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Cultivation of host-associated bacteria under sulfide-enriched microoxic and anoxic conditions
<p>Three images of cell colonies on culture plates inoculated with gill tissue homogenate from <em>Bathymodiolus brooksi</em>. The colonies grew under the following conditions: </p> <ul> <li>IMG_2467: microoxic, low H2S, low ammonium</li> <li>IMG_2468: microoxic, low H2S, low ammonium, organics</li> <li>IMG_2474: microoxic, low H2S, high ammonium, organics, 1 mM thiosulfate</li> </ul> <p>Image of a control plate without cultures inoculated with heat sterilized aliquot of <em>Bathymodiolus brooksi</em> gill homogenate:</p> <ul> <li>IMG_2475</li> </ul> <p>Two images of pH controls plated with homogenization medium that did not contain gill homogenate:</p> <ul> <li>IMG_2477: phenol red</li> <li>IMG_2479: bromothymol blue</li> </ul> <p>Two close up photos of colonies on agar plates</p> <ul> <li>IMG_2485</li> <li>IMG_2488</li> </ul>
Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells
<p>Single cell gene expression data for the paper "Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells" to appear in PLOS Pathogens.</p> <p>Package contains two single cell data sets, one consisting of single cells from PBMCs in three animals, and the other three tissues from one animal.</p> <p>The single-cells are grouped based on the SIV viral genes that they express.</p> <p> </p>
The morphologically glossed Rigveda - The Zurich annotation corpus revised and extended. Hosted by VedaWeb - Online Research Platform for Old Indic Texts.
<p>This file contains morphological and lexicographic annotations for the Rigveda. It was created in the DFG-funded research project Vedaweb and used as source data for the linguistic research platform <a href="https://vedaweb.uni-koeln.de">vedaweb.uni-koeln.de</a>.</p> <p>Prof. Dr. Paul Widmer and Dr. Salvatore Scarlata from the "Institut für Vergleichende Sprachwissenschaft" (Universität Zürich) provided the VedaWeb project a Filemaker file that was later transformed in Cologne into an Excel file. This data contained a version of the Rigveda by Prof. Dr. A. Lubotsky ("Indo-European Linguistics", Leiden University) that had been morphosytactically annotated over the course of more than 10 years at the University of Zurich. It also contained for each token, if available, a reference to an entry in Grassmann's dictionary for the Rigveda.</p> <p> </p> <p><strong>Modifications made by Jakob Halfmann and Natalie Korobzow to the data in 2020:</strong></p> <p>Disambiguation of the relevant categories, if unspecified in Zurich data, according to the Grassmann dictionary (updates from 6th edition partially included up to page 274):</p> <ul> <li>case, gender and number for nouns, pronouns (columns G–I)</li> <li>number, person, mood, tense and voice for verbs (columns I–M) up to line 109216</li> <li>case, gender, number, tense and voice for participles (columns G–I, L–M) up to line 109216</li> <li>absolutives are marked as Abs. in columns N and V</li> <li>Inconsistencies between the original file from Zurich and the Grassmann dictionary as well as internal inconsistencies in Grassmann are noted in column AE, whenever they were noticed.</li> <li>Zurich data was overwritten by conflicting Grassmann data in columns G–M but retained elsewhere.</li> <li>Verb classes according to Whitney (1885) and Jamison (1983) for class 10 in column Y, differences in root spelling between Whitney and Grassmann are noted in column Z. All potential verb classes provided by Whitney are given for every occurrence of the root.</li> <li>Local particles and verbal forms containing them are marked as LP in column AF.</li> <li>Comparatives and superlatives are marked as such in column X and desideratives as Des. in column Y.</li> </ul> <p> </p> <p><strong>Modifications made by Anna Fischer (data transformation, technical realisation) to the data:</strong></p> <p>New structure of data table for linguistic annotations with new column titles:</p> <ul> <li>A - "VERS_NR": renamed column (from "belege::stelleMMSSSRR")</li> <li>B - "PADA_NR": renamed column (from "belege::pada")</li> <li>C - "PADA_TEXT_LUBOTSKY": renamed column (from "belege::lubotskypada")</li> <li>D - "TOKEN_NR_VERS": renamed column (from "belege::wortnummer rc")</li> <li>E - "TOKEN_NR_PADA": renamed column (from "belege::wortnummer pada")</li> <li>F - "FORM": renamed column (from "belege::form")</li> <li>G - "KASUS": renamed column (from "belege::kasus")</li> <li>H - "GENUS": renamed column (from "belege::genus")</li> <li>I - "NUMERUS": renamed column (from "belege::numerus")</li> <li>J - "PERSON": renamed column (from "belege::person")</li> <li>K - "TEMPUS": moved and renamed column (from L "belege::tempus")</li> <li>L - "PRAESENSKLASSE": created new column for present stem class for each form</li> <li>M - "LEMMA_PRAESENSKLASSEN": created column for present stem classes of respective lemma: Moved and renamed column (from Y "formen::zusätzliche merkmale verb"), moved values "Abs." and "Inf." to column P "INFINIT", moved values "Prek." and "si-Ipv." to column N "MOOD", moved value "Des." to column Q "ABGELEITETE_KONJUGATION": moved value "se-Form" to column W "WEITERE_WERTE"</li> <li>N - "MODUS": moved and renamed column (from K "belege::modus")</li> <li>O - "DIATHESE": moved and renamed column (from M "belege::diathese")</li> <li>P - "INFINIT": created new column for infinite forms "Abs.", "Inf.", "Ptz.", "ta-Ptz.", "na-Ptz."</li> <li>Q - "ABGELEITETE_KONJUGATION": created new column for secondary conjugation "Des.", "Int.", "Kaus."</li> <li>R - "GRADUS": created new column for degree: "Comp.", "Sup."</li> <li>S - "LOKALPARTIKEL": moved and renamed column (from AF "LP")</li> <li>T - "LEMMA_ZÜRICH": moved and renamed column (from AA "lemmata klassisch::lemma")</li> <li>U - "LEMMA_ZÜRICH_LEMMATYP": moved and renamed column (from AB "lemmata klassisch::lemmatyp")</li> <li>V - "LEMMA_ZÜRICH_BEDEUTUNG": moved and renamed column (from AC "lemmata klassisch::bedeutung")</li> <li>W - "WEITERE_WERTE": created new column for all miscellaneous values: e.g. "Hyperchar.", "n-haltig", "se-Form"</li> <li>X - "KOMMENTAR": created new column merging former columns Z "formen::HELPformbestimmung", AD "lemmata klassisch::HELPbedeutung" and AE "anmerkungen abweichungen"</li> </ul> <p>Columns that were removed due to redundant information:</p> <ul> <li>"formen::zusätzliche merkmale nomen": values "superlative" And "comparative" were renamed "sup." and "comp." and moved to new column R "GRADUS", all other values were moved to new column for miscellaneous W "WEITERE_WERTE"</li> <li>"belege::belegbestimmung summe simpel": values "Ptz.", "ta-Ptz." and "na-Ptz." were moved to new new column P "INFINIT"</li> <li>"belege::kasus bestof"</li> <li>"belege::genus bestof"</li> <li>"belege::numerus bestof"</li> <li>"belege::person bestof"</li> <li>"belege::modus bestof"</li> <li>"belege::tempus bestof"</li> <li>"belege::diathese bestof"</li> <li>"belege::belegbestimmung bestof summe sophistiziert"</li> </ul> <p> </p> <p><strong>Revisions and additions made by Antje Casaretto to the data in 2023:</strong></p> <ul> <li>F-T: - revision and correction (wherever necessary) of all annotations (books 1-7)</li> <li>G,H,I - disambiguation of case forms, reg. pronouns and nominal forms, if unspecified in Zurich data (books 1-7)</li> <li>L - disambiguation of present stem classes (book 7 and book 1 up to line 21050 vers 01.125.01)</li> <li>M - disambiguation of denominal verbs from primary verbs of the 10th class (books 1-10)</li> <li>N - disambiguation of precative and optative forms wherever possible (books 1-7)</li> <li>Q - new annotations for "Int." (intensives) and "Kaus." (causatives) (books 1-7)</li> </ul> <p> </p> <p dir="ltr"><strong>Revisions and additions made by Antje Casaretto to the data in 2024 with support in data modeling and automation by Anna Fischer:</strong></p> <ul> <li>F-T: revision and correction (wherever necessary) of all annotations (books 8-10)</li> <li>G,H,I: disambiguation of case and gender forms in nominal and pronominal forms, if unspecified in Zurich data (books 8-10)</li> <li>L, M: disambiguation of present stem classes (books 1-10)</li> <li>N: disambiguation of precative and optative forms wherever possible (books 8-10)</li> <li>P: new annotations for "Gdv." (gerundives)</li> <li>Q: new annotations for "Den." (denominatives) (books 1-10) and further annotations of “Kaus.” (causatives) and “Int.” (intensives) (books 8-10)</li> <li>T: revision of lemmatization (books 1-10)</li> <li>V: update of meanings according to revised lemmatization; minimal revision</li> <li>W: revised annotation of ending -se (“se-Form”) (books 1-10); no systematic revision</li> <li>X: no systematic revision</li> <li>A-U: general revision of formal inconsistencies and typing errors (book 1-10)</li> </ul> <p> </p> <p dir="ltr"><strong>Revisions made by Natalie Korobzov and Pascal Coenen to the data in 2024 with computational support by Anna Fischer:</strong></p> <ul> <li>Y - "LEMMA_GRASSMANN_ID": new column for references to Grassmann dictionary (books 1-10) and revision of Grassmann references</li> </ul>
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
<p>Summary statistics for "Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation" </p><p>Files are organized in the following directory structure:</p><p><strong>G2G/</strong> - Summary statistics of G2G associations (SNPs, HLA, and gene-level analysis). </p><p><strong>HLA/ </strong>- Peptide binding prediction results</p><p><strong>preS1_haplotypes/ - </strong>Resolved intra-host haplotypes of the preS1 binding region. </p><p><strong>DnDs/</strong> - Calculation of intra-host positive selection, within the preS1 binding region. </p><p> </p>
Host biomarkers and combinatorial scores for the detection of serious and invasive bacterial infection in pediatric patients with fever without source
<h3><span>Background </span></h3> <p><span>Improved tools are required to detect bacterial infection in children with fever without source (FWS), especially when younger than 3 years old. The aim of the present study was to investigate the diagnostic accuracy of a host signature combining for the first time two viral-induced biomarkers, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and interferon </span><span>γ</span><span>-induced protein-10 (IP-10), with a bacterial-induced one, C-reactive protein (CRP), to reliably predict bacterial infection in children with fever without source (FWS) and to compare its performance to routine individual biomarkers (CRP, procalcitonin (PCT), white blood cell and absolute neutrophil counts, TRAIL, and IP-10) and to the Labscore.</span></p> <h3><span>Methods</span></h3> <p><span>This was a prospective diagnostic accuracy study conducted in a single tertiary center in children aged less than 3 years old presenting with FWS. Reference standard etiology (bacterial or viral) was assigned by a panel of three independent experts. Diagnostic accuracy (AUC, sensitivity, specificity) of host individual biomarkers and combinatorial scores was evaluated in comparison to reference standard outcomes (expert panel adjudication and microbiological diagnosis). </span></p> <h3><span>Results </span></h3> <p><span>241 patients were included. 68 of them (28%) were diagnosed with a bacterial infection and 5 (2%) with invasive bacterial infection (IBI). Labscore, ImmunoXpert, and CRP attained the highest AUC values for the detection of bacterial infection, respectively 0.854 (0.804–0.905), 0.827 (0.764–0.890), and 0.807 (0.744–0.869). Labscore and ImmunoXpert outperformed the other single biomarkers with higher sensitivity and/or specificity and showed comparable performance to one another although slightly reduced sensitivity in children < 90 days of age.</span></p> <h3><span>Conclusion </span></h3> <p><span>Labscore and ImmunoXpert demonstrate high diagnostic accuracy for safely discriminating bacterial infection in children with FWS aged under and over 90 days, </span><span>supporting their adoption in the assessment of febrile patients. </span></p>
Robust evidence for bats as reservoir hosts is lacking in most African virus studies – a review and call to optimize sampling and conserve bats
<p><span>Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoirs and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded, and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for </span><em>Orthoebolavirus</em> (formerly <em>Ebolavirus</em>) versus <em>Orthomarburgvirus</em> (formerly <em>Marburgvirus</em>) as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.</p>
Fig. 36 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 36. Salicopsallus lucidus: Male genitalia (male 1, AMNH_PBI 00071869; male 2, 00062261; male
Fig. 44 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 44. Taxon-host cladogram for Phymatopsallus-group taxa (see text for explanation).
Fig. 33 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 33. Phymatopsallus rinconae: Male genitalia (male 1, AMNH_PBI 00063106; male 2, 00063104).
Map 5 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Map 5. Distribution of Cercocarpopsallus and Knightopsallus spp.
Fig. 28 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 28. Knightopsallus portalensis: Male genitalia (AMNH_PBI 00062707).
Map 6 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Map 6. Distribution of Phymatopsallus acaciae–P. rinconae.
Map 7 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Map 7. Distribution of Phymatopsallus tuberculatus.
Fig. 23 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 23. Ceratopsallus vauqueliniae: Male genitalia (AMNH_PBI 00063230).
Fig. 31 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 31. Phymatopsallus dubiosus: Male genitalia (male 1, AMNH_PBI 00062339; male 2, 00074205).
Fig. 34 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 34. Phymatopsallus tuberculatus: Male genitalia (male 1, AMNH_PBI 00062428; male 2,
Fig. 26 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 26. Cercocarpopsallus gracilis: Male genitalia (AMNH_PBI 00075917).
Fig. 37 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 37. Salicopsallus schwartzi: Male genitalia (AMNH_PBI 00063162).
Fig. 15 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Fig. 15. Ceratopsallus croceus: Male genitalia (AMNH_PBI 00074847); female genitalia
Map 3 in Revision, Phylogenetic, Biogeographic, And Host Analyses Of The Endemic Western North American Phymatopsallus Group, With The Description Of 9 New Genera And 15 New Species (Insecta: Hemiptera: Miridae: Phylinae)
Map 3. Distribution of Ceratopsallus aquilonius–C. plautus.
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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)
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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.