10 Works

Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa

Rafal S. Sobota, Catherine M. Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P. Igo, Albert Magohe, LaShaunda L. Malone, Keith Chervenak, Noemi B. Hall, Mecky Matee, Harriet Mayanja-Kizza, Moses Joloba, Jason H. Moore, William K. Scott, Timothy Lahey, W. Henry Boom, C. Fordham Von Reyn, Scott M. Williams & Giorgio Sirugo
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Water vascular system architecture in an Ordovician ophiuroid

Elizabeth G. Clark, Bhart-Anjan S. Bhullar, Simon A. F. Darroch & Derek E. G. Briggs
Understanding the water vascular system (WVS) in early fossil echinoderms is critical to elucidating the evolution of this system in extant forms. Here we present the first report of the internal morphology of the water vascular system of a stem ophiuroid. The radial canals are internal to the arm, but protected dorsally by a plate separate to the ambulacrals. The canals zig-zag with no evidence of constrictions, corresponding to sphincters, which control pairs of tube...

Data from: Inference of facultative mobility in the enigmatic Ediacaran organism Parvancorina

Simon A.F. Darroch, Imran A. Rahman, Brandt Gibson, Rachel A. Racicot, Marc Laflamme & Simon A. F. Darroch
Establishing how Ediacaran organisms moved and fed is critical to deciphering their ecological and evolutionary significance, but has long been confounded by their non-analogue body plans. Here, we use computational fluid dynamics to quantitatively analyze water flow around the Ediacaran taxon Parvancorina, thereby testing between competing models for feeding mode and mobility. The results show that flow was not distributed evenly across the organism, but was directed towards localized areas; this allows us to reject...

Data from: Transcriptional profile and differential fitness in a specialist milkweed insect across host plants varying in toxicity

Stephanie S.L. Birnbaum, David C. Rinker, Nicole M. Gerardo, Patrick Abbot & Stephanie S. L. Birnbaum
Interactions between plants and herbivorous insects have been models for theories of specialization and coevolution for over a century. Phytochemicals govern many aspects of these interactions and have fostered the evolution of adaptations by insects to tolerate or even specialize on plant defensive chemistry. While genomic approaches are providing new insights into the genes and mechanisms insect specialists employ to tolerate plant secondary metabolites, open questions remain about the evolution and conservation of insect counter-defenses,...

Data from: Loss of mTORC2 signaling in oligodendrocyte precursor cells delays myelination

Mark D. Grier, Kathryn L. West, Nathaniel D. Kelm, Cary Fu, Mark D. Does, Brittany Parker, Eleanor McBrier, Andre H. LaGrange, Kevin C. Ess & Robert P. Carson
Myelin abnormalities are increasingly being recognized as an important component of a number of neurologic developmental disorders. The integration of many signaling pathways and cell types are critical for correct myelinogenesis. The PI3-K and mechanistic target of rapamycin (mTOR) pathways have been found to play key roles. mTOR is found within two distinct complexes, mTORC1 and mTORC2. mTORC1 activity has been shown to play a major role during myelination, while the role of mTORC2 is...

Data from: Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal

Esteban J. Parra, Andrew Mazurek, Christopher R. Gignoux, Alexandra Sockell, Michael Agostino, Andrew P. Morris, Lauren E. Petty, Craig L. Hanis, Nancy J. Cox, Adan Valladares-Salgado, Jennifer E. Below & Miguel Cruz
We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this...

Data from: An alternative pathway to eusociality: exploring the molecular and functional basis of fortress defense

Sarah P. Lawson, Leah Sigle, Abigail L. Lind, Andrew W. Legan, Jessica N. Mezzanotte, Hans-Willi Honegger, Patrick Abbot & Leah T. Sigle
Some animals express a form of eusociality known as 'fortress defense', in which defense rather than brood care is the primary social act. Aphids are small plant-feeding insects, but like termites, some species express division of labor and castes of aggressive juvenile 'soldiers'. What is the functional basis of fortress defense eusociality in aphids? Previous work showed that the acquisition of venoms might be a key innovation in aphid social evolution. We show that the...

Data from: Audio-visual interactions uniquely contribute to resolution of visual conflict in people possessing absolute pitch

Sujin Kim, Randolph Blake, Minyoung Lee & Chai-Youn Kim
Individuals possessing absolute pitch (AP) are able to identify a given musical tone or to reproduce it without reference to another tone. The present study sought to learn whether this exceptional auditory ability impacts visual perception under stimulus conditions that provoke visual competition in the form of binocular rivalry. Nineteen adult participants with 3 - 19 years of musical training were divided into two groups according to their performance on a task involving identification of...

Data from: Reconstructing geographic range size dynamics from fossil data

Simon A.F. Darroch & Erin E. Saupe
Ecologists and paleontologists alike are increasingly using the fossil record as a spatial data set, in particular to study the dynamics and distribution of geographic range sizes among fossil taxa. However, no attempts have been made to establish how accurately range sizes and range-size dynamics can be preserved. Two fundamental questions are: Can common paleo range-size reconstruction methods accurately reproduce known species’ ranges from locality (i.e., point) data? And, are some reconstruction methods more reliable...

Registration Year

  • 2017

Resource Types

  • Dataset


  • Vanderbilt University
  • University of Toronto
  • Vanderbilt University Medical Center
  • Fred Hutchinson Cancer Research Center
  • University of Pennsylvania
  • University of Washington
  • Stanford University
  • Columbia University
  • Natural History Museum of Los Angeles County
  • Duke University