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Code and data set for data analysis published as manuscript "Bacttle: a microbiology educational board game for lay public and schools"
<p>Code that processed raw data and plots the figures of the manuscript "Bacttle: a microbiology educational board game for lay public and schools"</p> <p>Below is a table with the original survey questions. The ID corresponds to the column displayed on the data set. When letters are followed by a number (1 or 2), it means that the question was answered before playing the game (1) and after playing the game (2).</p> <table> <tbody> <tr> <td> <p><em>ID<sup>1</sup></em></p> </td> <td> <p><em>Question text</em></p> </td> <td> <p><em>Possible answers<sup>2</sup></em></p> </td> </tr> <tr> <td> <p><em>A</em></p> </td> <td> <p>How old are you?</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p><em>B</em></p> </td> <td> <p>Do you know what a bacterium is?</p> </td> <td> <p>y/n</p> </td> </tr> <tr> <td> <p><em>C</em></p> </td> <td> <p>Do you know what a bacterial capsule is?</p> </td> <td> <p>y/n</p> </td> </tr> <tr> <td> <p><em>D</em></p> </td> <td> <p>Do bacteria have tools to harm each other?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>E</em></p> </td> <td> <p>Do bacteria reproduce at the same pace?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>F</em></p> </td> <td> <p>What is sporulation?</p> </td> <td> <p>A resistant state that some bacteria can achieve under unfavorable conditions.</p> </td> </tr> <tr> <td> <p>The release of toxins by bacteria.</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>G</em></p> </td> <td> <p>What are flagella used for?</p> </td> <td> <p>Sticking to surfaces.</p> </td> </tr> <tr> <td> <p>Motility in liquid environments.</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>H</em></p> </td> <td> <p>What does it mean to be lithotrophic?</p> </td> <td> <p>A bacterium can get energy from minerals.</p> </td> </tr> <tr> <td> <p>A bacterium can get energy from the sunlight.</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>I</em></p> </td> <td> <p>Can bacteria be infected by viruses?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>J</em></p> </td> <td> <p>Are all bacteria harmful for humans?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>K</em></p> </td> <td> <p>How many bacteria are in a coffee spoon of yoghurt?</p> </td> <td> <p>Millions</p> </td> </tr> <tr> <td> <p>Hundreds</p> </td> </tr> <tr> <td> <p>idk</p> </td> </tr> <tr> <td> <p><em>L</em></p> </td> <td> <p>How easy did you find the gameplay?</p> </td> <td> <p>VE/E/A/D/VD</p> </td> </tr> <tr> <td> <p><em>M</em></p> </td> <td> <p>Did you find the card content easy to understand?</p> </td> <td> <p>VE/E/A/D/VD</p> </td> </tr> <tr> <td> <p><em>N</em></p> </td> <td> <p>Did you like the setup of the game?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>O</em></p> </td> <td> <p>Would you like to play this game again?</p> </td> <td> <p>y/n/idk</p> </td> </tr> <tr> <td> <p><em>P</em></p> </td> <td> <p>What can we improve?</p> </td> <td> <p> </p> </td> </tr> </tbody> </table> <p>1) Question A categorizes the player’s age; B and C assess the initial level of knowledge in microbiology (none -both questions are answered negatively-, basic -player knows what a bacterium is but not a bacterial capsule-, or advanced -both answers are positive-); questions D-I score knowledge acquisition; J and K are control questions; L-O evaluate the appreciation of the game; and P is an optional free text-entry answer for additional feedback. <br>2) y= yes, n=no, idk=I don’t know, VE=very easy, E=easy, A=adequate, D=difficult, VD=very difficult.</p>
Microbiological data from studies to optimise depuration of viruses from Pacific oysters (Crassotrea gigas)
<p>Viral contamination of bivalve molluscan shellfish is a recognised cause of foodborne gastroenteritis. Unlike bacterial contaminants, viruses such as norovirus are not easily removed once shellfish become contaminated. Therefore the normal practice of depurating following harvest may not effectively reduce the risk of become ill following consumption of shellfish.</p> <p>As part of the SeafoodTomorrow consortium project (Horizon 2020), studies were undertaken to determine the optimal conditions under which Pacific oysters (Crassostrea gigas) are depurated (purified) following harvest.</p> <p>This dataset includes levels of norovirus, F specific coliphage genogroup II and E. coli found in oysters following several experiments in which depuration conditions were varied.</p>
Burmese MicroBiology 1K Dataset
<div> <h1>Burmese-Microbiology-1K</h1> <br> <h3>Min Si Thu, min@globalmagicko.com</h3> <br> <div>Clinical Microbiology 1K QA pairs in Burmese Language</div> <br>Purpose</div> <div><br> <div>Before this Burmese Clinical Microbiology 1K dataset, the open-source resources to train the Burmese Large Language Model in Medical fields were rare.</div> <div>Thus, the high-quality dataset needs to be curated to cover medical knowledge for the development of LLM in the Burmese language.</div> <br> <div>Motivation</div> <br> <div>I found an old notebook in my box. The book was from 2019. It contained written notes on microbiology when I was a third-year medical student. Because of the need for Burmese language resources in medical fields, I added more facts, and more notes and curated a dataset on microbiology in the Burmese language.</div> <br> <div>About</div> <br> <div>The dataset for microbiology in the Burmese language contains <strong>1262 rows of instruction and output pairs in CSV format</strong>.</div> <div>The dataset mainly focuses on clinical microbiology foundational knowledge, abstracting basic facts on culture medium, microbes - bacteria, viruses, fungi, parasites, and diseases caused by these microbes.</div> <br> <div>Examples</div> <br> <div> <ul> <li>ငှက်ဖျားရောဂါဆိုတာ ဘာလဲ?,ငှက်ဖျားရောဂါသည် Plasmodium ကပ်ပါးကောင်ကြောင့် ဖြစ်ပွားသော အသက်အန္တရာယ်ရှိနိုင်သည့် သွေးရောဂါတစ်မျိုးဖြစ်သည်။ ၎င်းသည် ငှက်ဖျားခြင်ကိုက်ခြင်းမှတဆင့် ကူးစက်ပျံ့နှံ့သည်။</li> </ul> </div> <br> <div> <ul> <li>Influenza virus အကြောင်း အကျဉ်းချုပ် ဖော်ပြပါ။,Influenza virus သည် တုပ်ကွေးရောဂါ ဖြစ်စေသော RNA ဗိုင်းရပ်စ် ဖြစ်သည်။ Orthomyxoviridae မိသားစုဝင် ဖြစ်ပြီး type A၊ B၊ C နှင့် D ဟူ၍ အမျိုးအစား လေးမျိုး ရှိသည်။</li> </ul> </div> <br> <div> <ul> <li>Clostridium tetani ဆိုတာ ဘာလဲ,Clostridium tetani သည် မေးခိုင်ရောဂါ ဖြစ်စေသော gram-positive၊ anaerobic bacteria တစ်မျိုး ဖြစ်သည်။ မြေဆီလွှာတွင် တွေ့ရလေ့ရှိသည်။</li> </ul> </div> <br> <div> <ul> <li>Onychomycosis ဆိုတာ ဘာလဲ?,Onychomycosis သည် လက်သည်း သို့မဟုတ် ခြေသည်းများတွင် ဖြစ်ပွားသော မှိုကူးစက်မှုဖြစ်သည်။ ၎င်းသည် လက်သည်း သို့မဟုတ် ခြေသည်းများကို ထူထဲစေပြီး အရောင်ပြောင်းလဲစေသည်။</li> </ul> </div> <br> <div>GitHub Repository</div> <br> <div>https://github.com/MinSiThu/Burmese-Microbiology-1K/blob/main/data/Microbiology.csv</div> </div> <div> </div> <div>Applications</div> <div><br> <div>Burmese Microbiology 1K Dataset can be used in building various medical-related NLP applications.</div> <div> </div> <div> <ul> <li>The dataset can be used for pretraining or finetuning the dataset on Burmese Large Langauge Models.</li> <li>The dataset is ready to use in building RAG-based Applications.</li> </ul> </div> <br> <div>Acknowledgments</div> <br> <div>Special thanks to magickospace.org for supporting the curation process of **Burmese Microbiology 1K Dataset**.</div> <div> </div> <div>Contact</div> <div> </div> <div>LinkedIn - https://www.linkedin.com/in/min-si-thu/</div> </div>
Chemical and microbiological properties of soils in the Andrews Experimental Forest (1994 REU Study)
To conduct a comprehensive study of soil chemical and microbiological properties at the HJA during the week of July 11,1994.
Datasets of Twitter mentions and publications in Information Science & Library Science and Microbiology
<p>Datasets used in the study 'Identifying and characterizing social media communities: a socio-semantic network approach to altmetrics'.</p> <p><strong>Microbiology publications (mic_publiccations.tsv).</strong> Dataset of 101,206 Microbiology publications with their author keywords.</p> <p><strong>Microbiology mentions (mic_mentions.tsv).</strong> Dataset of 328,110 Twitter mentions to Microbiology publications.</p> <p><strong>Information Science & Library Science publications (lis_publications.tsv).</strong> Dataset of 8452 Information Science & Library Science publications with their author keywords.</p> <p><strong>Information Science & Library Science mentions (lis_mentions.tsv).</strong> Dataset of 35,411 Twitter mentions to Information Science & Library Science publications.</p>
Microbiological agents as notified to EFSA
<p>This is the list of “Microbiological agents as notified to EFSA” from 2007, in the context of technical dossiers to EFSA Units, for intentional use in feed and/or food or as sources of food and feed additives, enzymes and plant protection products (PPPs) for safety assessment.</p> <p>This is supplementing the QPS statements part 11, part 12, part 13, part 14, part 15, part 16, part 17, part 18, part 19, part 20, part 21, part 22 and the 2022 Scientific Opinion of the BIOHAZ Panel of EFSA - see related identifiers.</p> <p>EFSA topic on QPS: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.efsa.europa.eu%2Fen%2Ftopics%2Ftopic%2Fqualified-presumption-safety-qps&data=02%7C01%7C%7Ca3e4d3a851c84defc2a008d7aa44f9e5%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637165085527366985&sdata=TlcglouTWhBY24K5ApAoawNpADKgyl%2FefxVUEbxjQo0%3D&reserved=0">https://www.efsa.europa.eu/en/topics/topic/qualified-presumption-safety-qps</a></p>
Dataset of Chen et al. (2023) "MCount: An automated colony counting tool for high-throughput microbiology"
<p>Folder "96 well colonies" contains 10 microplate images with the original resolution. Folder "results" contains a segmentation and quantification results from the microplate images. Folder "Codes" includes Python source code.</p>
Data for Water inputs across the Namib Desert: implications for dryland edaphic microbiology
<p>These are the data files required to run the analyses in Water inputs across the Namib Desert: implications for dryland edaphic microbiology.</p>
Data of microbiological decomposition monitoring of pine coniferous litter in the soils at the Moscow region by the ICP IM method
<p>Данные мониторинга микробиологического разложения хвойного опада сосны в почвах Московской области по методу ICP IM</p> <p>Data of microbiological decomposition monitoring of pine coniferous litter in the soils at the Moscow region by the ICP IM method</p> <p> </p> <p>Исследования проведены на базе двух особо охраняемых природных территориях (далее ООПТ) в Московской области и г. Москве, расположенных на расстоянии 90 км друг от друга. На обеих ООПТ работы проводились на постоянных пробных площадках (ППП) площадью 1 га.</p> <p>Эталон – Приокско-Террасный государственный природных биосферный заповедник. В заповеднике заложены 4 ППП, расположенные в бассейне малой реки Тоденка, большая часть бассейна которой находится в границах Заповедника. ППП расположены не далее 2 км от русла реки, в преобладающих по площади в ООПТ типах лесах: сосняке сложном (две ППП), березняке сложном широкотравном и дубраве широкотравной. В сосняках Заповедника были заложены 2 ППП, различающиеся по увлажнению и месторасположению, на террасе и на коренном берегу.</p> <p>Модельная находится под более высокой антропогенной нагрузкой в г. Москве с лесопарковая часть природно-исторического парка «Кузьминки-Люблино» (далее – Лесопарк), имеющая также схожий с Заповедником рельеф и породный состав лесов. Территории Заповедника и Лесопарка имеют сходство физико-географических условий формирования: обе ООПТ расположены на надпойменных террасах крупных рек Волжского бассейна (рек Оки и Москвы соответственно), на обеих территориях формируются слабо дифференцированные дерново-подзолистые почвы ржавоземы на флювиогляциальных песках (Brunic Arenosols) под сосновыми и березовыми лесами. Основные физико-химические свойства почв Лесопарка соответствуют естественным аналогам.</p> <p><strong>Метод изучения скорости разложения опада.</strong> Методической основой проводимых измерений скорости биоразложения опада является метод подпрограммы «MB Microbial decomposition» программы ICP IM [https://www.syke.fi/en-US/Research__development/Nature/Monitoring/Integrated_Monitoring/Manual_for_Integrated_Monitoring] с некоторыми изменениями.</p> <p>Изменения методики касались срока экспозиции. Мы использовали стандартный срок экспозиции в 1 год и отказались от экспозиции иголок более 1 года, как рекомендовано в методике ICP IM. Такая модификация метода позволила существенно сократить трудозатраты при получении сравнимых результатов.</p> <p>Измерение разложения опада проводились методом закладки конвертов из нейлоновой сетки 8 на 8 см с ячеей 1 мм с упакованными в них пробами на срок 1 год. Конверты запечатывались металлическими скобами. Пробы закладывались и снимались в последней декаде октября – начале ноября. В таблицах и тексте год указывается по году снятия образца, соответственно, пробы, заложенные в 2013 г. и собранные в 2014 г. относятся к 2014 г.</p> <p>Согласно методике, в экспериментах по изучению разложения опада использовались иголки сосны обыкновенной (<em>Pinus</em> <em>sylvestris</em> L.), которые собирались с ветвей невысоких деревьев (10–20 лет) в одном и том же квартале Заповедника и только пожелтевшие, перед их массовым опадом (обычно в начале октября). Предварительно все пробы высушивались до абсолютно сухого веса при 85 <sup>0</sup>С и взвешивались перед упаковкой в конверты. Взвешивание осуществлялось с точностью до 0.001 г, вес проб соснового опада 1 г.</p> <p>Конверты каждый год раскладывались на каждой ППП размерами 100×100 м возле углов и в центре пробных площадей в пределах квадрата 3×3 м в фиксированных точках. Конверты располагались в верхних 5 см почвы, под углом в 15<sup>0</sup>, под моховым покровом (при его наличии) или подстилкой и привязывались леской для удобства поиска. Не допускалось размещение конверта в приствольном круге деревьев. После экспозиции в течение 12 месяцев (350–380 суток) конверты снимались, а содержимое проб аккуратно с использованием пинцета промывалось дистиллированной водой от твердых частиц субстрата и мицелия грибов до остатков иголок и высушивалось до абсолютно сухого веса. Измерение потери массы каждой пробы проводилось методом взвешивания с точностью 0.001 г. Ежегодно закладывалось по 5 проб на каждой ППП в сосняке и березняке, но через год не всегда удавалось найти все заложенные конверты, так как происходили ветровалы и иные нарушения. На ППП в дубняке закладывалось по 10 конвертов.</p>
NGS in the clinical microbiology settings
<p>This dataset contains bam files from 16s rRNA targeted NGS sequencing from a variety of clinical specimens. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing. </p> <p>NGS: We sequenced the amplified V1-2 or V4 regions of 16s rRNA gene with Ion S5™ System (Thermo Fisher Scientific). Data were analyzed using the Ion Reporter bioinformatics Software pipeline (Thermo Fisher Scientific), using a threshold of 1000 mapped reads for designating significant pathogens. BAM files uploaded to the Ion Reporter were mapped to the Silva 138 SSU database.</p>
Data and code for: a behavioural and microbiological study of wound care in Camponotus floridanus
<p><span>Open wounds pose a major infection and mortality risk in animals. To reduce these risks, many animal species apply antimicrobial compounds on their wounds.<sup> </sup>Ant societies use antimicrobial secretions from the metapleural gland to combat pathogens<sup> </sup>but this gland has been lost over evolutionary time in several genera including <em>Camponotus</em>. Using behavioral and microbiological experiments, we studied how <em>Camponotus floridanus</em> handles infected wounds without the use of antimicrobial secretions. When we experimentally injured a worker's leg at the femur, nestmates amputated the injured limb by biting the base (trochanter) of the leg until it was severed, thereby significantly increasing survival compared to ants that did not receive amputations. However, when the experimental injury was more distal (at the tibia), nestmates did not amputate the leg and instead directed more wound care to the injury site. Experimental amputations also failed to improve survival in ants with infected tibia injuries unless the leg was amputated immediately after pathogen exposure. Micro CT-scans revealed that the muscles likely responsible for leg hemolymph circulation are predominantly in the femur. Thus, it is likely that femur injuries, by attenuating hemolymph flow, provide sufficient time for workers to perform amputations before pathogen spread. Overall, this study provides the first example of the use of amputations to treat infected individuals in a non-human animal and demonstrates that ants can adapt their type of treatment depending on the location of wounds.</span></p>
Po delta to Gulf of Trieste: Microbiological connectivity study and field testing of a Video-CTD probe prototype (JERICO-S3 PoGo project)
<p>ADCP and CTD data from field campaigns at S1-GB site (Po delta, Italy) performed in the scope of the JERICO-S3 PoGo project. This is raw data as collected by both instruments. The CTD prototype is under development at National Institute of Biology, Marine Biology Station Piran and hasn't been fully calibrated. The new recalibrated values have been added to mini-CTD-recalibrated archive.<br>The project report is available in this repository and at: https://www.jerico-ri.eu/ta/call-program/third-call/</p>
FIG. 9 in Two-phase medium - a new approach to microbiological culturing
FIG. 9. — Colonization of rock fragments in two-phase medium: A, Klebsormidium dissectum (F.Gay) H.Ettl & Gärtner with sandstone; B, with granite;C, Trentepohlia umbrina (Kütz.) Bornet with limeston; D, Vischeria polyphem (Pitschmann) Kryvenda, Rybalka, Wolf & Friedl with limesone. Scale bars: A, 1000 µm; B-D, 100 µm.
FIG. 8 in Two-phase medium - a new approach to microbiological culturing
FIG. 8. — Halos formed around rock fragments in two-phase media: A, medium with granite; B, medium with sandstone; C, medium with basalt; D, medium with limestone (thermal mapping images made with CorelDraw). Scale bars: 5 mm.
FIG. 6 in Two-phase medium - a new approach to microbiological culturing
FIG. 6. — Fungal development on two-phase medium containing granite: A, Penicillium sp.; B, Chaetomium globusom Kunze. Scale bars: A, 1 cm; B, 200 µm.
FIG. 4 in Two-phase medium - a new approach to microbiological culturing
FIG. 4. — Klebsormidium dissectum (F.Gay) H.Ettl & Gärtner. Thread-like (filamentous) clusters and single cells developed in two-phase media: A, containing limestone; B, containing granite. Scale bars: 10 µm.
FIG. 5 in Two-phase medium - a new approach to microbiological culturing
FIG. 5. — Microorganism development on two-phase medium containing limestone (marl): A, Aspergillus tubingensis R.Mosseray formed on surface of gel phase; B, A. tubingensis on limestone (solid phase); C, D, bacterial biofilms formed on surface of medium near limestone. Scale bars: 500 µm.
FIG. 3 in Two-phase medium - a new approach to microbiological culturing
FIG. 3. — Development of Klebsormidium dissectum (F.Gay) H.Ettl & Gärtner after 28 days of culture on two-phase media containing rock: A, granite; B, sandstone; C, basalt; D, limestone. Scale bars: 5 mm.
FIG. 2 in Two-phase medium - a new approach to microbiological culturing
FIG. 2. — Algal species growing on two-phase media with granite: A, Muriella decolor Vischer; B, Vischeria polyphem (Pitschmann) Kryvenda, Rybalka, Wolf & Friedl; C, Klebsormidium dissectum (F.Gay) H.Ettl & Gärtner. Scale bars: 10 µm.
FIG. 7 in Two-phase medium - a new approach to microbiological culturing
FIG. 7. — Mosses developed on two-phase media within: A, 2 weeks; B, 4 weeks. Scale bars: A, 2 mm; B, 1000 µm.
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.