A strategy to advance the evidence base in palliative medicine: formation of a palliative care research cooperative group.

BACKGROUND: Palliative medicine has made rapid progress in establishing its scientific and clinical legitimacy, yet the evidence base to support clinical practice remains deficient in both the quantity and quality of published studies. Historically, the conduct of research in palliative care populations has been impeded by multiple barriers including health care system fragmentation, small number and size of potential sites for recruitment, vulnerability of the population, perceptions of inappropriateness, ethical concerns, and gate-keeping. METHODS: A group of experienced investigators with backgrounds in palliative care research convened to consider developing a research cooperative group as a mechanism for generating high-quality evidence on prioritized, clinically relevant topics in palliative care. RESULTS: The resulting Palliative Care Research Cooperative (PCRC) agreed on a set of core principles: active, interdisciplinary membership; commitment to shared research purposes; heterogeneity of participating sites; development of research capacity in participating sites; standardization of methodologies, such as consenting and data collection/management; agile response to research requests from government, industry, and investigators; focus on translation; education and training of future palliative care researchers; actionable results that can inform clinical practice and policy. Consensus was achieved on a first collaborative study, a randomized clinical trial of statin discontinuation versus continuation in patients with a prognosis of less than 6 months who are taking statins for primary or secondary prevention. This article describes the formation of the PCRC, highlighting processes and decisions taken to optimize the cooperative group's success.

Fate of products of degradation processes: consequences for climatic change.

The end products of atmospheric degradation are not only CO2 and H2O but also sulfate and nitrate depending on the chemical composition of the substances which are subject to degradation processes. Atmospheric degradation has thus a direct influence on the radiative balance of the earth not only due to formation of greenhouse gases but also of aerosols. Aerosols of a diameter of 0.1 to 2 micrometer, reflect short wave sunlight very efficiently leading to a radiative forcing which is estimated to be about -0.8 watt per m2 by IPCC. Aerosols also influence the radiative balance by way of cloud formation. If more aerosols are present, clouds are formed with more and smaller droplets and these clouds have a higher albedo and are more stable compared to clouds with larger droplets. Not only sulfate, but also nitrate and polar organic compounds, formed as intermediates in degradation processes, contribute to this direct and indirect aerosol effect. Estimates for the Netherlands indicate a direct effect of -4 watt m-2 and an indirect effect of as large as -5 watt m-2. About one third is caused by sulfates, one third by nitrates and last third by polar organic compounds. This large radiative forcing is obviously non-uniform and depends on local conditions.

Discharge competence and pattern formation in peatlands: a meta-ecosystem model of the Everglades ridge-slough landscape.

Regular landscape patterning arises from spatially-dependent feedbacks, and can undergo catastrophic loss in response to changing landscape drivers. The central Everglades (Florida, USA) historically exhibited regular, linear, flow-parallel orientation of high-elevation sawgrass ridges and low-elevation sloughs that has degraded due to hydrologic modification. In this study, we use a meta-ecosystem approach to model a mechanism for the establishment, persistence, and loss of this landscape. The discharge competence (or self-organizing canal) hypothesis assumes non-linear relationships between peat accretion and water depth, and describes flow-dependent feedbacks of microtopography on water depth. Closed-form model solutions demonstrate that 1) this mechanism can produce spontaneous divergence of local elevation; 2) divergent and homogenous states can exhibit global bi-stability; and 3) feedbacks that produce divergence act anisotropically. Thus, discharge competence and non-linear peat accretion dynamics may explain the establishment, persistence, and loss of landscape pattern, even in the absence of other spatial feedbacks. Our model provides specific, testable predictions that may allow discrimination between the self-organizing canal hypotheses and competing explanations. The potential for global bi-stability suggested by our model suggests that hydrologic restoration may not re-initiate spontaneous pattern establishment, particularly where distinct soil elevation modes have been lost. As a result, we recommend that management efforts should prioritize maintenance of historic hydroperiods in areas of conserved pattern over restoration of hydrologic regimes in degraded regions. This study illustrates the value of simple meta-ecosystem models for investigation of spatial processes.

Global Rates of Free Hydrogen (H2) Production by Serpentinization and other Abiogenic Processes within Young Ocean Crust

The main conclusion of this dissertation is that global H2 production within young ocean crust (<10 Mya) is higher than currently recognized, in part because current estimates of H2 production accompanying the serpentinization of peridotite may be too low (Chapter 2) and in part because a number of abiogenic H2-producing processes have heretofore gone unquantified (Chapter 3). The importance of free H2 to a range of geochemical processes makes the quantitative understanding of H2 production advanced in this dissertation pertinent to an array of open research questions across the geosciences (e.g. the origin and evolution of life and the oxidation of the Earth’s atmosphere and oceans).

The first component of this dissertation (Chapter 2) examines H2 produced within young ocean crust [e.g. near the mid-ocean ridge (MOR)] by serpentinization. In the presence of water, olivine-rich rocks (peridotites) undergo serpentinization (hydration) at temperatures of up to ~500°C but only produce H2 at temperatures up to ~350°C. A simple analytical model is presented that mechanistically ties the process to seafloor spreading and explicitly accounts for the importance of temperature in H2 formation. The model suggests that H2 production increases with the rate of seafloor spreading and the net thickness of serpentinized peridotite (S-P) in a column of lithosphere. The model is applied globally to the MOR using conservative estimates for the net thickness of lithospheric S-P, our least certain model input. Despite the large uncertainties surrounding the amount of serpentinized peridotite within oceanic crust, conservative model parameters suggest a magnitude of H2 production (~1012 moles H2/y) that is larger than the most widely cited previous estimates (~1011 although previous estimates range from 1010-1012 moles H2/y). Certain model relationships are also consistent with what has been established through field studies, for example that the highest H2 fluxes (moles H2/km2 seafloor) are produced near slower-spreading ridges (<20 mm/y). Other modeled relationships are new and represent testable predictions. Principal among these is that about half of the H2 produced globally is produced off-axis beneath faster-spreading seafloor (>20 mm/y), a region where only one measurement of H2 has been made thus far and is ripe for future investigation.

In the second part of this dissertation (Chapter 3), I construct the first budget for free H2 in young ocean crust that quantifies and compares all currently recognized H2 sources and H2 sinks. First global estimates of budget components are proposed in instances where previous estimate(s) could not be located provided that the literature on that specific budget component was not too sparse to do so. Results suggest that the nine known H2 sources, listed in order of quantitative importance, are: Crystallization (6x1012 moles H2/y or 61% of total H2 production), serpentinization (2x1012 moles H2/y or 21%), magmatic degassing (7x1011 moles H2/y or 7%), lava-seawater interaction (5x1011 moles H2/y or 5%), low-temperature alteration of basalt (5x1011 moles H2/y or 5%), high-temperature alteration of basalt (3x1010 moles H2/y or <1%), catalysis (3x108 moles H2/y or <<1%), radiolysis (2x108 moles H2/y or <<1%), and pyrite formation (3x106 moles H2/y or <<1%). Next we consider two well-known H2 sinks, H2 lost to the ocean and H2 occluded within rock minerals, and our analysis suggests that both are of similar size (both are 6x1011 moles H2/y). Budgeting results suggest a large difference between H2 sources (total production = 1x1013 moles H2/y) and H2 sinks (total losses = 1x1011 moles H2/y). Assuming this large difference represents H2 consumed by microbes (total consumption = 9x1011 moles H2/y), we explore rates of primary production by the chemosynthetic, sub-seafloor biosphere. Although the numbers presented require further examination and future modifications, the analysis suggests that the sub-seafloor H2 budget is similar to the sub-seafloor CH4 budget in the sense that globally significant quantities of both of these reduced gases are produced beneath the seafloor but never escape the seafloor due to microbial consumption.

The third and final component of this dissertation (Chapter 4) explores the self-organization of barchan sand dune fields. In nature, barchan dunes typically exist as members of larger dune fields that display striking, enigmatic structures that cannot be readily explained by examining the dynamics at the scale of single dunes, or by appealing to patterns in external forcing. To explore the possibility that observed structures emerge spontaneously as a collective result of many dunes interacting with each other, we built a numerical model that treats barchans as discrete entities that interact with one another according to simplified rules derived from theoretical and numerical work, and from field observations: Dunes exchange sand through the fluxes that leak from the downwind side of each dune and are captured on their upstream sides; when dunes become sufficiently large, small dunes are born on their downwind sides (“calving”); and when dunes collide directly enough, they merge. Results show that these relatively simple interactions provide potential explanations for a range of field-scale phenomena including isolated patches of dunes and heterogeneous arrangements of similarly sized dunes in denser fields. The results also suggest that (1) dune field characteristics depend on the sand flux fed into the upwind boundary, although (2) moving downwind, the system approaches a common attracting state in which the memory of the upwind conditions vanishes. This work supports the hypothesis that calving exerts a first order control on field-scale phenomena; it prevents individual dunes from growing without bound, as single-dune analyses suggest, and allows the formation of roughly realistic, persistent dune field patterns.

ARFGAP1 plays a central role in coupling COPI cargo sorting with vesicle formation.

Examining how key components of coat protein I (COPI) transport participate in cargo sorting, we find that, instead of ADP ribosylation factor 1 (ARF1), its GTPase-activating protein (GAP) plays a direct role in promoting the binding of cargo proteins by coatomer (the core COPI complex). Activated ARF1 binds selectively to SNARE cargo proteins, with this binding likely to represent at least a mechanism by which activated ARF1 is stabilized on Golgi membrane to propagate its effector functions. We also find that the GAP catalytic activity plays a critical role in the formation of COPI vesicles from Golgi membrane, in contrast to the prevailing view that this activity antagonizes vesicle formation. Together, these findings indicate that GAP plays a central role in coupling cargo sorting and vesicle formation, with implications for simplifying models to describe how these two processes are coupled during COPI transport.

Unveiling Protein Kinase A Targets in Cryptococcus neoformans Capsule Formation.

The protein kinase A (PKA) signal transduction pathway has been associated with pathogenesis in many fungal species. Geddes and colleagues [mBio 7(1):e01862-15, 2016, doi:10.1128/mBio.01862-15] used quantitative proteomics approaches to define proteins with altered abundance during protein kinase A (PKA) activation and repression in the opportunistic human fungal pathogen Cryptococcus neoformans. They observed an association between microbial PKA signaling and ubiquitin-proteasome regulation of protein homeostasis. Additionally, they correlated these processes with expression of polysaccharide capsule on the fungal cell surface, the main virulence-associated phenotype in this organism. Not only are their findings important for microbial pathogenesis, but they also support similar associations between human PKA signaling and ubiquitinated protein accumulation in neurodegenerative diseases.

Multimode Atomic Pattern Formation via Enhanced Light-atom Interactions

The nonlinear interaction between light and atoms is an extensive field of study with a broad range of applications in quantum information science and condensed matter physics. Nonlinear optical phenomena occurring in cold atoms are particularly interesting because such slowly moving atoms can spatially organize into density gratings, which allows for studies involving optical interactions with structured materials. In this thesis, I describe a novel nonlinear optical effect that arises when cold atoms spatially bunch in an optical lattice. I show that employing this spatial atomic bunching provides access to a unique physical regime with reduced thresholds for nonlinear optical processes and enhanced material properties. Using this method, I observe the nonlinear optical phenomenon of transverse optical pattern formation at record-low powers. These transverse optical patterns are generated by a wave- mixing process that is mediated by the cold atomic vapor. The optical patterns are highly multimode and induce rich non-equilibrium atomic dynamics. In particular, I find that there exists a synergistic interplay between the generated optical pat- terns and the atoms, wherein the scattered fields help the atoms to self-organize into new, multimode structures that are not externally imposed on the atomic sample. These self-organized structures in turn enhance the power in the optical patterns. I provide the first detailed investigation of the motional dynamics of atoms that have self-organized in a multimode geometry. I also show that the transverse optical patterns induce Sisyphus cooling in all three spatial dimensions, which is the first observation of spontaneous three-dimensional cooling. My experiment represents a unique means by which to study nonlinear optics and non-equilibrium dynamics at ultra-low required powers.

Molecular Insights of CD4+ T Cell Differentiation, Effector Formation and Helper Function

CD4+ T cells play a crucial in the adaptive immune system. They function as the central hub to orchestrate the rest of immunity: CD4+ T cells are essential governing machinery in antibacterial and antiviral responses by facilitating B cell affinity maturation and coordinating the innate and adaptive immune systems to boost the overall immune outcome; on the contrary, hyperactivation of the inflammatory lineages of CD4+ T cells, as well as the impairments of suppressive CD4+ regulatory T cells, are the etiology of various autoimmunity and inflammatory diseases. The broad role of CD4+ T cells in both physiological and pathological contexts prompted me to explore the modulation of CD4+ T cells on the molecular level.

microRNAs (miRNAs) are small RNA molecules capable of regulating gene expression post-transcriptionally. miRNAs have been shown to exert substantial regulatory effects on CD4+ T cell activation, differentiation and helper function. Specifically, my lab has previously established the function of the miR-17-92 cluster in Th1 differentiation and anti-tumor responses. Here, I further analyzed the role of this miRNA cluster in Th17 differentiation, specifically, in the context of autoimmune diseases. Using both gain- and loss-of-function approaches, I demonstrated that miRNAs in miR-17-92, specifically, miR-17 and miR-19b in this cluster, is a crucial promoter of Th17 differentiation. Consequently, loss of miR-17-92 expression in T cells mitigated the progression of experimental autoimmune encephalomyelitis and T cell-induced colitis. In combination with my previous data, the molecular dissection of this cluster establishes that miR-19b and miR-17 play a comprehensive role in promoting multiple aspects of inflammatory T cell responses, which underscore them as potential targets for oligonucleotide-based therapy in treating autoimmune diseases.

To systematically study miRNA regulation in effector CD4+ T cells, I devised a large-scale miRNAome profiling to track in vivo miRNA changes in antigen-specific CD4+ T cells activated by Listeria challenge. From this screening, I identified that miR-23a expression tightly correlates with CD4+ effector expansion. Ectopic expression and genetic deletion strategies validated that miR-23a was required for antigen-stimulated effector CD4+ T cell survival in vitro and in vivo. I further determined that miR-23a targets Ppif, a gatekeeper of mitochondrial reactive oxygen species (ROS) release that protects CD4+ T cells from necrosis. Necrosis is a type of cell death that provokes inflammation, and it is prominently triggered by ROS release and its consequent oxidative stress. My finding that miR-23a curbs ROS-mediated necrosis highlights the essential role of this miRNA in maintaining immune homeostasis.

A key feature of miRNAs is their ability to modulate different biological aspects in different cell populations. Previously, my lab found that miR-23a potently suppresses CD8+ T cell cytotoxicity by restricting BLIMP1 expression. Since BLIMP1 has been found to inhibit T follicular helper (Tfh) differentiation by antagonizing the master transcription factor BCL6, I investigated whether miR-23a is also involved in Tfh differentiation. However, I found that miR-23a does not target BLIMP1 in CD4+ T cells and loss of miR-23a even fostered Tfh differentiation. This data indicate that miR-23a may target other pathways in CD4+ T cells regarding the Tfh differentiation pathway.

Although the lineage identity and regulatory networks for Tfh cells have been defined, the differentiation path of Tfh cells remains elusive. Two models have been proposed to explain the differentiation process of Tfh cells: in the parallel differentiation model, the Tfh lineage is segregated from other effector lineages at the early stage of antigen activation; alternatively, the sequential differentiation model suggests that naïve CD4+ T cells first differentiate into various effector lineages, then further program into Tfh cells. To address this question, I developed a novel in vitro co-culture system that employed antigen-specific CD4+ T cells, naïve B cells presenting cognate T cell antigen and BAFF-producing feeder cells to mimic germinal center. Using this system, I were able to robustly generate GC-like B cells. Notably, well-differentiated Th1 or Th2 effector cells also quickly acquired Tfh phenotype and function during in vitro co-culture, which suggested a sequential differentiation path for Tfh cells. To examine this path in vivo, under conditions of classical Th1- or Th2-type immunizations, I employed a TCRβ repertoire sequencing technique to track the clonotype origin of Tfh cells. Under both Th1- and Th2- immunization conditions, I observed profound repertoire overlaps between the Teff and Tfh populations, which strongly supports the proposed sequential differentiation model. Therefore, my studies establish a new platform to conveniently study Tfh-GC B cell interactions and provide insights into Tfh differentiation processes.