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Harnessing single cell RNA sequencing to identify dendritic cell types, characterize their biological states and infer their activation trajectory

Summary: Dendritic cells (DCs) orchestrate innate and adaptive immunity, by translating the sensing of distinct danger signals into the induction of different effector lymphocyte responses, to induce different defense mechanisms suited to face distinct types of threats. Hence, DCs are very plastic, which results from two key characteristics. First, DCs encompass distinct cell types specialized in different functions. Second, each DC type can undergo different activation states, fine-tuning its functions depending on its tissue microenvironment and the pathophysiological context, by adapting the output signals it delivers to the input signals it receives. Hence, to better understand DC biology and harness it in the clinic, we must determine which combinations of DC types and activation states mediate which functions, and how. To decipher the nature, functions and regulation of DC types and their physiological activation states, one of the methods that can be harnessed most successfully is ex vivo single cell RNA sequencing (scRNAseq). However, for new users of this approach, determining which analytics strategy and computational tools to choose can be quite challenging, considering the rapid evolution and broad burgeoning of the field. In addition, awareness must be raised on the need for specific, robust and tractable strategies to annotate cells for cell type identity and activation states. It is also important to emphasize the necessity of examining whether similar cell activation trajectories are inferred by using different, complementary methods. In this chapter, we take these issues into account for providing a pipeline for scRNAseq analysis and illustrating it with a tutorial reanalyzing a public dataset of mononuclear phagocytes isolated from the lungs of naïve or tumor-bearing mice. We describe this pipeline step-by-step, including data quality controls, dimensionality reduction, cell clustering, cell cluster annotation, inference of the cell activation trajectories and investigation of the underpinning molecular regulation. It is accompanied with a more complete tutorial on Github. We anticipate that this method will be helpful for both wet lab and bioinformatics researchers interested in harnessing scRNAseq data for deciphering the biology of DCs or other cell types, and that it will contribute to establishing high standards in the field.   Data: 1. negative_cDC1_relative_signatures.csv : Negative signatures for performing Connectivity Map (cMAP) Analysis 2. positive_cDC1_relative_signatures.csv : Positive signatures for performing Connectivity Map (cMAP) Analysis

Figs 24–26 in Halyomorpha halys fixed as the type species of the genus Halyomorpha (Hemiptera: Heteroptera: Pentatomidae)

Figs 24–26. Pentatoma halys Stål, 1855, female syntype (NHRS): 24 – dorsal view, 25 – ventral view, 26 – labels. Scale bar in mm. Orig. D. Rédei.

Figs 18–20 in Halyomorpha halys fixed as the type species of the genus Halyomorpha (Hemiptera: Heteroptera: Pentatomidae)

Figs 18–20. Halyomorpha timorensis (Westwood, 1837), female syntype: 18 – external scent efferent system of the metathoracic scent gland; 19–20 – external genitalia (19 – posterior view, 20 – ventral view, angle on posterior margin of lt8 shown by yellow arrows). Abbreviations: lt8–9 – laterotergites 8–9, o – ostiole, pe – peritreme in form of peritremal ruga, t8 – tergite 8, vf8–9 – valvifers 8–9, x – segment X. Orig. P. Kment.

Figs 4–9 in Halyomorpha halys fixed as the type species of the genus Halyomorpha (Hemiptera: Heteroptera: Pentatomidae)

Figs 4–9. Halyomorpha halys (Stål, 1855), male genitalia of the specimen from Mayr collection (NHMW). 4–8 – genital capsule (4 – posterior view, magnification 55×; 5 – dorsoposterior view, 47×; 6 – ventral view, 35×; 7 – dorsal view, 37×; 8 – lateral view, 47×); 9 – paramere in posterior mediolateral view (170×). Abbreviations: pa – parameres, plp – posterolateral lobes of genital capsule. Scale bars: 4–8 – 0.5 mm, 9 – 0.2 mm. Orig. P. Kment.

Figs 10–14 in Halyomorpha halys fixed as the type species of the genus Halyomorpha (Hemiptera: Heteroptera: Pentatomidae)

Figs 10–14. Halyomorpha picus (Fabricius, 1794), male genitalia of the specimen from Mayr collection (NHMW). 10–13 – genital capsule (10 – posterior view, magnification 42×; 11 – lateral view, 42×; 12 – ventral view, 30×; 13 – dorsal view, 32×); 14 – paramere in posterior mediolateral view (100×). Abbreviations: pa – parameres, plp – posterolateral lobes of genital capsule. Scale bars: 0.5 mm. Orig. P. Kment.

# Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease

Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern target gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, it is still challenging to understand how cell type networks work abnormally under AD. To address this, we integrated single-cell multi-omics data and predicted the gene regulatory networks in AD and control for four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes. Importantly, we applied network biology approaches to analyze the changes of network characteristics across these cell types, and between AD and control. For instance, many hub TFs target different genes between AD and control (rewiring). Also, these networks show strong hierarchical structures in which top TFs (master regulators) are largely common across cell types, whereas different TFs operate at the middle levels in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell type-specific TF-TF cooperativities in gene regulation. The cell type networks are highly modular and several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes and putative targets of approved and pending AD drugs, suggesting possible cell-type genomic medicine in AD. Finally, using the cell type gene regulatory networks, we developed machine learning models to classify and prioritize additional AD genes. We found that top prioritized genes predict clinical phenotypes (e.g., cognitive impairment) with reasonable accuracy. Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals dysregulated cell type gene dysregulatory mechanisms in AD.

CrossDomainTypes4Py: A Python Dataset for Cross-Domain Evaluation of Type Inference Systems

This dataset contains python repositories mined on GitHub on January 20, 2021. It allows a cross-domain evaluation of type inference systems. For this purpose, it consists of two sub-datasets, each containing only projects from the web or scientific calculation domain, respectively. Therefore we searched for projects with dependencies to either <a href="https://numpy.org/">NumPy</a> or <a href="https://flask.palletsprojects.com/en/2.0.x/">Flask</a>. Furthermore, only projects with dependencies to <a href="http://mypy-lang.org/">mypy</a> were considered, because this should ensure that at least parts of the projects have type annotations. These can be used later as ground truth. Further details about the dataset will be described in an upcoming paper, as soon as it is published it will be linked here. The dataset consists of two files for the two sub-datasets. The web domain dataset contains 3129 repositories and the scientific calculation domain dataset contains 4783 repositories. The files have two columns with the URL to the GitHub repository and the used commit hash. Thus, it is possible to download the dataset using shell or python scripts, for example, the pipeline provided by <a href="https://github.com/saltudelft/many-types-4-py-dataset">ManyTypes4Py</a> can be used. If repositories do not exist anymore or are private, you can contact us via the following email address: bernd.gruner@dlr.de. We have a backup of all repositories and will be happy to help you.

Correlation of urban avian species diversity present in heterogenous habitat types of the Silk city, Odisha, Eastern India

This is the complete metadata and the R code required to do the analysis of the paper regarding birds of Berhampur city.

Bacterial F-type ATP synthases follow a well-choreographed assembly pathway

The raw data provided here are referenced in the manuscript ''Bacterial F-type ATP synthases follow a well-choreographed assembly pathway'', which is in preparation for publication. The raw data files have the same name as the figures generated from the respective raw data. Content of the dataset: 1) raw spectra from LILBID measurements 2) raw spectra from nESI measurements 3) raw spectra from HPLC measurements 4) absorbance measurements and calculations for activity assays

How much hydrogen is in Type Ib and IIb supernova progenitors?

Input files and simulation results for stellar evolution tracks computed for the paper "How much hydrogen is in Type Ib and IIb supernova progenitors?", as well as synthetic photometry generated and used in the analysis. Version 10398 of MESA was used for the simulations. More details in the README.txt file and in the paper.

PGIR 20eid (SN 2020qmp): A Type IIP Supernova at 15.6 Mpc discovered by the Palomar Gattini-IR survey

We present a detailed analysis of SN 2020qmp, a nearby Type IIP core-collapse supernova (CCSN), discovered by the Palomar Gattini-IR (PGIR) survey in the galaxy UGC07125 (distance of ≈ 15.6 ± 4 Mpc). SN 2020qmp displays characteristic hydrogen lines in its optical spectra, as well as a plateau in its optical LC, hallmarks of a Type IIP SN. We analyze data from observations in various bands: radio, NIR, optical and X-rays. We do not detect linear polarization during the plateau phase, with a 3σ upper limit of 0.78%. Through hydrodynamical LC modeling and an analysis of its nebular spectra, we estimate a progenitor mass of around 11 solar masses, and an explosion energy of around 0.8e51 erg. We find that the spectral energy distribution cannot be explained by a simple CSM interaction model, assuming a constant shock velocity and steady mass-loss rate. In particular, the excess X-ray luminosity compared with the synchrotron radio luminosity suggests deviations from equipartition. Finally, we simulate a sample of CCSNe with plausible distributions of brightness and extinction, within 40 Mpc, and test what fraction of the sample is detectable at peak light by NIR surveys versus optical surveys. Our simulations show that the Wide-Field Infrared Transient Explorer will detect about 14 more CCSNe out of 75 expected in its footprint within 40 Mpc, over five years than an optical survey equivalent to the Zwicky Transient Facility would detect. We have determined or constrained the main properties of SN 2020qmp and of its progenitor, highlighting the value of multiwavelength follow-up observations of nearby CCSNe, as well as demonstrated the advantages of NIR surveys over optical surveys for the detection of dust-obscured CCSNe in the local universe.

Dataset - The cGAS-STING pathway drives type I IFN immunopathology in COVID-19

Dataset corresponding to the LoC studies in the manuscript titled The cGAS-STING pathway drives type I IFN immunopathology in COVID-19. The following data are included: BioEM.zip: Volumetric electron microscopy - representative movies of volumetric scans of fields of view of the vascular face of uninfected control and SARS-CoV-2 infected LoCs. Blender file containing reconstruction of mitochondria. Cleaved-caspase3.zip: Imaris files for analysis of 3D stacks from two- and three-component LoCs immunostained for cleaved-caspase 3. IFN beta.zip: Imaris files for analysis of 3D stacks from two- and three-component LoCs immunostained for IFN beta. PhosphoSTING.zip: Imaris files for analysis of 3D stacks from two component LoCs immunostained for phosphoSTING. Proteomics_R_code.Rmd: Annotated custom scripts in R for the analysis of the proteomics data.

opencc-by-4.0Sep 2021View details →

Data for: Trap type affects dung beetle taxonomic and functional diversity in Bornean tropical forests

Dung beetle community composition data. Data was collected using either dung-baited pitfall traps or flight interception traps. Each row represents one trap, with the author/study information, name of study site, sampling period, trap type and habitat type. Dung beetle species and their abundances are listed. See "metadata" tab for more details. Paper abstract: Baited pitfall traps (BPTs) and flight intercept traps (FITs) are the most common methods employed for sampling dung beetle communities. These methods vary in their efficacy and are affected by factors such as the bait types used and the dispersal abilities of different dung beetle species. We present the first quantitative comparison of the taxonomic and functional diversity, and community composition of dung beetles caught in BPTs and FITs in Bornean tropical forests. We show that BPTs and FITs captured complementary communities with different functional traits, and that BPTs captured more functionally diverse communities. We therefore recommend using a combination of both baited BPTs and FITs for studies assessing the composition of dung beetles across habitat types. Our results also highlight that it is important to consider how trap type affects the trait composition of communities when relating dung beetle communities and functional traits to ecological functioning. We suggest modifications to FITs based on the design of harp traps to increase their effectiveness in capturing larger-bodied beetles.

Family Type, Mental and Physical Health of in-school Female Adolescents in Ado-Ekiti, Nigeria

This dataset is based on a cross-sectional survey conducted in Ado-Ekiti, Nigeria among in-school female adolescents. The general objective of the study was to examine the influence of family type on the physical and mental health of in-school female adolescents. The data were obtained in 2017 from in-school female adolescents aged 10-18 years old. The respondents were randomly selected from four purposively selected secondary schools. Two schools were selected from the government-owned public schools and two from schools owned by individuals or private organizations. Nigeria operates a six-year secondary education; three years at the junior secondary school  (JSS 1-3) and three years at the senior secondary (SS 1-3). The population for this study excluded students in SS3 because they had just concluded their terminal examination at the time of this study. Using the formula proposed by (Krejcie & Morgan, 1970) for deriving a small sample when the population is known, a sample size of 383 was derived from a population of 1656 female students in the four schools. With 10% added to adjust for non-response, a total of 421 students were involved in the study. The number of respondents allocated to each school was proportional to the size of the female students' population in each school. In each school, respondents were assigned to classes proportional to the size, and the particular respondents were identified using a random number. Data were collected with a self-administered structured questionnaire which was piloted before the actual survey. The data is saved in Stata format.  A scale for measuring self-reported mental well was designed using questions adapted from Ross, Mirowsky, & Goldsteen (1990) and (Langton & Berger, 2011). The scale reliability coefficient was 0.85. The students were asked to state how often they experience 22 conditions such as feeling sad, discouraged, lonely, hopeless, worthless, wishing you were dead, having trouble concentrating, having difficulty sleeping, crying, and worried among others.  Physical health was measured using a scale generated with questions adapted from (Langton & Berger, 2011; Ross et al., 1990).  The students were asked to state the frequency of experiencing seven conditions in the month before the survey: feeling sick, tired, dizzy, having chest pain, a headache, muscle or joint pain, and stomach ache. The response options were every day, more than two times, two times, once, and never, graded 1-5. Family type was categorised in four ways: 1) two-parent and single parent. Two parents comprised of couples who were legally married and those who were living together in a consensual union whereas single parents comprised never married, widowed, divorced, and separated mother or father. 2) two-parent (monogamous), two-parent (polygynous), and single parent 3) two-parent, single father, and single mother 4) two-parent, never married, widowed, divorced, and separated

Towards identifying industrial crop types and associated agronomies to improve biomass production from marginal lands in Europe

Background: Growing industrial crops on marginal lands has been proposed as a strategy to minimize competition for arable land and food production. In the present study, eight experimental sites in three different climatic zones in Europe (Mediterranean, Atlantic and Continental), seven advanced industrial crop species [giant reed (two clones), miscanthus (M. × giganteus and two new seed-based hybrids), saccharum (one clones), switchgrass (one variety), tall wheatgrass (one variety), industrial hemp (three varieties) and willow (eleven clones)], and six marginality factors alone or in combination (dryness, unfavorable texture, stoniness, shallow soil, topsoil acidity, heavy metal and metalloid contamination) were investigated. At each site, biophysical constraints and low-input management practices were combined with prevailing climatic conditions. Results: The relative yield of a site-specific low-input system compared with the site-specific control was from small to large (i.e., from -99% in industrial hemp in the Mediterranean to +210% in willow in the Continental zone), due to the genotype-by-management interaction along with climatic variation between growing seasons. Genotype selection and improved knowledge on crop response to changing environmental, site-specific biophysical constraint and input application has been detected as key to profitably grow industrial crops on marginal areas. Conclusions: This study may act to provide hints on how to scale-up investigated cropping systems, through low-input practices, under similar environmental and soil conditions tested at each site. However, further attention to detail on the agronomy of early plant development and management in larger multi-year and multi-location field studies with commercially scalable agronomies are needed in order to validate yield performances, and thereby to inform on the best industrial crop options.

NMR data of Lanostane Type Triterpenoids isolated from Leplaea mayombensis

This folder contains NMR datasets of new compounds described in the publication entitled: Antiplasmodial and Cytotoxic Activity of Lanostane Type Triterpenoids isolated from Leplaea mayombensis   NMR processing : Topspin 4.1.13

CSV files and R script: writing process data of typed picture description by 15 cognitively impaired patients and 15 healthy controls

Writing process data of 15 cognitively impaired patients and 15 age- and gender-matched healthy controls were obtained. Each of them completed two typed picture description tasks that were logged with Inputlog, a keystroke logging tool. Variables included time on task; number of characters, pauses and Pause-bursts per minute; proportion of pause time; duration of Pause-bursts; and pause time between words. For pause time between words, also the effect of pauses preceeding specific word categories was analyzed. The data were used to explore if the observation of writing behavior can assist in the screening and follow-up of mild cognitive impairment (MCI) and mild dementia due to Alzheimer’s disease (AD). This data set contains the CSV files that were used for the analyses and the corresponding R script.

opencc-by-4.0Mar 2022View details →

Dataset of the determination of the topographic spatial resolution of a confocal point sensor with a type ASG material measure

These original measurement data relate to the publication: J. Schaude, A. C. Gröschl, T. Hausotte: Effect of a Misidentified Centre of a Type ASG Material Measure on the Determined Topographic Spatial Resolution of an Optical Point Sensor, Metrology 2(1), p. 19-32, 2022, <a href="https://doi.org/10.3390/metrology2010002">https://doi.org/10.3390/metrology2010002</a>. Please refer to this open access publication for a detailed description of the measurement setup and procedure. All data are in ASCII-format. Each file contains four columns, where column one to three are the x, y, and z-coordinates of the positioning system and column four is the signal of the photodetector. Content of the folders 10_Plane: Axial probings on 18 points just outside the grooves. 20_Edges: Lateral probings from each point just outside the grooves in the direction of the roughly determined centre of the material measure. 30_PlaneArea: Repeated axial probing on a plane area near the material measure. 40_RadialMeasurement: Radial measurement of the material measure by lateral (radial) probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), and radii (referring to the centre of the circle fitted to the edges determined in 20_Edges). Each radial probing has its own data file, with the name of the data file being “radial_probing {radius in m} {height in m} {data and time of probing}.txt”. 50_LineMeasurement: Lateral probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), different lateral offsets (referring to the centre of the circle fitted to the edges determined in 20_Edges) and on two angles (on the groove (0°) and the adjacent top level (10°)). Please refer to sec. 5.2 of the aforementioned publication for a detailed description. Each lateral probing has its own data file, with the name of the file being “lateral probing {angle in °} {offset in m} {height in m} {data and time of probing}.txt”. Acknowledgement This project 20IND07 TracOptic has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme. Funder name: European Metrology Programme for Innovation and Research (EMPIR); Funder ID: 10.13039/10001413

opencc-by-4.0Mar 2022View details →

Types of Custom Boxes For Bath Bombs

There are many types of bath bomb boxes available, which are given below: Boxes By Style 1. Boxes With Transparent Window Some <a href="https://www.thecosmeticboxes.com/product/bath-bomb-boxes/">Boxes For Bath Bombs</a> feature a transparent window, allowing customers to check the product before buying it.  2. Boxes With Colored Ribbons Others have colored ribbons to enhance the presentation of Bath Bombs Boxes Wholesale.  Regardless of the type of box you choose, it must meet your brand guidelines. These tips will help you create the most appealing packaging for your bath bombs.  Examples Of Bath Bomb Boxes <ul> <li>Custom Printed  Boxes For Bath Bombs</li> </ul> <a href="https://www.thecosmeticboxes.com/product/bath-bomb-boxes/">Custom Bath Bomb Boxes</a> for bath bombs are an excellent way to show off your products. They're durable and attractive, so customers will want to keep them around. You can add window panes and even your company's logo or product-related information to these boxes.  Show Your Brand UP A unique box can give your brand a distinct advantage over your competition. While a typical bath bomb box can be purchased anywhere, a unique and beautiful box can make your bath bombs stand out among the crowd. Whether your product is a luxury item or an essential item, a beautiful box will help your brand shine. Mailer bath bomb boxes are an environmentally-friendly choice, and they're versatile and easy to tailor.  <a href="https://www.thecosmeticboxes.com/product/bath-bomb-boxes/">Eco Friendly Bath Bomb Packaging</a> is ideal for products that don't need external packaging and need to stay dry for transport. They're also lightweight and cheap to ship compared to other types of packaging. Order free samples and try out different designs to make your bath bombs more visually appealing.

Maps of depths are created for the site of 50 m length. Flow types are turbulent, broken standing waves, unbroken standing waves, and rippled. The average width was 8 m and varied from 5.5 to 12 m. Bed elements included bars, rocks, and step/pools. The average depth was 0.35 m, with a maximum of 0.6 m. The average velocity was 0.4 m/s, with a maximum of 1.2 m/s (figs 10). Distribution of bottom habitats at the locations with the crayfish are as follows: megalital — 5 %, macrolithal — 30 %, mesolithal — 25 %, microlithal — 15 %, psammal — 15 %, CPOM — 10 %. Assessment by hydrobiological parameters showed that the presence of Lyngbya and Oscillatoria, as well as the increase of the number of Oligochae- in New Findings Of White Clawed Crayfish, Austropotamobius Pallipes (Decapoda, Astacidae), And Peculiarities Of Its Spatial Distribution In Neretvica (Bosnia And Herzegovina)

Maps of depths are created for the site of 50 m length. Flow types are turbulent, broken standing waves, unbroken standing waves, and rippled. The average width was 8 m and varied from 5.5 to 12 m. Bed elements included bars, rocks, and step/pools. The average depth was 0.35 m, with a maximum of 0.6 m. The average velocity was 0.4 m/s, with a maximum of 1.2 m/s (figs 10). Distribution of bottom habitats at the locations with the crayfish are as follows: megalital — 5 %, macrolithal — 30 %, mesolithal — 25 %, microlithal — 15 %, psammal — 15 %, CPOM — 10 %. Assessment by hydrobiological parameters showed that the presence of Lyngbya and Oscillatoria, as well as the increase of the number of Oligochae-