cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14845254.v2
title: Images of selected cells of TbGOS02 recombinant Trypanosoma brucei brucei cell line

description: A novel experimental setup for measuring fluorescence in live trypanosome (FILT) cells was established as described in Borg (2015) and Borg et al. (2021), a study which will be linked to this dataset upon publication. The FILT set up was used to capture 60 fluorescent and 60 brightfield images of a field of vision which encompassed 88 cells of the recombinant <i>Trypanosoma brucei brucei</i> cell line, TbGOS02. All these images are provided in the file within this dataset labelled, "TbGOS02 All Frames 88 cells 140619.pdf".<br> Each of the 88 cells in the image was enumerated as detailed in Borg et al. (2021). For cell number 08, 60 fluorescent and 60 brightfield cropped images featuring only this cell are provided in the file within this dataset labelled, " TbGOS02 All Frames Cell 08 140619.pdf ". Equivalent images for cells numbered 17, 63 and 76 are provided in the remaining three PDF files of this dateset, as summarised below. <b>TbGOS02 All Frames 88 cells 140619.pdf</b>All 120 captured images captured in the FILT setup, 60 fluorescent and 60 brightfield, of the 88 cells in view field. <b>TbGOS02 All Frames Cell 08 140619.pdf</b>All 120 captured images captured in the FILT setup, 60 fluorescent and 60 brightfield, of cell 08.<b> </b><b>TbGOS02 All Frames Cell 17 140619.pdf</b>All 120 captured images captured in the FILT setup, 60 fluorescent and 60 brightfield, of cell 17 <b>TbGOS02 All Frames Cell 63 140619.pdf</b>All 120 captured images captured in the FILT setup, 60 fluorescent and 60 brightfield, of cell 63 <b>TbGOS02 All Frames Cell 76 140619.pdf</b>All 120 captured images captured in the FILT setup, 60 fluorescent and 60 brightfield, of cell 76<br> References<i>Borg Y (2015). Design, Mathematical Modelling, Construction and Testing of Synthetic Gene Network Oscillators to Establish Roseobacter Clade Bacteria and the Protozoan Trypanosoma brucei as Synthetic Biology Chassis. Doctoral thesis, University College London. https://discovery.ucl.ac.uk/id/eprint/1472672</i><i> </i><i>Borg Y, Alsford S, Pavlika V, Zaikin A, Nesbeth D (2021). Synthetic biology tools for engineering Goodwin oscillation in Trypanosoma brucei brucei. In preparation.</i>
DOI: 10.5281/zenodo.5032528
title: EvolvingSTEM Bioinformatics mutant colony sequencing

description: Mutant colony sequencing for EvolvingSTEM Bioinformatics
DOI: 10.15482/usda.adc/1522652
title: Feedstock Readiness Level (FSRL) evaluation: Thlaspi arvense (pennycress), hydroprocessing (HEFA), Midwest, Jun. 2021
DOI: 10.15468/7v75wp
title: A checklist of the millipedes (Diplopoda) of Laos

description: This dataset contains the digitized treatments in Plazi based on the original journal article Likhitrakarn, Natdanai, Golovatch, Sergei I., Panha, Somsak (2014): A checklist of the millipedes (Diplopoda) of Laos. Zootaxa 3754 (4): 473-482, DOI: http://dx.doi.org/10.11646/zootaxa.3754.4.8
DOI: 10.6073/pasta/b910ee01efffa80e6ee5fdeaccbf30d5
title: Effects of Warming on Tree Species Recruitment at Harvard Forest and Duke Forest since 2009

description: Climate change is restructuring forests of the United States, although the details of this restructuring are currently uncertain. Rising temperatures of 2 to 8 deg C and associated changes in soil moisture will shift the competitive balance between species that compete for light and water, changing their abilities to produce seed, germinate, grow, and survive. We are using large scale experiments to determine the effects of warming on the most sensitive stage of species distributions, i.e., recruitment, in mixed deciduous forests in southern New England and in the Piedmont region of North Carolina. Two questions organize our proposed research: (1) Might temperate tree species near the "warm" end of their range in the eastern United States decline in abundance during the coming century due to projected warming? and (2) Might trees near the "cool" end of their range in the eastern United States increase in abundance, or extend their range, during the coming 100 years because of projected warming? To explore these questions, we are exposing seedlings to air and soil warming experiments in two eastern deciduous forest sites; one at the Harvard Forest (HF) in central Massachusetts, and the other at the Duke Forest (DF) in the Piedmont region of North Carolina. We focus on tree species common to both Harvard and Duke Forests (such as red, black, and white oaks), those near northern range limits (black oak, tulip poplar), and those near southern range limits (yellow birch, sugar maple). At each site, we plant seeds in common gardens established in temperature-controlled, open-top chambers. The experimental design is replicated and fully factorial and involves three temperature regimes (ambient, +3 deg C and +5 deg C) and two light regimes (closed forest canopy (low light) and gap conditions (high light)). Measured variables include Fall/Spring responses to temperature and mid-Summer responses to low soil moisture. This research will advance our understanding of how the abundances and geographic distributions of several important eastern tree species near the cool and warm ends of their ranges will change during the century because of projected warming. Warming-induced changes in eastern tree abundances and distributions have the potential to affect both the quality and quantity of goods and services provided by eastern forests, and will therefore be of importance to society.
DOI: 10.25386/genetics.14842779
title: Supplementary Files for Garge, Cha et al., 2021 (post accept)

description: Supplementary files and figures
DOI: 10.25386/genetics.14842779.v1
title: Supplementary Files for Garge, Cha et al., 2021 (post accept)

description: Supplementary files and figures
DOI: 10.18746/bmth.data.00000172
title: In pursuit of visual attention: SSVEP frequency-tagging moving targets
DOI: 10.6073/pasta/206d0cb265080617d4c2ea4c9f7a20e1
title: Carbon and Nitrogen Across Two ULTRA-Ex Urban to Rural Gradients in Massachusetts since 2010

description: As part of the Boston University-led, Urban Long-Term Research Area - Exploratory Award (ULTRA-Ex), we established 135 circular, 15 m radius biometric plots extending across two Boston urban-to-rural gradients (Boston MA to Petersham MA and Boston MA to Worcester MA). The plots were stratified based on neighborhood (1 km2 surrounding area) characteristics for population density, impervious surface area fraction, and land cover. Within each plot we measured aboveground live and dead biomass, species characteristics, ground cover characteristics, and soil properties.
DOI: 10.6073/pasta/692d46308ed5ff14658de66fb92cc1c6
title: Carbon and Nitrogen Across Two ULTRA-Ex Urban to Rural Gradients in Massachusetts 2010

description: As part of the Boston University-led, Urban Long-Term Research Area - Exploratory Award (ULTRA-Ex), we established 135 circular, 15 m radius biometric plots extending across two Boston urban-to-rural gradients (Boston MA to Petersham MA and Boston MA to Worcester MA). The plots were stratified based on neighborhood (1 km2 surrounding area) characteristics for population density, impervious surface area fraction, and land cover. Within each plot we measured aboveground live and dead biomass, species characteristics, ground cover characteristics, and soil properties.
DOI: 10.5281/zenodo.4426205
title: WALIS Spreadsheet Thompson Creveling v2.0

description: A compilation of Marine Isotope Stage 5a/5c relative sea level proxies and associated age data as it appears in the World Atlas of Last Interglacial Shorelines (WALIS) Database. Version 2 incorporates changes post review process. PDF included which details changes since version 1.
DOI: 10.6073/pasta/8b66de8723a38cfdfb8795bc16889dcd
title: Ungulate-Forest Interactions in Partially Harvested Oak-Pine Stands in Central Massachusetts 2009

description: Ungulates are attracted to forest openings created by natural disturbance and timber harvesting due to the abundance of high quality browse in these openings. Despite the increased activity and browsing of ungulates in forest openings, the importance of browsing relative to abiotic factors such as light on forest regeneration is often unclear. In southern New England, medium-intensity harvesting is the predominant forest disturbance attracting white-tailed deer and moose. Oaks are the foundation hardwood taxon and predominant timber tree in the region and are in decline. Hence, the effects of ungulate browsing on oak forests are of great interest to ecologists, conservationists and forest and wildlife managers. We sampled tree regeneration and ungulate foraging activity across a range of canopy disturbances (35-90% basal area removed) in 34 stands of the Quabbin and Ware River Watershed Forests. Browsing was very high across the plots with about 80% of red maple and oak stems browsed. Taller stems were generally browsed more frequently than shorter stems. Oak regeneration in the smaller size classes was generally lower in stands with higher percent cover of hay-scented fern. The proportion of browsed red maples and oaks generally increased with increasing density of these taxa. Despite intensive herbivory, oaks appear to be regenerating well with increased light in these partially harvested stands.
DOI: 10.6073/pasta/1191704f5865514b04a27a9f7f329fc9
title: Demography of Sarracenia Purpurea in Massachusetts and Vermont since 1997

description: The northern pitcher plant Sarracenia purpurea is a model system for forecasting extinction risk in the face of environmental change. We have monitored demographic variables of two mapped cohorts of S. purpurea in ombrotrophic bogs of northern New England from 1997-2005 (Hawley Bog, Massachusetts) and 1997-present (Molly Bog, Vermont). Growth, survivorship, and reproduction are in close balance, and matrix-models with four life stages (seeds, seedlings/juvenile plants, non-flowering adult plants, flowering adults) predicted population growth rates close to zero, with long doubling times. To further assess seed-to-seedling transitions, we measured and weighed Sarracenia seeds, and conducted a greenhouse experiment on density-dependent dynamics of newly germinated seedlings of S. purpurea.
DOI: 10.6073/pasta/eb9d87863fbdabc918c47b882e4cb817
title: Ungulate-Disturbance Interactions in Hemlock Ecosystems at Harvard Forest since 2012

description: Densities of ungulates are often associated with recent forest disturbances such as fire, logging and insect outbreaks, as increased resources stimulate tree regeneration, leading to abundant available browse. Despite the often significant role that ungulates play in disturbed forests, surprisingly little is known about ungulate-disturbance interactions, and ungulate herbivory is often excluded from examinations of forest response to disturbance. In the Northeastern United States, a large-scale insect outbreak, the hemlock wooly adelgid (HWA), has begun to have important effects on hemlock forests both directly and indirectly (i.e., by preemptive salvage logging). No studies have examined the interactions of both moose and deer activity with these associated canopy disturbances. Our objectives are twofold: to determine (1) the response of ungulates to varying disturbance types and intensities and (2) the influence of ungulate interactions with canopy disturbance on vegetation, other biota, and ecosystem processes. We will examine the relative abundance of moose and deer in four treatments (2 replicates) at the Hemlock Removal Experiment using three indices of ungulate activity: pellet group density, evidence of past browsing on seedlings and saplings, and the occurrence of animals using game cameras. We will also monitor the response of vegetation to ungulate browsing by sampling woody and herbaceous vegetation in fenced exclosures and paired controls in disturbed and undisturbed plots.
DOI: 10.6084/m9.figshare.14847975
title: DataSet

description: Japan Arrival Times.
DOI: 10.6073/pasta/b1c626d0294facafcf1eb9ebcbbec375
title: Regional Conservation Partnerships in New England 2009-2012

description: Across New England, a new model of regional collaboration is increasingly being used by land conservation trusts, watershed associations, state agencies and others. Regional conservation partnerships (RCPs) serve multiple purposes, such as coordinating among the various active groups in the region and allowing them to leverage funding and staff capacity. However, their essential missions are the same--protect more land from development. We use interviews, geographic information systems (GIS), and statistical analysis on 20 case studies to document RCP growth and characteristics and to analyze which attributes most contribute to their ability to conserve land. Along with well-known factors of organizational development, we find that the RCPs that match the size of the partnership region with the territory and capacity of the host partner organization are better able to achieve measurable conservation gains.
DOI: 10.6084/m9.figshare.12943454
title: Microbes increase thermal sensitivity in the mosquito Aedes aegypti, with the potential to change disease distributions

description: The mosquito <i>Aedes aegypti</i> is the primary vector of many disease-causing viruses, including dengue (DENV), Zika, chikungunya, and yellow fever. As consequences of climate change, we expect an increase in both global mean temperatures and extreme climatic events. When temperatures fluctuate, mosquito vectors will be increasingly exposed to temperatures beyond their upper thermal limits. Here, we examine how DENV infection alters <i>Ae. aegypti</i> thermotolerance by using a high-throughput physiological ‘knockdown’ assay modeled on studies in <i>Drosophila</i>. Such laboratory measures of thermal tolerance have previously been shown to accurately predict an insect’s distribution in the field. We show that DENV infection increases thermal sensitivity, an effect that may ultimately limit the geographic range of the virus. We also show that the endosymbiotic bacterium <i>Wolbachia pipientis</i>, which is currently being released globally as a biological control agent, has a similar impact on thermal sensitivity in <i>Ae. aegypti</i>. Surprisingly, in the coinfected state, <i>Wolbachia</i> did not provide protection against DENV-associated effects on thermal tolerance, nor were the effects of the two infections additive. The latter suggests that the microbes may act by similar means, potentially through activation of shared immune pathways or energetic tradeoffs. Models predicting future ranges of both virus transmission and <i>Wolbachia’s</i> efficacy following field release may wish to consider the effects these microbes have on host survival.
DOI: 10.6084/m9.figshare.12943454.v2
title: Microbes increase thermal sensitivity in the mosquito Aedes aegypti, with the potential to change disease distributions

description: The mosquito <i>Aedes aegypti</i> is the primary vector of many disease-causing viruses, including dengue (DENV), Zika, chikungunya, and yellow fever. As consequences of climate change, we expect an increase in both global mean temperatures and extreme climatic events. When temperatures fluctuate, mosquito vectors will be increasingly exposed to temperatures beyond their upper thermal limits. Here, we examine how DENV infection alters <i>Ae. aegypti</i> thermotolerance by using a high-throughput physiological ‘knockdown’ assay modeled on studies in <i>Drosophila</i>. Such laboratory measures of thermal tolerance have previously been shown to accurately predict an insect’s distribution in the field. We show that DENV infection increases thermal sensitivity, an effect that may ultimately limit the geographic range of the virus. We also show that the endosymbiotic bacterium <i>Wolbachia pipientis</i>, which is currently being released globally as a biological control agent, has a similar impact on thermal sensitivity in <i>Ae. aegypti</i>. Surprisingly, in the coinfected state, <i>Wolbachia</i> did not provide protection against DENV-associated effects on thermal tolerance, nor were the effects of the two infections additive. The latter suggests that the microbes may act by similar means, potentially through activation of shared immune pathways or energetic tradeoffs. Models predicting future ranges of both virus transmission and <i>Wolbachia’s</i> efficacy following field release may wish to consider the effects these microbes have on host survival.
DOI: 10.6084/m9.figshare.12943454.v1
title: Microbes increase thermal sensitivity in the mosquito Aedes aegypti, with the potential to change disease distributions

description: The mosquito <i>Aedes aegypti</i> is the primary vector of many disease-causing viruses, including dengue (DENV), Zika, chikungunya, and yellow fever. As consequences of climate change, we expect an increase in both global mean temperatures and extreme climatic events. When temperatures fluctuate, mosquito vectors will be increasingly exposed to temperatures beyond their upper thermal limits. Here, we examine how DENV infection alters <i>Ae. aegypti</i> thermotolerance by using a high-throughput physiological ‘knockdown’ assay modeled on studies in <i>Drosophila</i>. Such laboratory measures of thermal tolerance have previously been shown to accurately predict an insect’s distribution in the field. We show that DENV infection increases thermal sensitivity, an effect that may ultimately limit the geographic range of the virus. We also show that the endosymbiotic bacterium <i>Wolbachia pipientis</i>, which is currently being released globally as a biological control agent, has a similar impact on thermal sensitivity in <i>Ae. aegypti</i>. Surprisingly, in the coinfected state, <i>Wolbachia</i> did not provide protection against DENV-associated effects on thermal tolerance, nor were the effects of the two infections additive. The latter suggests that the microbes may act by similar means, potentially through activation of shared immune pathways or energetic tradeoffs. Models predicting future ranges of both virus transmission and <i>Wolbachia’s</i> efficacy following field release may wish to consider the effects these microbes have on host survival.
DOI: 10.6073/pasta/f6eb10a3faae5157589f1b8585764851
title: Thresholds and Tipping Points in a Sarracenia Microecosystem at Harvard Forest 2012-2013

description: The primary goal of this project is to determine experimentally the amount of lead time required to prevent a state change. To achieve this goal, we will (1) experimentally induce state changes in a natural aquatic ecosystem - the Sarracenia microecosystem; (2) use proteomic analysis to identify potential indicators of states and state changes; and (3) test whether we can forestall state changes by experimentally intervening in the system. This work uses state-of-the art molecular tools to identify early warning indicators in the field of aerobic to anaerobic state changes driven by nutrient enrichment in an aquatic ecosystem. The study tests two general hypotheses: (1) proteomic biomarkers can function as reliable indicators of impending state changes and may give early warning before increasing variances and statistical flickering of monitored variables; and (2) well-timed intervention based on proteomic biomarkers can avert future state changes in ecological systems.
DOI: 10.5066/p9chy45i
title: Data supporting an analysis of the recurrence interval of post-fire debris-flow generating rainfall in the southwestern United States

description: This data release supports the analysis of the recurrence interval of post-fire debris-flow generating rainfall in the southwestern United States. We define the recurrence interval of the peak 15-, 30-, and 60-minute rainfall intensities for 316 observations of post-fire debris-flow occurrence in 18 burn areas, 5 U.S. states, and 7 climate types. These data support the analysis described in Staley et al. (2020). Debris flow occurrence data and corresponding peak rainfall intensities are from Staley et al. (2016). Recurrence interval data are from NOAA Atlas 14 Volume 1: semiarid southwestern United States (Bonnin et al., 2004), Volume 6: California (Perica et al., 2014) and Volume 8: Midwestern States (Perica et al., 2013). Climate types are from Beck et al. (2018). References Beck, H.E., Zimmermann, N.E., McVicar, T.R., Vergopolan, N., Berg, A., Wood, E.F., 2018. Present and future Koppen-Geiger climate classification maps at 1-km resolution. Scientific Data, 5(1), 180214. doi:10.1038/sdata.2018.214 Bonnin, G.M., Martin, D., Lin, B., Parzybok, T., Yekta, M., Riley, D., 2004. NOAA Atlas 14 Precipitation-Frequency Atlas of the United States Volume 1 Version 5.0: Semiarid Southwest (Arizona, Southeast Californa, Nevada, New Mexico, Utah). 265pp pp. Perica, S., Dietz, S., Heim, S., Hiner, L., Maitaria, K., Martin, D., Pavlovic, S., Roy, I., Trypaluk, C., Unruh, D., Yan, F., Yekta, M., Zhao, T., Bonnin, G., Brewer, D., Chen, L.-C., Parzybok, T., Yarchoan, J., 2014. NOAA Atlas 14 Precipitation-Frequency Atlas of the United States Volume 6 Version 2.3: California, Silver Springs, MD. Perica, S., Martin, D., Pavlovic, S., Roy, I., St. Laurent, M., Trypaluk, C., Unruh, D., Yekta, M., Bonnin, G., 2013. NOAA Atlas 14 Precipitation-Frequency Atlas of the United States Volume 8 Version 2.0: Midwestern States (Colorado, Iowa, Kansas, Michigan, Minnesota, Missouri, Nebraska, North Dakota, Oklahoma, South Dakota, Wisconsin), Silver Springs, MD. Staley, D.M., Kean, J.W., Rengers, F.K., 2020. The recurrence interval of post-fire debris-flow generating rainfall in the southwestern United States. Geomorphology, XX, xxx-xxx. xxxx-x--x-xxxxxxxxx. Staley, D.M., Negri, J.A., Kean, J.W., Laber, J.L., Tillery, A.C., Youberg, A.M., 2016. Updated Logistic Regression Equations for the Calculation of Post-Fire Debris-Flow Likelihood in the Western United States. U. S. Geological Survey Open-File Report 2016-1106, 13p. 10.3133/ofr20161106.
DOI: 10.5281/zenodo.5033143
title: Data from Schmitt et al. 2020: A causal role of area hMST for self-motion perception in humans. Cerebral Cortex Communications

description: <strong>Dataset associated with the following publication:</strong> Constanze Schmitt, Bianca R Baltaretu, J Douglas Crawford, Frank Bremmer, A Causal Role of Area hMST for Self-Motion Perception in Humans, <em>Cerebral Cortex Communications</em>, Volume 1, Issue 1, 2020, tgaa042, https://doi.org/10.1093/texcom/tgaa042 Published 2020 July 20. <strong>Description of dataset:</strong> In our study we presented an optic flow stimulus simulating forward self-motion across a ground plane in one of three directions (30° to the left, straight ahead, 30° to the right) to eight human participants. In 57% of all trials TMS pulses were applied either to right hemisphere hMST or a control area while the optic flow stimulus was presented. Participants indicated the perceived heading of the self-motion stimulus. The dataset contains the responses (perceived headings) of all eight participants (s1 to s8). The responses are reported here in degrees with 0 degrees representing a movement straight ahead, negative values describing movements forward to the left and positive values describing movements forward to the right.
description: This work was supported by Deutsche Forschungsgemeinschaft (IRTG-1901 and CRC/TRR-135, project number 222641018) and Natural Sciences and Engineering Council of Canada (NSERC).