33 Works

Data from: Climate-associated tundra thaw pond formation and range expansion of boreal zooplankton predators

Derek J. Taylor, Matthew J. Ballinger, Andrew S. Medeiros & Alexey A. Kotov
Most of the freshwater component of the Earth's surface is composed of shallow tundra ponds. These high latitude ecosystems have been exposed to a variety of abiotic disturbances associated with recent environmental change. However, the biological significance of these changes remains poorly understood. Here, we characterize the abiotic disturbance to the shallow tundra ponds of northwest Alaska. We used historical aerial imagery to determine that up to 53% of the sampled ponds have formed during...

Thermal plasticity of setae of the second limb of Daphnia

Derek Taylor & Keonho Kim
These data are associated with a study that tests the hypothesis of thermal plasticity in the rigid setae of the second limb of Daphnia. The data are body size and length measurements (mm) of three limb setae (limb 2; endite 2). The second seta is often called the "rigid" seta because it is heavily chitinized. In all, 300 specimens of Daphnia (including Daphnia umbra and Daphnia galeata) were dissected from four sets of clonal thermal...

Data from: The evolution of hominoid cranial diversity: a quantitative genetic approach

Lauren Schroeder & Noreen Von Cramon-Taubadel
Hominoid cranial evolution is characterized by substantial phenotypic diversity, yet the cause of this variability has rarely been explored. Quantitative genetic techniques for investigating evolutionary processes underlying morphological divergence are dependent on the availability of good ancestral models, a problem in hominoids where the fossil record is fragmentary and poorly understood. Here, we use a maximum likelihood approach based on a Brownian motion model of evolutionary change to estimate nested hypothetical ancestral forms from 15...

Masked language models directly encode linguistic uncertainty

Cassandra Jacobs, Ryan J. Hubbard & Kara D. Federmeier

Data from: Structure-function covariation with nonfeeding ecological variables influences evolution of feeding specialization in Carnivora

Jack Tseng & John J. Flynn
Skull shape convergence is pervasive among vertebrates. Although this is frequently inferred to indicate similar functional underpinnings, neither the specific structure-function linkages nor the selective environments in which the supposed functional adaptations arose are commonly identified and tested. We demonstrate that nonfeeding factors relating to sexual maturity and precipitation-related arboreality also can generate structure-function relationships in the skulls of carnivorans (dogs, cats, seals, and relatives) through covariation with masticatory performance. We estimated measures of masticatory...

Data from: Mlh3 mutations in baker's yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide

Najla Al-Sweel, Vandana Raghavan, Abhishek Dutta, V. P. Ajith, Luigi Di Vietro, Nabila Khondakar, Carol M. Manhart, Jennifer Surtees, K. T. Nishant, Eric Alani & Jennifer A. Surtees
Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in baker's yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45...

Data from: Enzyme architecture: modeling the operation of a hydrophobic clamp in catalysis by triosephosphate isomerase

Yashraj S. Kulkarni, Qinghua Liao, Dušan Petrovic, Dennis M. Krüger, Birgit Strodel, Tina L. Amyes, John P. Richard & Shina Caroline Lynn Kamerlin
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (I170 and L230), over the carboxylate side chain of E165. This is critical...

Data from: Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberley M. Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T. Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F. Shibata, Shuji Shigenobu … & Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient...

Data from: Feeding capability in the extinct giant Siamogale melilutra and comparative mandibular biomechanics of living Lutrinae

Z. Jack Tseng, Denise F. Su, Xiaoming Wang, Stuart C. White & Xueping Ji
At 50 kg in estimated weight, the extinct Siamogale melilutra is larger than all living otters, and ranks among the largest fossil otters. The biomechanical capability of S. melilutra jaws as related to their large size is unknown but crucial to reconstructing the species’ potentially unique ecological niche. Here we compare the mandibular biomechanics of S. melilutra using engineering-based performance measures against ten extant otter biomechanical models. Despite a wide range of feeding preferences from...

Data from: An integrated iterative annotation technique for easing neural network training in medical image analysis

Brendon Lutnick, Brandon Ginley, Darshana Govind, Sean D. McGarry, Peter S. LaViolette, Rabi Yacoub, Sanjay Jain, John E. Tomaszewski, Kuang-Yu Jen & Pinaki Sarder
Neural networks promise to bring robust, quantitative analysis to medical fields. However, their adoption is limited by the technicalities of training these networks and the required volume and quality of human-generated annotations. To address this gap in the field of pathology, we have created an intuitive interface for data annotation and the display of neural network predictions within a commonly used digital pathology whole-slide viewer. This strategy used a ‘human-in-the-loop’ to reduce the annotation burden....

Coregonus spp. opsin amplicon sequence alignments

Katherine Eaton & Trevor Krabbenhoft
Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were sequenced for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific...

Oak galls exhibit ant-dispersal convergent with myrmecochorous seeds

Robert Warren, Antoine Guiguet, Chloe Mokadam, John Tooker & Andrew Deans
Ants disperse oak galls of some cynipid wasp species similarly to how they disperse seeds with elaiosomes. We conducted choice assays in field and lab settings, with ant-dispersed seeds and wasp-induced galls found in ant nests and found that seed-dispersing ants retrieve these galls as they do myrmecochorous seeds. We also conducted manipulative experiments in which we removed the putative ant-attracting appendages (“kapéllos”) from galls and found ants are specifically attracted to kapéllos. Finally, we...

Landmarks and 3D scan data of Macaca fascicularis

Hyunwoo Jung, Evan Simons & Noreen Von Cramon-Taubadel
Objectives: Magnitudes of morphological integration may constrain or facilitate craniofacial shape variation. The aim of this study was to analyze how the magnitude of integration in the skull of Macaca fascicularis changes throughout ontogeny in relation to developmental and/or functional modules. Materials and Methods: Geometric morphometric methods were used to analyze the magnitude of integration in the macaque cranium and mandible in 80 juvenile and 40 adult M. fascicularis specimens. Integration scores in skull modules...

What Don't RNN Language Models Learn About Filler-Gap Dependencies?

Rui P. Chaves

Assessing the ability of Transformer-based Neural Models to represent structurally unbounded dependencies

Jillian K. Da Costa & Rui P. Chaves

Dual spring force couples yield multifunctionality and ultrafast, precision rotation in tiny biomechanical systems

S. N. Patek, Ryan St. Pierre, Greg Sutton, Suzanne Cox, Sarah Bergbreiter, Adam Summers & Chi-Yun Kuo
Small organisms use propulsive springs rather than muscles to repeatedly actuate high acceleration movements, even when constrained to tiny displacements and limited by inertial forces. Through integration of a large kinematic dataset, measurements of elastic recoil, energetic math modeling, and dynamic math modeling, we tested how trap-jaw ants (Odontomachus brunneus) utilize multiple elastic structures to develop ultrafast and precise mandible rotations at small scales. We found that O. brunneus develops torque on each mandible using...

Look at that! BERT can be easily distracted from paying attention to morphosyntax

Rui P. Chaves & Stephanie N. Richter

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)

Moisés Bernal, Daniel Yule, Wendylee Stott, Lori Evrard, Thomas Dowling & Trevor Krabbenhoft
Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex...

Intracranial aneurysm risk scores, hemodynamics and vessel wall enhancement values

Sricharan Veeturi
Vessel wall enhancement (VWE) in contrast-enhanced magnetic resonance imaging (MRI) is a potential biomarker for intracranial aneurysm (IA) risk stratification. In this study, we investigated the relationship between VWE features, risk metrics, morphology, and hemodynamics in 41 unruptured aneurysms. We reconstructed the IA geometries from MR angiography and mapped pituitary stalk-normalized MRI intensity on the aneurysm surface using an in-house tool. For each case, we calculated the maximum intensity (CRstalk) and IA risk (via size...

An early dog from Southeast Alaska supports a coastal route for the first dog migration into the Americas

Flavio Augusto Da Silva Coelho, Stephanie Gill, Crystal Tomlin, Timothy Heaton & Charlotte Lindqvist
The oldest confirmed remains of domestic dogs in North America are from mid-continent archeological sites dated ~9,900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs are unclear. Here, we present a complete mitochondrial genome of a dog from Southeast Alaska, dated to 10,150 ± 260 cal BP. We compared this high-coverage...

Data from: Using artificial intelligence classification of videos to examine the environmental, evolutionary and physiological constraints on provisioning behavior

Heather M. Williams & Robert L. DeLeon
The use of artificial intelligence (AI) technologies can revolutionize how we approach data collection and analysis in behavioral ecology. One such example is in provisioning behavior. Parents of altricial species are selected to provide parental care (such as food provisioning) for their offspring, but there is substantial variation in the level of this care. Provisioning rate may be determined environmentally, by the physiological ability of parents and needs of nestlings, or by evolutionary incentives. We...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Data from: The effects of experimental sleep apnea on cardiac and respiratory functions in 6 and 18 Month Old dystrophic mdx mice

Milind R. Chaudhari, James A. Fallavollita & Gaspar A. Farkas
Duchenne muscular dystrophy (DMD) is a fatal disease where over 90% of patients succumb to respiratory or cardiac failure. Sleep apnea and sleep disordered breathing (SDB) are noted in a plurality of DMD patients, and the resulting nocturnal episodic hypoxia (EH) cannot be ruled out as a contributing factor to cardiac and respiratory dysfunction. In this study, we investigated the impact of long-term episodic hypoxia, which mimics the cyclic hypoxia seen in sleep apnea, on...

Data from: Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high-latitudes

Jocelyn P Colella, Tian-Ying Lan, Stephan C Schuster, Sandra L Talbot, Joseph A Cook & Charlotte Lindqvist
At high-latitude, climatic shifts hypothetically drove episodes of divergence during isolation in glacial refugia, or ice-free pockets of land that enabled terrestrial species persistence. Upon glacial recession, populations can expand and often come into contact, resulting in admixture between previously isolated groups. To understand how recurrent periods of isolation and contact have impacted evolution at high latitudes, we investigated introgression in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two...

Healing with Poisons

Yan Liu
At first glance, medicine and poison might seem to be opposites. But in China’s formative era of pharmacy (200–800 CE), poisons were strategically deployed as healing agents to cure everything from chills to pains to epidemics. Healing with Poisons explores the ways physicians, religious devotees, court officials, and laypeople used powerful substances to both treat intractable illnesses and enhance life. It illustrates how the Chinese concept of du—a word carrying a core meaning of “potency”—led...

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