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Figure 1. - Sample sites of Palaemoncarteri, Palaemonivonicus and Palaemonyuna sp. n. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas; AC-Acre; AM-Amazonas; AP-Amapá; MS-Mato Grosso do Sul; MT-Mato Grosso; PA-Pará and RO-Rondônia.
Figure 1. - Sample sites of Palaemoncarteri, Palaemonivonicus and Palaemonyuna sp. n. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas; AC-Acre; AM-Amazonas; AP-Amapá; MS-Mato Grosso do Sul; MT-Mato Grosso; PA-Pará and RO-Rondônia.
Daily climate data for Pousada Aguape, MS, Brazil, November 2021-October 2022
<p class="MsoNormal"><span>The extent to which animals may compensate for rising temperatures through behavioral thermoregulation is an important unknown in predicting responses to climate change. Flexibility in temporal activity in particular may be an important factor in determining species' vulnerability. In this study, we examine whether the white-lipped peccary, a predominantly diurnal Neotropical mammal, shifts its temporal activity and microclimate selection in response to daily temperature variation in the Pantanal biome of Brazil. From November 2021 to October 2022, we deployed camera traps and microclimate data loggers to record white-lipped peccary activity and air temperature on a fine spatiotemporal scale. We found that the percentage of peccary activity that is nocturnal increased with maximum daily temperature at a rate of 3.7% per 1°C past a threshold of 31.2°C, and increased with maximum daily wet-bulb temperature at a rate of 4.7% per 1°C past a threshold of 24.9°C. The afternoon period (i.e. solar noon to sunset) went from having the highest frequency of peccary activity at the lower end of our observed temperature range to having the lowest frequency of activity at the higher end. We did not find evidence of microclimate selection. Our findings indicate that white-lipped peccaries in the Pantanal demonstrate substantial behavioral flexibility in their response to high temperatures, which may help to buffer them against the impact of rising temperatures caused by climate change.</span></p> <p class="MsoNormal"><span>This dataset includes all data from the microclimate date loggers. Camera trap records can be accessed through Wildlife Insights.</span></p>
Algoa Bay 2018/2019 LC-MS/MS DOM study
<p>This dataset contains the raw and processed data for a nontargeted tandem mass spectrometry study of dissolved organic matter (DOM) in surface water collected from the Algoa Bay system in the Eastern Cape of South Africa in 2018/2019</p>
STAVER: A Standardized Benchmark Dataset-Based Algorithm for Effective Variation Reduction in Large-Scale DIA-MS Data
<p>This project focuses on developing and applying STAVER, an innovative DIA algorithm designed to eliminate non-biological noise and variability from the large-scale DIA-MS study dataset analyses. STAVER is a flexible framework that utilizes prior knowledge regarding peptide separation coordinates (RT) and fragment ion intensities from the standard benchmark datasets, which effectively mitigates non-biological noise potential during library searches, enhancing spectrum identifications and protein quantification accuracy. Furthermore, the robustness and broad applicability of STAVER were validated in multiple large-scale DIA datasets from different platforms and laboratories, demonstrating significantly improved precision and reproducibility of protein quantification. It facilitates the comparative and integrative analysis of DIA datasets across different platforms and laboratories, enhancing the consistency and reliability of findings in clinical research. The project aims to promote the adoption of hybrid library search and improve the sensitivity and quality of DIA proteomics data through the open-source STAVER software package.</p>
DRAFT dataset for MS on Greenland's subglacial geologic provinces by MacGregor et al.
<p>DRAFT dataset for MS on Greenland's subglacial geologic provinces</p>
lc_ms_method_params
Test upload of a dataset
Quantification of phosphorylated metabolites, organic acids, and intermediates of the TCA cycle using capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) following treatment of Escherichia coli with ciprofloxacin
<p>Capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) was used to quantify phosphorylated metabolites, organic acids, and intermediates of the TCA cycle of Escherichia coli treated with ciprofloxacin, BTP-001 (a novel antimicrobial peptide), and a combination of the two . Metabolite extracts were analyzed with a Xevo TQ-XS triple quadrupole mass spectrometer (Waters, USA).</p><p>Samples were gathered from E. coli cultures grown in batch cultivations using 1 liter bioreactors. Briefly, intracellular metabolites were extracted by cycling samples between −20 °C EtOH and N2 (<i>l</i>) in three consecutive freeze–thaw cycles, with vortexing every 10 min during the thawing phase. Filters were removed and the cell debris was pelleted (4500 rcf, 10 min, -9 °C). The supernatants were transferred to a new tube, snap frozen in N2 (<i>l</i>), and lyophilized. Lyophilized extracts were reconstituted in 500 µL cold Milli-Q H2O and cleared by spin-filtration with a 10 kDa molecular cutoff (20817 rcf, 10 min, 0 °C). A mix of 80 µL centrifuged sample and 20 µL 13C-labeled ISTD extract from yeast was sent to analysis. </p><p>Data processing and absolute quantification was performed as earlier described using the TargetLynx application manager of MassLynx v 4.1 (Waters) to interpolate calibration curves made with appropriate dilutions of analytical grade standards (Sigma-Aldrich). The response factor of the corresponding U13C-isotopologues were used to correct the standard and sample extract response factors. Extract concentrations were normalized to the CDW, which was calculated from interpolation of the OD600 vs. CDW (g/L) curve. </p><p>Further statistical analysis in MetaboAnalyst v 5.0 replaced missing values with 1/5 of the minimum value of the respective metabolite. An unpaired T-test with unequal variance determined differential enriched metabolites with a false discovery rate (FDR) < 0.05 which are presented as log2 fold-change compared to control. </p>
collected PTR-ToF-MS data, optical-based data, food frequency questionairre results, adipose tissue measurements, and anthroprometrics
<p><span>This file contains the collected PTR-ToF-MS data, optical-based data, food frequency questionairre results, adipose tissue measurements, and anthroprometrics. These data were used in the Periodic Technical Report Part B covering M37-M54. Graph generated from these data are Figure 16 and Figure 17 under Taks 7.5.</span></p> <p><span> </span></p> <p><span>Abbreviation<span> </span>Explanation</span></p> <p><span>BMI<span> </span>Body Mass Index</span></p> <p><span>SAT<span> </span>Subcutaneous adipose tissue</span></p> <p><span>VAT<span> </span>Visceral adipose tissue</span></p> <p><span>DHD1<span> </span>Vegetable intake</span></p> <p><span>DHD2<span> </span>Fruit intake</span></p> <p><span>DHD3<span> </span>Whole wheat products</span></p> <p><span>DHD4<span> </span>Legumes</span></p> <p><span>DHD5<span> </span>Nuts/seeds</span></p> <p><span>DHD6<span> </span>Dairy</span></p> <p><span>DHD7<span> </span>Fish</span></p> <p><span>DHD8<span> </span>Fat/oils</span></p> <p><span>DHD9<span> </span>High-fat and processed meat</span></p> <p><span>DHD10<span> </span>Sugar-containing beverages</span></p> <p><span>DHD11<span> </span>Unhealthy choices</span></p>
Dataset for MS 2023-04-06217B
<p>Dataset belonging to manuscript submitted as: MS 2023-04-06217B</p>
Deciphering the impacts of main inflowing rivers on dissolved organic matter in Lake Daye using isotopes, optical spectroscopy, and FT-ICR-MS during non-flood season
<p>The uploaded data include water quality data, isotopes, DOM fluorescence index and FT ICR MS data of Daye Lake and its inflowing rivers.</p>
UVSL MS 950 Tamiḻneṟiviḷakkam
<p>டாக்டர் உ.வே.சா. நூலகம், Ṭākṭar u.Vē.Cā. Nūlakam, Ceṉṉai</p> <p><a href="https://www.tamildigitallibrary.in/palms_detail?id=jZY9lup2kZl6TuXGlZQdjZl6kuUy" rel="nofollow">https://www.tamildigitallibrary.in/palms_detail?id=jZY9lup2kZl6TuXGlZQdjZl6kuUy</a></p> <p>This is an archive copy of the manuscript images provided by the Tamil Digital Library.</p>
LA-ICP-MS data files
<p>These are the data files needed to recreate the LA-ICP-MS trace element maps of steatite accessory minerals as presented in my MPhil thesis: <em>Chmielowski, R. M. (2024). Viking Age Steatite in Sweden: Accessory Mineral Provenancing and the Biographical Approach, Durham University. </em></p> <p>The target user is anyone who wishes to compare this data with their own archaeological research results to determine the provenance of steatite artefacts. However, this data set would also lend itself well as part of a study to investigate the geologic history and/or metamorphic fluid flow studies in these areas. Furthermore, this dataset would lend itself well as a practice set for students learning to process LA-ICP-MS data to produce trace element composition maps of single crystals in a rock matrix as it contains a variety of mineral types and different types of crystal zoning. In all cases see the thesis itself for information about the context of the data sets, and for images of the maps I created with this raw data.</p> <p>There are 32 folders, one for each trace element map created [there is no sample map M30, as it proved not to be steatite].</p> <p>It is not recommended to attempt to read the .csv files yourself. Best results are obtained using a program such as Iolite4 <https://iolite.xyz/> to read and interact with the files. </p> <p>Each folder contains:</p> <ul> <li><strong>A back-scatter electron image, in .jpg format</strong>, of the mapped sample area, with a file name in the format of M1, M2, etc., were “M1” is the name of the trace element map as used in this thesis. Where possible this image was taken before the laser ablation session. If there is no “before” image then the provided jpg was taken after laser ablation.</li> <li><strong>A folder of .csv data files from the ICP-MS</strong>, where the folder name takes the format “M1 ICP-MS files”, “M2 ICP-MS files”, etc., were “M1” is the name of the trace element map as used in this thesis. <ul> <li>The individual ICP-MS data files are in .csv format, and were named automatically by the ICP-MS computer. </li> <li>Their names take the form of “2019-04-20sulphidemap_1”, where the numbers give the date of the experiment laser ablation session, the text gives the name for the experiment used on the day, and the number after the underscore shows where in the sequence of the files a given file takes.</li> <li>The first and final set of these files correspond to the “Standards”, the laser ablation of the standard reference materials and “blanks” (laser firing, but at zero percent power, so that the ICP-MS is measuring the “background” levels of the day). There are typically, but not always 10 files for each set of standards: <ul> <li> one blank</li> <li>followed by two spots of the standard reference material (SRM) “Nist612”</li> <li>followed by a blank</li> <li>followed by two spots of the SRM “MASS1”</li> <li>followed by a blank</li> <li>followed by two spots of SRM “Fe-S1”</li> <li>followed by one blank.</li> </ul> </li> <li>Between the standards is the map data, with each file containing the total ICP-MS analysis collected during an interval of time that was slightly longer than needed to laser ablate one row of the map. Because the ICP-MS starts analysing before the laser starts firing, and continues after it stops, each of these files have an additional “blank” period before and after the line. (Save for one example where the ICP-MS stopped early for for several rows of data.)<br>Each of these files starts with a header section which records the name of the line, the date, and various settings of the ICP-MS. Below that is the actual comma separated data showing the time stamp, and the measured counts per second for each analysed elements.</li> </ul> </li> <li><strong>A folder of .csv data of laser log files</strong>, from the laser computer, where the folder name takes the format “M1 laser log files”, “M2 laser log files”, etc., were “M1” is the name of the trace element map as used in this thesis. <ul> <li>The individual data files are in .csv format, and their file names were generated automatically by the laser computer, and take the form of “ScanLog_19-04-30_09-02-45”, where the first set of numbers is a date stamp (year, month day), and the second set of numbers is a time stamp (hour, minutes, and seconds).</li> <li>The files themselves contain a series of time stamps that correspond to each time the laser fired for a specific “spot” or “line”, the cosponsoring X-Y position (in µm) of the laser stage at that moment in time, details about the laser spot size and speed of movement.</li> </ul> </li> </ul> <p>If you use this data please let me know, I would love to hear if it is being used for archaeological, geological, or educational, or other purposes.</p>
Photoreceptor-induced LHL4 protects photosystem II monomer - XL-MS and Alphafold2 intergrative modelling
<p>This dataset refers to the following preprint: https://www.biorxiv.org/content/10.1101/2024.02.23.581703v1 </p> <p>It provides:</p> <ul> <li>readable XL_MS annotate fragmentattion spectra for the crosslinks detected involved in the LHL4 interaction with CP43 and CP47. These complements the raw files submited in PRIDE (accession PXD049352) and the Supplementary Table 1 annexed to teh manuscript supplementray materials</li> <li>The complete output files for the AlphaFold2 multimer prediciotn of the pairwise interactions between LHL4 and CP43/CP47</li> </ul> <p> </p>
Chromatograms obtained by GC-MS of the four essential oils (Mentha pulegium, Origanum vulgare, Rosmarinus officinalis, Myrtus communis).
<p>The four selected bioactive EOs (Mentha pulegium, Origanum vulgare, Rosmarinus officinalis, Myrtus communis) was performed using gas chromatography (GC) (Agilent 7890A Series) coupled to mass spectrometry (MS) equipped with a multimode injector and a 123-BD11 column of dimension (15 m × 320 μm × 0.1 μm) at Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR) Institute.</p> <p>This file showed the outputs of the chromatogram obtained by GC-MS of the four essential oils (Mentha pulegium, Origanum vulgare, Rosmarinus officinalis, Myrtus communis).</p>
X-ray diffraction data, crystallographic information file, infrared spectra, and LA-ICP-MS depthprofiles of davemaoite
<p>Calcium silicate perovskite, CaSiO3, is arguably the most geochemically important phase in the lower mantle, because it concentrates elements that are incompatible in the upper mantle, including the heat-generating elements thorium and uranium, which have half-lives longer than the geologic history of Earth. We report CaSiO3-perovskite as an approved mineral (IMA2020-12a) with the name davemaoite. The natural specimen of davemaoite proves the existence of compositional heterogeneity within the lower mantle. Our observations indicate that davemaoite also hosts potassium in addition to uranium and thorium in its structure. Hence, the regional and global abundances of davemaoite influence the heat budget of the deep mantle, where the mineral is thermodynamically stable.</p>
Implementación del proyecto Fortalecimiento de la capacidad instalada del laboratorio de cromatografía líquida, HPLC-MS (Bioanalitics) de la Universidad del Valle, para la investigación en la región pacífico - Valle del Cauca"
<p>Dentro del Plan Estratégico de Desarrollo 2015-2025 de la Universidad del Valle (UNIVALLE)1, se creó el Programa para el Fortalecimiento del Sistema de Laboratorios. De manera complementaria, se plantea crear el sistema de laboratorios articuladores tipo core facilities también llamados laboratorios centralizados, laboratorios articuladores o Laboratorios Estratégicos Compartidos (LEC´s). Este mismo tipo de sistemas de laboratorios ya se encuentran funcionando en otras universidades en Colombia2-5. Para determinar cuál debería ser el primer LEC de la Universidad del Valle, se procedió a hacer una investigación de las necesidades más apremiantes de los grupos de investigación dentro de la Institución, y que también puedan fortalecer las necesidades de la región pacífico desde el centro universitario. Es por ello que con el estudio realizado, se determina que la Universidad cuenta con más de 30 grupos de investigación y más de 15 laboratorios investigando en temas relacionados con biodiversidad, agroindustria, sistemas agropecuarios, alimentos, medio ambiente y salud. Pero la universidad no cuenta con la tecnología necesaria que respalde la realización de investigaciones que permitan la caracterización e identificación de compuestos conocidos y desconocidos en las muestras relacionadas con las áreas anteriormente mencionadas. Para fortalecer la infraestructura tecnológica para el desarrollo de actividades que sirvan a la identificación y caracterización de compuestos (análisis molecular) se propone crear el laboratorio articulador BIOANALITICS. Un laboratorio de uso compartido e interdisciplinario para los grupos de investigación que impactan en los focos Agroindustria y Agropecuario, Salud (farmacia y nutrición), Biodiversidad y Medio Ambiente. BIOANALITICS tendrá como base la compra de un equipo de cromatografía líquida (LC) acoplado a espectrometría de masas de alta resolución (HRMS). Con este trabajo se pretende presentar el desarrollo investigativo que se llevó a cabo desde la propuesta del programa de Fortalecimiento del Sistema de Laboratorios hasta la puesta en marcha del laboratorio bioanalitics financiado por el Sistema General de Regalías con recursos que provienen del fondo de ciencia, tecnología e innovación de las regiones del Cauca, Chocó, Nariño y Valle del Cauca, complementado con recursos propios de la Universidad del Valle, y al mismo tiempo se pretende presentar cómo se proyecta el laboratorio y como plantea su funcionamiento de acuerdo a los principios básicos de los laboratorios tipo core-shell6 Entre los resultados esperados se encuentran la articulación de grupos de investigación en proyectos interdisciplinarios, apoyar los procesos de formación para estudiantes de maestría y doctorado, y tener posgrados competitivos a nivel internacional con atracción de nuevos estudiantes de maestría y doctorado, incluso internacionales, con lo que se espera fomentar las publicaciones de alto impacto, permitiendo el retorno de la diáspora de investigadores colombianos que deseen hacer investigación aplicando estas técnicas analíticas. Se discutirá acerca de los problemas, y los beneficios que se han identificado durante la implementación de Bioanalitics, desde su concepción, hasta la realidad transformada al día de hoy, al igual que la implementación de políticas para la administración, manejo y uso de los laboratorios articuladores dentro del sistema de gestión de calidad de la UNIVALLE.</p>
A novel UPLC-MS metabolomic analysis-based strategy to monitor the course and extent of iPSC differentiation to hepatocytes
<p>ms2 raw data, peak tables generated in Quantitative Analysis Software from Agilent and Matlab functions for QC-SVRC, data clean-up and analysis for the publication with title "Monitoring the differentiation of iPSC to hepatocytes by means of UPLC-MS metabolomics".</p>
In vitro shoot regeneration and root induction of Hylocereus polyrhizus 'Da Hong' from Murashige and Skoog (MS) medium supplemented with 0.05–0.20 mg/L α-naphthaleneacetic acid (NAA).
<p>Figure S1. <em>In vitro </em>shoot regeneration and root induction of <em>Hylocereus polyrhizus</em> ‘Da Hong’ from Murashige and Skoog (MS) medium supplemented with 0.05–0.20 mg/L α-naphthaleneacetic acid (NAA). Treatments: CS, control; TS01, 0.05 mg/L NAA; TS02, 0.10 mg/L NAA; TS03, 0.20 mg/L NAA. Bar = 5 cm.</p>
Chromatin-IP-MS raw data
<p>Immunoprecipitated proteins by Flag-Polη were resolved by SDS-PAGE, excised and in-gel digested with trypsin, and analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) on a Thermo Orbitrap Fusion Lumos mass spectrometer.</p>
Plantlet weight, including shoots and roots, and root/shoot ratio of Hylocereus polyrhizus 'Da Hong' grown on Murashige and Skoog (MS) medium supplemented with α-naphthaleneacetic acid (NAA) alone.
<p>Figure S2. Plantlet weight, including shoots and roots, and root/shoot ratio of <em>Hylocereus polyrhizus</em> ‘Da Hong’ grown on Murashige and Skoog (MS) medium supplemented with α-naphthaleneacetic acid (NAA) alone. Treatment: CS, control; TS01, 0.05 mg/L NAA; TS02, 0.10 mg/L NAA; TS03, 0.20 mg/L NAA. Mean ± SE (n = 3, 5 segments per replicate). Means followed by different letters near the column and circle are significantly different at <em>p </em>= 0.05 using Fisher’s protected LSD test.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.