Showing papers by "University of Missouri published in 2016"
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TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
7,299 citations
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TL;DR: The Global Burden of Disease 2015 Study provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015, finding several countries in sub-Saharan Africa had very large gains in life expectancy, rebounding from an era of exceedingly high loss of life due to HIV/AIDS.
4,804 citations
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Nicholas J Kassebaum1, Megha Arora1, Ryan M Barber1, Zulfiqar A Bhutta2 +679 more•Institutions (268)
TL;DR: In this paper, the authors used the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2015.
1,533 citations
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TL;DR: In this paper, an adeno-associated virus was used to deliver the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system to the mdx mouse model of Duchenne muscular dystrophy (DMD) to remove the mutated exon 23 from the dystrophin gene.
Abstract: Duchenne muscular dystrophy (DMD) is a devastating disease affecting about 1 out of 5000 male births and caused by mutations in the dystrophin gene. Genome editing has the potential to restore expression of a modified dystrophin gene from the native locus to modulate disease progression. In this study, adeno-associated virus was used to deliver the clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 system to the mdx mouse model of DMD to remove the mutated exon 23 from the dystrophin gene. This includes local and systemic delivery to adult mice and systemic delivery to neonatal mice. Exon 23 deletion by CRISPR-Cas9 resulted in expression of the modified dystrophin gene, partial recovery of functional dystrophin protein in skeletal myofibers and cardiac muscle, improvement of muscle biochemistry, and significant enhancement of muscle force. This work establishes CRISPR-Cas9–based genome editing as a potential therapy to treat DMD.
894 citations
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University of Ljubljana1, University of Birmingham2, Czech Technical University in Prague3, Linköping University4, Austrian Institute of Technology5, Carnegie Mellon University6, Parthenope University of Naples7, University of Isfahan8, Autonomous University of Madrid9, University of Ottawa10, University of Oxford11, Hong Kong Baptist University12, Kyiv Polytechnic Institute13, Middle East Technical University14, Hacettepe University15, King Abdullah University of Science and Technology16, Pohang University of Science and Technology17, University of Nottingham18, University at Albany, SUNY19, Chinese Academy of Sciences20, Dalian University of Technology21, Xi'an Jiaotong University22, Indian Institute of Space Science and Technology23, Hong Kong University of Science and Technology24, ASELSAN25, Australian National University26, Commonwealth Scientific and Industrial Research Organisation27, University of Missouri28, University of Verona29, Universidade Federal de Itajubá30, United States Naval Research Laboratory31, Marquette University32, Graz University of Technology33, Naver Corporation34, Imperial College London35, Electronics and Telecommunications Research Institute36, Zhejiang University37, University of Surrey38, Harbin Institute of Technology39, Lehigh University40
TL;DR: The Visual Object Tracking challenge VOT2016 goes beyond its predecessors by introducing a new semi-automatic ground truth bounding box annotation methodology and extending the evaluation system with the no-reset experiment.
Abstract: The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment. The dataset, the evaluation kit as well as the results are publicly available at the challenge website (http://votchallenge.net).
744 citations
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The Chinese University of Hong Kong1, University of Pittsburgh2, The Catholic University of America3, Barts Health NHS Trust4, Pontifícia Universidade Católica do Rio Grande do Sul5, University of Montana6, Cliniques Universitaires Saint-Luc7, Kyungpook National University8, University of Missouri9, University of Amsterdam10, University of Colorado Hospital11, Princess Alexandra Hospital12
TL;DR: Recommendations under the auspices of the International Society for Peritoneal Dialysis (ISPD) were first published in 1983 and revised in 1993, 1996, 2000, 2005, and 2010 are revised.
Abstract: Peritonitis is a common and serious complication of peritoneal dialysis (PD). Although less than 5% of peritonitis episodes result in death, peritonitis is the direct or major contributing cause of death in around 16% of PD patients (1-6). In addition, severe or prolonged peritonitis leads to structural and functional alterations of the peritoneal membrane, eventually leading to membrane failure. Peritonitis is a major cause of PD technique failure and conversion to long-term hemodialysis (1,5,7,8). Recommendations under the auspices of the International Society for Peritoneal Dialysis (ISPD) were first published in 1983 and revised in 1993, 1996, 2000, 2005, and 2010 (9-14). The present recommendations are organized into 5 sections: 1. Peritonitis rate 2. Prevention of peritonitis 3. Initial presentation and management of peritonitis 4. Subsequent management of peritonitis 5.
724 citations
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TL;DR: GBHs are the most heavily applied herbicide in the world and usage continues to rise; Worldwide, GBHs often contaminate drinking water sources, precipitation, and air, especially in agricultural regions and regulatory estimates of tolerable daily intakes for glyphosate in the United States and European Union are based on outdated science.
Abstract: The broad-spectrum herbicide glyphosate (common trade name “Roundup”) was first sold to farmers in 1974. Since the late 1970s, the volume of glyphosate-based herbicides (GBHs) applied has increased approximately 100-fold. Further increases in the volume applied are likely due to more and higher rates of application in response to the widespread emergence of glyphosate-resistant weeds and new, pre-harvest, dessicant use patterns. GBHs were developed to replace or reduce reliance on herbicides causing well-documented problems associated with drift and crop damage, slipping efficacy, and human health risks. Initial industry toxicity testing suggested that GBHs posed relatively low risks to non-target species, including mammals, leading regulatory authorities worldwide to set high acceptable exposure limits. To accommodate changes in GBH use patterns associated with genetically engineered, herbicide-tolerant crops, regulators have dramatically increased tolerance levels in maize, oilseed (soybeans and canola), and alfalfa crops and related livestock feeds. Animal and epidemiology studies published in the last decade, however, point to the need for a fresh look at glyphosate toxicity. Furthermore, the World Health Organization’s International Agency for Research on Cancer recently concluded that glyphosate is “probably carcinogenic to humans.” In response to changing GBH use patterns and advances in scientific understanding of their potential hazards, we have produced a Statement of Concern drawing on emerging science relevant to the safety of GBHs. Our Statement of Concern considers current published literature describing GBH uses, mechanisms of action, toxicity in laboratory animals, and epidemiological studies. It also examines the derivation of current human safety standards. We conclude that: (1) GBHs are the most heavily applied herbicide in the world and usage continues to rise; (2) Worldwide, GBHs often contaminate drinking water sources, precipitation, and air, especially in agricultural regions; (3) The half-life of glyphosate in water and soil is longer than previously recognized; (4) Glyphosate and its metabolites are widely present in the global soybean supply; (5) Human exposures to GBHs are rising; (6) Glyphosate is now authoritatively classified as a probable human carcinogen; (7) Regulatory estimates of tolerable daily intakes for glyphosate in the United States and European Union are based on outdated science. We offer a series of recommendations related to the need for new investments in epidemiological studies, biomonitoring, and toxicology studies that draw on the principles of endocrinology to determine whether the effects of GBHs are due to endocrine disrupting activities. We suggest that common commercial formulations of GBHs should be prioritized for inclusion in government-led toxicology testing programs such as the U.S. National Toxicology Program, as well as for biomonitoring as conducted by the U.S. Centers for Disease Control and Prevention.
638 citations
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TL;DR: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets.
Abstract: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.
605 citations
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Haidong Wang1, Zulfiqar A Bhutta2, Zulfiqar A Bhutta3, Matthew M Coates1 +610 more•Institutions (263)
TL;DR: The Global Burden of Disease 2015 Study provides an analytical framework to comprehensively assess trends for under-5 mortality, age-specific and cause-specific mortality among children under 5 years, and stillbirths by geography over time and decomposed the changes in under- 5 mortality to changes in SDI at the global level.
591 citations
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University of Western Australia1, University of Leeds2, The Chinese University of Hong Kong3, University of Missouri4, International Crops Research Institute for the Semi-Arid Tropics5, University of Sydney6, John Innes Centre7, University of Pretoria8, Case Western Reserve University9, University of Alberta10, Monash University11, Zhejiang University12
TL;DR: The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner ‘nutritious seeds for a sustainable future’, but the current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.
Abstract: The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner ‘nutritious seeds for a sustainable future’. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.
547 citations
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TL;DR: A surge in diabetic cardiomyopathy research is highlighted, current understanding of the molecular mechanisms underpinning this condition is summarized, and potential preventive and therapeutic strategies are explored.
Abstract: Insulin resistance, type 2 diabetes mellitus and associated hyperinsulinaemia can promote the development of a specific form of cardiomyopathy that is independent of coronary artery disease and hypertension. Termed diabetic cardiomyopathy, this form of cardiomyopathy is a major cause of morbidity and mortality in developed nations, and the prevalence of this condition is rising in parallel with increases in the incidence of obesity and type 2 diabetes mellitus. Of note, female patients seem to be particularly susceptible to the development of this complication of metabolic disease. The diabetic cardiomyopathy observed in insulin- resistant or hyperinsulinaemic states is characterized by impaired myocardial insulin signalling, mitochondrial dysfunction, endoplasmic reticulum stress, impaired calcium homeostasis, abnormal coronary microcirculation, activation of the sympathetic nervous system, activation of the renin-angiotensin-aldosterone system and maladaptive immune responses. These pathophysiological changes result in oxidative stress, fibrosis, hypertrophy, cardiac diastolic dysfunction and eventually systolic heart failure. This Review highlights a surge in diabetic cardiomyopathy research, summarizes current understanding of the molecular mechanisms underpinning this condition and explores potential preventive and therapeutic strategies.
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University of California, San Francisco1, Group Health Research Institute2, University of Iowa3, Columbia University4, State University of New York Upstate Medical University5, National Institutes of Health6, Harvard University7, Duke University8, Virginia Commonwealth University9, Yale University10, University of Alabama at Birmingham11, University of Missouri12, University of California, Los Angeles13, University of Washington14, Stanford University15, Brown University16, University of Texas at Austin17
TL;DR: The USPSTF concludes that the current evidence is insufficient to assess the balance of benefits and harms of initiating statin use in adults 76 years and older.
Abstract: Importance Cardiovascular disease (CVD) is the leading cause of morbidity and mortality in the United States, accounting for 1 of every 3 deaths among adults. Objective To update the 2008 US Preventive Services Task Force (USPSTF) recommendation on screening for lipid disorders in adults. Evidence Review The USPSTF reviewed the evidence on the benefits and harms of screening for and treatment of dyslipidemia in adults 21 years and older; the benefits and harms of statin use in reducing CVD events and mortality in adults without a history of CVD events; whether the benefits of statin use vary by subgroup, clinical characteristics, or dosage; and the benefits of various treatment strategies in adults 40 years and older without a history of CVD events. Conclusions and Recommendations The USPSTF recommends initiating use of low- to moderate-dose statins in adults aged 40 to 75 years without a history of CVD who have 1 or more CVD risk factors (dyslipidemia, diabetes, hypertension, or smoking) and a calculated 10-year CVD event risk of 10% or greater (B recommendation). The USPSTF recommends that clinicians selectively offer low- to moderate-dose statins to adults aged 40 to 75 years without a history of CVD who have 1 or more CVD risk factors and a calculated 10-year CVD event risk of 7.5% to 10% (C recommendation). The USPSTF concludes that the current evidence is insufficient to assess the balance of benefits and harms of initiating statin use in adults 76 years and older (I statement).
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University of Würzburg1, University of Texas at El Paso2, University of Pennsylvania3, Pohang University of Science and Technology4, University of Manchester5, University of Missouri6, University of Sydney7, Maastricht University8, University of Toyama9, Heriot-Watt University10, University of Tokyo11, University of Pisa12, University of Otago13, Tsinghua University14, Wake Forest Institute for Regenerative Medicine15, Utrecht University16
TL;DR: A refined working definition of Biofabrication is proposed, including Bioprinting and Bioassembly as complementary strategies within Biofabrica, with special focus on its relation to and application for Tissue Engineering and Regenerative Medicine.
Abstract: Biofabrication is an evolving research field that has recently received significant attention. In particular, the adoption of Biofabrication concepts within the field of Tissue Engineering and Regenerative Medicine has grown tremendously, and has been accompanied by a growing inconsistency in terminology. This article aims at clarifying the position of Biofabrication as a research field with a special focus on its relation to and application for Tissue Engineering and Regenerative Medicine. Within this context, we propose a refined working definition of Biofabrication, including Bioprinting and Bioassembly as complementary strategies within Biofabrication.
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TL;DR: A thin-film nanocomposite (TFN) membrane containing graphene oxide (GO) nanosheets was prepared by the in-situ interfacial polymerization process as mentioned in this paper.
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University of Florida1, University of Minnesota2, University of Oklahoma3, United States Department of Agriculture4, Donald Danforth Plant Science Center5, Stony Brook University6, Eckerd College7, Purdue University8, Cold Spring Harbor Laboratory9, University of Rhode Island10, University of California, Berkeley11, Colorado State University12, University of California, Riverside13, University of California, Davis14, Boyce Thompson Institute for Plant Research15, Stanford University16, Iowa State University17, University of Missouri18, University of Tennessee19
TL;DR: The state of plant transformation is reviewed and innovations needed to enable genome editing in crops are pointed to, including a potential game-changer in crop genetics when plant transformation systems are optimized.
Abstract: Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than thirty years of technological advances. Genome editing provides new opportunities to enhance crop productivity, but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Herein we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimize time in culture. Currently, specialized facilities exist for crop transformation. Single cell and robotic techniques should be developed for high throughput genomic screens. Utilization of plant genes involved in developmental reprogramming, wound response, and/or homologous recombination could boost recovery of transformed plants. Engineering universal Agrobacterium strains and recruitment of other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.
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TL;DR: It is shown that ultrasmall (< 10 nm in diameter) poly(ethylene glycol) (PEG)-coated silica nanoparticles, functionalized with melanoma-targeting peptides, can induce a form of programmed cell death known as ferroptosis in starved cancer cells and cancer-bearing mice.
Abstract: The design of cancer-targeting particles with precisely tuned physicochemical properties may enhance the delivery of therapeutics and access to pharmacological targets. However, a molecular-level understanding of the interactions driving the fate of nanomedicine in biological systems remains elusive. Here, we show that ultrasmall (<10 nm in diameter) poly(ethylene glycol)-coated silica nanoparticles, functionalized with melanoma-targeting peptides, can induce a form of programmed cell death known as ferroptosis in starved cancer cells and cancer-bearing mice. Tumour xenografts in mice intravenously injected with nanoparticles using a high-dose multiple injection scheme exhibit reduced growth or regression, in a manner that is reversed by the pharmacological inhibitor of ferroptosis, liproxstatin-1. These data demonstrate that ferroptosis can be targeted by ultrasmall silica nanoparticles and may have therapeutic potential. Starved cancer cells and xenograft tumours in mice treated with ultrasmall silica nanoparticles undergo ferroptosis — a form of programmed cell death.
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TL;DR: It is shown in a number of examples that CIs do not necessarily have any of the properties of confidence intervals, and can lead to unjustified or arbitrary inferences, and is suggested that other theories of interval estimation should be used instead.
Abstract: Interval estimates – estimates of parameters that include an allowance for sampling uncertainty – have long been touted as a key component of statistical analyses. There are several kinds of interval estimates, but the most popular are confidence intervals (CIs): intervals that contain the true parameter value in some known proportion of repeated samples, on average. The width of confidence intervals is thought to index the precision of an estimate; CIs are thought to be a guide to which parameter values are plausible or reasonable; and the confidence coefficient of the interval (e.g., 95 %) is thought to index the plausibility that the true parameter is included in the interval. We show in a number of examples that CIs do not necessarily have any of these properties, and can lead to unjustified or arbitrary inferences. For this reason, we caution against relying upon confidence interval theory to justify interval estimates, and suggest that other theories of interval estimation should be used instead.
18 Nov 2016
TL;DR: Though inflammation is crucial in the onset and the progression of neurodegenerative diseases, anti-inflammatory drugs do not provide significant therapeutic effects in these patients till date, as the disease pathogenesis is not yet clearly understood.
Abstract: Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and Multiple Sclerosis (MS) are characterized by neuronal degeneration and neuronal death in specific regions of the central nervous system (CNS). In AD, neurons of the hippocampus and entorhinal cortex are the first to degenerate, whereas in PD, dopaminergic neurons in the substantia nigra degenerate. MS patients show destruction of the myelin sheath. Once the CNS neurons are damaged, they are unable to regenerate unlike any other tissue in the body. Neurodegeneration is mediated by inflammatory and neurotoxic mediators such as interleukin-1beta (IL-1β), IL-6, IL-8, IL-33, tumor necrosis factor-alpha (TNF-α), chemokine (C-C motif) ligand 2 (CCL2), CCL5, matrix metalloproteinase (MMPs), granulocyte macrophage colony-stimulating factor (GM-CSF), glia maturation factor (GMF), substance P, reactive oxygen species (ROS), reactive nitrogen species (RNS), mast cells-mediated histamine and proteases, protease activated receptor-2 (PAR-2), CD40, CD40L, CD88, intracellular Ca+ elevation, and activation of mitogen-activated protein kinases (MAPKs) and nuclear factor kappa-B (NF-kB). Activated microglia, astrocytes, neurons, T-cells and mast cells release these inflammatory mediators and mediate neuroinflammation and neurodegeneration in a vicious manner. Further, immune and inflammatory cells and inflammatory mediators from the periphery cross the defective blood-brain-barrier (BBB) and augment neuroinflammation. Though inflammation is crucial in the onset and the progression of neurodegenerative diseases, anti-inflammatory drugs do not provide significant therapeutic effects in these patients till date, as the disease pathogenesis is not yet clearly understood. In this review, we discuss the possible factors involved in neuroinflammation-mediated neurodegeneration.
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26 Feb 2016
TL;DR: In this paper, the authors provide a summary of achievements made in recent studies of thermoelectric transport properties, and demonstrate how they have led to improvements in thermal performance by the integration of modern theory and experiment.
Abstract: During the last two decades, we have witnessed great progress in research on thermoelectrics. There are two primary focuses. One is the fundamental understanding of electrical and thermal transport, enabled by the interplay of theory and experiment; the other is the substantial enhancement of the performance of various thermoelectric materials, through synergistic optimisation of those intercorrelated transport parameters. Here we review some of the successful strategies for tuning electrical and thermal transport. For electrical transport, we start from the classical but still very active strategy of tuning band degeneracy (or band convergence), then discuss the engineering of carrier scattering, and finally address the concept of conduction channels and conductive networks that emerge in complex thermoelectric materials. For thermal transport, we summarise the approaches for studying thermal transport based on phonon–phonon interactions valid for conventional solids, as well as some quantitative efforts for nanostructures. We also discuss the thermal transport in complex materials with chemical-bond hierarchy, in which a portion of the atoms (or subunits) are weakly bonded to the rest of the structure, leading to an intrinsic manifestation of part-crystalline part-liquid state at elevated temperatures. In this review, we provide a summary of achievements made in recent studies of thermoelectric transport properties, and demonstrate how they have led to improvements in thermoelectric performance by the integration of modern theory and experiment, and point out some challenges and possible directions.
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Duke University1, North Carolina State University2, New York University3, Saint Louis University4, University of North Carolina at Chapel Hill5, Wright State University6, University of Missouri7, Hospital of the University of Pennsylvania8, Indiana University – Purdue University Indianapolis9, Durham University10
TL;DR: In this article, the authors used logistic regression to calculate odds ratios (ORs) for variables associated with fracture nonunion and found that increased nonunion risk was associated with severe fracture (e.g., open fracture, multiple fractures), high body mass index, smoking, and alcoholism.
Abstract: Importance Failure of bone fracture healing occurs in 5% to 10% of all patients. Nonunion risk is associated with the severity of injury and with the surgical treatment technique, yet progression to nonunion is not fully explained by these risk factors. Objective To test a hypothesis that fracture characteristics and patient-related risk factors assessable by the clinician at patient presentation can indicate the probability of fracture nonunion. Design, Setting, and Participants An inception cohort study in a large payer database of patients with fracture in the United States was conducted using patient-level health claims for medical and drug expenses compiled for approximately 90.1 million patients in calendar year 2011. The final database collated demographic descriptors, treatment procedures as per Current Procedural Terminology codes; comorbidities as per International Classification of Diseases, Ninth Revision codes; and drug prescriptions as per National Drug Code Directory codes. Logistic regression was used to calculate odds ratios (ORs) for variables associated with nonunion. Data analysis was performed from January 1, 2011, to December 31, 2012, Exposures Continuous enrollment in the database was required for 12 months after fracture to allow sufficient time to capture a nonunion diagnosis. Results The final analysis of 309 330 fractures in 18 bones included 178 952 women (57.9%); mean (SD) age was 44.48 (13.68) years. The nonunion rate was 4.9%. Elevated nonunion risk was associated with severe fracture (eg, open fracture, multiple fractures), high body mass index, smoking, and alcoholism. Women experienced more fractures, but men were more prone to nonunion. The nonunion rate also varied with fracture location: scaphoid, tibia plus fibula, and femur were most likely to be nonunion. The ORs for nonunion fractures were significantly increased for risk factors, including number of fractures (OR, 2.65; 95% CI, 2.34-2.99), use of nonsteroidal anti-inflammatory drugs plus opioids (OR, 1.84; 95% CI, 1.73-1.95), operative treatment (OR, 1.78; 95% CI, 1.69-1.86), open fracture (OR, 1.66; 95% CI, 1.55-1.77), anticoagulant use (OR, 1.58; 95% CI, 1.51-1.66), osteoarthritis with rheumatoid arthritis (OR, 1.58; 95% CI, 1.38-1.82), anticonvulsant use with benzodiazepines (OR, 1.49; 95% CI, 1.36-1.62), opioid use (OR, 1.43; 95% CI, 1.34-1.52), diabetes (OR, 1.40; 95% CI, 1.21-1.61), high-energy injury (OR, 1.38; 95% CI, 1.27-1.49), anticonvulsant use (OR, 1.37; 95% CI, 1.31-1.43), osteoporosis (OR, 1.24; 95% CI, 1.14-1.34), male gender (OR, 1.21; 95% CI, 1.16-1.25), insulin use (OR, 1.21; 95% CI, 1.10-1.31), smoking (OR, 1.20; 95% CI, 1.14-1.26), benzodiazepine use (OR, 1.20; 95% CI, 1.10-1.31), obesity (OR, 1.19; 95% CI, 1.12-1.25), antibiotic use (OR, 1.17; 95% CI, 1.13-1.21), osteoporosis medication use (OR, 1.17; 95% CI, 1.08-1.26), vitamin D deficiency (OR, 1.14; 95% CI, 1.05-1.22), diuretic use (OR, 1.13; 95% CI, 1.07-1.18), and renal insufficiency (OR, 1.11; 95% CI, 1.04-1.17) (multivariate P Conclusions and Relevance The probability of fracture nonunion can be based on patient-specific risk factors at presentation. Risk of nonunion is a function of fracture severity, fracture location, disease comorbidity, and medication use.
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TL;DR: Gene-edited pigs are protected from porcine reproductive and respiratory syndrome virus by being resistant to the PRRSV isolate NVSL 97-7895, a well-characterized, relatively virulent viral isolate that is commonly used in experimentalPRRSV infection trials.
Abstract: VOLUME 34 NUMBER 1 JANUARY 2016 NATURE BIOTECHNOLOGY To the Editor: Porcine reproductive and respiratory syndrome (PRRS) is the most economically important disease of swine in North America, Europe and Asia, costing producers in North America more than $600 million annually1. The disease syndrome was first recognized in the United States in 1987 and described in 1989 (ref. 2). The causative agent, porcine reproductive and respiratory syndrome virus (PRRSV), was subsequently isolated and characterized in Europe in 1991 (ref. 3). Vaccines have been unable to control the disease. It has been suggested that CD163 is the receptor for entry of PRRSV into cells4. Thus, we hypothesized that pigs with defective CD163 would be immune to PRRSV. Previously we used CRISPRCas9 to generate pigs lacking functional CD163 (ref. 5). Here we demonstrate that these animals are resistant to the PRRSV isolate NVSL 97-7895, a well-characterized, relatively virulent viral isolate that is commonly used in experimental PRRSV infection trials. After infection, they showed no clinical signs (fever or respiratory signs), lung pathology, viremia or antibody response and remained healthy for the 35 d after infection measured in this study. Because CD163 was edited using CRISPR-Cas9, the pigs challenged in this study do not contain any transgenes5. PRRSV is a member of the mammalian arterivirus group, which also includes murine lactate dehydrogenase-elevating virus, simian hemorrhagic fever virus and equine arteritis virus. The arteriviruses share important pathogenesis properties, including macrophage tropism and the capacity to cause both severe disease and persistent infection. In young pigs, infection with PRRSV results in respiratory disease, including cough and fever and reduced growth performance. In pregnant sows, PRRSV infection can result in reproductive failure, as well as persistently infected and low birth weight piglets.The virus is associated with polymicrobial disease syndromes, including porcine respiratory Gene-edited pigs are protected from porcine reproductive and respiratory syndrome virus
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TL;DR: This work analyzes simulation data stemming from detailed large-scale agent-based models previously designed and calibrated to study how realistic social networks and disease transmission characteristics shape early epidemic growth patterns, general transmission dynamics, and control of international disease emergencies such as the 2009 A/H1N1 influenza pandemic and the 2014-2015 Ebola epidemic in West Africa.
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Oklahoma State University Center for Health Sciences1, Stony Brook University2, University of Texas at Austin3, Ohio University4, University of Missouri5, Hull York Medical School6, Sam Houston State University7, University of Toronto8, University of Vienna9, Humboldt University of Berlin10, University of Utah11, University of Chicago12, Villanova University13, Brown University14
TL;DR: A critical review of the recent contributions to iodine‐based, contrast‐enhanced CT research is provided to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies.
Abstract: Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.
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University of Queensland1, University of Western Australia2, University of Warwick3, Michigan State University4, Korea Research Institute of Bioscience and Biotechnology5, Cold Spring Harbor Laboratory6, University of Georgia7, University of Missouri8, National Research Council9, Fujian Agriculture and Forestry University10, J. Craig Venter Institute11
TL;DR: Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.
Abstract: There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.
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TL;DR: The second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function, was conducted by as mentioned in this paper. But the results of the CAFA2 assessment are limited.
Abstract: BACKGROUND: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. RESULTS: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. CONCLUSIONS: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.
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TL;DR: The signal processing algorithms and techniques involved in elderly fall detection using radar are described, including fall features determination and classification and some of the challenges facing technology developments for fall detection are reported on.
Abstract: Radar is considered an important technology for health monitoring and fall detection in elderly assisted living due to a number of attributes not shared by other sensing modalities. In this article, we describe the signal processing algorithms and techniques involved in elderly fall detection using radar. A human?s radar signal returns differ in their Doppler characteristics, depending on the nature of the human gross motor activities. These signals are nonstationary in nature, inviting time-frequency analysis in both its linear and bilinear aspects, to play a fundamental role in motion identification, including fall features determination and classification. This article employs real fall data to demonstrate the success of existing detection algorithms as well as to report on some of the challenges facing technology developments for fall detection.
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TL;DR: It is shown that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes, and that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements.
Abstract: We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
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TL;DR: The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement.
Abstract: 3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/.
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The Peregrine Fund1, Mbarara University of Science and Technology2, University of British Columbia3, Wageningen University and Research Centre4, University of Reading5, Centre national de la recherche scientifique6, University of York7, University of Missouri8, Makerere University9, Endangered Wildlife Trust10, University of Swaziland11
TL;DR: The first estimates of a 30-year Pan African vulture decline were presented in this article, confirming that declines have occurred on a scale broadly comparable with those seen in Asia, where the ecological, economic, and human costs are already documented.
Abstract: Vultures provide critical ecosystem services, yet populations of many species have collapsed worldwide. We present the first estimates of a 30-year PanAfrican vulture decline, confirming that declines have occurred on a scale broadly comparable with those seen in Asia, where the ecological, economic, and human costs are already documented. Populations of eight species we assessed had declined by an average of 62%; seven had declined at a rate of 80% or more over three generations. Of these, at least six appear to qualify for uplisting to Critically Endangered. Africa’s vultures are facing a range of specific threats, the most significant of which are poisoning and trade in traditional medicines, which together accounted for 90% of reported deaths. We recommend that national governments urgently enact and enforce legislation to strictly regulate the sale and use of pesticides and poisons, to eliminate the illegal trade in vulture body parts, as food or medicine, and to minimize mortality caused by power lines and wind turbines.
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TL;DR: It is shown that 3 months of rapamycin treatment is sufficient to increase life expectancy by up to 60% and improve measures of healthspan in middle-aged mice and this transient treatment is also associated with a remodeling of the microbiome, including dramatically increased prevalence of segmented filamentous bacteria in the small intestine.
Abstract: The FDA approved drug rapamycin increases lifespan in rodents and delays age-related dysfunction in rodents and humans. Nevertheless, important questions remain regarding the optimal dose, duration, and mechanisms of action in the context of healthy aging. Here we show that 3 months of rapamycin treatment is sufficient to increase life expectancy by up to 60% and improve measures of healthspan in middle-aged mice. This transient treatment is also associated with a remodeling of the microbiome, including dramatically increased prevalence of segmented filamentous bacteria in the small intestine. We also define a dose in female mice that does not extend lifespan, but is associated with a striking shift in cancer prevalence toward aggressive hematopoietic cancers and away from non-hematopoietic malignancies. These data suggest that a short-term rapamycin treatment late in life has persistent effects that can robustly delay aging, influence cancer prevalence, and modulate the microbiome.