Digital Commons Network^™

Editorial: Ethylene’S Role In Plant Mineral Nutrition, Francisco J. Romera, Aaron P. Smith, Rafael Pérez-Vicente

Faculty Publications

No abstract provided.

Empprior: Using Outside Empirical Data To Inform Branch-Length Priors For Bayesian Phylogenetics, John J. Andersen, Bradley J. Nelson, Jeremy M. Brown

Faculty Publications

© 2016 The Author(s). Background: Branch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informative and lead to branch- and tree-length estimates that are unreasonable. Alternatively, priors may be uninformative, but lead to diffuse posterior estimates. Despite the widespread availability of relevant datasets from other groups, biologists rarely leverage outside information to specify branch-length priors that are specific to the analysis they are conducting. Results: We developed the software package EmpPrior to facilitate the collection and incorporation of relevant, outside information when setting branch-length …

Local Versus Generalized Phenotypes In Two Sympatric Aurelia Species: Understanding Jellyfish Ecology Using Genetics And Morphometrics, Luciano M. Chiaverano, Keith Bayha, William M. Graham

Faculty Publications

For individuals living in environmentally heterogeneous environments, a key component for adaptation and persistence is the extent of phenotypic differentiation in response to local environmental conditions. In order to determine the extent of environmentally induced morphological variation in a natural population distributed along environmental gradients, it is necessary to account for potential genetic differences contributing to morphological differentiation. In this study, we set out to quantify geographic morphological variation in the moon jellyfish Aurelia exposed at the extremes of a latitudinal environmental gradient in the Gulf of Mexico (GoM). We used morphological data based on 28 characters, and genetic data …

Oviposition And Sex Ratio Of The Redbanded Stink Bug, Piezodorous Guildinii, In Soybean, Joshua H. Temple, Jeffrey A. Davis, Jarrod T. Hardke, Paul P. Price, B. Rogers Leonard

Faculty Publications

Redbanded stink bug, Piezodorus guildinii (Westwood), is a significant soybean pest across the mid-south region of the United States. The objectives of these studies were to characterize: (1) redbanded stink bug oviposition in relationship to soybean maturity group (MG), plant structure, crop phenology, and vertical distribution within the plant canopy; and (2) redbanded stink bug adult sex ratios in relationship to soybean phenology. A total of 5645 redbanded stink bug eggs in 421 egg masses (clusters) were field collected from naturally-occurring populations in MG IV and V soybean over a three year period (2009 to 2011). The mean number of …

Crystal Structure Of Di-Aqua-Bis-(7-Di-Ehtyl-Amino-3-Formyl-2-Oxo-2h-Chromen-4-Olato-Κ(2) O (3), O (4))Zinc(Ii) Dimethyl Sulfoxide Disolvate, Aaron B. Davis, Frank R. Fronczek, Karl J. Wallace

Faculty Publications

The structure of the title coordination complex, [Zn(C₁₄H₁₄NO₄)₂(H₂O)₂]·2C₂H₆OS, shows that the Zn^II cation adopts an octa­hedral geometry and lies on an inversion center. Two organic ligands occupy the equatorial positions of the coordination sphere, forming a chelate ring motif via the O atom on the formyl group and another O atom of the carbonyl group (a pseudo--diketone motif). Two water mol­ecules occupy the remaining coordination sites of the Zn^II cation in the axial positions. The water mol­ecules are each hydrogen bonded to …

A Cross-Species Bi-Clustering Approach To Identifying Conserved Co-Regulated Genes, Jiangwen Sun, Zongliang Jiang, Xiuchun Tian, Jinbo Bi

Faculty Publications

© 2016 The Author 2016. Published by Oxford University Press. Motivation: A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified …

Performance And Cross-Crop Resistance Of Cry1f-Maize Selected Spodoptera Frugiperda On Transgenic Bt Cotton: Implications For Resistance Management, Fei Yang, David L. Kerns, Sebe Brown, Ryan Kurtz, Tim Dennehy, Bo Braxton, Graham Head, Fangneng Huang

Faculty Publications

Transgenic crops producing Bacillus thuringiensis (Bt) proteins have become a primary tool in pest management. Due to the intensive use of Bt crops, resistance of the fall armyworm, Spodoptera frugiperda, to Cry1F maize has occurred in Puerto Rico, Brazil, and some areas of the southeastern U.S. The sustainability of Bt crops faces a great challenge because the Cry1F-maize resistant S. frugiperda may also infest other Bt crops in multiple cropping ecosystems. Here we examined the survival and plant injury of a S. frugiperda population selected with Cry1F maize on three single-gene and five pyramided Bt cotton products. Larvae of Cry1F-susceptible …

Use Of Protein Cross-Linking And Radiolytic Labeling To Elucidate The Structure Of Psbo Within Higher-Plant Photosystem Ii, Manjula P. Mummadisetti, Laurie K. Frankel, Henry D. Bellamy, Larry Sallans, Jost S. Goettert, Michal Brylinski, Terry M. Bricker

Faculty Publications

© 2016 American Chemical Society. We have used protein cross-linking with the zero-length cross-linker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, and radiolytic footprinting coupled with high-resolution tandem mass spectrometry, to examine the structure of higher-plant PsbO when it is bound to Photosystem II. Twenty intramolecular cross-linked residue pairs were identified. On the basis of this cross-linking data, spinach PsbO was modeled using the Thermosynechococcus vulcanus PsbO structure as a template, with the cross-linking distance constraints incorporated using the MODELLER program. Our model of higher-plant PsbO identifies several differences between the spinach and cyanobacterial proteins. The N-terminal region is particularly interesting, as this region has …

Use Of Protein Cross-Linking And Radiolytic Labeling To Elucidate The Structure Of Psbo Within Higher-Plant Photosystem Ii, Manjula P. Mummadisetti, Laurie K. Frankel, Henry D. Bellamy, Larry Sallans, Jost S. Goettert, Michal Brylinski, Terry M. Bricker

Faculty Publications

© 2016 American Chemical Society. We have used protein cross-linking with the zero-length cross-linker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, and radiolytic footprinting coupled with high-resolution tandem mass spectrometry, to examine the structure of higher-plant PsbO when it is bound to Photosystem II. Twenty intramolecular cross-linked residue pairs were identified. On the basis of this cross-linking data, spinach PsbO was modeled using the Thermosynechococcus vulcanus PsbO structure as a template, with the cross-linking distance constraints incorporated using the MODELLER program. Our model of higher-plant PsbO identifies several differences between the spinach and cyanobacterial proteins. The N-terminal region is particularly interesting, as this region has …

Sustained Deposition Of Contaminants From The Deepwater Horizon Spill, Beizhan Yan, Uta Passow, Jeffrey P. Chanton, Eva-Maria Nöthig, Vernon Asper, Julia Sweet, Masha Pitiranggon, Arne Diercks, Dorothy Pak

Faculty Publications

The 2010 Deepwater Horizon oil spill resulted in 1.6–2.6 × 10¹⁰ grams of petrocarbon accumulation on the seafloor. Data from a deep sediment trap, deployed 7.4 km SW of the well between August 2010 and October 2011, disclose that the sinking of spill-associated substances, mediated by marine particles, especially phytoplankton, continued at least 5 mo following the capping of the well. In August/September 2010, an exceptionally large diatom bloom sedimentation event coincided with elevated sinking rates of oil-derived hydrocarbons, black carbon, and two key components of drilling mud, barium and olefins. Barium remained in the water column for months …

Cellulose Structural Polymorphism In Plant Primary Cell Walls Investigated By High-Field 2d Solid-State Nmr Spectroscopy And Density Functional Theory Calculations, Tuo Wang, Hui Yang, James D. Kubicki, Mei Hong

Faculty Publications

© 2016 American Chemical Society. The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) …

Sources And Transformations Of Dissolved Lignin Phenols And Chromophoric Dissolved Organic Matter In Otsuchi Bay, Japan, Chia-Jung Lu, Ronald Benner, Cedric Fichot, Hideki Fukuda, Youhei Yamashita, Hiroshi Ogawa

Faculty Publications

Dissolved lignin phenols and optical properties of dissolved organic matter (DOM) were measured to investigate the sources and transformations of terrigenous DOM (tDOM) in Otsuchi Bay, Japan. Three rivers discharge into the bay, and relatively high values of syringyl:vanillyl phenols (0.73 ± 0.07) and cinnamyl:vanillyl phenols (0.33 ± 0.10) indicated large contributions of non-woody angiosperm tissues to lignin and tDOM. The physical mixing of river and seawater played an important role in controlling the concentrations and distributions of lignin phenols and chromophoric DOM (CDOM) optical properties in the bay. Lignin phenol concentrations and the CDOM absorption coefficient at 350 nm, …

A Compilation Of Global Bio-Optical In Situ Data For Ocean-Colour Satellite Applications, André Valente, Shubba Sathyendranath, Vanda Brotas, Steve Groom, Michael Grant, Malcolm Taberner, David Antoine, Robert A. Arnone Prof, William M. Balch, Kathryn Baker, Ray Barlow, Simon Bélanger, Jean-François Berthon, Sükrü Beşiktepe, Vittorio Brando, Elisabetta Canuti, Francisco Chavez, Hervé Claustre, Richard Crout, Robert Frounin, Carlos García-Soto, Stuart W. Gibb, Richard Gould, Stanford Hooker, Mati Kahru, Holger Klein, Susanne Kratzer, Hubert Loisel, David Mckee, Brian G. Mitchell, Tiffany Moisan, Frank Muller-Karger, Leonie O'Dowd, Michael Ondrusek, Alex J. Poulton, Michel Repecaud, Timothy Smythe, Heidi M. Sosik, Michael Twardowski, Kenneth Voss, Jeremy Werdell, Marcel Wernand, Giuseppe Zibordi

Faculty Publications

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet …

Aflatoxin-Exposure Of Vibrio Gazogenes As A Novel System For The Generation Of Aflatoxin Synthesis Inhibitors, Phani M. Gummadidala, Yung Pin Chen, Kevin R. Beauchesne, Kristen P. Miller, Chandrani Mitra, Michelle Velez-Martinez, Peter D. R. Moeller, John L. Ferry, Alan W. Decho, Anindya Chanda

Faculty Publications

Aflatoxin is a mycotoxin and a secondary metabolite, and the most potent known liver carcinogen that contaminates several important crops, and represents a significant threat to public health and the economy. Available approaches reported thus far have been insufficient to eliminate this threat, and therefore provide the rational to explore novel methods for preventing aflatoxin accumulation in the environment. Many terrestrial plants and microbes that share ecological niches and encounter the aflatoxin producers have the ability to synthesize compounds that inhibit aflatoxin synthesis. However, reports of natural aflatoxin inhibitors from marine ecosystem components that do not share ecological niches with …

Integration Of General Education Into The Senior Capstone Class In Engineering, Patricia Backer, Laura Sullivan-Green

Faculty Publications

Over the past few years, San Jose State University (SJSU) has mandated that all of the undergraduate degree programs including engineering degrees be set at 120 units. With the existing number of units for the BS engineering degrees, this mandatory requirement has led to new innovations in General Education (GE) at SJSU. We have created a two-course sequence to support the integration of upper division General Education into the engineering major. Advanced GE at SJSU is designed to help students become integrated thinkers who can see connections between and among a variety of concepts and ideas. In the College of …

Assessment Of Tick Antioxidant Responses To Exogenous Oxidative Stressors And Insight Into The Role Of Catalase In The Reproductive Fitness Of The Gulf Coast Tick, Amblyomma Maculatum, D. Kumar, K. Budachetri, V.C. Meyers, Shahid Karim

Faculty Publications

As obligate blood‐sucking ectoparasites, to avoid tissue damage, ticks must neutralize the reactive oxygen species (ROS) generated from uptake and digestion of a bloodmeal. Consequently, ticks utilize a battery of antioxidant molecules, including catalase (CAT), an enzyme that converts hydrogen peroxide (H₂O₂) into water and oxygen. Here, we investigated the tick antioxidant machinery by exogenous injection of sublethal doses of H₂O₂ or paraquat. The relative transcript levels of selected Amblyomma maculatum antioxidant targets in tissues were determined by quantitative reverse transcriptase PCR following treatment. The results showed 2–16‐fold increases in target antioxidant gene …

Bridging The Justice Gap In Family Law: Repurposing Federal Iv-D Funding To Expand Community-Based Legal And Social Services For Parents, Lisa V. Martin, Stacy Brustin

Faculty Publications

Parents in family court overwhelmingly proceed pro se; however, in child support courtrooms, government attorneys representing the state child support agency frequently play a pivotal role. These attorneys represent the state’s ostensible interests in ensuring that children are financially supported and in preventing welfare dependence; they do not represent individual parents. The outcomes of child support proceedings have profound, long-term constitutional and financial implications for parents, yet litigants rarely understand their rights or the role of the government.

Originally, the goal of state child support enforcement efforts was to recapture the costs of welfare expenditures. In 1990, two-thirds of cases …

A Conceptual Framework For Graduate Teaching Assistant Professional Development Evaluation And Research, Todd D. Reeves, Gili Marbach-Ad, Kristen R. Miller, Judith Ridgway, Grant E. Gardner, Elisabeth E. Schussler, E. William Wischusen

Faculty Publications

© 2016 T. D. Reeves et al. Biology graduate teaching assistants (GTAs) are significant contributors to the educational mission of universities, particularly in introductory courses, yet there is a lack of empirical data on how to best prepare them for their teaching roles. This essay proposes a conceptual framework for biology GTA teaching professional development (TPD) program evaluation and research with three overarching variable categories for consideration: outcome variables, contextual variables, and moderating variables. The framework’s outcome variables go beyond GTA satisfaction and instead position GTA cognition, GTA teaching practice, and undergraduate learning outcomes as the foci of GTA TPD …

Transcriptional Truncation Of The Long Coding Imprinted Gene Usp29, Hongzhi He, An Ye, Joomyeong Kim

Faculty Publications

© 2016 He et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Usp29 (Ubiquitin-specific protease 29) is a paternally expressed gene located upstream of another imprinted gene Peg3. In the current study, the transcription of this long coding gene spanning a 250-kb genomic distance was truncated using a knockin allele. According to the results, paternal transmission of the mutant allele resulted in reduced body and litter sizes whereas the maternal transmission caused no …

Persistence Of Neighborhood Demographic Influences Over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation In Tropical Forests, Christopher Wills, Kyle E. Harms, Thorsten Wiegand, Ruwan Punchi-Manage, Gregory S. Gilbert, David Erickson, W. John Kress, Stephen P. Hubbell, C. V.Savitri Gunatilleke, I. A.U.Nimal Gunatilleke

Faculty Publications

© 2016, Public Library of Science. All rights reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an …

The Abiotic And Biotic Drivers Of Rapid Diversification In Andean Bellflowers (Campanulaceae), Laura P. Lagomarsino, Fabien L. Condamine, Alexandre Antonelli, Andreas Mulch, Charles C. Davis

Faculty Publications

© 2016 New Phytologist Trust. The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are …

Hepatic Autophagy Contributes To The Metabolic Response To Dietary Protein Restriction, Tara M. Henagan, Thomas Laeger, Alexandra M. Navard, Diana Albarado, Robert C. Noland, Krisztian Stadler, Carrie M. Elks, David Burk, Christopher D. Morrison

Faculty Publications

© 2016 Elsevier Inc. All rights reserved. Autophagy is an essential cellular response which acts to release stored cellular substrates during nutrient restriction, and particularly plays a key role in the cellular response to amino acid restriction. However, there has been limited work testing whether the induction of autophagy is required for adaptive metabolic responses to dietary protein restriction in the whole animal. Here, we found that moderate dietary protein restriction led to a series of metabolic changes in rats, including increases in food intake and energy expenditure, the downregulation of hepatic fatty acid synthesis gene expression and reduced markers …

The Raf-Like Kinase Ilk1 And The High Affinity K+ Transporter Hak5 Are Required For Innate Immunity And Abiotic Stress Response, Elizabeth K. Brauer, Nagib Ahsan, Renee Dale, Naohiro Kato, Alison E. Coluccio, Miguel A. Piñeros, Leon V. Kochian, Jay J. Thelen, Sorina C. Popescu

Faculty Publications

© 2016 American Society of Plant Biologists. All rights reserved. Plant perception of pathogen-associated molecular patterns (PAMPs) and other environmental stresses trigger transient ion fluxes at the plasma membrane. Apart from the role of Ca2+ uptake in signaling, the regulation and significance of PAMPinduced ion fluxes in immunity remain unknown. We characterized the functions of INTEGRIN-LINKED KINASE1 (ILK1) that encodes a Raf-like MAP2K kinase with functions insufficiently understood in plants. Analysis of ILK1 mutants impaired in the expression or kinase activity revealed that ILK1 contributes to plant defense to bacterial pathogens, osmotic stress sensitivity, and cellular responses and total ion …

Mechanisms Of Animal Diapause: Recent Developments From Nematodes, Crustaceans, Insects, And Fish, Steven C. Hand, David L. Denlinger, Jason E. Podrabsky, Richard Roy

Faculty Publications

© 2016 the American Physiological Society. Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, and the diapause state may or may not be associated with some degree of metabolic depression. In this review, we will evaluate current advancements in our understanding of the mechanisms responsible for the remarkable phenotype, as well as environmental cues that signal entry and termination of the state. The developmental stage at which diapause occurs dictates and constrains the mechanisms governing diapause. Considerable progress has been made in …

The Abiotic And Biotic Drivers Of Rapid Diversification In Andean Bellflowers (Campanulaceae), Laura P. Lagomarsino, Fabien L. Condamine, Alexandre Antonelli, Andreas Mulch, Charles C. Davis

Faculty Publications

© 2016 New Phytologist Trust. The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are …

Addressing Emerging Risks: Scientific And Regulatory Challenges Associated With Environmentally Persistent Free Radicals, Tammy R. Dugas, Slawomir Lomnicki, Stephania A. Cormier, Barry Dellinger, Margaret Reams

Faculty Publications

© 2016 by the authors; licensee MDPI, Basel, Switzerland. Airborne fine and ultrafine particulate matter (PM) are often generated through widely-used thermal processes such as the combustion of fuels or the thermal decomposition of waste. Residents near Superfund sites are exposed to PM through the inhalation of windblown dust, ingestion of soil and sediments, and inhalation of emissions from the on-site thermal treatment of contaminated soils. Epidemiological evidence supports a link between exposure to airborne PM and an increased risk of cardiovascular and pulmonary diseases. It is well-known that during combustion processes, incomplete combustion can lead to the production of …

Vector Species Richness Increases Haemorrhagic Disease Prevalence Through Functional Diversity Modulating The Duration Of Seasonal Transmission, Andrew W. Park, Christopher A. Cleveland, Tad A. Dallas, Joseph L. Corn

Faculty Publications

© Copyright Cambridge University Press 2015. SUMMARY Although many parasites are transmitted between hosts by a suite of arthropod vectors, the impact of vector biodiversity on parasite transmission is poorly understood. Positive relationships between host infection prevalence and vector species richness (SR) may operate through multiple mechanisms, including (i) increased vector abundance, (ii) a sampling effect in which species of high vectorial capacity are more likely to occur in species-rich communities, and (iii) functional diversity whereby communities comprised species with distinct phenologies may extend the duration of seasonal transmission. Teasing such mechanisms apart is impeded by a lack of appropriate …

A Generalized Reed Model With Application To Wildfire Risk In Even-Aged Southern United States Pine Plantations, Andres Susaeta, Douglas R. Carter, Sun Joseph Chang, Damian C. Adams

Faculty Publications

We develop a generalized Reed model to incorporate the risk of wildfires on optimal management of slash pine (Pinus elliotti var. elliotti) in the southern United States. Comparative static analyses are conducted to determine the impacts of the probability of increasing and constant wildfire risk as forest stand ages, and portion of stand that is salvageable following a wildfire, on slash pine harvest decisions. Our results reveal that increasing the current risk of wildfire damage would shorten the current optimal slash pine harvest age, while increasing the future risk of wildfire losses would lengthen the current optimal harvest age. We …

Cancer Stem-Like Cells Accumulated In Nickel-Induced Malignant Transformation, Lei Wang, Jia Fan, John Andrew Hitron, Young Ok Son, James T.F. Wise, Ram Vinod Roy, Donghern Kim, Jin Dai, Poyil Pratheeshkumar, Zhuo Zhang, Xianglin Shi

Faculty Publications

Nickel compounds are known as human carcinogens. Chronic environmental exposure to nickel is a worldwide health concern. Although the mechanisms of nickel-induced carcinogenesis are not well understood, recent studies suggest that stem cells/cancer stem cells are likely important targets. This study examines the role of cancer stem cells in nickelinduced cell transformation. The nontransformed human bronchial epithelial cell line (Beas-2B) was chronically exposed to nickel chloride for 12 months to induce cell transformation. Nickel induced Beas-2B cell transformation, and cancer stemlike cells were enriched in nickel-transformed cell (BNiT) population. The BNiT cancer stem-like cells demonstrated enhanced self-renewal and distinctive differentiation …

What Time Is It? Deep Learning Approaches For Circadian Rhythms, Forest Agostinelli, Nicholas Ceglia, Babak Shahbaba, Paolo Sassone-Corsi, Pierre Baldi

Faculty Publications

Motivation: Circadian rhythms date back to the origins of life, are found in virtually every species and every cell, and play fundamental roles in functions ranging from metabolism to cognition. Modern high-throughput technologies allow the measurement of concentrations of transcripts, metabolites and other species along the circadian cycle creating novel computational challenges and opportunities, including the problems of inferring whether a given species oscillate in circadian fashion or not, and inferring the time at which a set of measurements was taken.

Results: We first curate several large synthetic and biological time series datasets containing labels for both periodic and aperiodic …