RCN: Diadromous Species Restoration Research Network (DSRRN)

The primary goal of the Diadromous Species Restoration Research Network (DSRRN) was to advance the science of diadromous fish restoration, promote state-of-the-art scientific approaches to multiple-species restoration on a watershed scale, and facilitate interactions among scientists, managers, and stakeholders throughout the North Atlantic region. This goal was achieved by a series of conferences and workshops over a five-year period between 2008 and 2013. In all, DSRRN organized two multi-day conferences with over 160 participants in attendance and five multiday workshops with an average of 25 participants. The objective of these workshops was to produce new directions for restoration science by exploring key scientific issues related to interdisciplinary scientific approaches to diadromous species restoration

Completeness of algebraic CPS simulations

The algebraic lambda calculus and the linear algebraic lambda calculus are two extensions of the classical lambda calculus with linear combinations of terms. They arise independently in distinct contexts: the former is a fragment of the differential lambda calculus, the latter is a candidate lambda calculus for quantum computation. They differ in the handling of application arguments and algebraic rules. The two languages can simulate each other using an algebraic extension of the well-known call-by-value and call-by-name CPS translations. These simulations are sound, in that they preserve reductions. In this paper, we prove that the simulations are actually complete, strengthening the connection between the two languages.Comment: In Proceedings DCM 2011, arXiv:1207.682

Semantics of a Typed Algebraic Lambda-Calculus

Algebraic lambda-calculi have been studied in various ways, but their semantics remain mostly untouched. In this paper we propose a semantic analysis of a general simply-typed lambda-calculus endowed with a structure of vector space. We sketch the relation with two established vectorial lambda-calculi. Then we study the problems arising from the addition of a fixed point combinator and how to modify the equational theory to solve them. We sketch an algebraic vectorial PCF and its possible denotational interpretations

Lake Mead nutrient enhancement project

The Lake Mead Fertilization Project is a research program designed to investigate the potential for using large-scale artificial fertilization to enhance the game fisheries of this reservoir through an increase in the population of threadfin shad, the system\u27s primary forage species. A substantial decline in the population of largemouth bass, together with poor condition of adult striped bass, are the two major issues affecting the Lake Mead game fisheries. Both issues have been hypothesized to be a result of an inadequate amount of forage in the reservoir. Previous studies have in turn suggested that a major factor limiting the shad population may be low productivity levels at the base of the food chain. Approximately 20,000 gallons of liquid ammonium polyphosphate were applied to about 20,000 acres of the Overton Arm in each of the years 1987 through 1989. The fertilizer was applied in late May or early June. Approximately 300 volunteer boats were used to distribute fertilizer in the early stages of the program; these were subsequently replaced with barge applications. A series of stations in both treatment and control areas was intensively sampled to document the impact of fertilization at various levels of the Lake Mead food chain. Fertilizer additions were designed to temporarily increase epilimnetic total phosphorus concentrations by approximately 20 ug/1 and chlorophyll concentrations by 5-10 ug/1. These increases were achieved, although there were substantial horizontal movements of the fertilized water mass, particularly in 1988. Chlorophyll concentrations peaked about 5 days following fertilization and returned to base-line levels within two weeks. Although maximum chlorophyll levels recorded were about 12 ug/1, thirty-day mean concentrations were below 5 ug/l at all stations. Fertilization produced few adverse water quality impacts and all these were short-lived. Water clarity exhibited temporary decreases at some stations in some years. Taste and odor and disinfection by-product formation potentials exhibited weak correlations with chlorophyll concentrations, but the increases were also short-lived. The fertilizer-induced algal production slightly increased the rate at which epilimnetic concentrations of inorganic nitrogen are typically depleted during the growing season in Lake Mead. The phytoplankton community displayed a complex response to fertilization, with some species clearly increasing their abundance and others showing little or no effect. The proportional abundance of blue-greens decreased following the fertilizer additions. Temporal patterns of algal primary production closely followed those of algal biomass. Size-fractionated production measurements demonstrated that most of the production was occurring in the 20-50 Mm size class, and that this pattern remained essentially unchanged as total production levels increased following fertilization. While interesting questions remain concerning the relative importance of resource levels and other factors, for example predation, in determining shad population abundance, fertilization of the Overton Arm, as undertaken during the present study, clearly did not lead to any obvious increase in shad abundance. While a longer-term research program might be able to separate resource-related variance in shad densities from other factors contributing to inter-annual population fluctuations, large-scale artificial fertilization on the scale employed in the present project does not appear to represent a useful management tool for the Lake Mead game fisheries

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death

Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis

Stochastic fluctuations in gene expression give rise to cell-to-cell variability in protein levels which can potentially cause variability in cellular phenotype. For TRAIL (TNF-related apoptosis-inducing ligand) variability manifests itself as dramatic differences in the time between ligand exposure and the sudden activation of the effector caspases that kill cells. However, the contribution of individual proteins to phenotypic variability has not been explored in detail. In this paper we use feature-based sensitivity analysis as a means to estimate the impact of variation in key apoptosis regulators on variability in the dynamics of cell death. We use Monte Carlo sampling from measured protein concentration distributions in combination with a previously validated ordinary differential equation model of apoptosis to simulate the dynamics of receptor-mediated apoptosis. We find that variation in the concentrations of some proteins matters much more than variation in others and that precisely which proteins matter depends both on the concentrations of other proteins and on whether correlations in protein levels are taken into account. A prediction from simulation that we confirm experimentally is that variability in fate is sensitive to even small increases in the levels of Bcl-2. We also show that sensitivity to Bcl-2 levels is itself sensitive to the levels of interacting proteins. The contextual dependency is implicit in the mathematical formulation of sensitivity, but our data show that it is also important for biologically relevant parameter values. Our work provides a conceptual and practical means to study and understand the impact of cell-to-cell variability in protein expression levels on cell fate using deterministic models and sampling from parameter distributions

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

In situ nutrient assays of periphyton growth in a lowland Costa Rican stream

Nutrient limitation of primary production was experimentally assessed using an in situ bioassay technique in the Quebrada Salto, a third-order tropical stream draining the northern foothills of the Cordillera Central in Costa Rica. Bioassays employed artificial substrata enriched with nutrients that slowly diffuse through an agar-sand matrix (Pringle & Bowers, 1984). Multiple comparisons of regression coefficients, describing chlorophyll- a accrual through time for different nutrient treatments, revealed positive micronutrient effect(s). Micronutrient treatment combinations (Fe, B, Mn, Zn, Co, Mo, EDTA), supplemented with and without nitrate and phosphate, exhibited significantly greater chlorophyll- a accrual over all other treatments (P < 0.05), supporting over three times that of the control after 14-d of substratum colonization. Neither of the major nutrients (N or P) produced a significant stimulation, although the N treatment displayed ≃50% more chlorophyll- a than the control after 14-d. Similarly, Si, EDTA, and Si + N + P treatments did not exhibit chlorophyll- a response curves that were significantly different from the control. During the experiment, mean NH 4 -N and (NO 2 + NO 3 )-N concentrations in the Salto were 2.0 µM (28.6 µg · l −1 ) and 7.2 µM (100.2 µg · l −1 ), respectively. High concentrations of PO 4 -P ( = 2.0 µM; 60.9 µg · l −1 ) and TP ( = 3.0 µM; 94.0 µg · l −1 ) were also found, and consequently low molar N:P ratios = 4.7). Despite the potential for N limitation in the system, both N and P appear to be at growth saturating levels. This may be due to micronutrient limitation and/or light limitation of periphyton growth in densely shaded upstream portions of the stream.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42872/1/10750_2004_Article_BF00008489.pd

The ALICE experiment at the CERN LHC

ALICE (A Large Ion Collider Experiment) is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model. It is designed to address the physics of strongly interacting matter and the quark-gluon plasma at extreme values of energy density and temperature in nucleus-nucleus collisions. Besides running with Pb ions, the physics programme includes collisions with lighter ions, lower energy running and dedicated proton-nucleus runs. ALICE will also take data with proton beams at the top LHC energy to collect reference data for the heavy-ion programme and to address several QCD topics for which ALICE is complementary to the other LHC detectors. The ALICE detector has been built by a collaboration including currently over 1000 physicists and engineers from 105 Institutes in 30 countries. Its overall dimensions are 161626 m3 with a total weight of approximately 10 000 t. The experiment consists of 18 different detector systems each with its own specific technology choice and design constraints, driven both by the physics requirements and the experimental conditions expected at LHC. The most stringent design constraint is to cope with the extreme particle multiplicity anticipated in central Pb-Pb collisions. The different subsystems were optimized to provide high-momentum resolution as well as excellent Particle Identification (PID) over a broad range in momentum, up to the highest multiplicities predicted for LHC. This will allow for comprehensive studies of hadrons, electrons, muons, and photons produced in the collision of heavy nuclei. Most detector systems are scheduled to be installed and ready for data taking by mid-2008 when the LHC is scheduled to start operation, with the exception of parts of the Photon Spectrometer (PHOS), Transition Radiation Detector (TRD) and Electro Magnetic Calorimeter (EMCal). These detectors will be completed for the high-luminosity ion run expected in 2010. This paper describes in detail the detector components as installed for the first data taking in the summer of 2008