Taxonomic voucher specimens for study of post-wildfire forest habitat in Douglas County, Oregon

this publication provides data about voucher specimens deposited in the museum in conjunction with a research project on pollinators

Taxonomic voucher specimens for study of bee communities in intensively managed Douglas-fir forests in the Oregon Coast Range

Understanding how pollinators respond to anthropogenic land use is key to conservation of biodiversity and ecosystem services, but few studies have addressed this topic in coniferous forests, particularly those managed intensively for wood production. This study reports on voucher material generated as part of Zitomer et al. (2023), that assessed changes in wild bee communities with time since harvest in 60 intensively managed Douglas-fir (Pseudotsuga menziesii) stands in the Oregon Coast Range across a gradient in stand age spanning a typical harvest rotation (0-37 years post-harvest). We additionally assessed relationships of bee diversity and community composition to relevant habitat features, including availability of floral resources and nest sites, understory vegetation characteristics, and composition of the surrounding landscape. Specimens were collected using a combination of passive sampling methods-blue vane traps and white, blue, and yellow bowl traps- and hand-netting and were identified to the lowest possible taxonomic level by A.R. Moldenke and L.R. Best. Four hundred and ten taxonomic voucher specimens were deposited into the Oregon State Arthropod Collection (Accession# OSAC_AC_2023_01_09-001-01) to serve as a reference for future research

Effectiveness of a hand-held fan for breathlessness: a randomised phase II trial

<p>Abstract</p> <p>Background</p> <p>Breathlessness is common and distressing in advanced disease. This phase II study aimed to determine the use and acceptance of a hand-held fan (HHF) to relieve breathlessness, to test the effectiveness of the HHF and to evaluate the recruitment into the study.</p> <p>Methods</p> <p>RCT embedded within a longitudinal study testing a HHF over time compared to a wristband. Patients were included in the longitudinal study when suffering from breathlessness due to advanced cancer or COPD III/IV and could opt in the RCT. Primary outcome was use of the HHF and the wristband after two months. Secondary outcomes were recruitment into the trial and change of breathlessness severity after two months, measured on the modified Borg scale. Baseline data were collected in a personal interview and follow-up data by monthly postal questionnaires.</p> <p>Results</p> <p>109 patients were recruited in the longitudinal study of which 70 patients (64%) participated in the RCT. Non-participants had statistically significant less breathlessness (Borg mean 2.6 (SD 1.48) versus 3.7 (SD 1.83); p = 0.003) and a better functional status (Karnofsky status mean 61.9 (SD 11.2) versus 66.7 (SD 11.0); p = 0.03). Attrition due to drop out or death was high in both groups. After two months, about half of the patients used the HHF but only 20% the wristband without a statistical difference (Fisher's exact test p = 0.2). 9/16 patients judged the HHF as helpful after two months and 4/5 patients the wristband. There was no difference in mean breathlessness change scores between the HHF (Borg change score: mean 0.6 (SD 2.10)) and the wristband (mean 0.8 (SD 2.67)) after two months (p = 0.90).</p> <p>Conclusions</p> <p>Symptom burden and low functional status did not restrain patients from participation in the study. Finding a control for a visible intervention is challenging and needs careful consideration to what is acceptable to patients. The preliminary evidence of effectiveness of the HHF could not be proved. Patients often stopped using the HHF but a small group seemed to benefit which was not necessarily related to a relief in breathlessness. Therefore, more work is necessary on selecting and identifying those who might benefit from the HHF.</p> <p>Trial registration</p> <p>ClinicalTrials.gov Identifier: NCT01123902</p

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

An ARF GTPase module promoting invasion and metastasis through regulating phosphoinositide metabolism

The signalling pathways underpinning cell growth and invasion use overlapping components, yet how mutually exclusive cellular responses occur is unclear. Here, we report development of 3-Dimensional culture analyses to separately quantify growth and invasion. We identify that alternate variants of IQSEC1, an ARF GTPase Exchange Factor, act as switches to promote invasion over growth by controlling phosphoinositide metabolism. All IQSEC1 variants activate ARF5- and ARF6-dependent PIP5-kinase to promote PI(3,4,5)P3-AKT signalling and growth. In contrast, select pro-invasive IQSEC1 variants promote PI(3,4,5)P3 production to form invasion-driving protrusions. Inhibition of IQSEC1 attenuates invasion in vitro and metastasis in vivo. Induction of pro-invasive IQSEC1 variants and elevated IQSEC1 expression occurs in a number of tumour types and is associated with higher-grade metastatic cancer, activation of PI(3,4,5)P3 signalling, and predicts long-term poor outcome across multiple cancers. IQSEC1-regulated phosphoinositide metabolism therefore is a switch to induce invasion over growth in response to the same external signal. Targeting IQSEC1 as the central regulator of this switch may represent a therapeutic vulnerability to stop metastasis