Find research datasets worth reusing

FIG. 8. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 8. — Paragiopagurus schnauzer n. sp., ♂ holotype 3.3 mm, BIOGEOCAL, stn CP 214, New Caledonia (MNHN-Pg 7615): A, propodus and dactyl of left fourth pereopod, lateral; B, propodus and dactyl of left fifth pereopod, lateral; C, thoracic region, ventral; D, anterior and posterior lobes of thoracic sternite XII (third pereopods), ventral; E, uropods and telson, dorsal; F, left first pleopod, mesial; G, left second pleopod, anterior. Scale bars: A-D, F, G, 1 mm; E, 0.5 mm.

FIG. 3. — Oncopagurus conicus n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 3. — Oncopagurus conicus n. sp., ♂ holotype 2.0 mm, HALIPRO 1, stn C 858, New Caledonia (MNHN-Pg 7612): A, left second pereopod, lateral; B, dactyl of same, mesial; C, left third pereopod, lateral; D, dactyl of same, mesial; E, propodus and dactyl of left fourth pereopod, lateral; F, propodus and dactyl of left fifth pereopod, lateral. Scale bars: A-D, 1 mm; E, F, 0.20 mm.

FIG. 4. — Oncopagurus conicus n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 4. — Oncopagurus conicus n. sp., ♂ holotype 2.0 mm, HALIPRO 1, stn C 858, New Caledonia (MNHN-Pg 7612); A, thoracic region, ventral;B, anterior and posterior lobes of thoracic sternite XII (third pereopods), ventral; C, uropods and telson, dorsal; D, left first pleopod, mesial; E, left second pleopod, anterior. Scale bars: A, 0.50 mm; B, D, E, 0.20 mm; C, 0.25 mm.

FIG. 9 in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 9. — Right ocular peduncle and cornea (stippling indicates weakly calcified portion): A-C, Typhlopagurus foresti de Saint Laurent, 1972, ♂ 3.7 mm, SALOMON 1, stn CP 1781 (USNM 1084207, ex MNHN-Pg 6706); D, Sympagurus acinops Lemaitre, 1989, ♂ paratype 3.2 mm, Tongue of the Ocean, Bahamas, 1438 m (USNM 231834); E, Parapagurus saintlaurentae Lemaitre, 1999, ♂ paratype 12.8 mm, N of Madagascar, 4810 m (USNM 276123); A, D, E, lateral; B, mesial; C, ventral. Scale bars: A-D, 0.25 mm; E, 1 mm.

FIG. 7. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 7. — Paragiopagurus schnauzer n. sp., ♂ holotype 3.3 mm, BIOGEOCAL, stn CP 214, New Caledonia (MNHN-Pg 7615): A, right second pereopod, lateral; B, dactyl of same, mesial; C, right third pereopod, lateral; D, dactyl of same, mesial. Scale bar: 1 mm.

FIG. 1. — Oncopagurus conicus n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 1. — Oncopagurus conicus n. sp., New Caledonia: A, ♀ paratype 2.0 mm, HALIPRO 1, stn C 858 (MNHN-Pg 7613); B-D, F-J, ♂ holotype 2.0 mm, HALIPRO 1, stn C 858 (MNHN-Pg 7612); E, ovig. ♀ paratype 2.1 mm, BIOGEOCAL, stn CP 214 (MNHN-Pg 7614); A, gill lamella; B, shield and cephalic appendages, dorsal (stippling indicates weakly calcified portion); C, right ocular peduncle and cornea, lateral; D, epistome, dorsolateral (es, epistomial spine; ls, labral spine); E, anterior portion of shield and cephalic appendages, dorsal; F, right antennal peduncle, lateral; G, right cheliped, dorsal; H, chela of same, lateral; I, same, mesial; J, left cheliped, dorsal. Scale bars: A, 0.10 mm; B, 0.50 mm; C-F, 0.25 mm; G-J, 1 mm.

FIG. 6. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 6. — Paragiopagurus schnauzer n. sp., ♂ paratype 3.2 mm, HALIPRO 2, stn BT 105, Loyalty Islands (MNHN-Pg 6705), left mouthparts, internal: A, mandible; B, maxillule; C, maxilla; D, first maxilliped; E, second maxilliped; F, third maxilliped. Scale bars: 0.25 mm.

FIG. 5. — Paragiopagurus schnauzer n in Two new species of Parapaguridae (Crustacea, Decapoda, Anomura, Paguroidea) with subconical corneas, and new data on biology of some rare species

FIG. 5. — Paragiopagurus schnauzer n. sp., ♂ holotype 3.3 mm, BIOGEOCAL, stn CP 214, New Caledonia (MNHN-Pg 7615): A, gill lamella; B, shield and cephalic appendages, dorsal (stippling indicates weakly calcified portion); C, right ocular peduncle and cornea, lateral; D, epistome, dorsolateral (es, epistomial spine; ls, labral spine); E, right antennal peduncle, lateral; F, right cheliped, dorsal; G, chela of same, lateral; H, same, mesial; I, left cheliped, dorsal. Scale bars: A, C, D, 0.25 mm; B, F-I, 1 mm; E, 0.50 mm.

opencc-by-4.0Dec 2021View details →

Dataset for "Evaluation of Publicly Available Information on Sex-related Differences in the Efficacy and Safety of New Molecular Entities and Therapeutic Biological Products"

Contains our extraction sheets with additional documents/notes on methods used in our study.

opencc-by-4.0Dec 2021View details →

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

dryad40/100

Evidence for continent-wide convergent evolution and stasis throughout 150 years of a biological invasion

The extent to which evolution can rescue a species from extinction, or facilitate range expansion, depends critically on the rate, duration, and geographical extent of the evolutionary response to natural selection. Adaptive evolution can occur quickly, but the duration and geographical extent of contemporary evolution in natural systems remains poorly studied. This is particularly true for species with large geographical ranges and for timescales that lie between 'long-term' field experiments and the fossil record. Here, we introduce the Virtual Common Garden (VCG) to investigate phenotypic evolution in natural history collections while controlling for phenotypic plasticity in response to local growing conditions. Reconstructing 150 years of evolution in Lythrum salicaria (purple loosestrife) as it invaded North America, we analyze phenology measurements of 3,429 herbarium records, reconstruct growing conditions from more than 12 million local temperature records, and validate predictions across three common gardens spanning 10 degrees of latitude. We find that phenology clines have evolved along parallel climatic gradients, repeatedly throughout the range, during the first century of evolution. Thereafter, the rate of microevolution stalls, recapitulating macroevolutionary stasis observed in the fossil record. Our study demonstrates that preserved specimens are a critical resource for investigating limits to evolution in natural populations. Our results show how natural selection and trade-offs measured in field studies predict adaptive divergence observable in herbarium specimens over 15 decades at a continental scale.

opencc-zeroJan 2022View details →

# 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.

Figure 3 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 3 Uvariopsis dicaprio. (A) habit, cauliflorous inflorescences on trunk; (B) leafy branch, one season's growth; (C) inflorescence, showing pedicel articulations, bracts and bracteoles; (D) flower, with one petal removed to show the staminal dome; (E) detail of sparse hairs on abaxial petal surface; (F) stamen, different views; (G) junction of base of leaf with stem, showing dome-like axillary bud. All drawn from MacKinnon 51 (K) by MEG GRIFFITHS. Full-size DOI: 10.7717/peerj.12614/fig-3

Figure 4 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 4 Global distribution of Uvariopsis dicaprio, together with U. korupensis and U. submontana. Full-size DOI: 10.7717/peerj.12614/fig-4

Figure 1 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 1 Uvariopsis dicaprio. Cauliflorous inflorescences on trunk. Photo Lorna MacKinnon. Full-size DOI: 10.7717/peerj.12614/fig-1

Figure 2 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 2 Uvariopsis dicaprio. Trunk apex with cauliflorous flowers and canopy. Photo Lorna MacKinnon. Full-size DOI: 10.7717/peerj.12614/fig-2

Molecular and biological characterization of an Asian-American isolate of Chikungunya Virus

This is a dataset of the figures used in the development of the manuscript Molecular and biological characterization of an Asian-American isolate of Chikungunya Virus

FIG. 6 in Biological and cultural history of domesticated dogs in the Americas

FIG. 6. — Selection of skulls of dog breeds originating in the Americas (selection not exhaustive). These dogs demonstrate the great variation in skull shape and body size of modern American breeds, from slender to short snouted and from giant to dwarf sized varieties, including hairless forms with oligodontia. A, Chesapeake Bay Retriever (NMBE 1051681);B, Alaskan Malamute (NMBE 1051387);C, Chihuahua (NMBE 1052001);D, Fila Brasileiro (I.f.H. 14005, mirrored);E, Mexican hairless dog (ZMUZH 13754); F, Peruvian hairless dog (NMBE 1062857); G, Boston Terrier (NMBE 1051959); H, Newfoundland (NMBE 1050502). Abbreviations: I.f.H., Zoologisches Institut/Populationsgenetik (former Institut für Haustierkunde), Christian-Albrechts-Universität zu Kiel, Germany; NMBE, collection of the Albert-Heim-Foundation at the Naturhistorisches Museum Bern, Switzerland;ZMUZH, Zoologisches Museum der Universität Zürich, Switzerland. Scale bar: 5 cm.

FIG. 3 in Biological and cultural history of domesticated dogs in the Americas

FIG. 3. — Drawings of skulls of pre-Columbian domestic dogs. These drawings were published as part of Alfred Nehring's work (1884) and show skulls of domestic dogs that have been excavated in the Inca burial ground of Ancon, Peru. The same skulls are also depicted in Figure 2. A, shepherd-like dog in ventral view; B, bulldog-like dog in ventral view; C, same dog as in B but from dorsal view. Drawings are not to scale.

FIG. 1 in Biological and cultural history of domesticated dogs in the Americas

FIG. 1. — "Canis mexicana", a domestic dog with peculiar humps and apparent muscle hypertrophy, as depicted in 1651 by Hernández in his Rerum medicarum Novae Hispaniae thesaurus (Hernández 1992). Previously dismissed as a caricature (Ueck 1961), it may actually illustrate a phenotype associated with mutations in the myostatin gene. Picture retrieved from Internet Archive https://archive.org/details/rerummedicarumno00hern/page/466/mode/1up, last consultation on 30 November 2021.