2,449 results on '"Tyler Smith"'
Search Results
2. Palaearctic flea beetle Phyllotreta ochripes (Curtis) (Coleoptera, Chrysomelidae, Galerucinae), herbivore of Alliaria petiolata (garlic mustard), new to North America
- Author
-
Hume Douglas, George Hammond, Tyler Smith, Jessie Mutz, and Alexander Konstantinov
- Subjects
invasive alien species ,adventive species ,biologi ,Biology (General) ,QH301-705.5 - Abstract
The univoltine leaf beetle Phyllotreta ochripes (Curtis, 1837b) is native to the Palaearctic Region from Japan to western Europe.This species was previously evaluated as a potential biological control agent against invasive populations of the woodland weed Alliaria petiolata (Bieb.) Cavara & Grande (Brassicaceae) in North America, but rejected because it could harm native and at-risk populations of Brassicaceae.First North American records are presented for Phyllotreta ochripes (Curtis, 1837). Specimens were examined from the USA: Illinois, Maryland, Michigan, Ohio and Pennsylvania. Internet photographs of apparent additional individuals from USA: Indiana, Michigan, Minnesota, Ohio, Pennsylvania, Tennessee, Wisconsin and Canada: Ontario were also examined. DNA barcoding analysis showed high genetic variability and possible cryptic species within European populations of P. ochripes. Diagnostic information is presented to distinguish P. ochripes. from other North American Chrysomelidae and a species distribution model to assess its potential spread in North America is presented.Phyllotreta ochripes breeds on invasive garlic mustard, Alliaria petiolata (Bieb.) Cavara & Grande (Brassicaceae) and also non-native Rorippa amphibia (L.) Besser and other species of Brassicaceae.A species distribution model and the range of its host plant A. petiolata, indicates the most suitable conditions for this species are in humid areas of eastern North America. However, most of the known records of this species were discovered in areas projected to have low suitability. This is likely a consequence of sampling bias towards western Europe and away from the eastern Asian portion of its native range. The United States of America and Canada are now known to be home to 72 or more species of adventive Chrysomelidae.
- Published
- 2024
- Full Text
- View/download PDF
3. Palearctic flea beetle and pest of hops and Cannabis, Psylliodes attenuata (Coleoptera, Chrysomelidae, Galerucinae), new to North America
- Author
-
Hume Douglas, Justin Renkema, Tyler Smith, Alexander Konstantinov, and Joseph Moisan-De Serres
- Subjects
invasive alien species ,adventive species ,crop pe ,Biology (General) ,QH301-705.5 - Abstract
The univoltine leaf beetle Psylliodes attenuata (Koch, 1803) is a pest of Cannabis and Humulus (Cannabaceae) and native to the Palaearctic Region, known from eastern Asia to western Europe.First North American records are presented for P. attenuata from Canada: Ontario and Québec. Adult beetle feeding damage to hops Humulus lupulus L. (Cannabacaea) plants is recorded from Québec. Diagnostic information is presented to distinguish P. attenuata from other North American Chrysomelidae and a preliminary assessment of its potential to spread in North America is presented. While our climate analysis is limited by a lack of data, it appears P. attenuata is physiologically capable of persisting throughout the range of Humulus in North America.The United States of America and Canada are now known to be home to 71 or more species of adventive Chrysomelidae.
- Published
- 2024
- Full Text
- View/download PDF
4. Endovascular retrieval of a migrated covered stent from the pulmonary artery
- Author
-
Ziga Cizman, MD, William Zachery Paden, MD, Tyler Smith, MD, Samuel Wilhite, MD, David Strain, MD, and Wael Saad, FSIR, MBBCh
- Subjects
Stent migration ,Tricuspid regurgitation ,Nutcracker syndrome ,Endovascular stent retrieval ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
Stent migration is a rare but significant complication following endovascular procedures. Techniques for managing dislodged stents have included surgical, endovascular, and conservative approaches. This case details a patient who had a covered stent placed within the left renal vein which later migrated to the pulmonary artery causing damage to the tricuspid valve. The migrated stent was successfully removed using a percutaneous endovascular approach utilizing fluoroscopy and transesophageal echocardiogram guidance.
- Published
- 2024
- Full Text
- View/download PDF
5. Multi‐method approach to assessing the floral‐visiting insect assemblage of rare, abophilous plant Baccharis vanessae in Southern California
- Author
-
Christina Simokat, Elizabeth L. Ferguson, Jessica Keatly, Tyler Smith, Mia Lorence, and Jasmine O'Hara
- Subjects
camera traps ,conservation management ,focal observations ,insect–plant interactions ,plant conservation ,pollination ,Ecology ,QH540-549.5 - Abstract
Abstract Insects are the major pollination vectors for angiosperms, and insects native to a given habitat can play an irreplaceable ecological role in food webs and plant reproduction. With precipitous declines in insect species over the last decades, it is urgent to document insect assemblages in native plant communities to support conservation efforts. Identifying pollinators and their pollination activity is challenging; however, emerging technological methods are providing new monitoring capabilities. In this study, we compare the accuracy of two different methods of monitoring to assess the flower‐visiting insect assemblage and likely pollinators of Encinitas baccharis (Baccharis vanessae): focal observations and video recordings from camera traps. B. vanessae is a rare, endemic species found in Coastal Sage Scrub communities in San Diego County. This federally listed species is threatened by habitat loss and fragmentation, which may also be affecting the availability of its insect pollinators. Results indicate that B. vanessae supports and is supported by a variety of flower‐visiting insect groups. The diversity of insect visitors at male and female plants were similar across all diversity measurements. The insect vectors identified were as expected given B. vanessae pollination syndrome. This syndrome also aligns with wind as a pollination vector, providing evidence of ambophily. While focal observations underreported insect activity by approximately half, the proportions of common diurnal visitors were similar with both methods. Camera traps were unable to provide sufficient detail to discern visually similar groups, but were able to record nocturnal insect activity, which was dominated by moths (Lepidoptera, 82%). While collection protocol in this study did not record the time an insect spent interacting with a flower, we anecdotally observed moths spent notably longer periods in contact with flowers than most diurnal insects. This study has implications for effective monitoring and conservation of endangered plant species and their affiliated pollinators.
- Published
- 2024
- Full Text
- View/download PDF
6. A summary of the main themes and findings presented at the ASM Intermountain Branch meeting (2024)
- Author
-
Jay Radke, Javier Ochoa-Repåraz, Jamee Nixon, Sajal Acharya, Haley Bridgewater, Joshua Burger, Abigail Cheever, Robert Darby, William Doyle, Alka Gaur, Eva Githuku, Rose Goodman, Topher Haynie, Hannah Hedelius, Kristina Hill, Misha Iqbal, Salma Laabi, Carlos Moreno, Melinda Moss, Nagama Parveen, Naomi Rapier-Sharman, Sara Sadeghi, Saeed Saleh, Sean Schumacher, Miranda Sharp, Noah Souza, Soni Thapa, Shule Aggabao, David Amsbury, Sheena Isabelle Bautista, Atalie Bogh, Aaron Bohn, Cade Brink, B. Shaun Bryner, James Cannon, Scot Carrington, Hayzen Chamberlain, Alex Cherry, McKaylin Cole, Edgar Corrales, Caz Cullimore, Sophie Daines, Payson Danielson, Monterey Domike, Matthew East, Bronwyn Ellis, Taryn Evans, Zach Fears, Paige Fellars, Tate Fisher, Braxton Floyd, Trenton Gibson, Mason Gueller, Heather Gupta, Jacob Gwilliam, Mackenzie Hansen, Jacob Hardy, Christopher Harrell, Rebecca Hassell, Wesley Hendricks, Colby Hendrix, Hirsche Henstrom, Kelly Hernandez Sanguino, George Higgins, Hyunbi Hwang, Matt Jackson, Conner Jensen, Austin Johnson, Chloe Kang, Sehi Kim, Alexandra LaFollette, Phoenix Larsen, Abbey Larson, Bryson Leary, Jayden Longhurst, Michael Mann, Isreal Martinez, Brooklyn Matthews, Cody McStraw, Ninahazwe Mireill, Rachel Moffat, Peter Mourik, Madelyn Mudrow, Mailon Odell, Blake Oler, Natalie Olsen, Nazanin Paymard, Spencer T. Payne, Levi Pearson, Josh Peter, Tiffani Peterson, Daniel Puentes Navarro, Kyla Radke, Joseph Richardson, Russell Ridd, Akir Rowe, Rylan Schmanski, Jacob Scott, Samuel Scott, Mya Simpkins, Madalyne Sisk, Tyler Smith, Brinley Smith, Jacob Sy, Gisselle Trejo, Bartel Van Oostendorp, Ethan Walbom, Rebecca Whetten, Dallin Zollinger, Miriam Braunstein, Donald P. Breakwell, Anirban Chakraborty, Matthew Crook, Michele Culumber, Wayne Hatch, Victor M. Jimenez, Jr., Wales P. Nematollahi, Michael Olson, Mark Poritz, Seth Ririe, Jeffrey Schachterle, Lisa Wiltbank, Todd Kelson, and Brett E. Pickett
- Subjects
branch meeting ,microbiology ,phages ,environmental biology ,infectious diseases ,clinical microbiology ,Microbiology ,QR1-502 - Abstract
ABSTRACT The annual meeting for the Intermountain Branch was held in April 2024 on the campus of Brigham Young University. There were 127 branch members from Utah, Idaho, and Nevada who attended the meeting and were composed of undergraduate students, graduate or medical students, and faculty. This report highlights the diversity of, and the emerging trends in, the research conducted by American Society for Microbiology members in the Intermountain Branch.
- Published
- 2024
- Full Text
- View/download PDF
7. Quantum computation of reactions on surfaces using local embedding
- Author
-
Tanvi P. Gujarati, Mario Motta, Triet Nguyen Friedhoff, Julia E. Rice, Nam Nguyen, Panagiotis Kl. Barkoutsos, Richard J. Thompson, Tyler Smith, Marna Kagele, Mark Brei, Barbara A. Jones, and Kristen Williams
- Subjects
Physics ,QC1-999 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Abstract Modeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a workflow to model the adsorption and reaction of molecules on surfaces using quantum computing algorithms. We develop and compare two local embedding methods for the systematic determination of active spaces. These methods are automated and based on the physics of molecule-surface interactions and yield systematically improvable active spaces. Furthermore, to reduce the quantum resources required for the simulation of the selected active spaces using quantum algorithms, we introduce a technique for exact and automated circuit simplification. This technique is applicable to a broad class of quantum circuits and critical to enable demonstration on near-term quantum devices. We apply the proposed combination of active-space selection and circuit simplification to the dissociation of water on a magnesium surface using classical simulators and quantum hardware. Our study identifies reactions of molecules on surfaces, in conjunction with the proposed algorithmic workflow, as a promising research direction in the field of quantum computing applied to materials science.
- Published
- 2023
- Full Text
- View/download PDF
8. Palaearctic leaf beetle Chrysolina fastuosa (Coleoptera, Chrysomelidae, Chrysomelinae) new to North America
- Author
-
Hume Douglas, Tyler Smith, and Patrice Bouchard
- Subjects
invasive alien species ,adventive species ,biologi ,Biology (General) ,QH301-705.5 - Abstract
The univoltine leaf beetle Chrysolina fastuosa (Scopoli, 1763) is native to in the Palearctic Region from eastern Siberia to western Europe.First North American records are presented for C. fastuosa (Scopoli, 1763) (Coleoptera, Chrysomelidae, Chrysomelinae), as confirmed by vouchered specimens from Canada: Nova Scotia. Additional citizen science records from USA: Vermont are also discussed. Diagnostic information is presented to distinguish C. fastuosa from other North American Chrysomelidae and a species distribution model to assess its potential spread in North America is presented. This insect is expected to cause some feeding damage to above-ground parts of ornamental and invasive Lamiaceae, especially species of Galeopsis L. The species distribution model and the range of its host plant Galeopsis tetrahit, suggest the north-eastern US and south-eastern Canada, from the Atlantic coast to the west end of Lake Superior provide the most suitable conditions for this species. The United States of America and Canada are now known to be home to 70 or more species of adventive Chrysomelidae.
- Published
- 2023
- Full Text
- View/download PDF
9. Compression and energy absorption characteristics of short fiber‐reinforced 2D composite lattices made by material extrusion
- Author
-
Seokpum Kim, Aslan Nasirov, Deepak Kumar Pokkalla, Vidya Kishore, Tyler Smith, Chad Duty, and Vlastimil Kunc
- Subjects
additive manufacturing ,composites ,compression ,energy absorption ,lattice ,material extrusion ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
AbstractWith the advent of additive manufacturing, lattice structures have been of increasing interest for engineering applications involving light‐weighting and energy absorption. Several studies have investigated mechanical properties of various lattices made up of mostly unreinforced polymers and lack numerical analysis for reinforced lattice structures. In this paper, mechanical response of short fiber reinforced lattice structures under compression is investigated through experiments and numerical simulations. Three different 2D lattices namely, square grid, honeycomb, and isogrid along with their rotated counterparts were fabricated using 15% wt carbon fiber‐acrylonitrile butadiene styrene and experimentally evaluated through uniaxial compression testing up to 30% strain. As simulations on fiber‐reinforced lattices under large compressive strains are rarely performed and published, finite element models accounting for fiber orientation induced anisotropic mechanical properties and geometrical imperfections were developed to predict the stress–strain characteristics up to 30% compressive strains. The stress–strain curves predicted from the numerical simulations matches well with the experimental responses for various lattice geometries. Various failure mechanisms such as thin strut buckling, contact within the lattice, and fracture of struts under large deformation were investigated. Analyzing energy absorption characteristics of these lattices revealed that the honeycomb structures in horizontal configuration exhibits superior energy absorption capability.
- Published
- 2023
- Full Text
- View/download PDF
10. Republication of 'Uses of Braces and Orthotics for Conservative Management of Foot and Ankle Disorders'
- Author
-
Osama Elattar MD, Tyler Smith DO, Adam Ferguson DO, Daniel Farber MD, and Keith Wapner MD
- Subjects
Orthopedic surgery ,RD701-811 - Abstract
Nonsurgical management is almost always considered the first-line treatment for the vast majority of foot and ankle pathologies. Foot orthoses, shoe modifications, and therapeutic footwear are considered essential tools for successful conservative management of different foot and ankle disorders. Orthopedic foot and ankle surgeons should have a meticulous understanding of the lower extremity biomechanics as well as the pathoanatomy and the sequelae of diseases affecting the foot and/or ankle. This is essential to the understanding of the desired effects of the different inserts, orthotics, shoe modifications, or braces that may be prescribed for these conditions. In this article, we will summarize the orthoses used for treatment of the most commonly encountered foot and ankle pathologies, with the exclusion of treatment for the diabetic foot because of the unique requirements of that disease process.
- Published
- 2023
- Full Text
- View/download PDF
11. Patients Have Poor Postoperative Recall of Information Provided the Day of Surgery but Report Satisfaction With and High Use of an E-mailed Postoperative Digital Media Package
- Author
-
Kyle Shultz, D.O., Marissa Mastrocola, M.D., Tyler Smith, D.O., and Brian Busconi, M.D.
- Subjects
Sports medicine ,RC1200-1245 - Abstract
Purpose: To understand what portions of the surgical day patients remember, what parts of an e-mailed media package regarding their surgery patients are used, and how that information affects their surgical experience. Methods: Patients undergoing an outpatient arthroscopic procedure were approached in the preoperative area and asked to remember 3 words. Postoperatively, they were seen by the surgeon to discuss surgical findings and instructions. They were then e-mailed a multimedia package containing a thank you letter, postoperative instructions, annotated arthroscopy images, and a personalized video from the surgeon. Patients were called 2 to 5 days after surgery to answer survey questions and recall the 3 words they were told on the day of surgery. Results: Of the 160 patients, 100% received and accessed the e-mail. When asked if they remembered the postoperative conversation, 125 (78.1%) patients responded yes and 35 (21.9%) responded no. When asked to rate how well they remembered the postoperative conversation, 75.2% patients rated their memory very poor (48, 38.4%) or poor (46, 36.8%). Similarly, 129 (80.6%) patients were unable to remember the 3 surgeon-related words. One hundred percent of patients strongly agreed (145, 90.6%) or agreed (15, 9.4%) the e-mail package enhanced their experience. In addition, 100% of patients strongly agreed (150, 93.8%) or agreed (10, 6.2%) the surgeon video enhanced their experience. The average e-mail shares per patient was 2.5, with 158 (98.7%) of patients sharing the e-mail at least once. Conclusions: This study shows that patients had poor memory of in-person conversations on the day of surgery. However, patients were satisfied with a postoperative multimedia package provided via e-mail after surgery. Patients interacted with the e-mail primarily on their cell phones, liked the surgeon video, and shared the e-mail with others. Level of evidence: Level IV, therapeutic case series.
- Published
- 2023
- Full Text
- View/download PDF
12. Acute decompensation of patient following an outpatient CT-guided needle biopsy: A case report
- Author
-
Danielle Fall, PA-C, Tyler Smith, MD, Ann Marie Prazak, PharmD, Ziga Cizman, MD, and Aidin Iravani, MD
- Subjects
Arterial air embolism ,Pneumothorax ,Hyperbaric oxygen therapy ,Lung biopsy ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
A 74-year-old female with history of type 2 diabetes, hypertension, and uterine adenocarcinoma presented for CT-guided lung biopsy that was ultimately complicated by an arterial air embolus requiring intensive care. Systemic air embolism is a very rare event but can be devastating. Prompt recognition can be difficult due to an often-vague presentation but is essential and should be considered upon rapid deterioration of a patient's status following high risk procedures. Hyperbaric oxygen therapy is preferred; however, if this is unavailable, additional treatments are predominately supportive care with 100% supplemental oxygen, rapid volume expansion, and ionotropic medications as needed.
- Published
- 2023
- Full Text
- View/download PDF
13. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies
- Author
-
Basile Tessier‐Cloutier, Jasleen K Grewal, Martin R Jones, Erin Pleasance, Yaoqing Shen, Ellen Cai, Chris Dunham, Lynn Hoang, Basil Horst, David G Huntsman, Diana Ionescu, Anthony N Karnezis, Anna F Lee, Cheng Han Lee, Tae Hoon Lee, David DW Twa, Andrew J Mungall, Karen Mungall, Julia R Naso, Tony Ng, David F Schaeffer, Brandon S Sheffield, Brian Skinnider, Tyler Smith, Laura Williamson, Ellia Zhong, Dean A Regier, Janessa Laskin, Marco A Marra, C Blake Gilks, Steven JM Jones, and Stephen Yip
- Subjects
biomarker ,diagnostic ,WGTA ,pathology ,precision medicine ,oncology ,Pathology ,RB1-214 - Abstract
Abstract In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular alterations and site/tissue of origin prediction. Two reviewers analyzed genomic reports, clinical history, and tumor pathology. We used National Comprehensive Cancer Network (NCCN) consensus guidelines, Food and Drug Administration (FDA) approvals, and provincially reimbursed treatments to define genomic biomarkers associated with approved targeted therapeutic options (TTOs). Tumor tissue/site of origin was reassessed for most cases using genomic analysis, including a machine learning algorithm (Supervised Cancer Origin Prediction Using Expression [SCOPE]) trained on The Cancer Genome Atlas data. WGTA was performed on 652 cases, including a range of primary tumor types/tumor sites and 15 malignant tumors of uncertain histogenesis (MTUH). At the time WGTA was performed, alterations associated with an approved TTO were identified in 39 (6%) cases; 3 of these were not identified through routine pathology workup. In seven (1%) cases, the pathology workup either failed, was not performed, or gave a different result from the WGTA. Approved TTOs identified by WGTA increased to 103 (16%) when applying 2021 guidelines. The histopathologic diagnosis was reviewed in 389 cases and agreed with the diagnostic consensus after WGTA in 94% of non‐MTUH cases (n = 374). The remainder included situations where the morphologic diagnosis was changed based on WGTA and clinical data (0.5%), or where the WGTA was non‐contributory (5%). The 15 MTUH were all diagnosed as specific tumor types by WGTA. Tumor board reviews including WGTA agreed with almost all initial predictive molecular profile and histopathologic diagnoses. WGTA was a powerful tool to assign site/tissue of origin in MTUH. Current efforts focus on improving therapeutic predictive power and decreasing cost to enhance use of WGTA data as a routine clinical test.
- Published
- 2022
- Full Text
- View/download PDF
14. Internal Jugular Central Venous Catheter Tip Migration: Patient and Procedural Factors
- Author
-
Tyler Smith, Claire Kaufman, and Keith Quencer
- Subjects
central venous catheter ,catheter dysfunction ,dialysis access ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Background: The ideal central venous catheter (CVC) tip position placement is controversial, and CVCs do not remain in a fixed position after placement. This study evaluates both patient and procedural factors which may influence CVC tip migration and subsequent catheter dysfunction. Materials and Methods: This study evaluates CVC placements at a single institution. Patient age, gender, body mass index (BMI), catheter laterality, CVC type and indication for central venous access were recorded. Catheter tip location relative to the carina was measured at time of placement and removal utilizing supine fluoroscopic imaging. Patients’ electronic medical records were reviewed for evidence of catheter dysfunction. Statistical analysis was performed utilizing odds ratios and two tailed Student’s t-test. Results: 177 patients were included (101 female; mean age 55; mean BMI 29.2). Catheter types included 122 ports, 50 tunneled large bore central venous catheters (≥9 French), and 5 tunneled small bore central venous catheters (p = 0.000008). Catheters that migrated cranially by >2 cm had more than 7× greater risk of dysfunction compared to catheters that migrated ≤2 cm (odds ratio of 7.2; p = 0.0001). Left sided CVCs were significantly more likely to have >2 cm of cranial migration (odds ratio 6.9, 95% CI 3.4–14.2, p < 0.0001) and had a higher rate of dysfunction, likely due to this cranial migration (32% vs. 4.7%; p = 0.00001). Gender and BMI were not found to be associated with catheter dysfunction or an increased odds ratio of >2 cm cranial migration. Conclusions: Left-sided CVCs migrate an average of 2.4 cm cranially more than right-sided catheters. Additionally, when migration occurs, left-sided catheters are more likely to be dysfunctional. These suggest that lower initial placement may be beneficial in left-sided catheters.
- Published
- 2022
- Full Text
- View/download PDF
15. Sensemaking in the Legal System: A Comparative Case Study of Changes to Monetary Sanction Laws
- Author
-
Tyler Smith, Kristina J. Thompson, and Michele Cadigan
- Subjects
legal change ,monetary sanctions ,courtroom communities ,Social Sciences - Abstract
Legal scholars have long studied why laws are implemented differently across local court contexts. Key to understanding this localized variation is understanding how new laws are communicated, interpreted, and negotiated within the legal field. Few studies, however, have directly examined the process by which court actors interpret and negotiate new laws within the court. We explore these sensemaking processes through interviews and observations of court actors in Washington and Missouri after changes to monetary sanction laws. We identify three primary forms of sensemaking and analyze contextual factors that shape these processes. We find key differences in sensemaking based on differing levels of regulatory oversight but also that normative and cultural factors were still important in determining legal interpretation and implementation within each state. These findings have important implications for our theoretical understanding of courtroom communities and for policymakers seeking to enact reform.
- Published
- 2022
- Full Text
- View/download PDF
16. County Dependence on Monetary Sanctions: Implications for Women’s Incarceration
- Author
-
Kate K. O’Neill, Tyler Smith, and Ian Kennedy
- Subjects
incarceration ,sex ,gender ,monetary sanctions ,sentencing ,Social Sciences - Abstract
Although men’s incarceration rates have declined in the United States, women’s have stayed steady and even risen in some areas. At the same time, courts have increased their use of monetary sanctions, especially for low-level offenses. We propose that women’s incarceration trends can be partially explained by county dependence on monetary sanctions as a source of revenue. We suggest that monetary sanctions expose female defendants to processes that increase their likelihood of incarceration, especially in counties more reliant on monetary sanctions as a source of revenue, and where women’s poverty rates are high. Using data from Washington State, we find county dependence on monetary sanctions is positively associated with rates of women sentenced to incarceration. Although rural counties’ rates are higher, they depend on monetary sanctions no more than nonrural counties do.
- Published
- 2022
- Full Text
- View/download PDF
17. Monetary Sanctions as Chronic and Acute Health Stressors: The Emotional Strain of People Who Owe Court Fines and Fees
- Author
-
Alexes Harris and Tyler Smith
- Subjects
health ,stress ,criminal legal system ,monetary sanctions ,fines and fees ,Social Sciences - Abstract
In this article, we explore the experiences of people who carry monetary sanction (or penal) debt across eight U.S. states. Using 519 interviews with people sentenced to fines and fees, we analyze the mental and emotional aspects of their experiences. Situating our analysis within research on the social determinants of health and the stress universe, we suggest that monetary sanctions create an overwhelmingly palpable sense of fear, frustration, anxiety, and despair. We theorize the ways in which monetary sanctions function as both acute and chronic health stressors for people who are unable to pay off their debts, highlight the mechanisms linking penal debt with mental and emotional burdens, and generalize our findings using national data from the U.S. Federal Reserve. We find that the system of monetary sanctions generates a great deal of stress and strain that becomes an internalized punishment affecting many realms of people’s lives.
- Published
- 2022
- Full Text
- View/download PDF
18. Embolization of pulmonary artery aneurysms in a patient with Behçet’s disease complicated by coil erosion into the airway
- Author
-
Nicole Law, MD, Keith Quencer, MD, Claire Kaufman, MD, Aidin Iravani, MD, Rulon Hardman, MD, PhD, and Tyler Smith, MD
- Subjects
Behcet’s disease ,Pulmonary artery aneurysm ,Coil migration ,Surgery ,RD1-811 ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Behçet’s disease is an inflammatory vasculitis with the unique feature of pulmonary artery aneurysms. We describe a patient with Behçet’s disease and pulmonary artery aneurysms who presented with massive hemoptysis treated by coil embolization. Although there was immediate resolution of hemoptysis and improvement in hemodynamic status, 2 months later the patient reported a refractory cough and feeling of foreign body in her throat. Imaging demonstrated partial coil migration into the bronchus and trachea. Although endovascular intervention is the first-line treatment for massive hemoptysis, in patients with Behçet’s disease, active inflammation and chronic steroid use may increase the risk of coil erosion and migration.
- Published
- 2022
- Full Text
- View/download PDF
19. Acupuncture for combat post-traumatic stress disorder: trial development and methodological approach for a randomized controlled clinical trial
- Author
-
Michael Hollifield, An-Fu Hsiao, Kala Carrick, Andrea Gory Munoz, Teresa Calloway, Karen Cocozza, Besa Smith, Tyler Smith, Tanja Jovanovic, Seth Norrholm, Estate Sokhadze, and Christopher Reist
- Subjects
Post-traumatic stress ,Acupuncture ,Combat ,Veterans ,Psychophysiology ,Medicine (General) ,R5-920 - Abstract
Abstract Background Post-traumatic stress disorder (PTSD) is a significant public health problem, affecting approximately 7% of the general population and 13–18% of the combat Veteran population. The first study using acupuncture for PTSD in a civilian population showed large pre- to post-treatment effects for an empirically developed verum protocol, which was equivalent to group cognitive behavior therapy and superior to a wait-list control. The primary objective of this study is to determine both clinical and biological effects of verum acupuncture for combat-related PTSD in treatment-seeking US Veterans. Methods This is a two-arm, parallel-group, prospective randomized placebo-controlled clinical trial. The experimental condition is verum acupuncture and the placebo control is sham (minimal) acupuncture in 1-h sessions, twice a week for 12 weeks. Ninety subjects will provide adequate power and will be allocated to group by an adaptive randomization procedure. The primary outcome is change in PTSD symptom severity from pre- to post-treatment. The secondary biological outcome is change from pre- to post-treatment in psychophysiological response, startle by electromyographic (EMG) eyeblink. Assessments will be conducted at pre-, mid-, post-, and 1-month post-treatment, blind to group allocation. Intent-to-treat analyses will be conducted. Discussion The study results will be definitive because both clinical and biological outcomes will be assessed and correlated. Issues such as the number needed for recruitment and improvement, use of sham acupuncture, choice of biological measure, and future research need will be discussed. Trial registration ClinicalTrials.gov NCT02869646 . Registered on 17 August 2016.
- Published
- 2021
- Full Text
- View/download PDF
20. Assessing the impact of PET estimation methods on hydrologic model performance
- Author
-
Dilhani Ishanka Jayathilake and Tyler Smith
- Subjects
budyko classification ,hydrologic model ,potential evapotranspiration ,uncertainty ,variability ,River, lake, and water-supply engineering (General) ,TC401-506 ,Physical geography ,GB3-5030 - Abstract
Evapotranspiration is a necessary input and one of the most uncertain hydrologic variables for quantifying the water balance. Key to accurately predicting hydrologic processes, particularly under data scarcity, is the development of an understanding of the regional variation of the impact of potential evapotranspiration (PET) data inputs on model performance and parametrization. This study explores this impact using four different potential evapotranspiration products (of varying quality). For each data product, a lumped conceptual rainfall–runoff model (GR4J) is tested on a sample of 57 catchments included in the MOPEX data set. Monte Carlo sampling is performed, and the resulting parameter sets are analyzed to understand how the model responds to differences in the forcings. Test catchments are classified as energy- or water-limited using the Budyko framework and by eco-region, and the results are further analyzed. While model performance (and parameterization) in water-limited sites was found to be largely unaffected by the differences in the evapotranspiration inputs, in energy-limited sites model performance was impacted as model parameterizations were clearly sensitive to evapotranspiration inputs. The quality/reliability of PET data required to avoid negatively impacting rainfall–runoff model performance was found to vary primarily based on the water and energy availability of catchments. HIGHLIGHTS Model sensitivity to potential evapotranspiration (PET) errors was explored based on eco-regional and Budyko classifications.; Although the model was not found to be sensitive to eco-region classification, the sensitivity varied along the water- to energy-limited continuum.; This information, critically, can be used to better allocate limited resources for performing data collection and modeling and has benefits in data-scarce regions.;
- Published
- 2021
- Full Text
- View/download PDF
21. A biological condition gradient for coral reefs in the US Caribbean Territories: Part I. Coral narrative rules
- Author
-
Deborah L Santavy, Susan K. Jackson, Benjamin Jessup, Jeroen Gerritsen, Caroline Rogers, William S. Fisher, Ernesto Weil, Alina Szmant, David Cuevas-Miranda, Brian K. Walker, Christopher Jeffrey, Patricia Bradley, David Ballantine, Loretta Roberson, Hector Ruiz-Torres, Brandi Todd, Tyler Smith, Randy Clark, Ernesto Diaz, Jorge Bauzá-Ortega, Christina Horstmann, and Sandy Raimondo
- Subjects
Coral reef condition ,Biocriteria ,Biological integrity ,Biological Condition Gradient (BCG) ,Coral reef protection ,Narrative rules ,Ecology ,QH540-549.5 - Abstract
As coral reef condition and sustainability continue to decline worldwide, losses of critical habitat and their ecosystem services have generated an urgency to understand and communicate reef response to management actions, environmental contamination, and natural disasters. Increasingly, coral reef protection and restoration programs emphasize the need for robust assessment tools for protecting high-quality waters and establishing conservation goals. Of equal importance is the need to communicate assessment results to stakeholders, beneficiaries, and the public so that environmental consequences of decisions are understood. The Biological Condition (BCG) model provides a structure to evaluate the condition of a coral reef in increments of change along a gradient of human disturbance. Communication of incremental change, regardless of direction, is important for decision makers and the public to better understand what is gained or lost depending on what actions are taken. We developed a narrative (qualitative) Biological Condition Gradient (BCG) from the consensus of a diverse expert panel to provide a framework for coral reefs in US Caribbean Territories. The model uses narrative descriptions of biological attributes for benthic organisms to evaluate reefs relative to undisturbed or minimally disturbed conditions. Using expert elicitation, narrative decision rules were proposed and deliberated to discriminate among six levels of change along a gradient of increasing anthropogenic stress. Narrative rules for each of the BCG levels are presented to facilitate the evaluation of benthic communities in coral reefs and provide specific narrative features to detect changes in coral reef condition and biological integrity. The BCG model can be used in the absence of numeric, or quantitative metrics, to evaluate actions that may encroach on coral reef ecosystems, manage endangered species habitat, and develop and implement management plans for marine protected areas, watersheds, and coastal zones. The narrative BCG model is a defensible model and communication tool that translates scientific results so the nontechnical person can understand and support both regulatory and non-regulatory water quality and natural resource programs.
- Published
- 2022
- Full Text
- View/download PDF
22. Effectiveness of Amniotic Fluid Injection in the Treatment of Trigger Finger: A Pilot Study
- Author
-
Michael T. Quinet, BS, Maya Raghavan, MSPH, Emily Morris, BS, Tyler Smith, MPH, MSW, Haley Cook, BS, Nathan Walter, BS, and Michael Shuler, MD
- Subjects
Amniotic fluid ,Diabetes ,Injection ,Stenosing tenosynovitis ,Trigger finger ,Surgery ,RD1-811 - Abstract
Purpose: To assess the efficacy and safety of amniotic fluid therapy injections in patients with mild to moderate trigger finger. Methods: All participants received 1 mL of amniotic fluid injected into the tendon sheath of the affected tendon. Pretreatment and posttreatment data were collected for triggering frequency, Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire scores, and numerical pain rating scale scores. Results: Of 111 digits from 96 patients, 51% experienced clinically notable improvement and did not receive an alternative treatment. Average length of follow-up was 11 months. From baseline to end of follow-up, average pain score (0–10) decreased from 5.19 to 1.19 (P < .001), median triggering per day decreased from 5 to 0 (P < .001), and median DASH score (1–100) decreased from 20 to 6.03 (P < .001). There was a 50% success rate in patients with diabetes and a 52.6% success rate in digits diagnosed with concomitant Dupuytren contracture in the same hand. Conclusions: Amniotic fluid therapy injections may offer a biologic alternative for conservative treatment of trigger finger, particularly for patients with diabetes. Decreased pain, decreased triggering, and improved DASH scores offer preliminary evidence supporting the use of amniotic injections for stenosing tenosynovitis. Type of study/level of evidence: Therapeutic IV.
- Published
- 2020
- Full Text
- View/download PDF
23. Using mobile phone data for epidemic response in low resource settings—A case study of COVID-19 in Malawi
- Author
-
Dylan Green, Michael Moszczynski, Samer Asbah, Cassie Morgan, Brandon Klyn, Guillaume Foutry, Simon Ndira, Noah Selman, Maganizo Monawe, Andrew Likaka, Rachel Sibande, and Tyler Smith
- Subjects
COVID-19 ,Malawi ,mobile network data ,Information technology ,T58.5-58.64 ,Political institutions and public administration (General) ,JF20-2112 - Abstract
The COVID-19 global pandemic has had considerable health impact, including sub-Saharan Africa. In Malawi, a resource-limited setting in Africa, gaining access to data to inform the COVID-19 response is challenging. Information on adherence to physical distancing guidelines and reducing contacts are nonexistent, but critical to understanding and communicating risk, as well as allocating scarce resources. We present a case study which leverages aggregated call detail records into a daily data pipeline which summarize population density and mobility in an easy-to-use dashboard for public health officials and emergency operations. From March to April 2021, we have aggregated 6-billion calls and text messages and continue to process 12 million more daily. These data are summarized into reports which describe, quantify, and locate mass gatherings and travel between subdistricts. These reports are accessible via web dashboards for policymakers within the Ministry of Health and Emergency Operations Center to inform COVID-19 response efforts and resource allocation.
- Published
- 2021
- Full Text
- View/download PDF
24. The risks and benefits of providing HIV services during the COVID-19 pandemic.
- Author
-
John Stover, Sherrie L Kelly, Edinah Mudimu, Dylan Green, Tyler Smith, Isaac Taramusi, Loveleen Bansi-Matharu, Rowan Martin-Hughes, Andrew N Phillips, and Anna Bershteyn
- Subjects
Medicine ,Science - Abstract
IntroductionThe COVID-19 pandemic has caused widespread disruptions including to health services. In the early response to the pandemic many countries restricted population movements and some health services were suspended or limited. In late 2020 and early 2021 some countries re-imposed restrictions. Health authorities need to balance the potential harms of additional SARS-CoV-2 transmission due to contacts associated with health services against the benefits of those services, including fewer new HIV infections and deaths. This paper examines these trade-offs for select HIV services.MethodsWe used four HIV simulation models (Goals, HIV Synthesis, Optima HIV and EMOD) to estimate the benefits of continuing HIV services in terms of fewer new HIV infections and deaths. We used three COVID-19 transmission models (Covasim, Cooper/Smith and a simple contact model) to estimate the additional deaths due to SARS-CoV-2 transmission among health workers and clients. We examined four HIV services: voluntary medical male circumcision, HIV diagnostic testing, viral load testing and programs to prevent mother-to-child transmission. We compared COVID-19 deaths in 2020 and 2021 with HIV deaths occurring now and over the next 50 years discounted to present value. The models were applied to countries with a range of HIV and COVID-19 epidemics.ResultsMaintaining these HIV services could lead to additional COVID-19 deaths of 0.002 to 0.15 per 10,000 clients. HIV-related deaths averted are estimated to be much larger, 19-146 discounted deaths per 10,000 clients.DiscussionWhile there is some additional short-term risk of SARS-CoV-2 transmission associated with providing HIV services, the risk of additional COVID-19 deaths is at least 100 times less than the HIV deaths averted by those services. Ministries of Health need to take into account many factors in deciding when and how to offer essential health services during the COVID-19 pandemic. This work shows that the benefits of continuing key HIV services are far larger than the risks of additional SARS-CoV-2 transmission.
- Published
- 2021
- Full Text
- View/download PDF
25. The Arabidopsis Protein Disulfide Isomerase Subfamily M Isoform, PDI9, Localizes to the Endoplasmic Reticulum and Influences Pollen Viability and Proper Formation of the Pollen Exine During Heat Stress
- Author
-
Elizabeth Feldeverd, Brad W. Porter, Christen Y. L. Yuen, Kaela Iwai, Rina Carrillo, Tyler Smith, Cheyenne Barela, Katherine Wong, Pengfei Wang, Byung-Ho Kang, Kristie Matsumoto, and David A. Christopher
- Subjects
protein folding ,protein disulfide isomerase ,heat stress ,pollen viability ,pollen exine biogenesis ,Plant culture ,SB1-1110 - Abstract
Plants adapt to heat via thermotolerance pathways in which the activation of protein folding chaperones is essential. In eukaryotes, protein disulfide isomerases (PDIs) facilitate the folding of nascent and misfolded proteins in the secretory pathway by catalyzing the formation and isomerization of disulfide bonds and serving as molecular chaperones. In Arabidopsis, several members of the PDI family are upregulated in response to chemical inducers of the unfolded protein response (UPR), including both members of the non-classical PDI-M subfamily, PDI9 and PDI10. Unlike classical PDIs, which have two catalytic thioredoxin (TRX) domains separated by two non-catalytic TRX-fold domains, PDI-M isoforms are orthologs of mammalian P5/PDIA6 and possess two tandem catalytic domains. Here, PDI9 accumulation was found to be upregulated in pollen in response to heat stress. Histochemical staining of plants harboring the PDI9 and PDI10 promoters fused to the gusA gene indicated they were actively expressed in the anthers of flowers, specifically in the pollen and tapetum. Immunoelectron microscopy revealed that PDI9 localized to the endoplasmic reticulum in root and pollen cells. transfer DNA (T-DNA) insertional mutations in the PDI9 gene disrupted pollen viability and development in plants exposed to heat stress. In particular, the pollen grains of pdi9 mutants exhibited disruptions in the reticulated pattern of the exine and an increased adhesion of pollen grains. Pollen in the pdi10 single mutant did not display similar heat-associated defects, but pdi9 pdi10 double mutants (DMs) completely lost exine reticulation. Interestingly, overexpression of PDI9 partially led to heat-associated defects in the exine. We conclude that PDI9 plays an important role in pollen thermotolerance and exine biogenesis. Its role fits the mechanistic theory of proteostasis in which an ideal balance of PDI isoforms is required in the endoplasmic reticulum (ER) for normal exine formation in plants subjected to heat stress.
- Published
- 2020
- Full Text
- View/download PDF
26. Isolated Large Glenoid Fracture in Acute Glenohumeral Dislocation in the Elderly: A Novel Indication for Reverse Shoulder Arthroplasty
- Author
-
Tyler Smith, Joseph D’Alonzo, Alfonso Arevalo, and Jack Kazanjian
- Subjects
Orthopedic surgery ,RD701-811 - Abstract
Case. Two elderly males presented with traumatic shoulder dislocation and bony Bankart fracture consisting of greater than 25% of the glenoid width. Due to several concomitant factors such as polytrauma, activity level, rotator cuff pathology, optimization of comorbidities, risk of complications, and potential for revision surgery, the patients were treated with reverse shoulder arthroplasty (RSA). Conclusion. RSA may be a satisfactory treatment option for isolated, large glenoid fractures associated with anterior glenohumeral instability in the elderly. These patients are susceptible to rapid deconditioning with prolonged immobilization and may not be medically suited to undergo the prolonged recovery period associated with open reduction internal fixation or potentially undergo revision operations.
- Published
- 2020
- Full Text
- View/download PDF
27. Combining Differential Scanning Calorimetry and Cooling-Heating Curve Thermal Analysis to Study the Melting and Solidification Behavior of Al-Ce Binary Alloys
- Author
-
Marta Aniolek, Tyler Smith, and Frank Czerwinski
- Subjects
aluminum-cerium alloys ,solidification ,differential scanning calorimetry ,cooling curve thermal analysis ,Mining engineering. Metallurgy ,TN1-997 - Abstract
Two common techniques of thermal analysis, Differential Scanning Calorimetry (DSC) and Cooling/Heating Curve Thermal Analysis (CCTA), based on different signal collected and utilizing samples with a weight difference of three orders of magnitude, were used to assess the solidification and melting behavior of Al-Ce binary alloys, containing from 5 to 20 wt. % Ce. Thermal analysis was accompanied by microscopic observations of solidified structures. For heating/cooling rates of 0.2–0.4 °C/s, temperatures of eutectic transformation L ↔ Al + Al11Ce3 in the Al-10Ce alloy along with additional proeutectic reactions L ↔ Al in the Al-5Ce hypoeutectic alloy and L ↔ Al11Ce3 in Al-15Ce and Al-20Ce hypereutectic alloys, were determined. Although there was a general agreement in major transformations, registered by DSC and CCTA during melting and solidification, differences in the reaction temperature determined exceeded the typical measurement errors for each technique. In addition, DSC and CCTA exhibited differences in detecting some proeutectic reactions and minor non-equilibrium effects, accompanying the eutectic transformation. Some factors that could contribute to differences observed and their implications for engineering practice were discussed.
- Published
- 2021
- Full Text
- View/download PDF
28. Uses of Braces and Orthotics for Conservative Management of Foot and Ankle Disorders
- Author
-
Osama Elattar MD, Tyler Smith DO, Adam Ferguson DO, Daniel Farber MD, and Keith Wapner MD
- Subjects
Orthopedic surgery ,RD701-811 - Abstract
Nonsurgical management is almost always considered the first-line treatment for the vast majority of foot and ankle pathologies. Foot orthoses, shoe modifications, and therapeutic footwear are considered essential tools for successful conservative management of different foot and ankle disorders. Orthopedic foot and ankle surgeons should have a meticulous understanding of the lower extremity biomechanics as well as the pathoanatomy and the sequelae of diseases affecting the foot and/or ankle. This is essential to the understanding of the desired effects of the different inserts, orthotics, shoe modifications, or braces that may be prescribed for these conditions. In this article, we will summarize the orthoses used for treatment of the most commonly encountered foot and ankle pathologies, with the exclusion of treatment for the diabetic foot because of the unique requirements of that disease process.
- Published
- 2018
- Full Text
- View/download PDF
29. Abundance of commercially important reef fish indicates different levels of over-exploitation across shelves of the U.S. Virgin Islands.
- Author
-
Elizabeth Kadison, Marilyn Brandt, Richard Nemeth, Justin Martens, Jeremiah Blondeau, and Tyler Smith
- Subjects
Medicine ,Science - Abstract
The United States Virgin Islands are comprised of two separate insular platforms separated by the deep water Anegada Passage. Although managed by the same regulations, as one fishery, several physical and spatial differences exist between the two northern shelf islands, St. Thomas and St. John, and isolated St. Croix. Based on two long-term fisheries independent datasets, collected by the U.S. Virgin Islands Territorial Coral Reef Monitoring Program and the National Oceanographic and Atmospheric Administration Center for Coastal Monitoring and Assessment, there were significant differences between the northern USVI and St. Croix in both the occurrence and size of several species of large and commercially important reef fishes. These fishes are primarily apex piscivores and generally the first species over-exploited in small-scale fisheries. The disparities between the fish communities on the two island shelves cannot be explained solely by differences in habitat (coral cover, rugosity) or fisheries management, such as relative amount of marine protected area in local waters. They are instead probably caused by a combination of several other interrelated factors including water depth, fishing methodology, fishable area, and the presence or absence of viable fish spawning areas. This study considers those aspects, and illustrates the need for management of island artisanal fisheries that is tailored to the physical and spatial constraints imposed by insular platforms.
- Published
- 2017
- Full Text
- View/download PDF
30. Ghost admixture in eastern gorillas.
- Author
-
Pawar, Harvinder, Rymbekova, Aigerim, Cuadros-Espinoza, Sebastian, Huang, Xin, de Manuel, Marc, van der Valk, Tom, Lobon, Irene, Alvarez-Estape, Marina, Haber, Marc, Dolgova, Olga, Han, Sojung, Esteller-Cucala, Paula, Juan, David, Ayub, Qasim, Bautista, Ruben, Kelley, Joanna L, Cornejo, Omar E, Lao, Oscar, Andrés, Aida M, Guschanski, Katerina, Ssebide, Benard, Cranfield, Mike, Tyler-Smith, Chris, Xue, Yali, Prado-Martinez, Javier, Marques-Bonet, Tomas, and Kuhlwilm, Martin
- Subjects
Human Genome ,Genetics ,Underpinning research ,1.1 Normal biological development and functioning - Abstract
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
- Published
- 2023
31. Paradoxical Reaction to Alprazolam in an Elderly Woman with a History of Anxiety, Mood Disorders, and Hypothyroidism
- Author
-
Daniel Kirkpatrick, Tyler Smith, Mitchell Kerfeld, Taylor Ramsdell, Hasnain Sadiq, and Arun Sharma
- Subjects
Psychiatry ,RC435-571 - Abstract
With less than 1% of patients who use benzodiazepines being affected, paradoxical responses to benzodiazepines are rare. In this case report, we outline the course of an 80-year-old female who developed a paradoxical response to benzodiazepines. Significant medical and psychiatric history includes anxiety, mood disorder, hypothyroidism, bilateral mastectomy, goiter removal, and triple bypass. The patient presented with mental status changes, anxiety, motor restlessness, and paranoia. Over time, a temporal relationship between the severity of the patient’s motor agitation and intake of alprazolam was observed. As doses of alprazolam were decreased, her motor agitation became less severe. In addition to motor agitation, the patient also demonstrated increased aggressiveness, a subjective feeling of restlessness, and increased talkativeness. As her dose of alprazolam decreased, many of the patient’s symptoms were observed to decrease. This case report also discusses theories regarding the pathophysiology of paradoxical reactions to benzodiazepines, known risk factors, and appropriate treatment.
- Published
- 2016
- Full Text
- View/download PDF
32. Graphene Quantum Dots Electrochemistry and Sensitive Electrocatalytic Glucose Sensor Development
- Author
-
Sanju Gupta, Tyler Smith, Alexander Banaszak, and John Boeckl
- Subjects
graphene quantum dots ,hydrothermal ,electrochemistry ,glucose oxidase ,biosensing ,Chemistry ,QD1-999 - Abstract
Graphene quantum dots (GQDs), derived from functionalized graphene precursors are graphene sheets a few nanometers in the lateral dimension having a several-layer thickness. They are zero-dimensional materials with quantum confinement and edge site effects. Intense research interest in GQDs is attributed to their unique physicochemical phenomena arising from the sp2-bonded carbon nanocore surrounded with edged plane functional moieties. In this work, GQDs are synthesized by both solvothermal and hydrothermal techniques, with the optimal size of 5 nm determined using high-resolution transmission electron microscopy, with additional UV-Vis absorption and fluorescence spectroscopy, revealing electronic band signatures in the blue-violet region. Their potential in fundamental (direct electron transfer) and applied (enzyme-based glucose biosensor) electrochemistry has been practically realized. Glucose oxidase (GOx) was immobilized on glassy carbon (GC) electrodes modified with GQDs and functionalized graphene (graphene oxide and reduced form). The cyclic voltammetry, differential pulse voltammetry, and electrochemical impedance spectroscopy are used for characterizing the direct electron transfer kinetics and electrocatalytical biosensing. The well-defined quasi-reversible redox peaks were observed under various electrochemical environment and conditions (pH, concentration, scan rate) to determine the diffusion coefficient (D) and first-order electron transfer rate (kET). The cyclic voltammetry curves showed homogeneous ion transport behavior for GQD and other graphene-based samples with D ranging between 8.45 × 10−9 m2 s−1 and 3 × 10−8 m2 s−1 following the order of GO < rGO < GQD < GQD (with FcMeOH as redox probe) < GOx/rGO < GOx/GO < HRP/GQDs < GOx/GQDs. The developed GOx-GQDs biosensor responds efficiently and linearly to the presence of glucose over concentrations ranging between 10 μM and 3 mM with a limit of detection of 1.35 μM and sensitivity of 0.00769 μA μM−1·cm−2 as compared with rGO (0.025 μA μM−1 cm−2, 4.16 μM) and GO (0.064 μA μM−1 cm−2, 4.82 μM) nanosheets. The relatively high performance and stability of GQDs is attributed to a sufficiently large surface-to-volume ratio, excellent biocompatibility, abundant hydrophilic edges, and a partially hydrophobic plane that favors GOx adsorption on the electrode surface and versatile architectures to ensure rapid charge transfer and electron/ion conduction (
- Published
- 2017
- Full Text
- View/download PDF
33. Leaf and life history traits predict plant growth in a green roof ecosystem.
- Author
-
Jeremy Lundholm, Amy Heim, Stephanie Tran, and Tyler Smith
- Subjects
Medicine ,Science - Abstract
Green roof ecosystems are constructed to provide services such as stormwater retention and urban temperature reductions. Green roofs with shallow growing media represent stressful conditions for plant survival, thus plants that survive and grow are important for maximizing economic and ecological benefits. While field trials are essential for selecting appropriate green roof plants, we wanted to determine whether plant leaf traits could predict changes in abundance (growth) to provide a more general framework for plant selection. We quantified leaf traits and derived life-history traits (Grime's C-S-R strategies) for 13 species used in a four-year green roof experiment involving five plant life forms. Changes in canopy density in monocultures and mixtures containing one to five life forms were determined and related to plant traits using multiple regression. We expected traits related to stress-tolerance would characterize the species that best grew in this relatively harsh setting. While all species survived to the end of the experiment, canopy species diversity in mixture treatments was usually much lower than originally planted. Most species grew slower in mixture compared to monoculture, suggesting that interspecific competition reduced canopy diversity. Species dominant in mixture treatments tended to be fast-growing ruderals and included both native and non-native species. Specific leaf area was a consistently strong predictor of final biomass and the change in abundance in both monoculture and mixture treatments. Some species in contrasting life-form groups showed compensatory dynamics, suggesting that life-form mixtures can maximize resilience of cover and biomass in the face of environmental fluctuations. This study confirms that plant traits can be used to predict growth performance in green roof ecosystems. While rapid canopy growth is desirable for green roofs, maintenance of species diversity may require engineering of conditions that favor less aggressive species.
- Published
- 2014
- Full Text
- View/download PDF
34. Desmosomal Component Expression in Normal, Dysplastic, and Oral Squamous Cell Carcinoma
- Author
-
Nagamani Narayana, Julie Gist, Tyler Smith, Daniel Tylka, Gavin Trogdon, and James K. Wahl
- Subjects
Dermatology ,RL1-803 - Abstract
Squamous cell carcinoma (oral SCC) is the most common oral cancer in the U.S., affecting nearly 30,000 Americans each year. Despite recent advances in detection and treatment, there has been little improvement in the five-year survival rate for this devastating disease. Oral cancer may be preceded by premalignant disease that appears histologically as dysplasia. Identification of molecular markers for cellular change would assist in determining the risk of dysplasia progressing to oral squamous cell carcinoma. The goal of this study was to determine if any correlation exists between histological diagnosed dysplasia and OSCC lesions and altered expression of desmosomal cell-cell adhesion molecules in the oral epithelium. Our data showed that oral SCC tissue samples showed decreased immunoreactivity of both desmoplakin and plakophilin-1 proteins compared to normal oral epithelium. Furthermore, significant decrease in desmoplakin immunoreactivity was observed in dysplastic tissue compared to normal oral epithelium. In contrast, the level of desmoglein-1 staining was unchanged between samples however desmoglein-1 was found localized to cell borders in oral SCC samples. These data suggest that changes in expression of desmoplakin and plakophilin-1 may prove to be a useful marker for changes in tissue morphology and provide a tool for identifying pre-neoplastic lesions of the oral cavity.
- Published
- 2010
- Full Text
- View/download PDF
35. Assembly of 43 human Y chromosomes reveals extensive complexity and variation
- Author
-
Hallast, Pille, Ebert, Peter, Loftus, Mark, Yilmaz, Feyza, Audano, Peter A., Logsdon, Glennis A., Bonder, Marc Jan, Zhou, Weichen, Höps, Wolfram, Kim, Kwondo, Li, Chong, Hoyt, Savannah J., Dishuck, Philip C., Porubsky, David, Tsetsos, Fotios, Kwon, Jee Young, Zhu, Qihui, Munson, Katherine M., Hasenfeld, Patrick, Harvey, William T., Lewis, Alexandra P., Kordosky, Jennifer, Hoekzema, Kendra, O’Neill, Rachel J., Korbel, Jan O., Tyler-Smith, Chris, Eichler, Evan E., Shi, Xinghua, Beck, Christine R., Marschall, Tobias, Konkel, Miriam K., and Lee, Charles
- Published
- 2023
- Full Text
- View/download PDF
36. HERC1 deficiency causes osteopenia through transcriptional program dysregulation during bone remodeling
- Author
-
Pedrazza, Leonardo, Martinez-Martinez, Arturo, Sánchez-de-Diego, Cristina, Valer, José Antonio, Pimenta-Lopes, Carolina, Sala-Gaston, Joan, Szpak, Michal, Tyler-Smith, Chris, Ventura, Francesc, and Rosa, Jose Luis
- Published
- 2023
- Full Text
- View/download PDF
37. Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers
- Author
-
Aghakhanian, Farhang, Hoh, Boon-Peng, Yew, Chee-Wei, Kumar Subbiah, Vijay, Xue, Yali, Tyler-Smith, Chris, Ayub, Qasim, and Phipps, Maude E.
- Published
- 2022
- Full Text
- View/download PDF
38. The genomic history of the Middle East
- Author
-
Almarri, Mohamed A., Haber, Marc, Lootah, Reem A., Hallast, Pille, Al Turki, Saeed, Martin, Hilary C., Xue, Yali, and Tyler-Smith, Chris
- Published
- 2021
- Full Text
- View/download PDF
39. The landscape of autosomal-recessive pathogenic variants in European populations reveals phenotype-specific effects
- Author
-
Fridman, Hila, Yntema, Helger G., Mägi, Reedik, Andreson, Reidar, Metspalu, Andres, Mezzavilla, Massimo, Tyler-Smith, Chris, Xue, Yali, Carmi, Shai, Levy-Lahad, Ephrat, Gilissen, Christian, and Brunner, Han G.
- Published
- 2021
- Full Text
- View/download PDF
40. Population Structure, Stratification, and Introgression of Human Structural Variation
- Author
-
Almarri, Mohamed A., Bergström, Anders, Prado-Martinez, Javier, Yang, Fengtang, Fu, Beiyuan, Dunham, Alistair S., Chen, Yuan, Hurles, Matthew E., Tyler-Smith, Chris, and Xue, Yali
- Published
- 2020
- Full Text
- View/download PDF
41. Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain
- Author
-
Lall, Gurdeep Matharu, Larmuseau, Maarten H. D., Wetton, Jon H., Batini, Chiara, Hallast, Pille, Huszar, Tunde I., Zadik, Daniel, Aase, Sigurd, Baker, Tina, Balaresque, Patricia, Bodmer, Walter, Børglum, Anders D., de Knijff, Peter, Dunn, Hayley, Harding, Stephen E., Løvvik, Harald, Dupuy, Berit Myhre, Pamjav, Horolma, Tillmar, Andreas O., Tomaszewski, Maciej, Tyler-Smith, Chris, Verdugo, Marta Pereira, Winney, Bruce, Vohra, Pragya, Story, Joanna, King, Turi E., and Jobling, Mark A.
- Published
- 2021
- Full Text
- View/download PDF
42. A Southeast Asian origin for present-day non-African human Y chromosomes
- Author
-
Hallast, Pille, Agdzhoyan, Anastasia, Balanovsky, Oleg, Xue, Yali, and Tyler-Smith, Chris
- Published
- 2021
- Full Text
- View/download PDF
43. Genomic analyses inform on migration events during the peopling of Eurasia
- Author
-
Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait
- Subjects
Human Genome ,Biotechnology ,Genetics ,Generic health relevance ,Africa ,Animals ,Asia ,Datasets as Topic ,Estonia ,Europe ,Fossils ,Gene Flow ,Genetics ,Population ,Genome ,Human ,Genomics ,Heterozygote ,History ,Ancient ,Human Migration ,Humans ,Native Hawaiian or Other Pacific Islander ,Neanderthals ,New Guinea ,Population Dynamics ,Racial Groups ,General Science & Technology - Abstract
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
- Published
- 2016
44. A genomic history of Aboriginal Australia
- Author
-
Malaspinas, Anna-Sapfo, Westaway, Michael C, Muller, Craig, Sousa, Vitor C, Lao, Oscar, Alves, Isabel, Bergström, Anders, Athanasiadis, Georgios, Cheng, Jade Y, Crawford, Jacob E, Heupink, Tim H, Macholdt, Enrico, Peischl, Stephan, Rasmussen, Simon, Schiffels, Stephan, Subramanian, Sankar, Wright, Joanne L, Albrechtsen, Anders, Barbieri, Chiara, Dupanloup, Isabelle, Eriksson, Anders, Margaryan, Ashot, Moltke, Ida, Pugach, Irina, Korneliussen, Thorfinn S, Levkivskyi, Ivan P, Moreno-Mayar, J Víctor, Ni, Shengyu, Racimo, Fernando, Sikora, Martin, Xue, Yali, Aghakhanian, Farhang A, Brucato, Nicolas, Brunak, Søren, Campos, Paula F, Clark, Warren, Ellingvåg, Sturla, Fourmile, Gudjugudju, Gerbault, Pascale, Injie, Darren, Koki, George, Leavesley, Matthew, Logan, Betty, Lynch, Aubrey, Matisoo-Smith, Elizabeth A, McAllister, Peter J, Mentzer, Alexander J, Metspalu, Mait, Migliano, Andrea B, Murgha, Les, Phipps, Maude E, Pomat, William, Reynolds, Doc, Ricaut, Francois-Xavier, Siba, Peter, Thomas, Mark G, Wales, Thomas, Wall, Colleen Ma’run, Oppenheimer, Stephen J, Tyler-Smith, Chris, Durbin, Richard, Dortch, Joe, Manica, Andrea, Schierup, Mikkel H, Foley, Robert A, Lahr, Marta Mirazón, Bowern, Claire, Wall, Jeffrey D, Mailund, Thomas, Stoneking, Mark, Nielsen, Rasmus, Sandhu, Manjinder S, Excoffier, Laurent, Lambert, David M, and Willerslev, Eske
- Subjects
Africa ,Australia ,Datasets as Topic ,Desert Climate ,Gene Flow ,Genetics ,Population ,Genome ,Human ,Genomics ,History ,Ancient ,Human Migration ,Humans ,Language ,Native Hawaiian or Other Pacific Islander ,New Guinea ,Phylogeny ,Population Dynamics ,Racial Groups ,Tasmania ,General Science & Technology - Abstract
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
- Published
- 2016
45. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
- Author
-
Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P, Song, Yun S, Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R, Behar, Doron M, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L, Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M, Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B, Metspalu, Ene, Parik, Jüri, Villems, Richard, Henn, Brenna M, Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph TS, Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F, Kivisild, Toomas, Klitz, William, Winkler, Cheryl A, Labuda, Damian, Bamshad, Michael, Jorde, Lynn B, Tishkoff, Sarah A, Watkins, W Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pääbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David
- Subjects
Human Genome ,Genetics ,Animals ,Australia ,Black People ,Datasets as Topic ,Genetic Variation ,Genetics ,Population ,Genome ,Human ,Genomics ,History ,Ancient ,Human Migration ,Humans ,Mutation Rate ,Native Hawaiian or Other Pacific Islander ,Neanderthals ,New Guinea ,Phylogeny ,Racial Groups ,Sequence Analysis ,DNA ,Species Specificity ,Time Factors ,General Science & Technology - Abstract
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
- Published
- 2016
46. YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data
- Author
-
Jostins, Luke, Xu, Yali, McCarthy, Shane, Ayub, Qasim, Durbin, Richard, Barrett, Jeff, and Tyler-Smith, Chris
- Subjects
Quantitative Biology - Populations and Evolution ,Quantitative Biology - Genomics - Abstract
Low-coverage short-read resequencing experiments have the potential to expand our understanding of Y chromosome haplogroups. However, the uncertainty associated with these experiments mean that haplogroups must be assigned probabilistically to avoid false inferences. We propose an efficient dynamic programming algorithm that can assign haplogroups by maximum likelihood, and represent the uncertainty in assignment. We apply this to both genotype and low-coverage sequencing data, and show that it can assign haplogroups accurately and with high resolution. The method is implemented as the program YFitter, which can be downloaded from http://sourceforge.net/projects/yfitter/
- Published
- 2014
47. Grapholita pallifrontana.
- Author
-
Yali Xue, Tyler-smith, Chris, and Dickerson, Barry
- Subjects
- *
GRAPHOLITA , *TORTRICIDAE - Abstract
The article focuses on the distribution and conservation of the Liquorice Piercer moth, Grapholita pallifrontana, in Huntingdonshire, VC31. Topics include the moth's status as a category 3 Red Data Book species, its reliance on Wild Liquorice (Astragalus glycophillus) as a foodplant, and the increasing interest in tracking its current distribution for conservation efforts.
- Published
- 2024
48. A global reference for human genetic variation
- Author
-
Auton, Adam, Abecasis, Gonçalo R, Altshuler, David M, Durbin, Richard M, Bentley, David R, Chakravarti, Aravinda, Clark, Andrew G, Donnelly, Peter, Eichler, Evan E, Flicek, Paul, Gabriel, Stacey B, Gibbs, Richard A, Green, Eric D, Hurles, Matthew E, Knoppers, Bartha M, Korbel, Jan O, Lander, Eric S, Lee, Charles, Lehrach, Hans, Mardis, Elaine R, Marth, Gabor T, McVean, Gil A, Nickerson, Deborah A, Schmidt, Jeanette P, Sherry, Stephen T, Wang, Jun, Wilson, Richard K, Barnes, Kathleen C, Beiswanger, Christine, Burchard, Esteban G, Bustamante, Carlos D, Cai, Hongyu, Cao, Hongzhi, Gerry, Norman P, Gharani, Neda, Gignoux, Christopher R, Gravel, Simon, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S, Keinan, Alon, Kent, Alastair, Kerasidou, Angeliki, Li, Yingrui, Mathias, Rasika, Moreno-Estrada, Andres, Ossorio, Pilar N, Parker, Michael, Resch, Alissa M, Rotimi, Charles N, Royal, Charmaine D, Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H, Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Brooks, Lisa D, Felsenfeld, Adam L, McEwen, Jean E, Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A, Garrison, Erik P, Min Kang, Hyun, Marchini, Jonathan L, and McCarthy, Shane
- Subjects
Human Genome ,Genetics ,Biotechnology ,2.1 Biological and endogenous factors ,Aetiology ,Datasets as Topic ,Demography ,Disease Susceptibility ,Exome ,Genetic Variation ,Genetics ,Medical ,Genetics ,Population ,Genome ,Human ,Genome-Wide Association Study ,Genomics ,Genotype ,Haplotypes ,High-Throughput Nucleotide Sequencing ,Humans ,INDEL Mutation ,Internationality ,Physical Chromosome Mapping ,Polymorphism ,Single Nucleotide ,Quantitative Trait Loci ,Rare Diseases ,Reference Standards ,Sequence Analysis ,DNA ,Genomes Project Consortium ,General Science & Technology - Abstract
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
- Published
- 2015
49. Global diversity, population stratification, and selection of human copy-number variation.
- Author
-
Krumm, Niklas, Huddleston, John, Coe, Bradley, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn, Posukh, Olga, Sahakyan, Hovhannes, Watkins, W, Yepiskoposyan, Levon, Abdullah, M, Bravi, Claudio, Capelli, Cristian, Hervig, Tor, Wee, Joseph, Tyler-Smith, Chris, van Driem, George, Romero, Irene, Jha, Aashish, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena, Ayodo, George, Beall, Cynthia, Di Rienzo, Anna, Hammer, Michael, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, Eichler, Evan, Mallick, Swapan, Nelson, Bradley, Hormozdiari, Fereydoun, Henn, Brenna, and Sudmant, Peter
- Subjects
Animals ,Black People ,DNA Copy Number Variations ,Evolution ,Molecular ,Gene Duplication ,Genome ,Human ,Hominidae ,Humans ,Native Hawaiian or Other Pacific Islander ,Phylogeny ,Polymorphism ,Single Nucleotide ,Population ,Selection ,Genetic ,Sequence Deletion - Abstract
In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.
- Published
- 2015
50. Global diversity, population stratification, and selection of human copy-number variation
- Author
-
Sudmant, Peter H, Mallick, Swapan, Nelson, Bradley J, Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B, Posukh, Olga L, Sahakyan, Hovhannes, Watkins, W Scott, Yepiskoposyan, Levon, Abdullah, M Syafiq, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Wee, Joseph TS, Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B, Ayodo, George, Beall, Cynthia M, Di Rienzo, Anna, Hammer, Michael F, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E
- Subjects
Genetics ,Human Genome ,Animals ,Black People ,DNA Copy Number Variations ,Evolution ,Molecular ,Gene Duplication ,Genome ,Human ,Hominidae ,Humans ,Native Hawaiian or Other Pacific Islander ,Phylogeny ,Polymorphism ,Single Nucleotide ,Population ,Selection ,Genetic ,Sequence Deletion ,General Science & Technology - Abstract
In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.
- Published
- 2015
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.