28 Works

Data from: Experimental evidence that primate trichromacy is well suited for detecting primate social colour signals

Chihiro Hiramatsu, Amanda D. Melin, William L. Allen, Constance Dubuc & James P. Higham
Primate trichromatic colour vision has been hypothesized to be well tuned for detecting variation in facial coloration, which could be due to selection on either signal wavelengths or the sensitivities of the photoreceptors themselves. We provide one of the first empirical tests of this idea by asking whether, when compared with other visual systems, the information obtained through primate trichromatic vision confers an improved ability to detect the changes in facial colour that female macaque...

Stage 2: Virome Sniff

Jose Vargas-Asencio, Roy Nunez, Rajeeva Musunuri, Michael McCormack, Patrick Hagerty, Raehash Shah & Martina Bradic

Creating noisy 3D shapes - an implementation using free and open source tools

Zoltan Derzsi & Robert Volcic
Distorting the shape of a three-dimensional object in a randomised manner is a very difficult task. We present a script in this paper that programmatically generates spheres with added radius noise, utilising Meshlab’s software back-end. We successfully tested the script on Mac OS, Windows, and Linux operating systems. We also have given instructions on how to set up the environment for each platform, and how to replicate what the script does manually.

Data from: The impact of bottlenecks on microbial survival, adaptation and phenotypic switching in host-pathogen interactions

Richard Moxon & Edo Kussell
Microbial pathogens and viruses can often maintain sufficient population diversity to evade a wide range of host immune responses. However, when populations experience bottlenecks, as occurs frequently during initiation of new infections, pathogens require specialized mechanisms to regenerate diversity. We address the evolution of such mechanisms, known as stochastic phenotype switches, which are prevalent in pathogenic bacteria. We analyze a model of pathogen diversification in a changing host environment that accounts for selective bottlenecks, wherein...

Data from: Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

Takashi Nozoe, Edo Kussell & Yuichi Wakamoto
Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness...

Data from: Is male rhesus macaque facial coloration under intrasexual selection?

Megan Petersdorf, Constance Dubuc, Alexander V. Georgiev, Sandra Winters & James P. Higham
Exaggerated male traits can evolve under intra- or intersexual selection, but it remains less clear how often both mechanisms act together on trait evolution. While the males of many anthropoid primate species exhibit colorful signals that appear to be badges of status under intrasexual selection, the red facial coloration of male rhesus macaques (Macaca mulatta) appears to have evolved primarily under intersexual selection and female mate choice. Nonetheless, experiments show that red color is salient...

Scission and Lightness Illusions

Jonathan Winawer & Barton Anderson
Images and files associated with two papers on scission and lightness illusions, by Barton L Anderson and Jonathan Winawer

Stimulus dependence of gamma oscillations in human visual cortex

Jonathan Winawer & Dora Hermes

Data from: A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

Yann X.C. Bourgeois, Boris Delahaie, Mathieu Gautier, Emeline Lhuillier, Pierre-Jean G. Malé, Joris A.M. Bertrand, Josselin Cornuault, Kazumasa Wakamatsu, Olivier Bouchez, Claire Mould, Jade Bruxaux, Hélène Holota, Borja Mila, Christophe Thébaud, Joris A. M. Bertrand & Yann X. C. Bourgeois
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird...

Data from: Development of visual cortical function in infant macaques: a BOLD fMRI study

Tom Van Grootel, Alan Meeson, Matthias H.J. Munk, Zoe Kourtzi, J. Anthony Movshon, Nikos K. Logothetis, Lynne Kiorpes & Tom J. Van Grootel
Functional brain development is not well understood. In the visual system, neurophysiological studies in nonhuman primates show quite mature neuronal properties near birth although visual function is itself quite immature and continues to develop over many months or years after birth. Our goal was to assess the relative development of two main visual processing streams, dorsal and ventral, using BOLD fMRI in an attempt to understand the global mechanisms that support the maturation of visual...

Data from: Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time

Liam Walker, Claire Boddington, Dafyd J. Jenkins, Ying Wang, Jesper T. Grønlund, Jo Hulsmans, Sanjeev Kumar, Dhaval Patel, Jonathan D. Moore, Anthony Carter, Siva Samavedam, Giovanni Bonomo, David S. Hersh, Gloria D. Coruzzi, Nigel J. Burroughs & Miriam L. Gifford
Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana, at an unprecedented level of temporal detail. We found that individual transcripts are...

Data from: From pristine forests to high-altitude pastures: an ecological approach to prehistoric human impact on vegetation and landscapes in the western Italian Alps

Roberta Pini, Cesare Ravazzi, Luca Raiteri, Antonio Guerreschi, Lorenzo Castellano & Roberto Comolli
1. This paper addresses the origin and development of the oldest prehistoric pasture in the timberline ecotone known so far in the Alps and its relation to anthropogenic pressure and natural climate change. 2. Paleoecological and geochemical techniques were applied on the Crotte Basse mire stratigraphy (2365 m asl, western Italy) to describe changes in vegetation composition, forest biomass, land use and fertilization between ca. 6400 - 1800 yrs cal BP. 3. Subalpine forests dominated...

Data from: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria

Olatunji Kolawole, Michael Oguntoye, Tina Dam & Rumi Chunara
Objective: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical (hospital) surveillance in Nigeria. Results: Children were selected via convenience sampling from communities and a tertiary care center (n = 91) during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority (79.1%) of subjects were under 6 years...

Standard Cortical Observer Model for Human fMRI of V1-V3

Jonathan Winawer, Noah Benson, William Broderick & Heiko Müller

Research Data Management Hands on Workshop

Kevin Read, Nicole Contaxis & Alisa Surkis
This project includes material designed for teaching a 1.5 hour research data management workshop. It involves a case study that requires workshop participants to navigate messy data to identify the data that corresponds with the data represented in a figure from an article. Workshop attendees are then required to modify the messy data to follow research data management best practices.

Identification of the ventral occipital visual field maps in the human brain

Jonathan Winawer & Nathan Witthoft
Data and code supplement to manuscript, 'Identification of the ventral occipital visual field maps in the human brain'

Container Strategies for Data and Software Preservation Workshop

Michael Hildreth, Natalie Meyers, Sandra Gesing, Richard Johnson, Elisabeth Long, Jaroslaw Nabrzyski, Douglas Thain, Mark Suhovecky, Vicky Rampin, Ian Taylor, Charles Vardeman, Alexander Vyushkov, Reid Boehm, daniel brake, Donald Brower, Lincoln Bryant, Ryan Chamberlain, Euan Cochrane, Anita de Waard, Mandy Havert, Lukas Heinrich, Kolin Hodgson, Cole Hudson, Greg Janée, Maciej Malawski … & Charles Williams
A workshop organized by the DASPOS project, to be held 19-20 May 2016.

Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

David R. Nelson, Basel Khraiwesh, Weiqi Fu, Saleh Alseekh, Ashish Jaiswal, Amphun Chaiboonchoe, Khaled Hazzouri, Matthew J. O’Connor, Glenn L. Butterfoss, Nizar Drou, Jillian D. Rowe, Jamil Harb, Alisdair R. Fernie, Kristin C. Gunsalus & Kourosh Salehi-Ashtiani
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero...

Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Jae Young Choi & Michael D. Purugganan
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between...

Data from: Symbiont community stability through severe coral bleaching in a thermally extreme lagoon

Edward G. Smith, Grace O. Vaughan, Remi N. Ketchum, Dain McParland & John A. Burt
Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals’ responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C,...

Open, Public Goods Infrastructure for Research Management & Discovery IASSIST 2017

Matthew Spitzer, Vicky Rampin & Cynthia Hudson Vitale
Presentations on open technical infrastructure that supports research reproducibility, open access mandates, and data management and sharing requirements. Panel on Thursday, May 25th, 2017 at 4pm

Resolving the complex genetic basis of phenotypic variation and variability of cellular growth

David Gresham & Mark L Siegal
Data and computer code associated with Ziv et al., 2017

Do puzzle pieces and autism puzzle piece logos evoke negative associations?

Morton Ann Gernsbacher, Adam Raimond, Jennifer Stevenson, Jilana Boston & Bev Harp
This study examined whether puzzle-piece images evoke negative associations in the general public.

Data from: Concurrent temporal channels for auditory processing: oscillatory neural entrainment reveals segregation of function at different scales

Xiangbin Teng, Xing Tian, Jess Rowland & David Poeppel
Natural sounds convey perceptually relevant information over multiple timescales, and the necessary extraction of multi-timescale information requires the auditory system to work over distinct ranges. The simplest hypothesis suggests that temporal modulations are encoded in an equivalent manner within a reasonable intermediate range. We show that the human auditory system selectively and preferentially tracks acoustic dynamics concurrently at 2 timescales corresponding to the neurophysiological theta band (4–7 Hz) and gamma band ranges (31–45 Hz) but,...

Data from: Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments

Edward G. Smith, Cecilia D'Angelo, Yoni Sharon, Dan Tchernov & Joerg Wiedenmann
The depth distribution of reef-building corals exposes their photosynthetic symbionts of the genus Symbiodinium to extreme gradients in the intensity and spectral quality of the ambient light environment. Characterizing the mechanisms used by the coral holobiont to respond to the low intensity and reduced spectral composition of the light environment in deeper reefs (greater than 20 m) is fundamental to our understanding of the functioning and structure of reefs across depth gradients. Here, we demonstrate...

Registration Year

  • 2017
    28

Resource Types

  • Dataset
    14
  • Text
    14

Affiliations

  • New York University
    28
  • Center For Open Science
    3
  • York University
    3
  • New York University Abu Dhabi
    2
  • University of Cambridge
    2
  • Columbia University
    1
  • University of Notre Dame
    1
  • Kyushu University
    1
  • Interuniversity Institute for Marine Sciences in Eilat
    1
  • University of Milan
    1