VISUALIZING THE DATA VISUALIZATION NETWORK: THE DVMAP PROJECT

Data visualization is a familiar buzzword. Experts in the humanities, social and natural sciences, as well as technology, along with semi-experts and the general public, reach people everywhere with trends and conclusions drawn from visualized data. Governments, industries, businesses, sciences, marketers, academics, students and others value data visualization methods and tools as critical, applicable tools for understanding the world, which provide rich information analyses for specialists and generalists alike. Unfortunately, no single resource offers a space where people working in the multifaceted field of data visualization can share projects they are working on, tools they created, educational opportunities in the field, nor where they (and their work) are situated geographically. A research group at New Mexico Institute of Mining and Technology seeks to fill this gap with a repository of data visualization resources called ―Data Visualization Map (DVMap).‖ The DVMap is an interactive network data and geographic representation graph that provides a data visualization space for people across the world to share, view and/or collaborate on projects and publications; tools deployed or under development; educational opportunities in data visualization, such as formal programs, summer seminars, conferences; and the geographical locations of the users, projects, tools and educational opportunities. Given the necessity of this repository, this paper outlines the structure, underlying methodology, and anticipated outcomes for the DVMap data visualization network. The paper also accounts for limitations of the project and the potential problems of creating a map that wants to share work – especially work in progress – with everyone

Century-scale changes in phytoplankton phenology in the Gulf of Maine

The phenology of major seasonal events is an important indicator of climate. We analyzed multiple datasets of in situ chlorophyll measurements from the Gulf of Maine dating back to the early 20th century in order to detect climate-scale changes in phenology. The seasonal cycle was consistently characterized by a two-bloom pattern, with spring and autumn blooms. The timing of both spring and autumn blooms has shifted later in the year at rates ranging from ∼1 to 9 days per decade since 1960, depending on the phenology metric, and trends only emerged at time scales of >40 years. Bloom phenology had only weak correlations with major climate indices. There were stronger associations between bloom timing and physical and chemical variables. Autumn bloom initiation correlated strongly with surface temperature and salinity, and spring bloom with nutrients. A later spring bloom also correlated with an increased cohort of Calanus finmarchicus, suggesting broader ecosystem implications of phytoplankton phenology

Activated mutant NRasQ61K drives aberrant melanocyte signaling, survival, and invasiveness via a rac1-Dependent mechanism

Around a fifth of melanomas exhibit an activating mutation in the oncogene NRas that confers constitutive signaling to proliferation and promotes tumor initiation. NRas signals downstream of the major melanocyte tyrosine kinase receptor c-kit and activated NRas results in increased signaling via the extracellular signal–regulated kinase (ERK)/MAPK/ERK kinase/mitogen-activated protein kinase (MAPK) pathways to enhance proliferation. The Ras oncogene also activates signaling via the related Rho GTPase Rac1, which can mediate growth, survival, and motility signaling. We tested the effects of activated NRasQ61K on the proliferation, motility, and invasiveness of melanoblasts and melanocytes in the developing mouse and ex vivo explant culture as well as in a melanoma transplant model. We find an important role for Rac1 downstream of NRasQ61K in mediating dermal melanocyte survival in vivo in mouse, but surprisingly NRasQ61K does not appear to affect melanoblast motility or proliferation during mouse embryogenesis. We also show that genetic deletion or pharmacological inhibition of Rac1 in NRasQ61K induced melanoma suppresses tumor growth, lymph node spread, and tumor cell invasiveness, suggesting a potential value for Rac1 as a therapeutic target for activated NRas-driven tumor growth and invasiveness

Rapid climate-driven circulation changes threaten conservation of endangered north atlantic right whales

As climate trends accelerate, ecosystems will be pushed rapidly into new states, reducing the potential efficacy of conservation strategies based on historical patterns. In the Gulf of Maine, climate-driven changes have restructured the ecosystem rapidly over the past decade. Changes in the Atlantic meridional overturning circulation have altered deepwater dynamics, driving warming rates twice as high as the fastest surface rates. This has had implications for the copepod Calanus finmarchicus, a critical food supply for the endangered North Atlantic right whale (Eubalaena glacialis). The oceanographic changes have driven a deviation in the seasonal foraging patterns of E. glacialis upon which conservation strategies depend, making the whales more vulnerable to ship strikes and gear entanglements. The effects of rapid climate-driven changes on a species at risk undermine current management approaches.publishedVersio

A tau homeostasis signature is linked with the cellular and regional vulnerability of excitatory neurons to tau pathology.

Excitatory neurons are preferentially impaired in early Alzheimer's disease but the pathways contributing to their relative vulnerability remain largely unknown. Here we report that pathological tau accumulation takes place predominantly in excitatory neurons compared to inhibitory neurons, not only in the entorhinal cortex, a brain region affected in early Alzheimer's disease, but also in areas affected later by the disease. By analyzing RNA transcripts from single-nucleus RNA datasets, we identified a specific tau homeostasis signature of genes differentially expressed in excitatory compared to inhibitory neurons. One of the genes, BCL2-associated athanogene 3 (BAG3), a facilitator of autophagy, was identified as a hub, or master regulator, gene. We verified that reducing BAG3 levels in primary neurons exacerbated pathological tau accumulation, whereas BAG3 overexpression attenuated it. These results define a tau homeostasis signature that underlies the cellular and regional vulnerability of excitatory neurons to tau pathology

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean : phylogeny, physiology and stable isotope fractionation

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 5 (2011): 1796–1808, doi:10.1038/ismej.2011.58.Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the north Pacific Ocean that have been maintained in laboratory culture for over three years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S rRNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and cDNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonium (NH4 +) to nitrite (NO2 -). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15εNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15εNH3 ranged from 13- 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15εNH3 is similar.This work was supported by a Woods Hole Oceanographic Institution (WHOI) Postdoctoral Scholar fellowship to AES and the WHOI Ocean Life Institute

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Pathogenesis and Prognosis of Hepatocellular Carcinoma at the Cellular and Molecular Levels

The relative roles of silicon (Si) and iron (Fe) as limiting nutrients in the eastern equatorial Pacific (EEP) were examined in a series of nine microcosm experiments conducted over two years between 110°W and 140°W longitude. Si and Fe additions had consistently different but synergistic effects on macronutrient use, phytoplankton biomass and phytoplankton community structure. Silicon addition increased silicic acid use and biogenic silica production, but had no significant effect on the use of inorganic nitrogen or orthophosphate, chlorophyll accumulation, particulate inorganic (PIC) carbon accumulation, or plankton community composition relative to controls. That result, together with observations that Si addition increased the cellular Si content of the numerically dominant diatom by not, vert, similar50%, indicates that the main effect of Si was to regulate diatom silicification. Like the effect of Si, Fe addition increased the rate of silicic acid use and biogenic silica production and had no effect on PIC production. Unlike the effect of Si, Fe addition also enhanced rates of organic matter production, had no effect on cellular Si content of diatoms, and resulted in the growth of initially rare, large (&gt;40 ?m) diatoms relative to controls, indicating that Fe limitation acts mainly through its effects on growth rate and phytoplankton community composition. A pennate diatom of the genus Pseudo-nitzschia dominated the diatom assemblage in situ, grew readily in the controls and did not show a strong growth response to either Fe or Si addition suggesting that its growth was regulated by other factors such as grazing or light. Addition of germanium, an inhibitor of diatom cell division, eliminated the effects of Fe on macronutrient use, biogenic silica production and chlorophyll accumulation and phytoplankton community composition, consistent with a predominantly diatom response to Fe addition. The lack of a response of PIC production to Fe suggests that coccolithophores were not Fe limited. Addition of Fe and Si together resulted in the greatest levels of nutrient drawdown and biomass accumulation through the effect of Fe in promoting the growth of large diatoms. The results suggest a form of co-limitation with Si regulating diatom silicification and the rate of biogenic silica production while Fe regulates the production of organic matter through limitation of phytoplankton growth rates, in particular those of large diatoms. The results argue against Si regulation of new production in the EEP under average upwelling conditions. Iron addition was necessary and sufficient to stimulate complete removal of nitrate within the equatorial upwelling zone suggesting that new production was restricted by low ambient dissolved Fe consistent with results from in situ Fe fertilization experiments conducted to the south of the equator outside of the equatorial upwelling zone

Rapid climate-driven circulation changes threaten conservation of endangered north atlantic right whales

As climate trends accelerate, ecosystems will be pushed rapidly into new states, reducing the potential efficacy of conservation strategies based on historical patterns. In the Gulf of Maine, climate-driven changes have restructured the ecosystem rapidly over the past decade. Changes in the Atlantic meridional overturning circulation have altered deepwater dynamics, driving warming rates twice as high as the fastest surface rates. This has had implications for the copepod Calanus finmarchicus, a critical food supply for the endangered North Atlantic right whale (Eubalaena glacialis). The oceanographic changes have driven a deviation in the seasonal foraging patterns of E. glacialis upon which conservation strategies depend, making the whales more vulnerable to ship strikes and gear entanglements. The effects of rapid climate-driven changes on a species at risk undermine current management approaches