13 Works

Neuronal activity in sensory cortex predicts the specificity of learning

Maria Geffen, Katherine Wood, Christopher Angeloni, Karmi Oxman & Claudia Clopath
Learning to avoid dangerous signals while preserving normal responses to safe stimuli is essential for everyday behavior and survival. Following identical experiences, subjects exhibit fear specificity ranging from high (specializing fear to only the dangerous stimulus) to low (generalizing fear to safe stimuli), yet the neuronal basis of fear specificity remains unknown. Here, we identified the neuronal code that underlies inter-subject variability in fear specificity using longitudinal imaging of neuronal activity before and after differential...

Data from: A generalist nematode destabilizes plant competition: no evidence for direct effects, but strong evidence for indirect effects on rhizobia abundance

Samantha Catella, Castilleja Olmsted, Shaniya Markalanda, Connor McFadden, Corlett Wood & Sara Kuebbing
1. Difficulties quantifying pathogen load and mutualist abundance limit our ability to connect disease dynamics to host community ecology. For example, specific predictions about how differential pathogen load is hypothesized to drive host competitive outcomes are rarely tested. Additionally, although infection is known to affect mutualists, we rarely measure the magnitude of pathogen effects on mutualist abundance across host competitive contexts. We tested for both mechanisms in a plant-rhizobia-nematode system. 2. We paired the legume...

Hand-written letters classification measurement data

Farshid Ashtiani, Alexander Geers & Firooz Aflatouni
Deep neural networks with applications from computer vision to medical diagnosis1-5 are commonly implemented using clock-based processors6-14, where computation speed is mainly limited by the clock frequency and the memory access time. In the optical domain, despite advances in photonic computation15-17, the lack of scalable on-chip optical nonlinearity and the loss of photonic devices limit the scalability of optical deep networks. Here we report the first integrated end-to-end photonic deep neural network (PDNN) that performs...

Energy expenditure does not explain step length-width choices during walking

Stephen Antos, Konrad Kording & Keith Gordon
Healthy young adults have a most preferred walking speed, step length, and step width that are close to energetically optimal. However, people can choose to walk with a multitude of different step lengths and widths, which can vary in both energy expenditure and preference. Here we further investigate step length-width preferences and their relationship to energy expenditure. In line with a growing body of research, we hypothesized that people's preferred stepping patterns would not be...

Memory array locations, delay times, and participant response

Kyra Schapiro, Kresimir Josic, Joshua Gold & Zachary Kilpatrick
Deliberative decisions based on an accumulation of evidence over time depend on working-memory, and working memory has limitations, but how these limitations affect deliberative decision-making is not understood. We used human psychophysics to assess the impact of working-memory limitations on the fidelity of a continuous decision variable. Participants decided the average location of multiple visual targets. This computed, continuous decision variable degraded with time and capacity in a manner that depended critically on the strategy...

Supplemental files for: A consensus view of the proteome of the last universal common ancestor

Aaron Goldman, Andrew Crapitto, Amy Campbell & AJ Harris
The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor of life (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We...

Census and phenotype data supporting Drosophila adaptive tracking

Seth Rudman, Paul Schmidt, Subhash Rajpurohit, Sharon Greenblum & Dmitri Petrov
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked evolution of fitness-associated phenotypes and allele frequencies genome-wide in ten replicate field populations of Drosophila melanogaster over ten generations from summer to late fall. Adaptation was evident over each sampling interval (1-4 generations) with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent...

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Lerato Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Essex & Marc Lipsitch
Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Results: Deep-sequence phylogenetic analysis...

Data from: Cortico-Fugal regulation of predictive coding

Maria Geffen, Alexandria Lesicko, Christopher Angeloni, Jennifer Blackwell & Mariella De Biasi
Sensory systems must account for both contextual factors and prior experience to adaptively engage with the dynamic external environment. In the central auditory system, neurons modulate their responses to sounds based on statistical context. These response modulations can be understood through a hierarchical predictive coding lens: responses to repeated stimuli are progressively decreased, in a process known as repetition suppression, whereas unexpected stimuli produce a prediction error signal. Prediction error incrementally increases along the auditory...

Individual and collective encoding of risk in animal groups

Matthew M.G. Sosna, Colin R. Twomey, Joseph Bak-Coleman, Winnie Poel, Bryan C. Daniels, Pawel Romanczuk & Iain D. Couzin
The need to make fast decisions under risky and uncertain conditions is a widespread problem in the natural world. While there has been extensive work on how individual organisms dynamically modify their behavior to respond appropriately to changing environmental conditions (and how this is encoded in the brain), we know remarkably little about the corresponding aspects of collective information processing in animal groups. For example, many groups appear to show increased “sensitivity” in the presence...

Divergent water requirements partition exposure risk to parasites in wild equids

Kaia Tombak, Laurel Easterling, Lindsay Martinez, Monica Seng, Liana Wait & Daniel Rubenstein
For grazing herbivores, dung density in feeding areas is an important determinant of exposure risk to faecal-orally transmitted parasites. When host species share the same parasite species, a non-random distribution of their cumulative dung density and/or non-random ranging and feeding behaviour may skew exposure risk and the relative selection pressure parasites impose on each host. The arid-adapted Grevy’s zebra (Equus grevyi) can range more widely than the water-dependent plains zebra (Equus quagga), with which it...

Wind and route choice affect performance of bees flying above versus within a cluttered obstacle field

Nicholas Burnett, Marc Badger & Stacey Combes
Bees flying through natural landscapes encounter physical challenges, such as wind and cluttered vegetation. The influence of these factors on the flight performance of bees remains unknown. We analyzed 548 videos of wild-caught honeybees (Apis mellifera) flying through an enclosure containing a field of vertical obstacles that bees could fly within (through open corridors, without maneuvering) or above. We examined how obstacle field height, wind presence and direction (headwinds or tailwinds) affected altitude, ground speed,...

No evidence that grooming is exchanged for coalitionary support in the short- or long-term via direct or generalized reciprocity in unrelated rhesus macaques

William O'Hearn, Angelina Ruiz-Lambides, Michael Platt & Lauren Brent
Reciprocity is a prominent explanation for cooperation between non-kin. Studies seeking to demonstrate reciprocity often focus on direct reciprocity in the timescale of minutes to hours, whereas alternative mechanisms like generalised reciprocity and the possibility of reciprocation over longer timescales of months and years are less often explored. Using a playback experiment, we tested for evidence of direct and generalised reciprocity, across short and longer timescales. We examined the exchange of grooming for coalitionary support...

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