88 Works

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Neural network learning of the Russian genitive of negation: optionality and structure sensitivity

Natalia Talmina & Tal Linzen

Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Michael D. Martin, Elizabeth A. Zimmer, Morten T. Olsen, Andrew D. Foote, M. Thomas P. Gilbert & Grace S. Brush
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North...

Data from: Phylogenetic, ecological, and allometric correlates of cranial shape in Malagasy lemuriforms

Karen L. Baab, Jonathan M. G. Perry, F. James Rohlf & William L. Jungers
Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences in diel activity patterns. This study examines the role of two key ecological variables, diet and activity patterns, in shaping the radiation of a diverse clade of primates, the Malagasy lemurs....

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Meredith M. Doellman, Scott P. Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H.Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil, Jeff L. Feder, Jeffrey L. Feder & Thomas H. Q. Powell
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency...

Data from: Neural correlates of domain-specific cognitive decline: the ARIC-NCS study

Andrea Lauren Christman Schneider, Matthew L Senjem, Aozhou Wu, Alden Gross, David S. Knopman, Jeffrey L Gunter, Christopher G Schwarz, Tom H. Mosley, Rebecca F. Gottesman, A. Richey Sharrett & Clifford R. Jack
Objective: To evaluate the association of cognitive declines in the domains of memory, language, and executive function with brain gray matter (GM) volume in old age. Methods: Prospective study of 1,846 participants in the Atherosclerosis Risk in Communities (ARIC) study who underwent 3T brain MRI scans in 2011-2013. Participants were categorized by cognitive domain performance trajectory over the prior 20 years (cut-point to define decline: 20th percentile). Associations between GM volume and cognitive declines were...

Data from: Achieving a step change in the tuberculosis epidemic through comprehensive community-wide intervention: A model-based analysis

Sourya Shrestha, Emily Kendall, Rebekah Chang, Roy Joseph, Parastu Kasaie, Laura Gillini, Anthony Todd Fojo, Michael Campbell, Nimalan Arinaminpathy & David Dowdy
Background: Global progress towards reducing tuberculosis (TB) incidence and mortality has consistently lagged behind World Health Organization targets leading to a perception that large reductions in TB burden cannot be achieved. However, several recent and historical trials suggest that intervention efforts that are comprehensive and focused can have substantial epidemiological impact. We aimed to quantify the potential epidemiological impact of an intensive but realistic, community-wide campaign utilizing existing tools, and designed to achieve a “step...

Gene-drive suppression of mosquito populations in large cages as a bridge between lab and field

Andrew Hammond, Paola Pollegioni, Tania Persampieri, Ace North, Roxana Minuz, Alessandro Trusso, Alessandro Bucci, Kyros Kyrou, Ioanna Morianou, Alekos Simoni, Tony Nolan, Ruth Müller & Andrea Crisanti
CRISPR-based gene-drives targeting the gene doublesex in the malaria vector Anopheles gambiae effectively suppressed the reproductive capability of mosquito populations reared in small laboratory cages. To bridge the gap between laboratory and the field, this gene-drive technology must be challenged with vector ecology. Here we report the suppressive activity of the gene-drive in age-structured An. gambiae populations in large indoor cages that permit complex feeding and reproductive behaviours. The gene-drive element spreads rapidly through the...

Projected climate risk of aquatic food system benefits

Michelle Tigchelaar, William Cheung, Essam Mohammed, Michael Phillips, Hanna Payne, Elizabeth Selig, Colette Wabnitz, Muhammed Oyinlola, Thomas Frölicher, Jessica Gephart, Christopher Golden, Edward Allison, Abigail Bennett, Ling Cao, Jessica Fanzo, Benjamin Halpern, Fiorenza Micheli, Rosamond Naylor, Rashid Sumaila, Alessandro Tagliabue & Max Troell
Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and culture of billions of people worldwide – but climate-related hazards may compromise their ability to provide these benefits. This analysis estimates national-level aquatic food system climate risk using a fuzzy logic modeling approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes, and vulnerability to losing those contributions....

Data from: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

Andrew Skol, Segun Jung, Ana Marija Sokovic, Siquan Chen, Sarah Fazal, Olukayode Sosina, Poulami Borkar, Amy Lin, Maria Sverdlov, Dingcai Cao, Anand Swaroop, Ionut Bebu, Barbara Stranger & Michael Grassi
We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association to diabetic retinopathy in a genome-wide association study meta-analysis. Expression Quantitative Trait Loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose...

Mass ratio effects underlie ecosystem responses to environmental change

Melinda Smith, Sally Koerner, Alan Knapp, Meghan Avolio, Francis Chaves, Elsie Denton, John Dietrich, David Gibson, Jesse Gray, Ava Hoffman, David Hoover, Kimberly Komatsu, Andrea Silletti, Kevin Wilcox, Qiang Yu & John Blair
1. Random species loss has been shown experimentally to reduce ecosystem function, sometimes more than other anthropogenic environmental changes. Yet, controversy surrounds the importance of this finding for natural systems where species loss is non-random. 2. We compiled data from 16 multi-year experiments located at a single site in native tallgrass prairie. These experiments included responses to 11 anthropogenic environmental changes, as well as non-random biodiversity loss - either the removal of uncommon/rare plant species...

Data from: EDAPHOLOG monitoring system: automatic, real-time detection of soil microarthropods

Miklós Dombos, Oxána Bánszegi, Katalin Szlávecz & Andrés Kosztolányi
Soil microarthropods as organic matter decomposers play an important role in soil functioning thus providing ecosystem services. However, ecosystem scale investigations on their abundance and dynamics are scarce because their high spatio-temporal heterogeneity requires huge sample size. Processing and identifying large number of individuals are extremely labour-intensive. We prototyped a device called EDAPHOLOG monitoring system that consists of (1) a probe that catches and detects microarthropods and estimates their body size; (2) a data logger...

2019 NSF Workshop on Connecting Large Facilities and Cyberinfrastructure

Ewa Deelman, Ilya Baldin, Brian Bockelman, Adam Bolton, Patrick Brady, Tom Cheatham, Laura Christopherson, Rafael Ferreira da Silva, Tom Gulbransen, Kate Keahey, Marina Kogan, Anirban Mandal, Angela Murillo, Jarek Nabrzyski, Valerio Pascucci, Steve Petruzza, Mats Rynge, Susan Sons, Dan Stanzione, Chaudhuri Surajit, Daryl Swensen, Alexander Szalay, Douglas Thain, John Towns, Charles Vardeman … & Jane Wyngaard

Emergent Gestural Scores in a Recurrent Neural Network Model of Vowel Harmony

Caitlin Smith, Charlie O'Hara, Eric Rosen & Paul Smolensky

Human-Model Divergence in the Handling of Vagueness

Elias Stengel-Eskin, Jimena Guallar-Blasco & Benjamin Van Durme

Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Stefan Dennenmoser, Fritz J. Sedlazeck, Michael C. Schatz, Janine Altmüller, Matthias Zytnicki & Arne W. Nolte
Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Fisher’s geometric model predicts the effects of random mutations when tested in the wild

Frank W. Stearns & Charles B. Fenster
Fisher's Geometric Model of Adaptation (FGM) has been the conceptual foundation for studies investigating the genetic basis of adaptation since the onset of the neo Darwinian synthesis. FGM describes adaptation as the movement of a genotype toward a fitness optimum due to beneficial mutations. To date, one prediction of FGM, the probability of improvement is related to the distance from the optimum, has only been tested in microorganisms under laboratory conditions. There is reason to...

Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters

J. B. Harmon, H. K. Gray, C. Young & K. J. Schwab
Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and...

Using GBIF to Demonstrate Colonial Legacies on Biodiversity Data

Ryan S. Mohammed, Melissa Kemp, Michelle J. LeFebvre, Alexis M. Mychajliw, Grace Turner, Kelly Fowler, Michael Pateman, Maria A. Nieves-Colón, Lanya Fanovich, Siobhan B. Cooke, Liliana M. Dávalos, Scott M. Fitzpatrick, Christina M. Giovas, Myles Stokowski & Ashley A. Wrean
Biologists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”, but do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. We discuss two case studies of the Caribbean’s fragmented natural history collections, the effects of differing legislation and governance by the region’s multiple nation states. We use digital natural history specimen data from GBIF to demonstrate how...

Costing data for implementing mHealth facilitated tuberculosis contact tracing in Uganda

Amanda J Gupta, Patricia Turimumahoro, J. Lucian Davis, David Dowdy, Austin Tucker, Radhika Tampi, Diana Babirye, Emmanuel Ochom, Joseph Ggita, Irene Ayakaka, Hojoon Sohn & Achilles Katamba
Introduction Mobile health (mHealth) applications may improve timely access to health services and improve patient-provider communication, but the upfront costs of implementation may be prohibitive, especially in resource-limited settings. Methods We measured the costs of developing and implementing an mHealth-facilitated, home-based strategy for tuberculosis (TB) contact investigation (CI) in Kampala, Uganda, between February 2014 and July 2017. We compared routine implementation involving community health workers (CHWs) screening and referring household contacts to clinics for TB...

Bone structural data for the Denver Longitudinal Growth Study

Christopher Ruff
Long bone structural dimensions have been shown to be responsive to mechanical loadings during life. Thus, they can be used to track behavioral changes as well as changes in body size during ontogeny. Radiographic measurements of long bone structural properties (lengths, cross-sectional geometric properties, articular breadths) were carried out for a sample of 20 children who had participated in the Denver Growth Study. An average of 36 longitudinal time points for each individual, taken at...

Improved household living standards can restore dry tropical forests

Ruth DeFries, Meghna Agarwala, Sandra Baquie, Pooja Choksi, Sarika Khanwilkar, Pinki Mondal, Harini Nagendra & Johannes Uperlainen.
Despite multiple approaches over the last several decades to harmonize conservation and development goals in the tropics, forest-depende­­­­­­nt households remain the poorest in the world. Durable housing and alternatives to fuelwood for cooking are critical needs to reduce multi-dimensional poverty. These improvements also potentially reduce pressure on forests and alleviate forest degradation. We test this possibility in dry tropical forests of the Central Indian Highlands where tribal and other marginalized populations rely on forests for...

Data from: Protein synthesis inhibition in the peri-infarct cortex slows motor recovery in rats

Maximilian Schubring-Giese, Susan Leemburg, Andreas Rüdiger Luft & Jonas Aurel Hosp
Neuroplasticity and reorganization of brain motor networks are thought to enable recovery of motor function after ischemic stroke. Especially in the cortex surrounding the ischemic scar (i.e., peri-infarct cortex), evidence for lasting reorganization has been found at the level of neurons and networks. This reorganization depends on expression of specific genes and subsequent protein synthesis. To test the functional relevance of the peri-infarct cortex for recovery we assessed the effect of protein synthesis inhibition within...

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