13,305 research outputs found
Solomon Raphael peddler's license
No full textContains Raphael's Pennsylvania peddler's license, for the year 1787-1788, signed by Benjamin Franklin, president of the Supreme Executive Council of Pennsylvania.Digital ImageDigital finding aid available:reviewe
Raw read counts and phased SNP counts for every single cell in the sequencing datasets of the breast cancer patient S1 from "Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL"
No full textThis dataset contains the raw read counts and phased SNP counts for every single cell in the sequencing datasets of breast cancer patient S1 from “Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL” [Zaccaria & Raphael, 2020]. These data enable the full reproduction of all the results in the related manuscript for breast cancer patient S1. Specifically, the data are provided in two files for every dataset DAT of patient S1 with the following format:
DAT.raw_read_counts.bed.gz is a multi-cell BED file containing the raw read counts in the following fields:
CHROMOSOME: the name of a human chromosome
START: the starting genomic position of a genomic bin in the chromosome
END: the ending genomic position of the genomic bin in the chromosome
CELL: the cell barcode that uniquely identifies a cell
NORMAL: the raw read count for the specified bin from a matched-normal sample
COUNT: the raw read count for the specified bin in the specified cell
RDR: the estimated read-depth ratio for the specified bin in the specified cell
DAT.phased_snps_counts.pos.gz is a multi-cell POS file containing the phased SNP counts in the following fields:
CHROMOSOME: the name of a human chromosome
POS: the genomic position in the chromosome of a germline SNP
CELL: the cell barcode that uniquely identifies a cell
COUNT_HAPLOTYPE_A: the count of reads that cover the SNP and that belong to haplotype A in the specified cell
COUNT_HAPLOTYPE_B: the count of reads that cover the SNP and that belong to haplotype B in the specified cell
All the files have been compressed using standard gzip
J.C. Painter letter to Benjamin Lundy
No full textLetter from J.E. Painter to (presumably) Benjamin Lundy, answering a request for information about the history and operations of the Underground Railroad. Letter includes details of a story of an ex-slave transported on the Underground Railroad through Ohio and stories of the plight of other fugitive slaves crossing the Ohio River.
Benjamin Lundy (1789-1839) was a prominent Quaker abolitionist best known for his development of abolitionist periodicals. His "Genius of Universal Emancipation" was first published in 1821 from his home in Mt. Pleasant, Ohio, and enjoyed a wide circulation across the antebellum United States. In the 1820s, the young William Lloyd Garrison came to work for The Genius. Benjamin Lundy traveled widely seeking subscriptions to The Genius, giving talks about the anti-slavery movement, and observing and documenting the conditions of enslaved people across the Americas. He was also involved in the establishment of freed slave colonies in Mexico
Mexican land grant contract to Benjamin Lundy, March 10, 1835 (English)
No full textLegal document from an unsigned officer to Benjamin Lundy, authorizing him rights as empresario to a tract of land in then-Mexico. The document extends a previous treaty made to Lundy by the government of Mexico from November 17, 1823 -- presumably, this land is to be the site of Lundy's freed slave colony. Original Spanish-language document is also a part of this collection. Benjamin Lundy (1789-1839) was a prominent Quaker abolitionist best known for his development of abolitionist periodicals. His Genius of Universal Emancipation was first published in 1821 from his home in Mt. Pleasant, Ohio, and enjoyed a wide circulation across the antebellum United States. In the 1820s, the young William Lloyd Garrison came to work for The Genius. Benjamin Lundy traveled widely seeking subscriptions to The Genius, giving talks about the anti-slavery movement, and observing and documenting the conditions of enslaved people across the Americas. He was also involved in the establishment of freed slave colonies in Mexico
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data
No full textRecent cancer sequencing studies provide a wealth of somatic mutation data from a large number of patients. One of the most intriguing and challenging questions arising from this data is to determine whether the temporal order of somatic mutations in a cancer follows any common progression. Since we usually obtain only one sample from a patient, such inferences are commonly made from cross-sectional data from different patients. This analysis is complicated by the extensive variation in the somatic mutations across different patients, variation that is reduced by examining combinations of mutations in various pathways. Thus far, methods to reconstruction tumor progression at the pathway level have restricted attention to known, a priori defined pathways.In this work we show how to simultaneously infer pathways and the temporal order of their mutations from cross-sectional data, leveraging on the exclusivity property of driver mutations within a pathway. We define the Pathway Linear Progression Model, and derive a combinatorial formulation for the problem of finding the optimal model from mutation data. We show that while this problem is NP-hard, with enough samples its optimal solution uniquely identifies the correct model with high probability even when errors are present in the mutation data. We then formulate the problem as an integer linear program (ILP), which allows the analysis of datasets from recent studies with large number of samples. We use our algorithm to analyze somatic mutation data from three cancer studies, including two studies from The Cancer Genome Atlas (TCGA) on large number of samples on colorectal cancer and glioblastoma. The models reconstructed with our method capture most of the current knowledge of the progression of somatic mutations in these cancer types, while also providing new insights on the tumor progression at the pathway level
Eli Nichols letter to Benjamin Lundy, March 17th, 1839
No full textFriendly note from Eli Nichols to Benjamin Lundy covering topics in contemporary abolition, ranging from the social status of abolitionists to the oppression of the poor. Much of the letter concerns a review of contemporary social movements in equality-based education, including Shaker and Quaker communities. The letter concludes in discussion of Nichols' and Lundy's interest in forming a freed slave colony or community in then-Mexico, and describes the climate and culture of those regions in detail. Benjamin Lundy (1789-1839) was a prominent Quaker abolitionist best known for his development of abolitionist periodicals. His Genius of Universal Emancipation was first published in 1821 from his home in Mt. Pleasant, Ohio, and enjoyed a wide circulation across the antebellum United States. In the 1820s, the young William Lloyd Garrison came to work for The Genius. Benjamin Lundy traveled widely seeking subscriptions to The Genius, giving talks about the anti-slavery movement, and observing and documenting the conditions of enslaved people across the Americas. He was also involved in the establishment of freed slave colonies in Mexico
Mexican land grant contract to Benjamin Lundy, March 10, 1835 (Spanish)
No full textLegal document in Spanish from the government of Tamaulipas, Mexico, to Benjamin Lundy, which appears to grant Lundy the rights of empresario for his proposed colony for freed slaves in Tamaulipas. This document appears to be truncated; it ends abruptly after 2 pages. Collection also includes a period translation of this contract with Lundy in English, which appears to contain the full text of the agreement. Benjamin Lundy (1789-1839) was a prominent Quaker abolitionist best known for his development of abolitionist periodicals. His Genius of Universal Emancipation was first published in 1821 from his home in Mt. Pleasant, Ohio, and enjoyed a wide circulation across the antebellum United States. In the 1820s, the young William Lloyd Garrison came to work for The Genius. Benjamin Lundy traveled widely seeking subscriptions to The Genius, giving talks about the anti-slavery movement, and observing and documenting the conditions of enslaved people across the Americas. He was also involved in the establishment of freed slave colonies in Mexico
General Benjamin Butler Letter Regarding the naming of Newport News, Virginia
No full textDigital images of an original letter written by Former Union Major-General Benjamin Butler in reply to a query by author, Edwin Everett Hale on how Newport News, Virginia had received it's name. both sides of the original letter are included along with a typed transcription of the letter
Theorie, Methode, Disziplinengeschichte, Hilfswissenschaften
No full textMartin Wallraff (Hg.): Geschichte als Argument? Historiografie und Apologetik (Raphael Brendel)
Malte Lorenzen: Zwischen Wandern und Lesen. Eine rezeptionshistorische Untersuchung des Literaturkonzepts der bürgerlichen deutschen Jugendbewegung (1896-1923) (Joachim Knoll)
Jörg Baberowski: Räume der Gewalt (Benjamin Ziemann
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A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements
No full textMotivation. Complex genome rearrangements, such as chromothripsis and chromoplexy, are common in cancer and have also been reported in individuals with various developmental and neurological disorders. These mutations are proposed to involve simultaneous breakage of the genome at many loci and rejoining of these breaks that produce highly rearranged genomes. Since genome sequencing measures only the novel adjacencies present at the time of sequencing, determining whether a collection of novel adjacencies resulted from a complex rearrangement is a complicated and ill-posed problem. Current heuristics for this problem often result in the inference of complex rearrangements that affect many chromosomes.
Results. We introduce a model for complex rearrangements that builds upon the methods developed for analyzing simple genome rearrangements such as inversions and translocations. While nearly all of these existing methods use a maximum parsimony assumption of minimizing the number of rearrangements, we propose an alternative maximum parsimony principle based on minimizing the number of chromosomes involved in a rearrangement scenario. We show that our model leads to inference of more plausible sequences of rearrangements that better explain a complex congenital rearrangement in a human genome and chromothripsis events in 22 cancer genomes
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