, Beraut, Eric, Fairbairn, Colin, Marimuthu, Mohan PA, Nguyen, Oanh, Perri, Ralph, Fisher, Robert N, Toffelmier, Erin, Shaffer, H Bradley, and Wang, Ian J
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Biological Sciences ,Bioinformatics and Computational Biology ,Ecology ,Genetics ,Human Genome ,Biotechnology ,Life on Land ,Animals ,Mexico ,Ecosystem ,Crotalus ,Venomous Snakes ,California Conservation Genomics Project ,conservation genetics ,reference genome ,snake ,Viperidae ,Evolutionary Biology ,Evolutionary biology - Abstract
Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.
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- 2023
20. A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus
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Westeen, Erin P, Escalona, Merly, Beraut, Eric, Marimuthu, Mohan PA, Nguyen, Oanh, Fisher, Robert N, Toffelmier, Erin, Shaffer, H Bradley, and Wang, Ian J
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Biological Sciences ,Ecology ,Genetics ,Biotechnology ,Life Below Water ,Animals ,Colubridae ,Genomics ,Genome ,North America ,Phylogeny ,California Conservation Genomics Project ,CCGP ,conservation genetics ,Dipsadinae ,reference genome ,snake ,Evolutionary Biology ,Evolutionary biology - Abstract
Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.
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- 2023
21. The reference genome assembly of the bright cobblestone lichen, Acarospora socialis
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Adams, Julia N, Escalona, Merly, Marimuthu, Mohan PA, Fairbairn, Colin W, Beraut, Eric, Seligmann, William, Nguyen, Oanh, Chumchim, Noravit, and Stajich, Jason E
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Biological Sciences ,Bioinformatics and Computational Biology ,Ecology ,Genetics ,Human Genome ,Biotechnology ,Climate Action ,Lichens ,Molecular Sequence Annotation ,Genomics ,Ascomycota ,California Conservation Genomics Project ,lichen genomics ,metagenomics ,mycobiont ,symbiosis ,Evolutionary Biology ,Evolutionary biology - Abstract
Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.
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- 2023
22. A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta
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Chaturvedi, Samridhi, Escalona, Merly, Marimuthu, Mohan PA, Nguyen, Oanh, Chumchim, Noravit, Fairbairn, Colin W, Seligmann, William, Miller, Courtney, Shaffer, H Bradley, and Whiteman, Noah K
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Animals ,Butterflies ,Aristolochia ,Genome ,Genomics ,Chromosomes ,California Conservation Genomics Project ,genomics ,Lepidoptera ,Papilionidae ,Evolutionary Biology ,Evolutionary biology - Abstract
The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.
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- 2023
23. A highly contiguous reference genome for the Steller’s jay (Cyanocitta stelleri)
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Benham, Phred M, Cicero, Carla, DeRaad, Devon A, McCormack, John E, Wayne, Robert K, Escalona, Merly, Beraut, Eric, Marimuthu, Mohan PA, Nguyen, Oanh, Nachman, Michael W, and Bowie, Rauri CK
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Animals ,Genome ,Passeriformes ,Genomics ,Base Sequence ,Chromosomes ,Sex Chromosomes ,California Conservation Genomics Project ,Corvidae ,transposable elements ,Evolutionary Biology ,Evolutionary biology - Abstract
The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.
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- 2023
24. Reference genome of California walnut, Juglans californica, and resemblance with other genomes in the order Fagales
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Fitz-Gibbon, Sorel, Mead, Alayna, O’Donnell, Scott, Li, Zhi-Zhong, Escalona, Merly, Beraut, Eric, Sacco, Samuel, Marimuthu, Mohan PA, Nguyen, Oanh, and Sork, Victoria L
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Life on Land ,Juglans ,Ecosystem ,Genome ,Genomics ,California ,California black walnut ,California Conservation Genomics Project ,CCGP ,Fagales ,Juglandaceae ,Juglans californica ,Juglans hindsii ,Juglans spp ,Evolutionary Biology ,Evolutionary biology - Abstract
Juglans californica, California walnut, is a vulnerable small tree that is locally abundant but restricted to woodland and chaparral habitats of Southern California threatened by urbanization and land use change. This species is the dominant species in a unique woodland ecosystem in California. It is one of 2 endemic California walnut species (family Juglandaceae). The other species, Northern California black walnut (J. hindsii), has been suggested controversially to be a variety of J. californica. Here, we report a new, chromosome-level assembly of J. californica as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP common methodology across ~150 genomes, we used Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 137 scaffolds spanning 551,065,703 bp, has a contig N50 of 30 Mb, a scaffold N50 of 37 Mb, and BUSCO complete score of 98.9%. Additionally, the mitochondrial genome has 701,569 bp. In addition, we compare this genome with other existing high-quality Juglans and Quercus genomes, which are in the same order (Fagales) and show relatively high synteny within the Juglans genomes. Future work will utilize the J. californica genome to determine its relationship with the Northern California walnut and assess the extent to which these 2 endemic trees might be at risk from fragmentation and/or climate warming.
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- 2023
25. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis
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Bishop, Anusha P, Westeen, Erin P, Yuan, Michael L, Escalona, Merly, Beraut, Eric, Fairbairn, Colin, Marimuthu, Mohan PA, Nguyen, Oanh, Chumchim, Noravit, Toffelmier, Erin, Fisher, Robert N, Shaffer, H Bradley, and Wang, Ian J
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Biological Sciences ,Bioinformatics and Computational Biology ,Ecology ,Genetics ,Biotechnology ,Life on Land ,Animals ,Mexico ,Genome ,Ecosystem ,Genomics ,Lizards ,California Conservation Genomics Project ,CCGP ,de novo genome assembly ,Iguania ,Phrynosomatidae ,reptile ,Squamata ,Evolutionary Biology ,Evolutionary biology - Abstract
Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.
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- 2023
26. Chromosome-level reference genome of stinkwort, Dittrichia graveolens (L.) Greuter: A resource for studies on invasion, range expansion, and evolutionary adaptation under global change
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McEvoy, Susan L, Lustenhouwer, Nicky, Melen, Miranda K, Nguyen, Oanh, Marimuthu, Mohan PA, Chumchim, Noravit, Beraut, Eric, Parker, Ingrid M, and Meyer, Rachel S
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Biological Sciences ,Genetics ,Genome ,Genomics ,Chromosomes ,Biological Evolution ,Phylogeny ,Asteraceae ,California ,Dovetail Omni-C ,organelle genomes ,Pacific Biosciences HiFi ,range shift ,Evolutionary Biology ,Evolutionary biology - Abstract
Dittrichia graveolens (L.) Greuter, or stinkwort, is a weedy annual plant within the family Asteraceae. The species is recognized for the rapid expansion of both its native and introduced ranges: in Europe, it has expanded its native distribution northward from the Mediterranean basin by nearly 7 °C latitude since the mid-20th century, while in California and Australia the plant is an invasive weed of concern. Here, we present the first de novo D. graveolens genome assembly (1N = 9 chromosomes), including complete chloroplast (151,013 bp) and partial mitochondrial genomes (22,084 bp), created using Pacific Biosciences HiFi reads and Dovetail Omni-C data. The final primary assembly is 835 Mbp in length, of which 98.1% are represented by 9 scaffolds ranging from 66 to 119 Mbp. The contig N50 is 74.9 Mbp and the scaffold N50 is 96.9 Mbp, which, together with a 98.8% completeness based on the BUSCO embryophyta10 database containing 1,614 orthologs, underscores the high quality of this assembly. This pseudo-molecule-scale genome assembly is a valuable resource for our fundamental understanding of the genomic consequences of range expansion under global change, as well as comparative genomic studies in the Asteraceae.
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- 2023
27. A highly contiguous genome assembly for the California quail (Callipepla californica)
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Benham, Phred M, Cicero, Carla, Escalona, Merly, Beraut, Eric, Marimuthu, Mohan PA, Nguyen, Oanh, Nachman, Michael W, and Bowie, Rauri CK
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Animals ,Genomics ,Quail ,Chromosomes ,DNA Transposable Elements ,California ,California Conservation Genomics Project ,Odontophoridae ,transposable elements ,upland game bird ,Evolutionary Biology ,Evolutionary biology - Abstract
The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.
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- 2023
28. Reference genome of the Virginia rail, Rallus limicola
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Hall, Laurie A, Wang, Ian J, Escalona, Merly, Beraut, Eric, Sacco, Samuel, Sahasrabudhe, Ruta, Nguyen, Oanh, Toffelmier, Erin, Shaffer, H Bradley, and Beissinger, Steven R
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Biological Sciences ,Bioinformatics and Computational Biology ,Evolutionary Biology ,Genetics ,Life on Land ,Animals ,Virginia ,Genome ,Genomics ,Chromosomes ,Birds ,California Conservation Genomics Project ,CCGP ,conservation genetics ,Gruiformes ,Rallidae ,Evolutionary biology - Abstract
The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.
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- 2023
29. Reference genome of the black rail, Laterallus jamaicensis
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Hall, Laurie A, Wang, Ian J, Escalona, Merly, Beraut, Eric, Sacco, Samuel, Sahasrabudhe, Ruta, Nguyen, Oanh, Toffelmier, Erin, Shaffer, H Bradley, and Beissinger, Steven R
- Subjects
Biological Sciences ,Genetics ,Human Genome ,Life on Land ,Animals ,Genome ,Birds ,Ecosystem ,Genomics ,Ecology ,Chromosomes ,California Conservation Genomics Project ,CCGP ,conservation genetics ,Gruiformes ,Rallidae ,Evolutionary Biology ,Evolutionary biology - Abstract
The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.
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- 2023
30. Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae)
- Author
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Adams, Seira A, Graham, Natalie R, Holmquist, Anna J, Sheffer, Monica M, Steigerwald, Emma C, Sahasrabudhe, Ruta, Nguyen, Oanh, Beraut, Eric, Fairbairn, Colin, Sacco, Samuel, Seligmann, William, Escalona, Merly, Shaffer, H Bradley, Toffelmier, Erin, and Gillespie, Rosemary G
- Subjects
Biological Sciences ,Ecology ,Genetics ,Animals ,Ecosystem ,Genome ,Spiders ,California Conservation Genomics Project ,CCGP ,arachnid ,spider genome ,Evolutionary Biology ,Evolutionary biology - Abstract
Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.
- Published
- 2023
31. Real roots of random orthogonal polynomials with exponential weights
- Author
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Do, Yen, Lubinsky, Doron, Nguyen, Hoi H., Nguyen, Oanh, and Pritsker, Igor
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Mathematics - Probability - Abstract
We consider random orthonormal polynomials $$ P_{n}(x)=\sum_{i=0}^{n}\xi_{i}p_{i}(x), $$ where $\xi_{0}$, . . . , $\xi_{n}$ are independent random variables with zero mean, unit variance and uniformly bounded $(2+\ep_0)$-moments, and $\{p_n\}_{n=0}^{\infty}$ is the system of orthonormal polynomials with respect to a general exponential weight $W$ on the real line. This class of orthogonal polynomials includes the popular Hermite and Freud polynomials. We establish universality for the leading asymptotics of the expected number of real roots of $P_n$, both globally and locally. In addition, we find an almost sure limit of the measures counting all roots of $P_n.$ This is accomplished by introducing new ideas on applications of the inverse Littlewood-Offord theory in the context of the classical three term recurrence relation for orthogonal polynomials to establish anti-concentration properties, and by adapting the universality methods to the weighted random orthogonal polynomials of the form $W P_n.$
- Published
- 2022
32. Multilevel Determinants of Digital Health Equity: A Literature Synthesis to Advance the Field
- Author
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Lyles, Courtney R, Nguyen, Oanh Kieu, Khoong, Elaine C, Aguilera, Adrian, and Sarkar, Urmimala
- Subjects
Generic health relevance ,Good Health and Well Being ,Humans ,Health Policy ,Health Equity ,Social Determinants of Health ,Health Status Disparities ,digital health ,health equity ,social determinants of health ,health technology ,Public Health and Health Services ,Public Health - Abstract
Current digital health approaches have not engaged diverse end users or reduced health or health care inequities, despite their promise to deliver more tailored and personalized support to individuals at the right time and the right place. To achieve digital health equity, we must refocus our attention on the current state of digital health uptake and use across the policy, system, community, individual, and intervention levels. We focus here on (a) outlining a multilevel framework underlying digital health equity; (b) summarizingfive types of interventions/programs (with example studies) that hold promise for advancing digital health equity; and (c) recommending future steps for improving policy, practice, and research in this space.
- Published
- 2023
33. Characterizing patients hospitalized without an acute care indication: A retrospective cohort study
- Author
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Rosenthal, Molly A, Ranji, Sumant R, Kanzaria, Hemal K, Ortiz, Gabriel M, Chase, Jack, Chodos, Anna H, Nguyen, Oanh K, Rodriguez, Eric G, and Makam, Anil N
- Subjects
Health Services and Systems ,Health Sciences ,Clinical Research ,Patient Safety ,Good Health and Well Being ,Humans ,Retrospective Studies ,Length of Stay ,Hospitalization ,Patient Discharge ,Critical Care ,Clinical Sciences ,General & Internal Medicine ,Health services and systems ,Nursing - Abstract
BackgroundHospitalizations by patients who do not meet acute inpatient criteria are common and overburden healthcare systems. Studies have characterized these alternate levels of care (ALC) but have not delineated prolonged (pALC) versus short ALC (sALC) stays.ObjectiveTo descriptively compare pALC and sALC hospitalizations-groups we hypothesize have unique needs.Designs, settings, and participantsA retrospective study of hospitalizations from March-April 2018 at an academic safety-net hospital.Main outcome and measuresLevels of care for pALC (>3 days) and sALC (1-3 days) were determined using InterQual©, an industry standard utilization review tool for determining the clinical appropriateness of hospitalization. We examined sociodemographic and clinical characteristics.ResultsOf 2365 hospitalizations, 215 (9.1%) were pALC, 277 (11.7%) were sALC, and 1873 (79.2%) had no ALC days. There were 17,683 hospital days included, and 28.3% (n = 5006) were considered ALC. Compared to patients with sALC, those with pALC were older and more likely to be publicly insured, experience homelessness, and have substance use or psychiatric comorbidities. Patients with pALC were more likely to be admitted for care meeting inpatient criteria (89.3% vs. 66.8%, p < .001), had significantly more ALC days (median 8 vs. 1 day, p < .001), and were less likely to be discharged to the community (p < .001).ConclusionsPatients with prolonged ALC stays were more likely to be admitted for acute care, had greater psychosocial complexity, significantly longer lengths of stay, and unique discharge needs. Given the complexity and needs for hospitalizations with pALC days, intensive interdisciplinary coordination and resource mobilization are necessary.
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- 2023
34. Temperature and Field Dependence of Ferromagnetic Magnon in Monolayer Honeycomb Spin Lattice
- Author
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Nguyen, Niem Tu, Bach, Giang Huong, Pham, Thao Huong, Nguyen, Huy Duy, Nguyen, Oanh Thi Kim, and Bach, Cong Thanh
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Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Materials Science - Abstract
Temperature and field dependence of collective spin excitations or magnon in monolayer honeycomb spin lattices is investigated using an anisotropic exchange XZ-Heisenberg model in an external field. Magnetic phase transition in the presence of the transverse field is the spin reorientation (SR) transition with magnon intensity existing above the SR temperature. The transverse field either decreases or sustains the spin-wave intensity in the temperature region below or above the SR temperature, respectively. The gap of the zero-momentum low-energy magnon branch closes at the SR transverse field, which is the critical quantum phase transition field at zero temperature. The application of the model to a two-dimensional CrI$_3$ explains the existence of the zero-momentum magnon mode above the Curie temperature and shows the suitable values of the exchange parameters compared with the DFT calculations. The estimated magnon velocity near the Dirac point in this material is about 1.74 km/s.
- Published
- 2022
35. Assessing the Hotline Services on Child Trafficking Victims: An Analysis of Vietnam
- Author
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Van Nguyen, Oanh and Luong, Hai Thanh
- Published
- 2023
- Full Text
- View/download PDF
36. Disposal-based scarcity: How overstock reduction methods influence consumer brand perceptions and evaluations
- Author
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Nguyen, Oanh Dinh Yen, Bucic, Tania, Ngo, Liem Viet, and Oppewal, Harmen
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- 2023
- Full Text
- View/download PDF
37. Subcritical epidemics on random graphs
- Author
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Nguyen, Oanh and Sly, Allan
- Subjects
Mathematics - Probability - Abstract
We study the contact process on random graphs with low infection rate $\lambda$. For random $d$-regular graphs, it is known that the survival time is $O(\log n)$ below the critical $\lambda_c$. By contrast, on the Erd\H{o}s-R\'enyi random graphs $\mathcal G(n,d/n)$, rare high-degree vertices result in much longer survival times. We show that the survival time is governed by high-density local configurations. In particular, we show that there is a long string of high-degree vertices on which the infection lasts for time $n^{\lambda^{2+o(1)}}$. To establish a matching upper bound, we introduce a modified version of the contact process which ignores infections that do not lead to further infections and allows for a shaper recursive analysis on branching process trees, the local-weak limit of the graph. Our methods, moreover, generalize to random graphs with given degree distributions that have exponential moments., Comment: 43 pages
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- 2022
38. Acute cancer-related symptoms and concerns among patients receiving chemotherapy: current state of the science
- Author
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Smith, Kristen S., Hoogland, Aasha I., Welniak, Taylor, Nguyen, Oanh L., Rodriguez, Yvelise, Li, Xiaoyin, Crowder, Sylvia L., Oswald, Laura B., Carpenter, Kristen M., Fischer, Stacy M., Li, Daneng, Kinney, Anita Y., Berry, Donna L., Gonzalez, Brian D., and Jim, Heather S. L.
- Published
- 2024
- Full Text
- View/download PDF
39. A draft reference genome of the red abalone, Haliotis rufescens , for conservation genomics
- Author
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Griffiths, Joanna S, Sahasrabudhe, Ruta M, Marimuthu, Mohan P A, Chumchim, Noravit, Nguyen, Oanh H, Beraut, Eric, Escalona, Merly, Whitehead, Andrew, and Lopez, Jose
- Published
- 2022
40. Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata
- Author
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Todd, Brian D, Jenkinson, Thomas S, Escalona, Merly, Beraut, Eric, Nguyen, Oanh, Sahasrabudhe, Ruta, Scott, Peter A, Toffelmier, Erin, Wang, Ian J, Shaffer, H Bradley, and Shapiro, Beth
- Published
- 2022
41. A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii
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Orland, Chloé, Escalona, Merly, Sahasrabudhe, Ruta, Marimuthu, Mohan P A, Nguyen, Oanh, Beraut, Eric, Marshman, Blythe, Moore, James, Raimondi, Peter, Shapiro, Beth, and Lopez, Jose V
- Published
- 2022
42. Reference genome of the California glossy snake, Arizona elegans occidentalis : A declining California Species of Special Concern
- Author
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Wood, Dustin A, Richmond, Jonathan Q, Escalona, Merly, Marimuthu, Mohan P A, Nguyen, Oanh, Sacco, Samuel, Beraut, Eric, Westphal, Michael, Fisher, Robert N, Vandergast, Amy G, Toffelmier, Erin, Wang, Ian J, Shaffer, H Bradley, and Shapiro, Beth
- Published
- 2022
43. A Reference Genome Assembly of the Bobcat, Lynx rufus
- Author
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Lin, Meixi, Escalona, Merly, Sahasrabudhe, Ruta, Nguyen, Oanh, Beraut, Eric, Buchalski, Michael R, Wayne, Robert K, and Blackmon, Heath
- Published
- 2022
44. Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems
- Author
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Bernardi, Giacomo, DeBiasse, Melissa, Escalona, Merly, Marimuthu, Mohan P A, Nguyen, Oanh, Sacco, Samuel, Beraut, Eric, Miller, Courtney, Toffelmier, Erin, Shaffer, H Bradley, and Murphy, William
- Published
- 2022
45. Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage
- Author
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Bernardi, Giacomo, Toy, Jason A, Escalona, Merly, Marimuthu, Mohan P A, Sahasrabudhe, Ruta, Nguyen, Oanh, Sacco, Samuel, Beraut, Eric, Toffelmier, Erin, Miller, Courtney, Shaffer, H Bradley, and Sethuraman, Arun
- Published
- 2022
46. Reference genome for the California ribbed mussel, Mytilus californianus , an ecosystem engineer
- Author
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Paggeot, Lisa X, DeBiasse, Melissa B, Escalona, Merly, Fairbairn, Colin, Marimuthu, Mohan P A, Nguyen, Oanh, Sahasrabudhe, Ruta, Dawson, Michael N, and Meyer, Rachel
- Published
- 2022
47. Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae)
- Author
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Grismer, Jesse L, Escalona, Merly, Miller, Courtney, Beraut, Eric, Fairbairn, Colin W, Marimuthu, Mohan P A, Nguyen, Oanh, Toffelmier, Erin, Wang, Ian J, Shaffer, H Bradley, and Meyer, Rachel
- Published
- 2022
48. A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus , a species severely impacted by wasting
- Author
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DeBiasse, Melissa B, Schiebelhut, Lauren M, Escalona, Merly, Beraut, Eric, Fairbairn, Colin, Marimuthu, Mohan P A, Nguyen, Oanh, Sahasrabudhe, Ruta, Dawson, Michael N, and Lopez, Jose
- Published
- 2022
49. The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi
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Kieran Blair, Shannon Rose, Hull, Joshua, Escalona, Merly, Finger, Amanda, Joslin, Shannon E K, Sahasrabudhe, Ruta, Marimuthu, Mohan P A, Nguyen, Oanh, Chumchim, Noravit, Morris, Emily Reister, Velazquez, Samantha, Schreier, Andrea, and Booth, Warren
- Published
- 2022
50. Reference genome assembly of the sunburst anemone, Anthopleura sola
- Author
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Cornwell, Brendan H, Beraut, Eric, Fairbairn, Colin, Nguyen, Oanh, Marimuthu, Mohan P A, Escalona, Merly, Toffelmier, Erin, and Olsen, Kenneth
- Published
- 2022
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