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Table S1: Genes involved in galactose derivatives metabolism used in this study.

The sequences of the six genes of all the 12 Andrena species analyzed in "Evolutionary adaptation of genes involved in galactose derivatives metabolism in oil-tea specialized Andrena species".

Data and Code for "A Ray-Based Input Distance Function to Model Zero-Valued Output Quantities: Derivation and an Empirical Application"

This data and code archive provides all the data and code for replicating the empirical analysis that is presented in the journal article "A Ray-Based Input Distance Function to Model Zero-Valued Output Quantities: Derivation and an Empirical Application" authored by Juan José Price and Arne Henningsen and published in the Journal of Productivity Analysis (DOI: <a href="https://doi.org/10.1007/s11123-023-00684-1">10.1007/s11123-023-00684-1</a>). We conducted the empirical analysis with the "R" statistical software (version 4.3.0) using the add-on packages "combinat" (version 0.0.8), "miscTools" (version 0.6.28), "quadprog" (version 1.5.8), sfaR (version 1.0.0), stargazer (version 5.2.3), and "xtable" (version 1.8.4) that are available at CRAN. We created the R package "micEconDistRay" that provides the functions for empirical analyses with ray-based input distance functions that we developed for the above-mentioned paper. Also this R package is available at CRAN (https://cran.r-project.org/package=micEconDistRay). This replication package contains the following files and folders: <ul> <li>README This file</li> <li>MuseumsDk.csv The original data obtained from the Danish Ministry of Culture and from Statistics Denmark. It includes the following variables: <ul> <li>museum: Name of the museum. </li> <li>type: Type of museum (Kulturhistorisk museum = cultural history museum; Kunstmuseer = arts museum; Naturhistorisk museum = natural history museum; Blandet museum = mixed museum).</li> <li>munic: Municipality, in which the museum is located.</li> <li>yr: Year of the observation.</li> <li>units: Number of visit sites.</li> <li>resp: Whether or not the museum has special responsibilities (0 = no special responsibilities; 1 = at least one special responsibility).</li> <li>vis: Number of (physical) visitors.</li> <li>aarc: Number of articles published (archeology).</li> <li>ach: Number of articles published (cultural history).</li> <li>aah: Number of articles published (art history).</li> <li>anh: Number of articles published (natural history).</li> <li>exh: Number of temporary exhibitions.</li> <li>edu: Number of primary school classes on educational visits to the museum.</li> <li>ev: Number of events other than exhibitions.</li> <li>ftesc: Scientific labor (full-time equivalents).</li> <li>ftensc: Non-scientific labor (full-time equivalents).</li> <li>expProperty: Running and maintenance costs [1,000 DKK].</li> <li>expCons: Conservation expenditure [1,000 DKK]. </li> <li>ipc: Consumer Price Index in Denmark (the value for year 2014 is set to 1).</li> </ul> </li> <li>prepare_data.R This R script imports the data set MuseumsDk.csv, prepares it for the empirical analysis (e.g., removing unsuitable observations, preparing variables), and saves the resulting data set as DataPrepared.csv.</li> <li>DataPrepared.csv This data set is prepared and saved by the R script prepare_data.R. It is used for the empirical analysis.</li> <li>make_table_descriptive.R This R script imports the data set DataPrepared.csv and creates the LaTeX table /tables/table_descriptive.tex, which provides summary statistics of the variables that are used in the empirical analysis.</li> <li>IO_Ray.R This R script imports the data set DataPrepared.csv, estimates a ray-based Translog input distance functions with the 'optimal' ordering of outputs, imposes monotonicity on this distance function, creates the LaTeX table /tables/idfRes.tex that presents the estimated parameters of this function, and creates several figures in the folder /figures/ that illustrate the results.</li> <li>IO_Ray_ordering_outputs.R This R script imports the data set DataPrepared.csv, estimates a ray-based Translog input distance functions, imposes monotonicity for each of the 720 possible orderings of the outputs, and saves all the estimation results as (a huge) R object allOrderings.rds.</li> <li>allOrderings.rds (not included in the ZIP file, uploaded separately) This is a saved R object created by the R script IO_Ray_ordering_outputs.R that contains the estimated ray-based Translog input distance functions (with and without monotonicity imposed) for each of the 720 possible orderings.</li> <li>IO_Ray_model_averaging.R This R script loads the R object allOrderings.rds that contains the estimated ray-based Translog input distance functions for each of the 720 possible orderings, does model averaging, and creates several figures in the folder /figures/ that illustrate the results.</li> <li>/tables/ This folder contains the two LaTeX tables table_descriptive.tex and idfRes.tex (created by R scripts make_table_descriptive.R and IO_Ray.R, respectively) that provide summary statistics of the data set and the estimated parameters (without and with monotonicity imposed) for the 'optimal' ordering of outputs.</li> <li>/figures/ This folder contains 48 figures (created by the R scripts IO_Ray.R and IO_Ray_model_averaging.R) that illustrate the results obtained with the 'optimal' ordering of outputs and the model-averaged results and that compare these two sets of results.</li> </ul>

Eurasia-fixed GNSS-derived velocity field for Turkey

The dataset and the analysis is described in the <a href="http://journals.tubitak.gov.tr/cgi/viewcontent.cgi?article=1844&context=earth">paper</a> and presented <a href="https://meetingorganizer.copernicus.org/EGU23/EGU23-12258.html">here</a>. The data fields are: longitude, latitude, E velocity, N velocity, sigma E, sigma N, rho, U velocity, sigma U, station. You can use the following code snippet to load your data to python: <pre><code class="language-python">fields = ['longitude', 'latitude', 've', 'vn', 'se', 'sn', 'rho', 'vu', 'su', 'station'] df = pd.read_csv('Kurt_etal_2023.csv', header=None, names=fields)</code></pre>

Satellite-derived sunshine duration product - DISSM/INPE

This dataset is the satellite-derived sunshine duration (SDU) product developed at the Satellite and Meteorological Sensors Division of the National Institute of Space Research for the period from September 2013 to December 2017. The data is delivered as daily SDU in hours, it has a spatial resolution of 0.04 degree on a regular latitude-longitude grid of 1800x1800 pixels within latitudes 50°S to 21.96°N and longitudes 100°W to 28.04°W. Each netCDF file correspond to a day and has a size of 26MB. Validation with in situ measurements and intercomparison with other satellite product is currently being submitted for peer review.

Making andesite through shallow hybridization of magmas derived from variably enriched lithospheric mantle

We integrate textural and in situ compositional information from plagioclase and clinopyroxene (Cpx) phenocrysts together with groundmass compositions in early Cretaceous andesite dykes within the Sulu belt of China to propose a new petrogenetic model for andesite. Plagioclase phenocrysts are mostly andesine; they are depleted in high field strength elements (HFSE). However, clinopyroxene (Cpx) phenocrysts are either reversely-zoned (type I) or homogeneous (type II), with the zoned Cpx divided into subtypes IA and IB. All Cpx has high Mg#, low Na2O and generally low Al2O3, with depletions in HFSE and variably high 87Sr/86Sr ratios, suggesting crystallization above the Moho from magmas derived from enriched lithospheric mantle. The cores of type IA/IB and type II Cpx have normal major- and trace-element compositional variations and similar 87Sr/86Sr ratios to each other and to plagioclase, consistent with fractional crystallization from a common magma (magma 1). The rims of type IA and IB Cpx also have normal major- and trace-element compositional variations, but these are not as evolved as the cores, and the rims have lower 87Sr/86Sr ratios, demonstrating crystallization from an isotopically-distinct magma (magma 2). Based on modelled major and rare earth element compositions of magmas inferred to have been in equilibrium with different Cpx (± plagioclase) domains, the measured groundmass compositions can be reproduced by variable mixing between the two magmas. Our study demonstrates for the first time that andesite magma can be made through fractionation and shallow hybridization of magmas derived from variably enriched lithospheric mantle.

opencc-zeroJun 2023View details →

Oxamniquine derivatives overcome praziquantel treatment limitations for schistosomiasis

Human schistosomiasis is a neglected tropical disease caused by S. mansoni, S. haematobium, and S. japonicum. Praziquantel (PZQ) is the method of choice for treatment. Due to constant selection pressure, there is an urgent need for new therapies for schistosomiasis. Previous treatment of S. mansoni included the use of Oxamniquine (OXA), a drug that activated by schistosomes' sulfotransferase (SULT). Guided by data from Xray crystallography and Schistosoma killing assays more than 350 OXA derivatives were designed, synthesized, and tested. We were able to identify CIDD-0150610 and CIDD-0150303 as powerful derivatives in vitro that kill (100%) of all three Schistosoma species at a final concentration of 143 µM. We evaluated the efficacy of the best OXA derivates in an in vivo model after treatment with a single dose of 100 mg/kg by oral gavage. The highest rate of worm burden reduction was achieved by CIDD -150303 (81.8%) against S. mansoni, CIDD-0149830 (80.2%) against S. haematobium and CIDD-066790 (86.7%) against S. japonicum. We have also evaluated the derivatives ability to kill immature stages since PZQ does not kill immature schistosomes. CIDD-0150303 demonstrated (100%) of killing for all life stages at a final concentration of 143 µM in vitro and effective reduction in worm burden in vivo. To understand how OXA derivatives fit in the SULT binding pocket, X-ray crystal structures of CIDD-0150303 and CIDD-0150610 demonstrate that the SULT active site will accommodate further modifications to our most active compounds as we tune them to increase favorable pharmacokinetic properties. Treatment with a single dose of 100 mg/kg by oral gavage of each PZQ and CIDD-0150303 reduced the worm burden in an animal model by (90.8%). Therefore, we conclude that CIDD-0150303, CIDD-0149830 and CIDD-066790 are the novel drugs that overcome OXA limitation, and CIDD-0150303 can be used with PZQ in combination therapy.

opencc-zeroJul 2023View details →

Data from: A mosaic of endogenous and plant-derived courtship signals in moths

Insects rely on olfaction to guide a wide range of adaptive behaviors, including mate- and food-localization, mate choice, oviposition site selection, kin recognition and predator avoidance. In nocturnal insects, such as moths and cockroaches, mate finding is stimulated predominantly by long-range species-specific sex pheromones, typically emitted by females. During courtship, at close-range, males in most moth species emit a blend of pheromone compounds from an everted, often large, pheromone gland. While long-distance communication with sex pheromones has been remarkably well characterized in thousands of moth species, close-range chemosensory sexual communication remains poorly understood. We reveal that in the moth Chloridea virescens, the male pheromone consists of three distinct classes of compounds: de novo biosynthesized alcohols, aldehydes, acetates and carboxylic acids that resemble the female's emissions, and newly identified compounds that are unique to the male pheromone: aliphatic polyunsaturated hydrocarbons and sequestered plant secondary compounds and hormone derivatives, including methyl salicylate (MeSA). Thus, males employ a mosaic pheromone blend of disparate origins that may serve multiple functions during courtship. We show that two olfactory receptors in female antennae are tuned to MeSA, which facilitates female acceptance of the male. Because MeSA is emitted by plants attacked by pathogens and herbivores, the chemosensory system of female moths was likely already tuned to this plant volatile, and males appear to exploit the female's preadapted sensory bias. Interestingly, while female moths (largely nocturnal) and butterflies (diurnal) diverged in their use of sensory modalities in sexual communication, MeSA is used by males of both lineages.

Aerosol indirect-effect-derived PM2.5 contributions during the development of convective clouds over the Yellow Sea in July of 2017

Meteorological processes are investigated during the development of deep convective clouds over the Yellow Sea inside a quasi-stationary rainy front in the East Asian region. WRF-Chem simulations were conducted to assess the aerosol-indirect-effect (AIE)-derived PM2.5 contributions to the cloud microphysical process in deep convective clouds and the associated precipitation. In our dataset, you can find output of WRF-Chem baseline simulations (BASE) and other sensitivity simulated outputs (CONTROL). Furthermore, model variables of precipitations, cloud top temperature (CTT), surface-level pressure (SLP), convective available potential energy (CAPE), and hydrometer mixing ratios of cloud water (qcloud), raindrops (qrain), and ice (qice) can be found in these zip files. If you have any difficulty downloading these datasets, please feel free to contact the first author, kimhsung@gmail.com. All references and acknowledgments can be found in our paper

Data Set for Copper-Catalyzed Benzylic Functionalization of Lignin-Derived Monomers

Raw NMR and HRMS data for the article entitled Copper-Catalyzed Benzylic Functionalization of Lignin-Derived Monomers. The folder names corrspond to the compound names.

Trellis Single-Cell Screening Reveals Stromal Regulation of Patient-Derived Organoid Drug Responses

Patient-derived organoids (PDOs) can model personalized therapy responses, however current screening technologies cannot reveal drug response mechanisms or how tumor microenvironment cells alter therapeutic performance. To address this, we developed a highly-multiplexed mass cytometry platform to measure post translational modification (PTM) signaling, DNA-damage, cell-cycle activity, and apoptosis in >2,500 colorectal cancer (CRC) PDOs and cancer associated fibroblasts (CAFs) in response to clinical therapies at single-cell resolution. To compare patient- and microenvironment-specific drug responses in thousands of single-cell datasets, we developed Trellis — a highly-scalable, hierarchical tree-based treatment effect analysis method. Trellis single-cell screening revealed that on-target cell-cycle blockage and DNA-damage drug effects are common, even in chemorefractory PDOs. However, drug-induced apoptosis is rare, patient-specific, and aligns with cancer cell PTM signaling. We find that CAFs can regulate cancer cell plasticity — shifting proliferative stem cells to slow-cycling revival stem cells via YAP to protect cancer cells from chemotherapy.   This repo contains the processed scRNA-seq Scanpy AnnData objects generated from the study. More information describing the data can be found at: https://github.com/TAPE-Lab/Ramos-et-al-Trellis

Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W4R4] Scaffold: Structural Studies and Correlation with Activity

Data for Publication “Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W4R4] Scaffold: Structural Studies and Correlation with Activity.” The file archive "WR_peptides_MD.zip" contains the starting structures of peptides, molecular topologies of peptides, representative MD trajectories of peptides in water and the DOPC/DOPG bilayer, as well as MD simulation parameters. See the README.txt file in this archive for details.

Endmember spectra and classified mosaics derived from CRISM mapping data at the south pole of Mars

Overview Multispectral mapping data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) provide a unique opportunity to characterize south polar ice deposits at higher spectral sampling, spatial resolution, or spatiotemporal coverage than previous work. This new perspective can help to constrain the nature and distribution of different mixtures of CO2 ice, H2O ice, and dust that influence the formation, evolution, and preservation of Mars climate records. We processed 1103 CRISM observations spanning southern summer of six Mars Years through a combination of k-means clustering and random forest classification. Using a set of 12 spectral endmembers directly tied to previous work with high-resolution CRISM targeted data, we made a series of temporally restricted mosaics showing surface spectral variation over time. The endmember set and classified mosaics produced in this work can provide critical context for future studies of the dynamic processes that shape south polar ice deposits. This is follow-on work to a previous study that produced a series of classified maps and a spectral library from CRISM targeted data. That work can be accessed with the following links: <ul> <li>Publication: <a href="https://doi.org/10.1029/2022JE007372">https://doi.org/10.1029/2022JE007372</a></li> <li>Repository: <a href="https://doi.org/10.5281/zenodo.6960943">https://doi.org/10.5281/zenodo.6960943</a></li> </ul> Contents The repository contains two .zip files, which can be expanded to access the files described below: <ul> <li>classified_mosaics.zip <ul> <li>lookup_files <ul> <li>SP_CRISM_RF_ColorMap.clr : An ESRI-formatted color map file that can be used to apply the endmember color scheme to random forest-classified maps in ArcGIS (see Symbology settings). Note that for continuity with Cartwright (2022), there are 21 colors in this file, though only endmembers associated with 12 of those colors are present in the classified mosaics.</li> <li>SP_CRISM_RF_ColorMap.txt : A text file that can be loaded into Python as a numpy array and used to generate a matplotlib color ramp. Row indices correspond to endmember numbers (see below) and columns are red, green, and blue values scaled from 0 to 1. Note that for continuity with Cartwright (2022), there are 21 colors in this file, though only endmembers associated with 12 of those colors are present in the classified mosaics.</li> <li>SP_CRISM_RF_Mapping_Endmember_Lookup.csv : A lookup table that can be used to cross-reference between endmember numbers (as stored in GeoTiffs or the indices of the colormaps above) and corresponding endmember names (C1m, Dc3m, etc.). Note that for continuity with Cartwright (2022), the endmember numbers are not sequential and instead correspond to the number of the original reference spectrum (e.g., C1m in this work has the same endmember number as C1 in Cartwright (2022)).</li> </ul> </li> <li>random_forest_classification <ul> <li>Contains GeoTiff mosaics of random forest classification results. Mosaics compile all observations falling in 10º bins of solar longitude (Ls) for a given year, provided that data was acquired in that range. Classified observations are stacked in ascending order of Ls. Mosaics of MSW data have a resolution of ~90 m/pixel while mosaics of MSP or combined MSP and MSW data have a resolution of ~180 m/pixel. Filenames indicate the observation type ("MSP", "MSW", or combined "MSP-MSW"), Mars Year ("MY28", "MY29", etc.) and Ls range ("Ls300-310" indicates all observations acquired between Ls 300º and Ls 310º). These images are not rendered to display colors consistent with the publication figures, but instead store the endmember classification for each pixel as a number from 0 to 21; use the contents of lookup_files to find the corresponding endmember name or render the image with the color scheme from the publication. To view rendered summary plots of each observation, see the contents of summary_plots below.</li> </ul> </li> <li>summary_plots <ul> <li>Contains summary plots of the endmember-classified mosaics provided in random_forest_classification above. Each plot presents the classified mosaic over a grey outline approximating the extent of high-albedo CO2 ice in the south polar residual cap (SPRC). Note that the summary view focuses on the area in and around the SPRC, but the full mosaics may extend beyond these bounds. </li> </ul> </li> </ul> </li> <li>spectral_library.zip <ul> <li>Contains spectral libraries with the median spectrum of each endmember as presented in Figure 3 in the publication. A basic text file listing the wavelength (WVL) and normalized reflectance values for each endmember is included (SP_CRISM_MappingEndmemberMedians.txt) as well as an ENVI-formatted spectral library (SP_CRISM_MappingEndmemberMedians_ENVI.sli). Note that a subset of the 55 wavelengths sampled in the source CRISM data were removed to avoid error-prone bands, leaving these spectral libraries with 51 bands. The spectra are normalized by the value at 1.330 µm.</li> </ul> </li> </ul>

opencc-by-4.0Aug 2023View details →

Data for "Derivative voltammetry: a simple tool to probe reaction selectivity in photoelectrochemical cells"

Data archive for "Derivative voltammetry: a simple tool to probe reaction selectivity in photoelectrochemical cells"  <a href="https://doi.org/10.1039/D2SE00692H">https://doi.org/10.1039/D2SE00692H</a>

opencc-by-4.0Aug 2023View details →

Transcriptomic profiles of MCF7-derived tamoxifen resistant cell lines

We report mRNA profiles of human breast cancer cell lines, MCF7 parental, and MCF7-derived tamoxifen-resistant cell lines MCF7-TR1 and MCF7-TR2. These cells have been previously described in  Ines Barone, Lauren Brusco, Guowei Gu, Jennifer Selever, Amanda Beyer, Kyle R. Covington, Anna Tsimelzon, Tao Wang, Susan G. Hilsenbeck, Gary C. Chamness, Sebastiano Andò, and Suzanne A.W. Fuqua. Loss of Rho GDIα and Resistance to Tamoxifen via Effects on Estrogen Receptor α. J Natl Cancer Inst. 2011 Apr 6; 103(7): 538–552. PMID: 21447808

opencc-zeroJul 2022View details →

Model simulation data used in "A global climatology of ice-nucleating particles under cirrus conditions derived from model simulations with EMAC-MADE3" (Beer et al., Atmos. Chem. Phys., 2022)

This dataset contains the output and the namelist setup of the EMAC-MADE3 global model simulations analysed and discussed in Beer et al. ("A global climatology of ice nucleating particles at cirrus conditions derived from model simulations with EMAC-MADE3", Atmos. Chem. Phys., 2022).

opencc-by-4.0Sep 2023View details →

Data from: In situ correlation between microplastic and suspended particulate matter concentrations in river-estuary systems support proxies for satellite-derived estimates of microplastic flux

Data from Sullivan et al., (in press) In situ correlation between microplastic and suspended particulate matter concentrations in river-estuary systems support proxies for satellite-derived estimates of microplastic flux, Marine Pollution Bulletin.  It contains the summary of the in situ measurements of TSM and microplastic counts and concentrations for each site. For more detail on the methods, users are directed to the methods section 2.2 of the open access paper.

opencc-zeroSep 2023View details →

Induction of daytime downward migration in a field-derived Daphnia population by the fish kairomone CPS – a mesocosm approach

The fish-borne bile salt 5α-cyprinol sulfate (CPS) has been identified as a kairomone inducing the predator avoidance behavior "diel vertical migration" (DVM) in Daphnia magna in response to fish. Conclusions about the ecological significance of CPS have been derived from laboratory experiments only. Using a mesocosm approach, we investigate whether the role of CPS as a kairomone can be confirmed in the field. We demonstrate that CPS induces downward migration during daytime in a field-derived Daphnia community consisting of D. longispina and D. cucullata and in D. longispina in particular. In the study lake, D. longispina shows a similar pattern of DVM. Quantification of CPS by HPLC-MS confirms that CPS in situ concentrations in the lake are sufficiently high for induction of daytime downward migration of D. longispina in this oligo-mesotrophic lake. Conclusively, we provide evidence for the significance of CPS as a kairomone in freshwater systems.

opencc-zeroSep 2023View details →

Data from: Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions

Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods have left DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scaled community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant derived eDNA analysis for large-scale biodiversity assessments that include information about community level interactions.

opencc-zeroOct 2023View details →

Data for: Simultaneous subset tracing and miRNA profiling of tumor-derived exosomes via dual-surface-protein orthogonal barcoding

The clinical potential of miRNA-based liquid biopsy has been largely limited by the heterogeneous sources in plasma and tedious assay processes. Here we develop a precise and robust one-pot assay called dual-surface-protein-guided orthogonal recognition of tumor-derived exosomes and in-situ profiling of microRNAs (SORTER) to detect tumor-derived exosomal miRNAs and enhance the diagnostic accuracy of prostate cancer (PCa). The SORTER utilizes two allosteric aptamers against exosomal marker CD63 and tumor marker EpCAM to create an orthogonal labeling barcode and achieve selective sorting of tumor-specific exosome subtypes. Furthermore, the labeled barcode on tumor-derived exosomes initiated targeted membrane fusion with liposome probes to import miRNA detection reagents, enabling in-situ sensitive profiling of tumor-derived exosomal miRNAs. With a signature of six miRNAs, SORTER differentiated PCa and benign prostatic hyperplasia with an accuracy of 100%. Notably, the diagnostic accuracy reached 90.6% in the classification of metastatic and non-metastatic PCa. We envision that the SORTER will promote the clinical adaptability of miRNA-based liquid biopsy.