25 Works

When in Rome… on local norms and sentencing decisions (LIEPP Working Paper, n°88)

David Abrams, Roberto Galbiati, Emeric Henry & Arnaud Philippe
The paper deals with legal intermediaries, as two streams of research apprehend and define them in recent and dynamic works. One, rooted in political science, studies regulatory intermediaries (LeviFaur et al., 2017; Bes, 2019), as actors between regulators and regulated, whereas the other, rooted in the Law and Society field and sociology, analyses legal intermediaries (Edelman, 2016; Talesh and Pélisse, 2019 ; Billows and alii 2019), as a broader and more bottom up category describing...

Splice altering variant predictions in four archaic hominin genomes

Colin Brand, Laura Colbran & John Anthony Capra
This file contains high-quality autosomal SNVs that occur among four high-coverage archaic genomes aligned to the hg19/GRCh37 reference genome. Each entry corresponds to a single variant with a distinct GENCODE, Human Release 24, annotation per genomic position. Data per variant includes the genomic position, reference/alternate alleles, archaic genotypes, gene annotation, and additional data relevant to the analysis of splicing variants: SpliceAI annotations gene constraint measured using data from gnomAD variant conservation measured using phyloP allele...

Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load

Beatriz Navarro-Dominguez, Ching-Ho Chang, Cara Brand, Christina Muirhead, Daven Presgraves & Amanda Larracuente
Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive- the driver and the target- linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic...

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...

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...

Parasites, niche modification and the host microbiome: A field survey of multiple parasites

Kayleigh R. O'Keeffe, Fletcher W. Halliday, Corbin D. Jones, Ignazio Carbone & Charles E. Mitchell
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity...

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...

Label-free three-photon imaging of intact human cerebral organoids: Tracking early events in brain development and deficits in Rett Syndrome

Murat Yildirim, Chloe Delepine, Danielle Feldman, Vincent Pham, Stephanie Chou, Jacque Ip, Alexi Nott, Li-Huei Tsai, Guo-Li Ming, Peter So & Mriganka Sur
Human cerebral organoids are unique in their development of progenitor-rich zones akin to ventricular zones from which neuronal progenitors differentiate and migrate radially. Analyses of cerebral organoids thus far have been performed in sectioned tissue or in superficial layers due to their high scattering properties. Here, we demonstrate label-free three-photon imaging of whole, uncleared intact organoids (~2 mm depth) to assess early events of early human brain development. Optimizing a custom-made three-photon microscope to image...

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...

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...

Parsing Early Modern English for Linguistic Search

Seth Kulick, Neville Ryant & Beatrice Santorini

Sample metadata for feline leukemia virus dataset

Raegan Petch, Roderick Gagne, Elliott Chiu, Clara Mankowski, Jaime Rudd, Melody Roelke-Parker, Winston Vickers, Kenneth Logan, Mathew Alldredge, Deana Clifford, Mark Cunningham, Dave Onorato & Sue VandeWoude
Feline leukemia virus (FeLV) is a gammaretrovirus with horizontally transmitted and endogenous forms. Domestic cats are the primary reservoir species, but FeLV outbreaks in endangered Florida panthers and Iberian lynx have resulted in mortalities. To assess prevalence and interspecific/intraspecific transmission, we conducted an extensive survey and phylogenetic analysis of FeLV infection in free-ranging pumas (n=641), bobcats (n=212) and shelter domestic cats (n=304). Samples were collected from coincident habitats across the United States between 1985-2018. FeLV...

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...

Observational data and model output for sediment nutrient cycling at Patagonian fjords

Hong Chin Ng, Jon R. Hawkings, Jemma L. Wadham, Katharine R. Hendry, Tim M. Conway, Sebastien Bertrand, Matthias Sieber, Brent A. Summers, Felipe S. Freitas, James P.J. Ward, Helena V. Pryer & Sandra Arndt
Glacier meltwater supplies a significant amount of silicon (Si) and iron (Fe) sourced from weathered bedrock to downstream ecosystems. However, the extent to which these essential nutrients reach the ocean is regulated by the nature of the benthic cycling of dissolved Si and Fe within fjord systems, given the rapid deposition of reactive particulate fractions at fjord heads. The dataset is used to examine the benthic cycling of the two nutrients at Patagonian fjord heads...

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...

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,...

Rhesus macaque cone ratio heritability

Rachel A. Munds, Eve Cooper, Mareike C. Janiak, Linh Gia Lam, Alex DeCasien, Sam Baumann Surratt, Mike Montague, Melween Martinez, Shoji Kawamura, James P. Higham & Amanda D. Melin
A defining feature of catarrhine primates is uniform trichromacy – the ability to distinguish red (long; L), green (medium; M), and blue (short; S) wavelengths of light. While the tuning of photoreceptors is conserved, the ratio of L:M cones in the retina is variable within and between species, with human cone ratios differing from other catarrhines. Yet, the sources and structure of variation in cone ratios are poorly understood, precluding a broader understanding of color...

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...

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...

Trends in Social Mobility in Post-Revolution China (LIEPP Working Paper, n°126)

Yu Xie, Dong HAO, Zhou Xiang & Xi Song
In this paper, we study long-term trends in social mobility in the People's Republic of China since its inception in 1949, with 2 operationalizations: (1) intergenerational occupational mobility, and (2) intergenerational educational mobility. We draw on an accumulation of administrative and survey data and provide comparable estimates of these measures for birth cohorts born after 1945. To help interpret the results, we compare trends in China to those in the US for the same birth...

Data from: Parallel processing in speech perception with local and global representations of linguistic context

Christian Brodbeck, Shohini Bhattasali, Aura A. L. Cruz Heredia, Philip Resnik, Jonathan Z. Simon & Ellen Lau
Speech processing is highly incremental. It is widely accepted that human listeners continuously use the linguistic context to anticipate upcoming concepts, words, and phonemes. However, previous evidence supports two seemingly contradictory models of how a predictive context is integrated with the bottom-up sensory input: Classic psycholinguistic paradigms suggest a two-stage process, in which acoustic input initially leads to local, context-independent representations, which are then quickly integrated with contextual constraints. This contrasts with the view that...

Predicting spatio-temporal population patterns of Borrelia burgdorferi, the Lyme disease pathogen

Tam Tran, Melissa A. Prusinski, Jennifer L. White, Richard C. Falco, John Kokas, Vanessa Vinci, Wayne K. Gall, Keith J. Tober, Jamie Haight, JoAnne Oliver, Lee Ann Sporn, Lisa Meehan, Elyse Banker, P. Bryon Backenson, Shane T. Jensen & Dustin Brisson
The causative bacterium of Lyme disease, Borrelia burgdorferi, expanded from an undetected human pathogen into the etiologic agent of the most common vector-borne disease in the United States over the last several decades. Systematic field collections of the tick vector reveal increases in the geographic range and population size of B. burgdorferi that coincided with increases in human Lyme disease incidence across New York State. Here we investigate the impact of environmental features on the...

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  • 2022

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  • University of Pennsylvania
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