Single cell RNA sequencing (scRNA-seq) has become a core tool for researchers to understand biology. As scRNA-seq has become more ubiquitous, many applications demand higher scalability and sensitivity. Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells, overcoming limitations of previous droplet based technologies. However, there is still a need for increased sensitivity for both droplet and combinatorial barcoding based scRNA-seq technologies. To meet this need, here we introduce an updated combinatorial barcoding method for scRNA-seq with dramatically improved sensitivity. To assess performance, we profile a variety of sample types, including cell lines, human peripheral blood mononuclear cells (PBMCs), mouse brain nuclei, and mouse liver nuclei. When compared to the previously best performing approach, we find up to a 2.6-fold increase in unique transcripts detected per cell and up to a 1.8-fold increase in genes detected per cell. These improvements to transcript and gene detection increase the resolution of the resulting data, making it easier to distinguish cell types and states in heterogeneous samples. Split-pool combinatorial barcoding already enables scaling to millions of cells, the ability to perform scRNA-seq on previously fixed and frozen samples, and access to scRNA-seq without the need to purchase specialized lab equipment. Our hope is that by combining these previous advantages with the dramatic improvements to sensitivity presented here, we will elevate the standards and capabilities of scRNA-seq for the broader community.
In 2019, the Author's Guild of the United States announced their intent to pursue federal legislation for Public Lending Rights (PLR). PLR provide remuneration to authors, publishers, and/or illustrators for the circulation of their works in public, and sometimes school, libraries. A number of countries, including the United Kingdom, Canada, and Australia, instituted PLR in the 1970s and 1980s. This paper aims to investigate how public libraries in those three nations responded to the movement for PLR and how the philosophical concerns they raised may inform librarians in the United States.
We surveyed the insect fauna associated with Urophora cardui L. (Diptera: Tephritidae) galls on Canada thistle, Cirsium arvense L. (Asterales, Asteraceae), in parts of the northern Great Plains, U.S., by field-collecting galls and rearing or dissecting out the insects. We also examined the relationships between gall biomass and insect density and biomass. Urophora cardui were widespread, and the gall biomass was positively correlated with fly density and fly biomass. We recovered Isohydnocera tabida (LeConte) (Coleoptera: Cleridae) from galls in two counties, which represents a new host record and provides vital information on the little-known immatures of this predatory species. Pteromalus elevatus (Walker) (Hymenoptera: Pteromalidae) was the dominant parasitoid that emerged from the U. cardui galls. Individual galls typically only had one insect species, and occasionally both U. cardui and P. elevatus were present, but it was rare for other insects to be present in galls housing I. tabida. This study adds to the taxonomic literature of gall-inhabiting insect species and provides new information on the predators of U. cardui, specifically a little-known clerid beetle species.
Objective -To learn how faculty members define plagiarism and what actions (if any) they are taking in their classes to educate students about plagiarism. Design -Online survey.Setting -A small private college in the Northeastern United States of America.
Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare tumor disease, which affects children and adolescents without history of primary liver disease. Beside surgical resection established treatment options are lacking for FL-HCC. Recently, the DNAJB1-PRKACA fusion transcript was identified as the oncogenic driver of tumor pathogenesis in 100% of FL-HCC patients. Here, we investigated the role of the DNAJB1-PRKACA fusion protein as a source for immunogenic neoepitopes and showed first immunotherapeutic application of these antigens in a FL-HCC patient.HLA class I- and class II-presented neoantigens derived from the DNAJB1-PRKACA fusion protein were predicted in silico using NetMHCpan 4.1 and SYFPEITHI 1.0, or NetMHCIIpan 4.0, respectively. With this workflow nine binding cores of nine amino acid length for a total of 1290 different HLA class II alleles, as well as 13 HLA class I ligands for the 20 most frequent HLA class I allotypes (European population, iedb.org) were identified. Cellular processing and HLA presentation of DNAJB1-PRKACA-derived peptides was proven by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) of DNAJB1-PRKACA-transduced HCC cell lines. Immunogenicity of DNAJB1-PRKACA-derived peptides was assessed for the HLA class II peptide (PII-1) and the HLA-A*24 peptide (PA*24) by in vitro priming experiments which showed an induction of multifunctional peptide-specific CD4+ and CD8+ T cells, respectively, with expression of CD107a, IFNγ, and TNF upon peptide-pulsing. Furthermore, PA*24-specific T cells showed antigen-specific lysis of autologous peptide-loaded target cells and single-cell next-generation sequencing (10x Genomics) of PA*24-specific CD8+ T cells further enabled the identification of DNAJB1-PRKACA-reactive T cell receptors. Based on these preclinical data we applied a peptide vaccine, consisting of three HLA class I ligands (PA*02, PB*44, and PC*05) and PII-1 spanning the DNAJB1-PRKACA fusion region, to a 15-year old patient with histologically confirmed FL-HCC, who experienced multiple tumor relapses after early liver transplant due to unresectable FL-HCC not responsive to chemotherapy. After two vaccinations in vivo induction of multifunctional CD4+ T cells targeting PII-1 and PB*44 was observed by IFNγ ELISPOT. Single-cell RNA sequencing of vaccine-induced CD4+ T cells revealed distinct gene expression clusters of T cell activation and high TCR clonality. DNAJB1-PRKACA-specific T cells persisted in peripheral blood and were accompanied by relapse free survival of the patient until now, more than one year post vaccination. These findings identified the DNAJB1-PRKACA fusion transcript as novel prime source for broadly applicable neoepitopes and corresponding TCRs and provide first evidence for their application in cancer immunotherapy of FL-HCC. Citation Format: Jens Bauer, Natalie Köhler, Yacine Maringer, Philip Bucher, Tatjana Bilich, Melissa Zwick, Severin Dicks, Annika Nelde, Marissa Dubbelaar, Jonas Scheid, Marcel Wacker, Jonas J. Heitmann, Sarah Schroeder, Jonas Rieth, Monika Denk, Marion Richter, Reinhild Klein, Irina Bonzheim, Julia Luibrand, Ursula Holzer, Martin Ebinger, Ines B. Brecht, Michael Bitzer, Melanie Boerries, Helmut R. Salih, Hans-Georg Rammensee, Stephan Hailfinger, Juliane S. Walz. The oncogenic fusion protein DNAJB1-PRKACA can be actively targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2008.
A Review of: Logan, J., & Spence, M. (2021). Content strategy in LibGuides: An exploratory study. The Journal of Academic Librarianship, 47(1), Article 102282. https://doi.org/10.1016/j.acalib.2020.102282 Abstract Objective – To determine what strategies academic libraries use to govern creation and maintenance of their LibGuides. Design – Online survey questionnaire. Setting – A selection of academic libraries that use Springshare’s LibGuide system, mainly in the United States and Canada. Subjects – Academic libraries with administrator level access to LibGuides at 120 large and small, private and public schools. Methods – Researchers made their online questionnaire available on a Springshare lounge and recruited participants through electronic mailing lists. Respondents were self-selected participants. The survey consisted of 35 questions, including several about their institution’s size and type, the number of LibGuides available through their library, and how their guides are created and reviewed. There was space available for comments. The survey stated that the researchers’ goal is to complete an “environmental scan of content strategies” in LibGuides at academic institutions. Main Results – Of the 120 responding institutions, 88% are located in either the United States or Canada and 53% reported that they do have content guidelines for LibGuide authors. Content guidelines might include parameters for topics, target audiences, or purpose. Parameters for structural elements, including page design, content reuse policies, naming conventions, and navigation, were most commonly represented at those institutions that reported having guidelines. Seventy-seven percent of respondents reported that their LibGuides do not go through a formal review process prior to publication. Regarding LibGuide maintenance, 58% reported that LibGuides are reviewed as needed, while 27% indicated a more systematic approach. In most cases, the LibGuide reviewer is the author, though sometimes a LibGuide administrator may take on a review role. The most common considerations for LibGuide review are currency, accuracy, usage, and consistency. Of the responding institutions, 74% reported that they do not conduct any user testing of their guides. Two of the biggest barriers to introducing and maintaining LibGuide guidelines identified in the survey were lack of time and a sense of librarian ownership over content and workflow. The strong culture of academic freedom may make some librarians resistant to following institutional guidelines. Survey respondents noted that, where content guidelines are present, they tend to address “low hanging fruit” issues, such as page design and naming conventions, rather than more complex issues around tone and messaging. Conclusion – Content creators tend to have many competing priorities, so a workflow and guideline system might help librarians spend less time on their guides. Despite a large amount of research on LibGuide best practices regarding content strategy, few institutions seem to be taking systematic steps to implement them. Further research examining the experiences of LibGuide authors and administrators and on the effectiveness of content strategy practices is necessary.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.