255 Works

Supplemental Material for Bruna et al., 2022

Tomáš Brůna, Rishi Aryal, Olga Dudchenko, Daniel James Sargent, Daniel Mead, Matteo Buti, Andrea Cavallini, Timo Hytönen, Javier Andrés, Melanie Pham, David Weisz, Flavia Mascagni, Gabriele Usai, Lucia Natali, Nahla Bassil, Gina E. Fernandez, Alexandre Lomsadze, Mitchell Armour, Bode Olukolu, Thomas Poorten, Caitlin Britton, Jahn Davik, Hamid Ashrafi, Erez Lieberman Aiden, Mark Borodovsky … & Margaret Worthington
Supplemental Material

Supplemental Material for Bruna et al., 2022

Tomáš Brůna, Rishi Aryal, Olga Dudchenko, Daniel James Sargent, Daniel Mead, Matteo Buti, Andrea Cavallini, Timo Hytönen, Javier Andrés, Melanie Pham, David Weisz, Flavia Mascagni, Gabriele Usai, Lucia Natali, Nahla Bassil, Gina E. Fernandez, Alexandre Lomsadze, Mitchell Armour, Bode Olukolu, Thomas Poorten, Caitlin Britton, Jahn Davik, Hamid Ashrafi, Erez Lieberman Aiden, Mark Borodovsky … & Margaret Worthington
Supplemental Material

Supplemental File 4- Replicate four data for array to F1 integrations

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing the array and F1 barcodes, counts, normalized frequencies, and delta frequency for replicate four.

Supplemental File 9- TARDIS Notebook #1

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
Notebook used for the HighSeq quality scoring, cleaning, demultiplexing, and trimming. Contains the python code used for the analysis of one individual worm from each of four TARDIS arrays (PX816, PX817, PX818 profiles 1 & 2). Contains the python code used for the analysis and visualization for all four replicates measuring the frequency from the array to the F1 integrations. Contains the python code used for the analysis and visualization of the injection mixture.

Supplemental File 5- Array 1 PX816 Barcode Count

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
An excel document containing all barcode sequences and frequencies found in array 1 PX816 across six individual worms.

Supplemental File 11- Promoter Images

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
Contains all unedited image files along with metadata, for the individual integrations and double integration lines In several cases, fluorescence was observed in multiple parts of the body, in which case the file notes the approximate location. Additionally, multiple worms were imaged per strain, which have been denoted alphanumerically.

Supplemental File 12- Plasmid Sequences

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
Plasmids used in this study and described in the manuscript

Supplemental File 13- Split Selection Landing Pad (SSLP) Sequences

Zachary Stevenson, Megan J Moerdyk-Schauwecker, Stephen Banse, Dhaval S Patel, Hang Lu & Patrick C. Phillips
All landing pad sequences along with limited surrounding genomic region used in this study and described in the manuscript

Additional file 1 of Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)

Yongbin Li, Rui Yang, Max M. Häggblom, Mengyan Li, Lifang Guo, Baoqin Li, Max Kolton, Zhiguo Cao, Mohsen Solemani, Zheng Chen, Zhimin Xu, Wenlong Gao, Bei Yan & Weimin Sun
Additional file 1: Table S1. The chemical properties of sample sites. Table S2. Node table for biotic interaction network in the less contaminatedsites. Table S3. Edge table for biotic interaction network in the lesscontaminated sites. Table S4. Node table for biotic interaction network in thehigh contaminated sites. Table S5. Edge table for biotic interaction network inthe high contaminated sites.

Pollutant Emissions Reporting for Ammonia Fuel Blends

Christopher M. Douglas, Robert Steele, Tom Martz, Bobby Noble, Benjamin Emerson & Tim C. Lieuwen

Surprisingly Popular, State Capitals, & Domain Knowledge

Justin Sukernek & Rick Thomas
A partial replication of the state capitals experiments in Prelec, Seung, & McCoy (2017) in which participants answer whether the most populous city in a state is also the state's capital. Participants also estimate the percentage of subjects that will answer 'Yes' on each question. An added novel layer is that participants will submit which of the 50 states they've lived in for at least 5 years, as a measure of latently implied domain knowledge.

Additional file 1 of Ascorbic acid 6-palmitate modulates microglia M1/M2 polarization in lipopolysaccharide-stimulated BV-2 cells via PERK/elF2α mediated endoplasmic reticulum stress

Qian Li, Yao Wu, Xue-shen Chen, Tao Zeng, Lin-ling Liu, Zi-qi Feng, Dan-yang Liu, Ling Zhu & Li-hong Wan
Additional file 1: Supplementary figure 1. A mRNA levels of grp78 and chop in TM-stimulated BV-2 cells; B mRNA levels of inos and il-10 in TM-stimulated BV-2 cells; C mRNA levels of grp78 and chop in 4-PBA-stimulated BV-2 cells. B mRNA levels of inos and il-10 4-PBA-stimulated BV-2 cells. Supplementary figure 2. A Full-length blots/gels of β-actin; B Full-length blots/gels of PERK; C Full-length blots/gels p-PREK. All of them were repeated three times. Supplementary figure...

Ascorbic acid 6-palmitate modulates microglia M1/M2 polarization in lipopolysaccharide-stimulated BV-2 cells via PERK/elF2α mediated endoplasmic reticulum stress

Qian Li, Yao Wu, Xue-shen Chen, Tao Zeng, Lin-ling Liu, Zi-qi Feng, Dan-yang Liu, Ling Zhu & Li-hong Wan
Abstract Background Neuroinflammation-mediated microglia polarization is a major process in various central nervous system (CNS) diseases. Endoplasmic reticulum (ER) stress contributes to the inflammatory signals as well as to microglia polarization in lipopolysaccharide (LPS) induced neuroinflammation. Ascorbic acid 6-palmitate (L-AP) has been broadly used as a dietary antioxidant in foods and demonstrated a strong inhibitory effect on 5-LOX; however, the specific anti-inflammation mechanisms remain unclear. In this study, we investigated the effects and possible mechanisms...

Additional file 2 of Impacts of metabolic disorders on short- and long-term mortality after coronary artery surgery in the elderly

Yuhong Fan, Jingjing Liu, Lei Jin, Zhonghe Liu, Lixiang Han, Yue Wang, Yangyang Zhang, Peiming Shen & Zhi Li
Additional file 2. Fig. S1: Standardized differences for each variable before and after PSM. The absolute standardized differences < 0.2 indicate balanced matching. Y axis represents the baseline of variables. X axis represents the standardized mean difference value. PSM, propensity score matching; EuroSCORE II, European system for cardiac operative risk evaluation II; IABP, intra-aortic balloon pump; PCI, percutaneous coronary intervention; COPD, chronic obstructive pulmonary disease; Scr, serum creatinine; LVEF, left ventricular ejection fraction; NYHA, New...

Additional file 1 of Impacts of metabolic disorders on short- and long-term mortality after coronary artery surgery in the elderly

Yuhong Fan, Jingjing Liu, Lei Jin, Zhonghe Liu, Lixiang Han, Yue Wang, Yangyang Zhang, Peiming Shen & Zhi Li
Additional file 1. Table S1: Independent risk factors of CCV mortality by multivariate cox regression analysis before and after matching.

Impacts of metabolic disorders on short- and long-term mortality after coronary artery surgery in the elderly

Yuhong Fan, Jingjing Liu, Lei Jin, Zhonghe Liu, Lixiang Han, Yue Wang, Yangyang Zhang, Peiming Shen & Zhi Li
Abstract Background Elderly patients undergoing cardiac operation often suffer various metabolic comorbidities, such as diabetes mellitus (DM) and obesity. The metabolic disorders in these individuals are widely considered to be possible predisposing factors for unfavourable prognosis. This retrospective study was aimed to determine the association of metabolic diseases with the mortality of elderly patients after coronary artery bypass grafting (CABG) and to identify the protective or risk factors related to their short- and long-term survival....

Impacts of metabolic disorders on short- and long-term mortality after coronary artery surgery in the elderly

Yuhong Fan, Jingjing Liu, Lei Jin, Zhonghe Liu, Lixiang Han, Yue Wang, Yangyang Zhang, Peiming Shen & Zhi Li
Abstract Background Elderly patients undergoing cardiac operation often suffer various metabolic comorbidities, such as diabetes mellitus (DM) and obesity. The metabolic disorders in these individuals are widely considered to be possible predisposing factors for unfavourable prognosis. This retrospective study was aimed to determine the association of metabolic diseases with the mortality of elderly patients after coronary artery bypass grafting (CABG) and to identify the protective or risk factors related to their short- and long-term survival....

Data from: Fluc­tu­a­tion domains in adap­tive evo­lu­tion

Carl Boettiger, Jonathan Dushoff & Joshua S. Weitz
We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains–parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined...

Data from: Intoxicated copepods: ingesting toxic phytoplankton leads to risky behaviour

Rachel S. Lasley-Rasher, Kathryn Nagel, Aakanksha Angra & Jeannette Yen
Understanding interactions between harmful algal bloom (HAB) species and their grazers is essential for determining mechanisms of bloom proliferation and termination. We exposed the common calanoid copepod, Temora longicornis to the harmful algal bloom species Alexandrium fundyense and examined effects on copepod survival, ingestion, egg production and swimming behaviour. A. fundyense was readily ingested by T. longicornis and significantly altered copepod swimming behaviour without affecting copepod survival or fitness. A. fundyense caused T. longicornis to...

The DART Project: using data management plans as a research tool

Amanda Whitmire, Jacob Carlson, Brian Westra, Patricia Hswe & Susan Parham
This is a two-year National Leadership Grant for Libraries Demonstration Project to facilitate a multi-university study of faculty data management plans (DMPs). The primary outputs of this project will be an analytic rubric to standardize the review of data management plans as a means to inform targeted expansion or development of research data services at academic libraries; and a study utilizing the rubric that presents the results of data management plan analyses at five universities....

Data from: Species colonisation, not competitive exclusion, drives community overdispersion over long-term succession

Shao-Peng Li, Marc W. Cadotte, Scott J. Meiners, Zheng-Shuang Hua, Lin Jiang & Wen-Sheng Shu
Ecological communities often transition from phylogenetic and functional clustering to overdispersion over succession as judged by space-for-time substitution studies. Such a pattern has been generally attributed to the increase in competitive exclusion of closely related species with similar traits through time, although colonisation and extinction have rarely been examined. Using 44 years of uninterrupted old-field succession in New Jersey, USA, we confirmed that phylogenetic and functional clustering decreased as succession unfolded, but the transition was...

Data from: Force encoding in muscle spindles during stretch of passive muscle

Kyle P. Blum, Boris Lamotte D’Incamps, Daniel Zytnicki & Lena H. Ting
Muscle spindle proprioceptive receptors play a primary role in encoding the effects of external mechanical perturbations to the body. During externally-imposed stretches of passive, i.e. electrically-quiescent, muscles, the instantaneous firing rates (IFRs) of muscle spindles are associated with characteristics of stretch such as length and velocity. However, even in passive muscle, there are history-dependent transients of muscle spindle firing that are not uniquely related to muscle length and velocity, nor reproduced by current muscle spindle...

Data from: Spatial storage effect promotes biodiversity during adaptive radiation

Jiaqi Tan, Jennifer B. Rattray, Xian Yang & Lin Jiang
Many ecological communities are enormously diverse. Variation in environmental conditions over time and space provides opportunities for temporal and spatial storage effects to operate, potentially promoting species coexistence and biodiversity. While several studies have provided empirical evidence supporting the significance of the temporal storage effect for coexistence, empirical tests of the role of the spatial storage effect are rare. In particular, we know little about how the spatial storage effect contributes to biodiversity over evolutionary...

Data from: Temperature-regulated guest admission and release in microporous materials

Gang Kevin Li, Jin Shang, Qinfen Gu, Rohan V. Awati, Nathan Jensen, Andrew Grant, Xueying Zhang, David S. Sholl, Jefferson Z. Liu, Paul A. Webley & Eric F. May
While it has long been known that some highly adsorbing microporous materials suddenly become inaccessible to guest molecules below certain temperatures, previous attempts to explain this phenomenon have failed. Here we show that this anomalous sorption behaviour is a temperature-regulated guest admission process, where the pore-keeping group’s thermal fluctuations are influenced by interactions with guest molecules. A physical model is presented to explain the atomic-level chemistry and structure of these thermally regulated micropores, which is...

Data from: Plant functional diversity modulates global environmental change effects on grassland productivity

Zhuwen Xu, Mai-He Li, Niklaus E. Zimmermann, Shaopeng Li, Hui Li, Haiyan Ren, Hao Sun, Xingguo Han, Yong Jiang, Lin Jiang & Shao-Peng Li
1. Although much research has explored changes in ecosystem functions associated with global environmental changes, the mechanistic pathways behind the observed changes remain poorly understood. 2. Using an 11-year experiment that increased growing season precipitation and nitrogen deposition in a temperate steppe, we explored the relative importance of direct and indirect environmental change effects on plant primary productivity. 3. We show that increases in water and nitrogen availability influenced plant productivity via both direct and...

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