415 Works

Data from: Adaptive dynamics of cuticular hydrocarbons in Drosophila

Subhash Rajpurohit, Robert Hanus, Vladimir Vrkoslav, Emily L. Behrman, Alan O. Bergland, Dmitri Petrov, Josef Cvacka & Paul S. Schmidt
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore,...

Data from: The magnitude of ivacaftor effects on fluid secretion via R117H-CFTR channels: human in vivo measurements

Jessica E. Char, Colleen Dunn, Zoe Davies, Carlos Milla, Richard B. Moss & Jeffrey J. Wine
We optically measured effects of orally available ivacaftor (Kalydeco®) on sweat rates of identified glands in 3 R117H subjects, each having a unique set of additional mutations, and compared them with 5 healthy control subjects tested contemporaneously. We injected β-adrenergic agonists intradermally to stimulate CFTR-dependent ‘C-sweat’ and methacholine to stimulate ‘M-sweat’, which persists in CF subjects. We focused on an R117H-7T/F508del subject who produced quantifiable C-sweat off ivacaftor and was available for 1 blinded, 3...

Data from: Characteristics and outcomes of women utilizing emergency medical services for third-trimester pregnancy-related complaints in India: a prospective observational study

Matthew C. Strehlow, Jennifer A. Newberry, Corey B. Bills, Hyeyoun Min, Ann E. Evensen, Lawrence Leeman, Elizabeth A. Pirrotta, G. V. Ramana Rao & S. V. Mahadevan
Objectives: Characterize the demographics, management, and outcomes of obstetric patients transported by emergency medical services (EMS). Design: Prospective observational study. Setting: Five Indian states utilizing a centralized EMS agency that transported 3.1 million pregnant women in 2014. Participants: This study enrolled a convenience sample of 1684 women in third trimester of pregnancy calling with a “pregnancy-related” complaint for free-of-charge ambulance transport. Calls were deemed “pregnancy-related” if categorized by EMS dispatchers as “pregnancy”, “childbirth”, “miscarriage”, or...

Data from: Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies

Alison Ravenscraft, Michelle Berry, Tobin Hammer, Kabir Peay & Carol Boggs
The relationship between animals and their gut flora is simultaneously one of the most common and most complex symbioses on Earth. Despite its ubiquity, our understanding of this invisible but often critical relationship is still in its infancy. We employed adult Neotropical butterflies as a study system to ask three questions: First, how does gut microbial community composition vary across host individuals, species and dietary guilds? Second, how do gut microbiota compare to food microbial...

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

Beth Morrison, Berry Brosi & Rodolfo Dirzo
Within ecological communities, species engage in myriad interaction types, yet empirical examples of hybrid species interaction networks composed of multiple types of interactions are still scarce. A key knowledge gap is understanding how the structure and stability of such hybrid networks are affected by anthropogenic disturbance. Using 15,169 interaction observations, we constructed 16 hybrid herbivore-plant-pollinator networks along an agricultural intensification gradient to explore changes in network structure and robustness to local extinctions. We found that...

Frequent burning causes large losses of carbon from deep soil layers in a temperate savanna

Adam Francis Pellegrini, Kendra K. McLauchlan, Sarah E. Hobbie, Michelle C. Mack, Abbey L. Marcotte, David M. Nelson, Steven Perakis, Peter B. Reich & Kyle Whittinghill
1. Fire activity is changing dramatically across the globe, with uncertain effects on ecosystem processes, especially belowground. Fire‐driven losses of soil carbon (C) are often assumed to occur primarily in the upper soil layers because the repeated combustion of aboveground biomass limits organic matter inputs into surface soil. However, C losses from deeper soil may occur if frequent burning reduces root biomass inputs of C into deep soil layers or stimulates losses of C via...

Data from: ClinicNet: machine learning for personalized order set recommendations

Jonathan Wang, Delaney Sullivan, Alex Wells & Jonathan Chen
Objective This study assesses whether neural networks trained on electronic health record (EHR) data can anticipate what individual clinical orders and existing institutional order set templates clinicians will use more accurately than existing decision support tools. Materials and Methods We process 57,624 patients-worth of clinical event EHR data from 2008-2014. We train a feed-forward neural network (ClinicNet) and logistic regression applied to the traditional problem structure of predicting individual clinical items as well as our...

Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function

Pagé Goddard, Kevin Keys, Angel Mak, Eunice Lee, Amy Liu, Lesly-Anne Samedy-Bates, Oona Risse-Adams, Maria Contreras, Jennifer Elhawary, Donglei Hu, Sam Oh, Sandra Salazar, Celeste Eng, Blanca Himes, Marquitta White & Esteban Burchard
Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung...

Data set for 'Lunge filter feeding biomechanics constrain rorqual foraging ecology across scale'...

Shirel Rachel Kahane-Rapport
Fundamental scaling relationships influence the physiology of vital rates, which in turn shape the ecology and evolution of organisms. For diving mammals, benefits conferred by large body size include reduced transport costs and enhanced breath-holding capacity, thereby increasing overall foraging efficiency. Rorqual whales feed by engulfing a large mass of prey-laden water at high speed and filter it through baleen plates. However, as engulfment capacity increases with body length across species (Engulfment Volume ∝ Body...

Contrasting fungal responses to wildfire across different ecosystem types

Gabriel Smith, Lucy Edy & Kabir Peay
We took topsoil samples in burned and unburned areas across two California ecosystem types (Sonoma, California, United States) with differing fire ecologies in the immediate aftermath of a damaging wildfire in 2017. From our soil samples, we extracted DNA, amplified and sequenced fungal communities, and also measured chemistry (C%, N% and pH). Soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. The latter are more strongly altered compositionally by...

Data for: Successful management of invasive rats across a fragmented landscape

Erin Rankin, Sarah Barney, Devin Leopold, Kainana Francisco, David Flaspohler, Tad Fukami, Christian Giardina, Daniel Gruner, Jessie Knowlton & William Pitt
This dataset is from the manuscript "Successful management of invasive rats across a fragmented landscape" and provides the details on snap trap and tracking card data in a broadscale rat removal effort 2011-2015 in the Upper Waiakea Forest Reserve on the Island of Hawai‘i. It describes the successful trapping efforts as well as long term tracking data, which allow us to describe patterns of habitat use of non-native vertebrate species in these naturally fragmented forests...

Land use impacts on parasitic infection: A cross-sectional epidemiological study on the role of irrigated agriculture in schistosome infection in a dammed landscape

Andrea Lund, David Rehkopf, Susanne Sokolow, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Gilles Riveau, Giulio De Leo & David Lopez-Carr
Background: Water resources development promotes agricultural expansion and food security. But are these benefits offset by increased infectious disease risk? Dam construction on the Senegal River in 1986 was followed by agricultural expansion and increased transmission of human schistosomes. Yet the mechanisms linking these processes at the individual and household levels remain unclear. We investigated the association between household land use and schistosome infection in children. Methods: We analyzed cross-sectional household survey data (n =...

Data from: Reverse diel vertical movements of oceanic manta rays off the northern coast of Peru and implications for conservation

Samantha Andrzejaczek, Robert Schallert, Kerstin Forsberg, Natalie Arnoldi, Mariano Cabanillas, Wilmer Purizaca & Barbara Block
An understanding of the vertical movements of elasmobranchs across their range is crucial to defining critical habitat use, its overlap with anthropogenic activities, and subsequently managing such interactions. In this study, satellite telemetry was used to investigate the vertical habitat use of three oceanic manta rays (Mobula birostris) tagged on the northern coast of Peru. All three oceanic mantas exhibited patterns of reverse diel vertical migration, where vertical movements were significantly deeper at night than...

Data from: Gene expression plasticity and desert adaptation in house mice

Noelle Bittner, Katya Mack & Michael Nachman
Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied evolved and plastic responses to water-stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments and measured gene expression and organismal phenotypes under control and water-stressed conditions. After many generations in the lab, desert mice consumed significantly less water...

Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis

Nalin Ratnayeke, Mingyu Chung & Tobias Meyer
A fundamental concept in eukaryotic DNA replication is the temporal separation of G1 origin licensing from S phase origin firing. Re-replication and genome instability ensue if licensing occurs after DNA synthesis has started. In humans and other vertebrates, the E3 ubiquitin ligase CRL4Cdt2 starts to degrade the licensing factor Cdt1 after origins fire, raising the question of how cells prevent re-replication in early S phase. Here, using quantitative microscopy, we show that Cdt1 inhibits DNA...

Data for: Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

Ming-Fu Lin, Narendra Singh, Shujia Liang, Mianzhen Mo, Joao Pedro Figueira Nunes, Kathryn Ledbetter, Jie Yang, Michael Kozina, Stephen Weathersby, Xiaozhe Shen, Amy Cordones, Thomas Wolf, Sri Chaitanya Das Pemmaraju, Matthias Ihme & Xijie Wang
The radiolysis of water is ubiquitous in nature and plays a critical role in numerous biochemical and technological applications. Although the elementary reaction pathways for the ionized water have been studied, the short-lived intermediate complex and structural dynamic response after the proton transfer reaction remain poorly understood. Using liquid-phase ultrafast electron diffraction technique to measure the intermolecular O··O and O··H bonds, we captured the short-lived radical-cation complex OH(H3O+) that was formed within 140 femtoseconds through...

Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging

John Hickey
We performed CODEX (co-detection by indexing) multiplexed imaging on four sections of the human colon (ascending, transverse, descending, and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies. Subsequently images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), and single cell segmentation. Output of this process was a dataframe of nearly 130,000 cells with fluorescence values quantified from each marker. We used this dataframe...

Projected climate risk of aquatic food system benefits

Michelle Tigchelaar, William Cheung, Essam Mohammed, Michael Phillips, Hanna Payne, Elizabeth Selig, Colette Wabnitz, Muhammed Oyinlola, Thomas Frölicher, Jessica Gephart, Christopher Golden, Edward Allison, Abigail Bennett, Ling Cao, Jessica Fanzo, Benjamin Halpern, Fiorenza Micheli, Rosamond Naylor, Rashid Sumaila, Alessandro Tagliabue & Max Troell
Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and culture of billions of people worldwide – but climate-related hazards may compromise their ability to provide these benefits. This analysis estimates national-level aquatic food system climate risk using a fuzzy logic modeling approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes, and vulnerability to losing those contributions....

Growth rates of populations evolved and assayed at two temperatures for 6500 generations

Jason Tarkington & Rebecca Zufall
Evolutionary biologists have long sought to understand what factors affect the repeatability of adaptive outcomes. To better understand the role of temperature in determining the repeatability of adaptive trajectories, we evolved populations of different genotypes of the ciliate Tetrahymena thermophila at low and high temperatures and followed changes in growth rate over 6,500 generations. As expected, growth rate increased with a decelerating rate for all populations; however, there were differences in the patterns of evolution...

Quantum mechanical double slit for molecular scattering

Haowen Zhou, William E. Perreault, Nandini Mukherjee & Richard N. Zare
Interference observed in a double-slit experiment most conclusively demonstrates the wave properties of particles. We construct a quantum mechanical double-slit interferometer by rovibrationally exciting D2 (v=2, j=2) molecules in a biaxial state using Stark-induced adiabatic Raman passage. In D2(v=2, j=2)→D2(v=2, j'=0) rotational relaxation via a cold collision with ground state He, the entangled bond axis orientations in the biaxial state act as two slits generating two indistinguishable quantum mechanical pathways connecting initial and final states...

Data from: Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance

Danielle Claar, Jamie McDevitt-Irwin, Melissa Garren, Rebecca Vega Thurber, Ruth Gates & Julia Baum
Coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae spp.) are both vitally important for the biological function of corals. Yet little is known about their co-occurrence within corals, how their diversity varies across coral species, or how they are impacted by anthropogenic disturbances. Here, we sampled coral colonies (n = 472) from seven species, encompassing a range of life history traits, across a gradient of chronic human disturbance (n = 11 sites on Kiritimati (Christmas) atoll) in...

Decrypting cryptic crosswords: Semantically complex wordplay puzzles as a target for NLP

Joshua Rozner, Christopher Potts & Kyle Mahowald
Cryptic crosswords, the dominant crossword variety in the UK, are a promising target for advancing NLP systems that seek to process semantically complex, highly compositional language. Cryptic clues read like fluent natural language but are adversarially composed of two parts: a definition and a wordplay cipher requiring character-level manipulations. Expert humans use creative intelligence to solve cryptics, flexibly combining linguistic, world, and domain knowledge. In this paper, we make two main contributions. First, we present...

Macrophage-derived IL-6 trans-signaling as a novel target in the pathogenesis of bronchopulmonary dysplasia (RNA-seq-P14-HYXvsNOX)

Dharmesh Hirani & Cristina Alvira
Rationale: Premature infants exposed to oxygen are at risk for bronchopulmonary dysplasia (BPD), which is characterized by lung growth arrest. Inflammation is important, but the mechanisms remain elusive. Here, we investigated inflammatory pathways and therapeutic targets in severe clinical and experimental BPD. Methods and Results: First, transcriptomic analysis with in-silico cellular deconvolution identified a lung-intrinsic M1-like-driven cytokine pattern in newborn mice after hyperoxia. These findings were confirmed by gene expression of macrophage-regulating chemokines (Ccl2, Ccl7,...

Fine particulate matter and neuroanatomic risk for Alzheimer’s disease in older women

Diana Younan, Xinhui Wang, Ramon Casanova, Ryan Barnard, Sarah Gaussoin, Santiago Saldana, Andrew Petkus, Daniel Beavers, Susan Resnick, JoAnn Manson, Marc Serre, William Vizuete, Victor Henderson, Bonnie Sachs, Joel Salinas, Margaret Gatz, Mark Espeland, Helena Chui, Sally Shumaker, Stephen Rapp & Jiu-Chiuan Chen
Objective: To examine whether late-life exposure to PM2.5 (particulate matter with aerodynamic diameters <2.5-µm) contributes to progressive brain atrophy predictive of Alzheimer’s disease (AD) using a community-dwelling cohort of women (aged 71-89) with up to two brain MRI scans (MRI-1: 2005-6; MRI-2: 2010-11). Methods: AD pattern similarity (AD-PS) scores, developed by supervised machine learning and validated with MRI data from the AD Neuroimaging Initiative, was used to capture high-dimensional gray matter atrophy in brain areas...

Reproduction Materials for: Anthropogenic Climate Change Has Slowed Global Agricultural Productivity Growth

Ariel Ortiz-Bobea, Toby R. Ault, Carlos M. Carrillo, Robert G. Chambers & David B. Lobell
Agricultural research has fostered productivity growth, but the historical influence of anthropogenic climate change on that growth has not been quantified. We develop a robust econometric model of weather effects on global agricultural total factor productivity (TFP) and combine this model with counterfactual climate scenarios to evaluate impacts of past climate trends on TFP. Our baseline model indicates that anthropogenic climate change has reduced global agricultural TFP by about 21% since 1961, a slowdown that...

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  • Stanford University
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