Harvesting Intensity and Aridity Are More Important Than Climate Change in Affecting Future Carbon Stocks of Douglas-Fir Forests

Improved forest management may offer climate mitigation needed to hold warming to below 2°C. However, uncertainties persist about the effects of harvesting intensity on forest carbon sequestration, especially when considering interactions with regional climate and climate change. Here, we investigated the combined effects of harvesting intensity, climatic aridity, and climate change on carbon stocks in Douglas-fir [Pseudotsuga menziesii Mirb. (Franco)] stands. We used the Carbon Budget Model of the Canadian Forest Sector to simulate the harvest and regrowth of seven Douglas-fir stand types covering a 900 km-long climate gradient across British Columbia, Canada. In particular, we simulated stand growth under three regimes (+17%, −17% and historical growth increment) and used three temperature regimes [historical, representative concentration pathways (RCP) 2.6 and RCP 8.5]. Increasing harvesting intensity led to significant losses in total ecosystem carbon stocks 50 years post-harvest. Specifically, forests that underwent clearcutting were projected to stock about 36% less carbon by 2,069 than forests that were left untouched. Belowground carbon stocks 50 years into the future were less sensitive to harvesting intensity than aboveground carbon stocks and carbon losses were greater in arid interior Douglas-fir forests than in humid, more productive forests. In addition, growth multipliers and decay due to the RCP’s had little effect on total ecosystem carbon, but aboveground carbon declined by 7% (95% confidence interval [−10.98, −1.81]) in the high emissions (RCP8.5) scenario. We call attention to the implementation of low intensity harvesting systems to preserve aboveground forest carbon stocks until we have a more complete understanding of the impacts of climate change on British Columbia’s forests

Harvest intensity effects on carbon stocks and biodiversity are dependent on regional climate in Douglas-fir forests of British Columbia

Temperate forests provide crucial ecosystems services as living sinks for atmospheric carbon (C) and repositories of biodiversity. Applying harvesting at intensities that minimize losses offers one means for mitigating global change. However, little is known of overstory retention levels that best conserve ecosystem services in different regional climates, and likewise as climate changes. To quantify the effect of harvest intensity on C stocks and biodiversity, we compared five harvesting intensities (clearcutting,seedtree retention, 30% patch retention, 60% patch retention, and uncut controls) across a climatic aridity gradient that ranged from humid to semi-arid in the Douglas-fir (Pseudostuga menziesii) forests of British Columbia. We found that increased harvesting intensity reduced total ecosystem, aboveground, and live tree C stocks one year post-harvest, and the magnitude of these losses were negatively correlated with climatic aridity. In humid forests, total ecosystem C ranged from 50% loss following clearcut harvest, to 30% loss following large patch retention harvest. In arid forests this range was 60% to 8% loss, respectively. Where lower retention harvests are sought, the small patch retention treatment protected both C stocks and biodiversity in the arid forests, whereas the seedtree method performed as well or better in the humid forests. Belowground C stocks declined by an average of 29% after harvesting, with almost all of the loss from the forest floor and none from the mineral soil. Of the secondary pools, standing and coarse deadwood declined in all harvesting treatments regardless of cutting intensity or aridity, while C stocks in fine fuels and stumps increased. The understory plant C pool declined across all harvesting intensities in the humid forests, but increased in arid forests. Shannon’s diversity and richness of tree and bryoid species declined with harvesting intensity, where tree species losses were greatest in the humid forests and bryoid losses greatest in arid forests. Shrub and herb species were unaffected. This study showed that the highest retention level was best at reducing losses in C stocks and biodiversity, and clearcutting the poorest, and while partial retention of canopy trees can reduce losses in these ecosystem services, outcomes will vary with climatic aridity

AltitudeOmics: Baroreflex Sensitivity During Acclimatization to 5,260 m.

<b>Introduction:</b> Baroreflex sensitivity (BRS) is essential to ensure rapid adjustment to variations in blood pressure (BP). Little is known concerning the adaptive responses of BRS during acclimatization to high altitude at rest and during exercise. <b>Methods:</b> Twenty-one healthy sea-level residents were tested near sea level (SL, 130 m), the 1st (ALT1) and 16th day (ALT16) at 5,260 m using radial artery catheterization. BRS was calculated using the sequence method (direct interpretation of causal link between BP and heartrate). At rest, subjects breathed a hyperoxic mixture (250 mmHg O <sub>2</sub> , end tidal) to isolate the preponderance of CO <sub>2</sub> chemoreceptors. End-tidal CO <sub>2</sub> varied from 20 to 50 mmHg to assess peripheral chemoreflex. Rebreathing provoked incremental increase in CO <sub>2</sub> , increasing BP to assess baroreflex. During incremental cycling exercise to exhaustion, subjects breathed room air. <b>Results:</b> Resting BRS decreased in ALT1 which was exacerbated in ALT16. This decrease in ALT1 was reversible upon additional inspired CO <sub>2</sub> , but not in ALT16. BRS decrease during exercise was greater and occurred at lower workloads in ALT1 compared to SL. At ALT16, this decrease returned toward SL values. <b>Discussion/Conclusion:</b> This study is the first to report attenuated BRS in acute hypoxia, exacerbated in chronic hypoxia. In ALT1, hypocapnia triggered BRS reduction whilst in ALT16 resetting of chemoreceptor triggered BRS reduction. The exercise BRS resetting was impaired in ALT1 but normalized in ALT16. These BRS decreases indicate decreased control of BP and may explain deteriorations of cardiovascular status during exposure to high altitude

AltitudeOmics: Spontaneous Baroreflex Sensitivity During Acclimatization to 5,260 m: A Comparison of Methods

Baroreflex sensitivity (BRS) is essential to ensure rapid adjustment to variations in blood pressure (BP). Spontaneous baroreflex function can be assessed using continuous recordings of blood pressure. The goal of this study was to compare four methods for BRS quantification [the sequence, Bernardi's (BER), frequency and transfer function methods] to identify the most consistent method across an extreme range of conditions: rest and exercise, in normoxia, hypoxia, hypocapnia, and hypercapnia. Using intra-radial artery BP in young healthy participants, BRS was calculated and compared using the four methods in normoxia, acute and chronic hypoxia (terrestrial altitude of 5,260 m) in hypocapnia (hyperventilation), hypercapnia (rebreathing) and during ramp exercise to exhaustion. The sequence and BER methods for BRS estimation showed good agreement during the resting and exercise protocols, whilst the ultra- and very-low frequency bands of the frequency and transfer function methods were more discrepant. Removing respiratory frequency from the blood pressure traces affected primarily the sequence and BER methods and occasionally the frequency and transfer function methods. The sequence and BER methods contained more respiratory related information than the frequency and transfer function methods, indicating that the former two methods predominantly rely on respiratory effects of BRS. BER method is recommended because it is the easiest to compute and even though it tends to overestimate BRS compared to the sequence method, it is consistent with the other methods, whilst its interquartile range is the smallest

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

Between-site reliability of startle prepulse inhibition across two early psychosis consortia

Prepulse inhibition (PPI) and reactivity of the acoustic startle response are widely used biobehavioral markers in psychopathology research. Previous studies have demonstrated that PPI and startle reactivity exhibit substantial within-site stability; between-site stability, however, has not been established. In two separate consortia investigating biomarkers of early psychosis, traveling subjects studies were performed as part of quality assurance procedures in order to assess the fidelity of data across sites. In the North American Prodromal Longitudinal Studies (NAPLS) Consortium, 8 normal subjects traveled to each of the 8 NAPLS sites and were tested twice at each site on the startle PPI paradigm. In preparation for a binational study, 10 healthy subjects were assessed twice in both San Diego and Mexico City. Intraclass correlations between and within sites were significant for PPI and startle response parameters, confirming the reliability of startle measures across sites in both consortia. There were between site differences in startle magnitude in the NAPLS study that did not appear to be related to methods or equipment. In planning multi-site studies, it is essential to institute quality assurance procedures early and establish between site reliability to assure comparable data across sites

Integrated Molecular Characterization of Uterine Carcinosarcoma

SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified