Arbor Groves 41HO02 Final Report

Arbor Groves, located in the heart of the Piney Woods and west of multiple large bodies of fresh water, was most likely a sanctuary for woodland animals and early Americans. In fact, artifacts from the Clovis period (ca. 10,000 BP) to the modern era have been excavated from the site. Most of the artifacts excavated during the 2016 field season dated to the late Archaic period (8000-500 BC) to the early Woodlands period (beginning approximately 500 BC). The amount of lithic debris and projectile points found strongly suggest that Arbor Groves was a lithic manufacturing site. The manufacture of projectile points and other tools result in many lithic flakes discarded from the parent material (Morrow 1996). Because manufacturing and disposing of the waste are often in the same area, evidence for these sites also include the presence of broken projectiles, cores, and various pecked cobbles. Rarely does one find complete points or the hammerstone and tools used to produce the objects, as those are carried by the maker

The Canadian Research Alliance for Community Innovation and Networking (CRACIN): A Research Partnership and Agenda for Community Networking in Canada

The Canadian Research Alliance for Community Innovation and Networking (CRACIN) is a collaborative partnership amongst academic researchers in Canada, international researchers in Community Informatics, the three principal federal government departments promoting the "Connecting Canadians" agenda, and community networking practitioners in Canada. CRACINs substantive goal is to review the progress of community-based information and communications technology (ICT) development in the context of Canadian government programs promoting the development and public accessibility of Internet services. Central issues to be explored include the sustainability of community networking initiatives, along with an examination of how the Canadian community-based initiatives contribute to: the amelioration of "digital divides"; the enhancement of economic, social, political and cultural capabilities; the creation, provision, and use of community-oriented learning opportunities; and the development of community-oriented cultural content, open source software, learning tools and broadband infrastructures. The over-arching goal of our research is to begin the systematic documentation and assessment of the development of community-oriented ICT capacity and services contributing to local learning, to the strengthening of relations in and between communities, and more generally to community-focused social and economic development in Canada

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut [version 2; referees: 3 approved]

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software

Intersection of Immune and Oncometabolic Pathways Drives Cancer Hyperprogression During Immunotherapy

Immune checkpoint blockade (ICB) can produce durable responses against cancer. We and others have found that a subset of patients experiences paradoxical rapid cancer progression during immunotherapy. It is poorly understood how tumors can accelerate their progression during ICB. In some preclinical models, ICB causes hyperprogressive disease (HPD). While immune exclusion drives resistance to ICB, counterintuitively, patients with HPD and complete response (CR) following ICB manifest comparable levels of tumor-infiltrating CD

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar ‘Chandler’ to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traitsWe would especially like to thank Gale McGranahan, Emeritus Professor of the Department of Plant Sciences at UC Davis, for providing tissue culture materials for the transcriptome sequencing and assembly and the California Walnut Board for supporting this study. We gratefully acknowledge the editor and two anonymous referees for their constructive criticism and helpful comments that improved the manuscriptPeer reviewe

When abortion was a crime: women, medicine, and law in the United States, 1867-1973/ Leslie J. Reagan.

"With a new preface."1 online resource