10 Works

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: Clinical presentation and management of SMART syndrome

Sebastian F. Winter, Joshua P. Klein, Eugene J. Vaios, Philipp Karschnia, Eudocia Q. Lee, Helen A. Shih, Franziska Loebel & Jorg Dietrich
Stroke-like migraine attacks after radiation therapy (SMART) syndrome represents a rare but serious condition manifesting years after cranial radiation therapy (RT). Characterized by migraine-type headaches, stroke-like deficits and/or seizures and MR imaging abnormalities, including cortical gyriform enhancement in irradiated brain regions, SMART remains diagnostically and therapeutically challenging. Distinction from tumor progression is difficult and treatment options are limited. Although frequently reversible, SMART episodes can recur and effectuate persistent neurologic and/or imaging sequelae.

Data from: Biallelic SQSTM1 mutations in early-onset, variably progressive neurodegeneration

Valentina Muto, Elisabetta Flex, Zachary Kupchinsky, Guido Primiano, Hamid Galehdari, Mohammadreza Dehghani, Serena Cecchetti, Giovanna Carpentieri, Teresa Rizza, Neda Mazaheri, Alireza Sedaghat, Mohammad Yahya Vahidi Mehrjardi, Alice Traversa, Michela Di Nottia, Maria M. Kousi, Yalda Jamshidi, Andrea Ciolfi, Viviana Caputo, Reza Azizi Malamiri, Francesca Pantaleoni, Simone Martinelli, Aaron R. Jeffries, Jawaher Zeighami, Amir Sherafat, Daniela Di Giuda … & Marco Tartaglia
Objective: To characterize clinically and molecularly an early-onset, variably progressive neurodegenerative disorder characterized by a cerebellar syndrome with severe ataxia, gaze palsy, dyskinesia, dystonia, and cognitive decline affecting 11 individuals from 3 consanguineous families. Methods: We used whole-exome sequencing (WES) (families 1 and 2) and a combined approach based on homozygosity mapping and WES (family 3). We performed in vitro studies to explore the effect of the nontruncating SQSTM1 mutation on protein function and the...

Data from: The epileptology of alternating hemiplegia of childhood

Julie Uchitel, Ashley Helseth, Lyndsey Prange, Melissa McLean, Ryan Ghusayni, Monisha Sachdev, Arsen Hunanyan & Mohamad Mikati
Objective: Report our experience and investigate five original hypotheses: 1) Multiple types of epileptic seizures occur in Alternating Hemiplegia of Childhood (AHC) and these can be the initial presentation. 2) Epileptiform abnormalities often appear well after clinical seizures. 3) Non-epileptic reduced awareness spells (RAS) occur frequently. 4) Epilepsy is commonly drug resistant but may respond to vagal nerve stimulation (VNS). 5) Status epilepticus (SE) is common and is usually refractory and recurrent. Methods: Analyze a...

Recurrent circuitry is required to stabilize piriform cortex odor representations across brain states

Kevin Bolding
Pattern completion, or the ability to retrieve stable neural activity patterns from noisy or partial cues, is a fundamental feature of memory. Theoretical studies indicate that recurrently connected auto-associative or discrete attractor networks can perform this process. Although pattern completion and attractor dynamics have been observed in various recurrent neural circuits, the role recurrent circuitry plays in implementing these processes remains unclear. In recordings from head-fixed mice, we found that odor responses in olfactory bulb...

Phenotypic divergence among threespine stickleback that differ in nuptial coloration

Clara Jenck, Whitley Lehto, Brian Ketterman, Lukas Sloan, Aaron Sexton & Robin Tinghitella
By studying systems in their earliest stages of differentiation, we can learn about the evolutionary forces acting within and among populations and how those forces could contribute to reproductive isolation. Such an understanding would help us better discern and predict how selection leads to the maintenance of multiple morphs within a species, rather than speciation. The postglacial adaptive radiation of the threespine stickleback (Gasterosteus aculeatus) is one of the best-studied cases of evolutionary diversification and...

Data from: Describing complex structure-function relationships in biomolecules at equilibrium

Homme W. Hellinga & Malin J. Allert
One of the great ambitions of structural biology is to describe structure-function relationships quantitatively. Statistical thermodynamics is a powerful, general tool for computing the behavior of biological macromolecules at equilibrium, because it establishes a direct link between structure and function. Complex behavior emerges as equilibria of multiple reactions are coupled. Analytical treatment of linked equilibria scales poorly with increasing numbers of reactions and states as the algebraic constructs rapidly become unwieldy. We therefore developed a...

Data from: Looking up: a dozen years of evolution of neurology clerkships in the United States

Joseph E. Safdieh, Adam D. Quick, Pearce J. Korb, Diego R. Torres-Russotto, Karissa L. Gable, Maggie M. Rock, Carolyn M. Cahill & Madhu Soni
Objective: To report a 2017 survey of all US medical school neurology clerkship directors (CDs) and to compare the results to similar surveys conducted in 2005 and 2012. Methods: An American Academy of Neurology (AAN) Consortium of Neurology Clerkship Directors (CNCD) workgroup developed the survey that was sent to all neurology CDs listed in the AAN CNCD database. Comparisons were made to similar 2005 and 2012 surveys. Results: The response rate was 92 of 146...

Data from: An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina

Jasper J. Visser, Yolanda Cheng, Steven C. Perry, Andrew Benjamin Chastain, Bayan Parsa, Shatha S. Masri, Ray Thomas A., Jeremy N. Kay, Woj M. Wojtowicz & Thomas A Ray
In the inner plexiform layer of the mouse retina, ~70 neuronal subtypes form a stereotyped circuit that underlies visual processing. During development, subtypes organize into an intricate laminar structure. This organization is choreographed by extracellular interactions that mediate cell recognition events. To identify recognition proteins involved in lamination, we utilized microarray data from 13 subtypes to identify differentially-expressed cell surface and secreted proteins. Using these candidates, we performed a biochemical screen and identified ~50 previously-unknown...

Data from: Improving rational use of ACTs through diagnosis-dependent subsidies: evidence from a cluster-randomized controlled trial in western Kenya

Wendy Prudhomme O'Meara, Diana Menya, Jeremiah Laktabai, Alyssa Platt, Indrani Saran, Elisa Maffioli, Joseph Kipkoech, Manoj Mohanan, Elizabeth L. Turner & Wendy Prudhomme O’Meara
Background: More than half of artemisinin combination therapies (ACTs) consumed globally are dispensed in the retail sector where diagnostic testing is uncommon, leading to overconsumption and poor targeting. In many malaria-endemic countries, ACTs sold over-the-counter are available at heavily subsidized prices, further contributing to their misuse. Inappropriate use of ACTs can have serious implications for the spread of drug resistance and leads to poor outcomes for non-malaria patients treated with incorrect drugs. We evaluated the...

Registration Year

  • 2021
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  • 2016

Resource Types

  • Dataset


  • Duke University School of Medicine
  • Duke University
  • Charité
  • Massachusetts General Hospital
  • Fred Hutchinson Cancer Research Center
  • The Ohio State University Wexner Medical Center
  • University of Washington
  • Columbia University
  • Agostino Gemelli University Polyclinic
  • University of California, Berkeley