cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Building a B Cell Differentiation Model for X-Linked Agammaglobulinemia Using Pluripotent Stem Cells
Creators: name: Hernández González, Elaine
name: Porteus, Matthew
Publisher: name: Stanford Digital Repository
Year: 2024
Subjects: subject: B cell
subject: Differentiation
subject: Transcription factors
subject: Pluripotent stem cells
subject: X-Linked Agammaglobulinemia

description: X-Linked Agammaglobulinemia (XLA) is the most common primary immunodeficiency in males in the United States. It is characterized by the inability to produce mature B cells due to mutations in the BTK gene. Current treatments involve repeated injection of immunoglobulins, but these have limitations, as patients can have adverse reactions and this treatment does not replace the entire immune response. As a result, gene correction is considered a viable therapy for XLA; however, a robust B cell differentiation model to study the effect of using gene therapy to treat XLA has not been established. Although cytokines are not sufficient to induce differentiation, studies have shown that transcription factor-driven differentiation systems have been proven to be successful in producing differentiated cells from pluripotent stem cells (PSCs). Therefore, this project aimed to study and replicate B cell development in vitro with the purpose of designing a new differentiation model using B cell-specific transcription factors (TFs), EBF1 and PAX5. This was approached by using the gene editing tool clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) and adeno-associated virus type 6 (AAV6) on human PSCs. First, assessment of wild type PSC potential to differentiate into B cells using cytokines confirmed inefficient B cell development. Then, an in-depth study of BTK mutations led to the generation of three pluripotent XLA-knockout cell lines that imitate the disease phenotype. The design and integration of GFP reporter constructs into the B-cell specific marker CD20 is still being studied. Finally, TF constructs were designed with the purpose of enhancing a cytokine-based B cell differentiation. These results support the development of PSC lines with transgenic B cell differentiation TFs as a model for XLA and other B cell-related malignancies, while eliminating the need for patients to provide bone marrow or hematopoietic stem cell samples.
Euchromius superbellus
Creators: name: Sinev, Sergey Yu.
name: Korb, Stanislav K.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Euchromius
Euchromius superbellus

description: * 131. Euchromius superbellus (Zeller, 1849)
Koro-Goo, 10.VII.2014, 5 males, 1 female; Toktogul, 13.VII.2015, 2 males, 1 female; Tortkol, 13.VII.2016, 1 male; Kekemeren, 26.VII.2016, 1 male.
Remark. This species recorded from Central Asia (Slamka 2008: 22).
description: Published as part of Sinev, Sergey Yu. & Korb, Stanislav K., 2022, A preliminary list of the Pyraloid moths (Lepidoptera: Pyraloidea) of Kyrgyzstan, pp. 101-136 in Zootaxa 5138 (2) on page 116, DOI: 10.11646/zootaxa.5138.2.1, http://zenodo.org/record/6556841
A Predictive Model of Human Transcriptional Activators and Repressors
Creators: name: Liongson, Ivan
name: Bintu, Lacramioara
Publisher: name: Stanford Digital Repository
Year: 2024
Subjects: subject: Biology
subject: Transcription factors
subject: Genetic transcription

description: The ability to predict which protein sequences can act as transcriptional activators or repressors is important for understanding the function of human and viral transcription factors (TFs) inside human cells and for building synthetic biology tools for gene control. Here, I integrate multiple high-throughput data sets acquired using a recently developed method (HT-Recruit) that tests hundreds of thousands of protein sequences for their effect on reporter genes in live human cells. I first created a data processing pipeline using ground truth validations to regularize results from multiple HT-Recruit screens, allowing cross-screen comparisons as well as proper model training. After processing these datasets, I built and trained convolutional neural network machine learning models that predict both activation and repression for protein sequences across the human transcription factors. These are the first models to be trained on human TF data, as well as the first to predict repressors. Some protein sequences are bifunctional in that they both activate and repress, so it is important to be able to predict both.
Sharing data pipelines: Why sharing data may not be enough, and what to do about it
Creators: name: Käthner, David
Publisher: name: ZPID (Leibniz Institute for Psychology)
Year: 2020
Subjects: subject: data pipeline
subject: data sciene
subject: data processing
subject: time series data
subject: multi variate data
subject: data fusion
subject: 150

description: New research challenges and low-cost technological solutions drive the motivation to record behavior in multivariate ways using high temporal resolution. Making such data accessible and usable is more complicated than it may seem. Methods like ECG, EEG, and eye tracking can produce very large amounts of data in a short time. Further, context data to explain the observed behavior must be recorded as well. E.g., in a field study using an instrumented research vehicle, the position of the vehicle and the distance to the vehicle in front could act as context data. To make this multitude of data analyzable, data must be cleaned and fused in data pipelines. Cleaning happens in multiple stages, and requires decisions which have direct effects on patterns in the data. Time series data are often up- or down sampled, potentially altering characteristics of signals of interest. Sharing the data pipeline alongside an uncleaned version of the data therefore should be the default when publishing research results. Data science has developed a number of solutions to store and document data and data pipelines, whose benefits and costs will be discussed in this talk. These approaches can be structured in three interdependent dimensions: data storage, data processing, and competencies required by developers and users of data pipelines. Data from empirical studies can be very challenging to store, process, and document. Solutions to these issues do exist, but they require a training which is yet to be implemented in the typical Psychology curriculum.
Additional file 1: of Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-Î˛ (TRIF) provides insights into its autoinhibited state
Creators: name: Jarjapu Mahita
name: Sowdhamini, Ramanathan
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Appendix S1. List of organisms used for co-evolution analysis (DOCX 16Â kb)
Myrmica pertinax
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica pertinax

description: 5. Myrmica pertinax.
M. rufo-fusca, nitida, sparse pilosa; capite longitudinaliter striate; metathorace mutico.
Worker. Length 1 1 / 2 - 2 lines. Rufo-fuscous, the head darker than the the body; the anterior portion of the head and the antennae bright rufo-ferruginous. The thorax smooth and shining, with a few fine punctures, the base and apex of the femora pale in some of the larger and darker examples; the abdomen pale at the base, the ex- treme apex pale and pubescent. Smaller specimens are usually paler than large ones.
Hab. Celebes (Tondano).
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on pages 46-47
Additional file 3: Figure S1. of Morphological and molecular characteristics of Malayfilaria sofiani Uni, Mat Udin & Takaoka n. g., n. sp. (Nematoda: Filarioidea) from the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia) in Peninsular Malaysia
Creators: name: Shigehiko Uni
name: Udin, Ahmad Mat
name: Agatsuma, Takeshi
name: Weerachai Saijuntha
name: Junker, Kerstin
name: Rosli Ramli
name: Hasmahzaiti Omar
name: Lim, Yvonne
name: Sivanandam, Sinnadurai
name: Lefoulon, Emilie
name: Martin, Coralie
name: Daicus Belabut
name: Saharul Kasim
name: Halim, Muhammad Abdullah
name: Zainuri, Nur
name: Bhassu, Subha
name: Fukuda, Masako
name: Matsubayashi, Makoto
name: Harada, Masashi
name: Low, Van
name: Chen, Chee
name: Narifumi Suganuma
name: Rosli Hashim
name: Takaoka, Hiroyuki
name: Mohd Azirun
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Taxonomic position of Malayfilaria sofiani n. g., n. sp., inferred using the neighbour-joining method, based on cox1 nucleotide sequences. The tree was based on the Kimura 2-parameter model with 10,000 bootstrap replicates (MEGA6). Numbers at the nodes are the bootstrap confidence values after 10,000 replicates. The percentage of replicate trees in which the associated taxa clustered together is shown next to the branches. Valuesâ  >â  50% are shown. There were a total of 569 positions in the final dataset. The scale-bar below the diagram indicates the number of changes inferred as having occurred along each branch. Red triangles indicate the sequences generated in this study. (PDF 290 kb)
Chrysoteuchia culmella
Creators: name: Sinev, Sergey Yu.
name: Korb, Stanislav K.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Chrysoteuchia
Chrysoteuchia culmella

description: * 132. Chrysoteuchia culmella (Linnaeus, 1758)
Katta-Karakol, 14.VII.2015, 1 male.
description: Published as part of Sinev, Sergey Yu. & Korb, Stanislav K., 2022, A preliminary list of the Pyraloid moths (Lepidoptera: Pyraloidea) of Kyrgyzstan, pp. 101-136 in Zootaxa 5138 (2) on page 117, DOI: 10.11646/zootaxa.5138.2.1, http://zenodo.org/record/6556841
Zorotypus medoensis Hwang
Creators: name: Yin, Zi-Wei
name: Li, Li-Zhen
name: Wu, Chao
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Zoraptera
Zorotypidae
Zorotypus
Zorotypus medoensis

description: Zorotypus medoensis Hwang
(Figs 6, 7)
Zorotypus medoensis Hwang, 1976: 225.
Material examined. 2 apteron ♂♂, 1 apteron ♀, 2 alate ♀♀, labeled: ‘ China, Xizang A. R. [= Tibet], Motuo Hsien [ffiRθ], Hanmi [R÷], 29°21’50’’N, 95°07’48’’E, under bark covered with moss, 15.vii.2013, 2100 m, Chao Wu leg.’ (pcWC, pcBW); 9 deälate ♀♀, labeled: ‘ China, Xizang A. R., Motuo Hsien, 80K, 29°39’18’’N, 95°29’25’’E, under bark, 2.viii.2013, 2100 m, Wen-Xuan Bi leg.’ (pcBW).
Biology. All individuals were collected under barks of large fallen decomposing logs (Fig. 7).
Distribution. Southwestern China: Xizang Autonomous Region.
Comments. According to Hwang (1976), Zorotypus medoensis is very similar to Z. sinensis in general morphology, and can be separated from the latter only by the chaetotaxy of male sternum VIII, and form of the male genitalia. For comparative purposes, important diagnostic features of Zorotypus medoensis from the type locality are figured (Fig. 6). Both Z. medoensis and Z. sinensis lack a strongly elongate and coiled flagellum, indicating that these two species may be more closely related to Z. ceylonicus Silverstri from Sri Lanka (Hwang 1974: 427) than to the southeastern Asian and central American species that share this structure (see ‘Comparative diagnosis’ of Z. hainanensis sp. n. above, and Mashimo et al. 2013: 512).
description: Published as part of Yin, Zi-Wei, Li, Li-Zhen & Wu, Chao, 2015, New and little known species of Zorotypus Silvestri (Zoraptera: Zorotypidae) from China, pp. 557-566 in Zootaxa 4007 (4) on page 565, DOI: 10.11646/zootaxa.4007.4.6, http://zenodo.org/record/240040
Additional file 1: Supplementary material. of A 3D in vitro model of the human breast duct: a method to unravel myoepithelial-luminal interactions in the progression of breast cancer
Creators: name: Carter, Edward
name: Gopsill, James
name: Jennifer. Gomm
name: J. Jones
name: Grose, Richard
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 60506 Virology

description: Figure S1. Promoter efficacy in primary cultures of myoepithelial and luminal cells. a Representative images of GFP expression in myoepithelial and luminal cells 48 h following infection with neuraminidase-treated lentiviral particles driving GFP expression under either human/mouse CMV, human/mouse EF1α, CAG, PGK and UBC promoters. Scale bar = 20 μm. b Mean fluorescence intensity (MFI) values of myoepithelial and luminal cells 48 h post-infection with lentiviral particles as in (a). Images and values are representative of cells derived from two donors. Figure S2. Spheroids formed in Matrigel cultures express markers of both luminal and myoepithelial cells. Expression of cytokeratin (CK) 8 and P-cadherin in spheroids formed in Matrigel from co-culture of isolated myoepithelial and luminal cells over 21 days. Images are representative of cells derived from at least three donors. Scale bar = 20 μm. Figure S3. Objective and systematic calculation of cell and spheroid volumes. Representative workflow of spheroid analysis. Raw DAPI z-sections (a) are converted into greyscale images and a greyscale distribution profile (b). Greyscale images are then converted to binary images using a calculated threshold to indicate cell presence (c). The pixels that indicate cells are then translated into a geometrically accurate point cloud using the known image resolutions (d). Further post-processing using density-based spatial clustering of applications with noise (DBSCAN) is performed to identify the main body of cells (e). The point cloud representing the main spheroid is then extracted (f). The alpha-shape algorithm is applied using thresholds set as a function of the image resolutions to form triangulated bodies that represent the cells and body (g). The volumes of these bodies are then calculated alongside the resultant cell/body ratio. (PDF 1342 kb)
Additional file 1: Table S1. of Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes
Creators: name: Diaz-Beltran, Leticia
name: Esteban, Francisco
name: Varma, Maya
name: Ortuzk, Alp
name: David, Maude
name: Wall, Dennis
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified

description: Information summary of the datasets selected. (DOCX 12Â kb)
Dispositiv(e) der Pandemie : Die Corona-Warn-App
Creators: name: Völkl, Paul
Publisher: name: Universität Regensburg
Year: 2023
Subjects: subject: Corona-Warn-App; Dispositiv; Pandemie; Subjektivierung
subject: 004 Informatik
subject: 610 Medizin

description: Die Corona-Warn-App wurde im Juni 2020 als Bluetooth-basiertes Warnsystem zur Eindämmung der Corona-Pandemie veröffentlicht. Die App, die auf dem GAEN-System (Google-Apple-Exposure-Notification) beruht, wurde während ihrer Dienstzeit um weitere Funktionen, wie ein digitales Kontakt-Tagebuch oder die Hinterlegung von Impf- und Testzerifikaten, ergänzt. Die App wird im folgenden Artikel aus einer medienwissenschaftli chen Perspektive als Teil eines pandemischen Dispositivs betrachtet, das ein netzartiges Ensemble aus institutionellen, diskursiven und medialen Ele menten um die Pandemie darstellt. Im Fokus der Untersu chung stehen die An- und Eingebundenheiten der App an/in das Dispositiv sowie die Subjektivierungsprozesse der Nutzer:innen in der und durch die Nutzung der App.
Myrmica vexator
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica vexator

description: 6. Myrmica vexator.
M. pallide flavo-testacea, laevis, nitidissima; abdomine apice fusco-nigro.
Worker. Length 1 line. Honey-yellow, very smooth and shining; the flagellum slightly fuscous towards the apex; the eyes small and placed forwards at the sides of the head; the metathorax not spined; the abdomen fuscous with the base pale.
Hab. Ternati.
This species resembles the House-ant, M. molesta; but it differs in several particulars from that species; its head is much larger, and it is entirely smooth and shining.
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on page 47
Myrmica insolens
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica insolens

description: 7. Myrmica insolens.
M. testaceo-ferruginea, sparse pilosa; capite thoraceque longitudinaliter striatim rugosis; metathorace spinis parvis acutis armato.
Worker. Length 1 3 / 4 line. Pale ferruginous; the head and thorax longitudinally, irregularly and roughly striated; the eyes and ocelli black; the antenna with three joints in the club; the metathorax with two straight acute spines, which are situated at the sides of the truncation of the metathorax; the abdomen smooth and shining.
Hab. Menado.
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on page 47
All about persistence: Challenges of misaligned incentives in the research ecosystem
Creators: name: Jones, Phill
Publisher: name: Zenodo
Year: 2021
Subjects: PIDs
RDA Plenary
Persistent Identifiers
open science
open research
Incentives

description: Individually, PIDs have almost no value. What would be the point of getting and ORCID ID, or registering a DOI for a research article if you were the only one to ever do it? On the other hand, they become increasingly valuable as more and more individuals and organisations adopt and use them, and even more valuable still when they are connected to each other. In other words, PIDs exhibit powerful network effects. 

One of the big challenges in driving PID adoption appears to be that data entered by one stakeholder, benefits other stakeholders in the ecosystem. For example, Funders require authors and institutions to return data about what was done with research funding. Institutions need to know who they’re collaborating with and where their funding is coming from, while publishers seek to connect objects in the broader research ecosystem to improve discoverability and help researcher comply with mandates. In other words, incentives to participate in the emergent knowledge graph that are PIDs are misaligned?

The question then becomes, how do we, as a community, develop incentives to participation that result in a more accurate, complete and timely PID and metadata landscape.
Myrmica opaca
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica opaca

description: 8. Myrmica opaca.
M. nigra, opaca, delicatule scabrosa; pedibus rufo-fuscis, tarsis pallide testaceis.
Worker. Length 2 lines. Opake-black, the head, thorax and nodes of the peduncle finely scabrous, on the head having a tendency to run into lines; behind the eyes is a longitudinal groove, apparently for the reception of the scape of the antennae; the antennae obscurely ferruginous with the tip pale; the mandibles ferruginous, striated and with several black teeth on their inner margin. Thorax armed posteriorly with two stout curved spines; the tarsi pale rufo-testaceous. The nodes of the peduncle large and globose; the abdomen thinly sprinkled with erect white setae.
Hab. Celebes (Tondano).
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on page 47
Crambus monochromellus Herrich-Schaffer 1852
Creators: name: Sinev, Sergey Yu.
name: Korb, Stanislav K.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Crambus
Crambus monochromellus

description: * 133. Crambus monochromellus Herrich-Schäffer, 1852
Ala-Archa, 24.VII.2015, 12 males.
Remark. This species recorded from Central Asia (Slamka 2008: 35).
description: Published as part of Sinev, Sergey Yu. & Korb, Stanislav K., 2022, A preliminary list of the Pyraloid moths (Lepidoptera: Pyraloidea) of Kyrgyzstan, pp. 101-136 in Zootaxa 5138 (2) on page 117, DOI: 10.11646/zootaxa.5138.2.1, http://zenodo.org/record/6556841
Additional file 1: Supplementary material. of A 3D in vitro model of the human breast duct: a method to unravel myoepithelial-luminal interactions in the progression of breast cancer
Creators: name: Carter, Edward
name: Gopsill, James
name: Jennifer. Gomm
name: J. Jones
name: Grose, Richard
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Virology

description: Figure S1. Promoter efficacy in primary cultures of myoepithelial and luminal cells. a Representative images of GFP expression in myoepithelial and luminal cells 48 h following infection with neuraminidase-treated lentiviral particles driving GFP expression under either human/mouse CMV, human/mouse EF1α, CAG, PGK and UBC promoters. Scale bar = 20 μm. b Mean fluorescence intensity (MFI) values of myoepithelial and luminal cells 48 h post-infection with lentiviral particles as in (a). Images and values are representative of cells derived from two donors. Figure S2. Spheroids formed in Matrigel cultures express markers of both luminal and myoepithelial cells. Expression of cytokeratin (CK) 8 and P-cadherin in spheroids formed in Matrigel from co-culture of isolated myoepithelial and luminal cells over 21 days. Images are representative of cells derived from at least three donors. Scale bar = 20 μm. Figure S3. Objective and systematic calculation of cell and spheroid volumes. Representative workflow of spheroid analysis. Raw DAPI z-sections (a) are converted into greyscale images and a greyscale distribution profile (b). Greyscale images are then converted to binary images using a calculated threshold to indicate cell presence (c). The pixels that indicate cells are then translated into a geometrically accurate point cloud using the known image resolutions (d). Further post-processing using density-based spatial clustering of applications with noise (DBSCAN) is performed to identify the main body of cells (e). The point cloud representing the main spheroid is then extracted (f). The alpha-shape algorithm is applied using thresholds set as a function of the image resolutions to form triangulated bodies that represent the cells and body (g). The volumes of these bodies are then calculated alongside the resultant cell/body ratio. (PDF 1342 kb)
Bulbocythere Coimbra & Morais, 2016, gen. nov.
Creators: name: Coimbra, João Carlos
name: De Morais, Anderson L. M.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Ostracoda
Podocopida
Hemicytheridae
Bulbocythere

description: Genus Bulbocythere gen. nov.
Type species. Bulbocythere calida sp. nov., by monotypy.
Diagnosis. A hemicytherid, subrectangular in lateral view with a delicate posteroventral caudal process. Eye spot pronounced. Anterior margin with an anterodorsal flange in LV. Surface ornamented with tubercles, mostly of them slightly aligned in rows. Hinge holamphidont with median element smooth and the posterior one bilobate. Central muscle scars an oblique row of four adductors, the middle two subdivided; two frontal scars. Inner margin with a delicate anterior vestibule. Radial pore canals straight, simple and numerous.
Remarks. The genus Ruggiericythere Aiello, Coimbra & Barra, 2004, a South American ostracode with a preference for temperate and cool waters, shows some similarity with Bulbocythere gen. nov. However, Ruggiericythere has a surface dominated by prominent ribs, which are primarily longitudinally disposed, and by intercostal coarse reticulation. Internally, Ruggiericythere shows three frontal muscle scars and line of concrescence coincident with the inner margin along the entire duplicature (Fig. 2).
Echinocythereis Puri, 1953 somewhat resembles Bulbocythere gen. nov. externally. However, the former shows an ornamentation constituted mostly by small spines, which are sometimes superimposed on a secondary reticulate ornamentation. In addition, Echinocythereis has the two median adductor muscle scars undivided, a line of concrescence coincident with the inner margin, and a hinge with the posterior element not bilobate (Fig. 2).
A superficial similarity between Bulbocythere gen. nov. and the monospecific hemicytherid genus Mimicocythere Titterton & Whatley, 2008 from the Solomon Islands, North Pacific Ocean, cannot be confirmed after in-depth comparison. Bulbocythere gen. nov. has an antimerodont hinge, line of concrescence and the inner margin coincident, and only the upper median adductor scar subdivided. Mimicocythere is inflated posteroventrally and possesses a spinose surface superimposed on the muri of a gentle reticulation.
Etymology. Latin origin, bulbosus = bulbous, with reference to the ornamentation constituted by tubercles.
description: Published as part of Coimbra, João Carlos & De Morais, Anderson L. M., 2016, On a new marine podocopid genus and species (Ostracoda: Hemicytheridae) from Brazil, pp. 167-176 in Zootaxa 4193 (1) on page 170, DOI: 10.11646/zootaxa.4193.1.8, http://zenodo.org/record/166659
Cerapachys antennatus
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Cerapachys
Cerapachys antennatus

description: 1. Cerapachys antennatus
, Smith, Proc. Linn. Soc. ii. 74. 1.
Hab. Celebes; Borneo.
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on page 47
Additional file 2: Figure S1. of Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-Î˛ (TRIF) provides insights into its autoinhibited state
Creators: name: Jarjapu Mahita
name: Sowdhamini, Ramanathan
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: The concatenated multiple sequence alignment of the N-terminal domain and TIR domain sequences from different organisms used for predicting co-evolving pair of residues. The region of the MSA corresponding to the N-terminal domain sequences is highlighted in purple while the region corresponding to the TIR domain is highlighted in green. Different colours for different co-evolving pair of residues with one colour for each pair have also been marked on the alignment. (PDF 4 MB)
Crambus pascuellus
Creators: name: Sinev, Sergey Yu.
name: Korb, Stanislav K.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Crambus
Crambus pascuellus

description: * 134. Crambus pascuellus (Linnaeus, 1758) (Fig. 27)
Alai, [18]85, [leg.] Haberhauer, 1 male (ZMHU); Aksu, 7.VII.2016, 1 male; Koro-Goo, 10–16.VII.2018, 1 male; Kyzyl-Eshme, 21–22.VII.2019, 1 male.
description: Published as part of Sinev, Sergey Yu. & Korb, Stanislav K., 2022, A preliminary list of the Pyraloid moths (Lepidoptera: Pyraloidea) of Kyrgyzstan, pp. 101-136 in Zootaxa 5138 (2) on page 117, DOI: 10.11646/zootaxa.5138.2.1, http://zenodo.org/record/6556841
Mechanisms of Ferroptosis Evasion Promoted by Extracellular Metabolites
Creators: name: Alchemy, Grace
name: Dixon, Scott
Publisher: name: Stanford Digital Repository
Year: 2024
Subjects: subject: Ferroptosis
subject: Cysteine
subject: Albumin
subject: Lysosome
subject: Monounsaturated Fatty Acids
subject: Spheroid
subject: Biology

description: Cancer cells require nutrients to grow and proliferate. The availability of the amino acid cysteine impacts whether cancer cells die by an iron-dependent, non-apoptotic form of cell death executed by lipid peroxidation called ferroptosis. Ferroptosis can be induced if the availability of the amino acid cysteine is limiting or by inhibiting the phospholipid hydroperoxidase glutathione peroxidase 4 (GPX4). Extracellular metabolites such as monounsaturated fatty acids (MUFAs) and cysteine can protect from ferroptosis. However, it is unclear how cancer cells acquire cysteine to evade ferroptosis or what MUFAs they can use to evade ferroptosis. Using human-derived cancer cell lines in both adherent (2D) and suspension (3D) culture, this study demonstrates that the cysteine-rich extracellular protein albumin protects from ferroptosis caused by cysteine deprivation. Albumin in combination with inhibition of the nutrient and energy sensing kinase, mammalian target of rapamycin complex 1 (mTORC1), is required to robustly protect from cysteine deprivation-induced ferroptosis in 2D. This combination treatment protects from ferroptosis by increasing intracellular levels of cysteine. Furthermore, this process is dependent on the catabolism of albumin into its amino acid constituents. Additionally, albumin protects from cystine deprivation-induced ferroptosis in 3D culture. This study reveals that a variety of exogenous MUFAs that have not previously been characterized as ferroptosis-protective metabolites protect HT-1080 cells in monolayer and HT-1080 and Panc-1 spheroids from GPX4 inhibition-induced ferroptosis. These MUFAs exhibit different protective abilities in adherent compared to spheroid culture and this suggests growth-context dependent differences in MUFA protection. These results describe novel metabolite-mediated strategies of ferroptosis evasion in 2D and 3D culture. Understanding how cells utilize exogenous protective metabolites such as albumin and MUFAs in death-inducing conditions can reveal novel ways to induce more complete cancer cell death by curtailing alternative avenues of protection. Targeting these mechanisms to induce more effective cell death in cancer cells reveals potential therapeutic relevance of this work.
Additional file 2: Figure S1. of Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes
Creators: name: Diaz-Beltran, Leticia
name: Esteban, Francisco
name: Varma, Maya
name: Ortuzk, Alp
name: David, Maude
name: Wall, Dennis
Publisher: name: Figshare
Year: 2017
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified

description: Box plots showing the distribution of the samples of each dataset after preprocessing; median-centered values indicate that the data are normalized and cross-comparable. (PDF 5181Â kb)
Dissecting the Parasympathetic Neural Circuits of the Heart
Creators: name: Nguyen, Annie
name: Krasnow, Mark
Publisher: name: Stanford Digital Repository
Year: 2024
Subjects: subject: parasympathetic
subject: cardiopulmonary
subject: Neural circuits
subject: intrinsic cardiac neurons

description: The autonomic nervous system carefully balances its sympathetic “fight or flight” and parasympathetic “rest and digest” divisions to mediate critical cardiopulmonary functions. Dysfunction between and within these divisions causes a broad range of disease, including heart failure, asthma, and chronic obstructive pulmonary disease (COPD). Here we examine postganglionic parasympathetic or intrinsic neurons, which are exceedingly rare and fragile and housed within the organ they innervate. Recent work has shown that activation of a major subset of cardiac intrinsic neurons by nucleus ambiguus cardiovascular (ACV) neurons evokes bradycardia, whereas activation of another subset of cardiac intrinsic neurons and lung intrinsic neurons that are jointly innervated by nucleus ambiguus cardiopulmonary (ACP) neurons evokes simultaneous bradycardia and bronchoconstriction1, demonstrating their role in controlling and coordinating critical cardiac and cardiopulmonary responses. Despite their functional importance, the molecular diversity and organization of these neural circuits, especially those under parasympathetic control, remain largely unknown. To characterize the anatomical, cellular, molecular, and functional properties of intrinsic lung and cardiac neurons, we use single-cell RNA- sequencing, immunohistochemistry, and single-molecule fluorescent in situ hybridization (smFISH). We reveal molecularly distinct populations of lung and cardiac intrinsic neurons and offer optimized protocols for procuring and analyzing these rare and fragile neurons. These studies aim to elucidate the characteristics and roles of intrinsic lung and cardiac neurons in mediating precise cardiopulmonary regulation and interrogate their interactions with neighboring neuronal populations.
Crematogaster ampullaris
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Crematogaster
Crematogaster ampullaris

description: 1. Crematogaster ampullaris.
C. rufo-niger; capite thorace mul-tum latiore; parte postica thoracis dilatata; abdomine cordata.
Worker. Length 2 lines. Obscure fusco-ferruginous; the antennae, sides of the head, the nodes of the petiole, and the legs of a brighter red; the head much wider than the thorax and more shining; the metathorax much swollen and wider than the prothorax, swelling out on each side. Abdomen, heart-shaped, palest at the base and shining.
Hab. Celebes (Tondano).
The swollen metathorax in this species, I apprehend, is a receptacle for saccharine fluid; on each side is a small orifice, and beneath it, adhering to the thorax, are particles of crystallized masses, apparently formed of the fluid which has exuded from the receptacle. Two species from Sarawak, having similar formations, are described in the second volume of the ' Proceedings of the Linnean Society.
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on pages 47-48
Solenopsis cephalotes
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Solenopsis
Solenopsis cephalotes

description: 1. Solenopsis cephalotes
, Smith, Proc. Linn. Soc. iii. 149. 1.
Hab. Celebes; Aru.
The worker major of this species has the head greatly enlarged, that of the worker minor being of the ordinary size.
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on page 48
Crambus perlellus
Creators: name: Sinev, Sergey Yu.
name: Korb, Stanislav K.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Crambus
Crambus perlellus

description: 135. Crambus perlellus (Scopoli, 1763)
Caradja 1916: 4, as Crambus rostellus var. nigerrimus nov. ([Kyrgyzstan] Karagaitau); Błeszyński 1965: 220, as ssp. nigerrimus Car.
Naryn, STAZR, 18.VII.1981, 1.VIII.1981, leg. Sinev, 4 males (ZIN); At-Bashi, 30.VII.1981, leg. Sinev, 1 male (ZIN); Karakol, 9.VII.2014, 17.VII.2015, 26.VII.2019, 7 males, 2 females; Koro-Goo, 10.VII.2014, 25– 26.VII.2017, 24–26.VII.2017, 10–16.VII.2018, 2–8.VII.2019, 33 males, 12 females; Ak-Kiya, 11.VII.2014, 4 males, 3 females; Toktogul, 13.VII.2015, 2 males; Katta-Karakol, 14.VII.2015, 8 males, 1 female; Kichi- Karakol, 15.VII.2015, 22.VII.2017, 7 males; Ottuk, 8.VII.2016, 20.VII.2018, 4 males; Tortkol, 13.VII.2016, 2 males, 2 females; Urumbash, 17.VII.2016, 2 males, 2 females; Kulanak, 21.VII.2016, 3 males; Kekemeren, 26.VII.2016, 30.IX.2019, 5 males; Tyup, 5.VIII.2016, 1 male; Archaty, 16–18.VII.2019, 2 males; Kyzyl-Eshme, 21–22.VII.2019, 8 males, 4 females; Kara-Suu, 24.VII.2019, 5 males.
description: Published as part of Sinev, Sergey Yu. & Korb, Stanislav K., 2022, A preliminary list of the Pyraloid moths (Lepidoptera: Pyraloidea) of Kyrgyzstan, pp. 101-136 in Zootaxa 5138 (2) on page 117, DOI: 10.11646/zootaxa.5138.2.1, http://zenodo.org/record/6556841
Additional file 4: Figure S2. of Morphological and molecular characteristics of Malayfilaria sofiani Uni, Mat Udin & Takaoka n. g., n. sp. (Nematoda: Filarioidea) from the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia) in Peninsular Malaysia
Creators: name: Shigehiko Uni
name: Udin, Ahmad Mat
name: Agatsuma, Takeshi
name: Weerachai Saijuntha
name: Junker, Kerstin
name: Rosli Ramli
name: Hasmahzaiti Omar
name: Lim, Yvonne
name: Sivanandam, Sinnadurai
name: Lefoulon, Emilie
name: Martin, Coralie
name: Daicus Belabut
name: Saharul Kasim
name: Halim, Muhammad Abdullah
name: Zainuri, Nur
name: Bhassu, Subha
name: Fukuda, Masako
name: Matsubayashi, Makoto
name: Harada, Masashi
name: Low, Van
name: Chen, Chee
name: Narifumi Suganuma
name: Rosli Hashim
name: Takaoka, Hiroyuki
name: Mohd Azirun
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Taxonomic position of Malayfilaria sofiani n. g., n. sp., inferred using the neighbour-joining method, based on 12S rDNA nucleotide sequences. The tree was based on the Kimura 2-parameter model with 10,000 bootstrap replicates (MEGA6). Gblocks (version 0.91b, 2002) was used to eliminate poorly aligned positions and divergent regions of the alignment [70]. There were 319 positions in the final dataset. The scale-bar indicates the number of changes inferred as having occurred along each branch. Red triangles indicate the sequences generated in this study. (PDF 297 kb)
Additional file 3: Table S1. of Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-Î˛ (TRIF) provides insights into its autoinhibited state
Creators: name: Jarjapu Mahita
name: Sowdhamini, Ramanathan
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Co-evolving pair of residues predicted by CMAT. The N-terminal domain corresponds to residues 1 to 153, while residues 154â  349 make up the TIR domain in the concatenated multiple sequence alignment. (DOCX 16Â kb)
Solenopsis laboriosa
Creators: name: Smith, F.
Publisher: name: Zenodo
Year: 1861
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Solenopsis
Solenopsis laboriosa

description: 2. Solenopsis laboriosa.
S. ferruginea: capite maximo, longi-tudinahter striato, postice transverso-striato; spinis metathoracis minu-tissimis.
Worker major. Length 3 lines. Dark ferruginous, with the legs pale; rufo-testaceous; the head very large, twice as wide as the abdomen, in front and at the sides roughly striated, posteriorly delicately striated; the sides of the head very slightly rounded, emarginate behind with a central impressed line running forwards and terminating opposite the eyes; the eyes very small and placed at the sides a little beyond the middle; the vertex smooth and shining, with a few scattered fine punctures. Thorax sub-rugose, convex anteriorly and shining, behind constricted and narrowed; the metathorax with two short, erect, acute spines. Abdomen smooth, shining and slightly pubescent. The mandibles have a single tooth at their apex.
Worker minor. Length 1 - 2 lines. This form is of a much paler colour, the larger individuals having the abdomen fuscous, except at the extreme base; in the smaller examples it is only fuscous at the apex; in large individuals the head is slightly striated in front, in small ones it is entirely smooth and shining; the head much smaller in proportion than in the worker major; the mandibles with two or three teeth on their inner margin.
Hab. Celebes (Tondano).
The different-sized workers were taken from the nest by Mr. Wallace.
description: Published as part of Smith, F., 1861, Catalogue of hymenopterous insects collected by Mr. A. R. Wallace in the Islands of Ceram, Celebes, Ternate, and Gilolo., pp. 36-48 in Journal of the Proceedings of the Linnean Society of London, Zoology 6 on page 48
Additional file 4: Figure S2. of Morphological and molecular characteristics of Malayfilaria sofiani Uni, Mat Udin & Takaoka n. g., n. sp. (Nematoda: Filarioidea) from the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia) in Peninsular Malaysia
Creators: name: Shigehiko Uni
name: Udin, Ahmad Mat
name: Agatsuma, Takeshi
name: Weerachai Saijuntha
name: Junker, Kerstin
name: Rosli Ramli
name: Hasmahzaiti Omar
name: Lim, Yvonne
name: Sivanandam, Sinnadurai
name: Lefoulon, Emilie
name: Martin, Coralie
name: Daicus Belabut
name: Saharul Kasim
name: Halim, Muhammad Abdullah
name: Zainuri, Nur
name: Bhassu, Subha
name: Fukuda, Masako
name: Matsubayashi, Makoto
name: Harada, Masashi
name: Low, Van
name: Chen, Chee
name: Narifumi Suganuma
name: Rosli Hashim
name: Takaoka, Hiroyuki
name: Mohd Azirun
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology
subject: Virology
subject: Computational Biology

description: Taxonomic position of Malayfilaria sofiani n. g., n. sp., inferred using the neighbour-joining method, based on 12S rDNA nucleotide sequences. The tree was based on the Kimura 2-parameter model with 10,000 bootstrap replicates (MEGA6). Gblocks (version 0.91b, 2002) was used to eliminate poorly aligned positions and divergent regions of the alignment [70]. There were 319 positions in the final dataset. The scale-bar indicates the number of changes inferred as having occurred along each branch. Red triangles indicate the sequences generated in this study. (PDF 297 kb)
Agriphila deliella
Creators: name: Sinev, Sergey Yu.
name: Korb, Stanislav K.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Agriphila
Agriphila deliella

description: *136. Agriphila deliella (Hübner, 1813)
Tyup, 5.VIII.2016, 1 male.
description: Published as part of Sinev, Sergey Yu. & Korb, Stanislav K., 2022, A preliminary list of the Pyraloid moths (Lepidoptera: Pyraloidea) of Kyrgyzstan, pp. 101-136 in Zootaxa 5138 (2) on page 117, DOI: 10.11646/zootaxa.5138.2.1, http://zenodo.org/record/6556841
Additional file 5: Figure S3. of Morphological and molecular characteristics of Malayfilaria sofiani Uni, Mat Udin & Takaoka n. g., n. sp. (Nematoda: Filarioidea) from the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia) in Peninsular Malaysia
Creators: name: Shigehiko Uni
name: Udin, Ahmad Mat
name: Agatsuma, Takeshi
name: Weerachai Saijuntha
name: Junker, Kerstin
name: Rosli Ramli
name: Hasmahzaiti Omar
name: Lim, Yvonne
name: Sivanandam, Sinnadurai
name: Lefoulon, Emilie
name: Martin, Coralie
name: Daicus Belabut
name: Saharul Kasim
name: Halim, Muhammad Abdullah
name: Zainuri, Nur
name: Bhassu, Subha
name: Fukuda, Masako
name: Matsubayashi, Makoto
name: Harada, Masashi
name: Low, Van
name: Chen, Chee
name: Narifumi Suganuma
name: Rosli Hashim
name: Takaoka, Hiroyuki
name: Mohd Azirun
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Taxonomic position of Malayfilaria sofiani n. g., n. sp., inferred using the neighbour-joining method, based on ITS1 nucleotide sequences. The tree was based on the Kimura 2-parameter model with 1,000 bootstrap replicates (MEGA6). Gblocks was used to eliminate poorly aligned positions and divergent regions of a DNA alignment [70]. There are 495 positions in the final dataset. The scale-bar indicates the number of changes inferred as having occurred along each branch. Red triangles indicate the sequences generated in this study. (PDF 170 kb)