An extension of the FRI framework for calcium transient detection

Two-photon calcium imaging of the brain allows the spatiotemporal activity of neuronal networks to be monitored at cellular resolution. In order to analyse this activity it must first be possible to detect, with high temporal resolution, spikes from the time series corresponding to single neurons. Previous work has shown that finite rate of innovation (FRI) theory can be used to reconstruct spike trains from noisy calcium imaging data. In this paper we extend the FRI framework for spike detection from calcium imaging data to encompass data generated by a larger class of calcium indicators, including the genetically encoded indicator GCaMP6s. Furthermore, we implement least squares model-order estimation and perform a noise reduction procedure ('pre-whitening') in order to increase the robustness of the algorithm. We demonstrate high spike detection performance on real data generated by GCaMP6s, detecting 90% of electrophysiologically-validated spikes

Non-consumptive predator effects indirectly influence marine plant biomass and palatability

1. Predators can reduce herbivory and increase plant biomass by consuming herbivores, lowering individual herbivore feeding rates, or both. We tested whether the presence of predators increases plant quality by non-consumptively reducing grazing pressure and thereby weakening the strength of the induced response in plant chemical defences. 2. We performed a 42-day outdoor mesocosm experiment in which the herbivorous amphipod Ampithoe longimana was cultured on the brown seaweed Sargassum filipendula in the presence and absence of olfactory cues of its principal fish predator, the pinfish Lagodon rhomboides. The presence of fish cues reduced per capita rates of amphipod grazing by nearly 50%. Over the span of the mesocosm experiment, this per capita reduction in feeding rate yielded at least a 40% lower growth rate of amphipod populations (i.e. r reduced from 1.01 to 0.61). The lower rates of amphipod grazing (overall or per capita) correlated with higher algal biomass. 3. We pursued a series of laboratory-based feeding choice assays with naive amphipods to determine tissue palatability and the plant traits that mediate feeding choices. Tissue from tanks without grazers was more palatable than tissue from tanks with grazers, a pattern of induced plant defences that has been documented previously. Surprisingly, however, plant tissue from tanks with grazers and fish cues was more palatable than tissue from tanks with grazers but without fish cues. All changes in algal palatability were mediated by polar, but not lipophilic metabolites. These results suggest that the non-consumptive effects of fish predators increases the food quality of Sargassum by weakening the strength of its induced chemical defences. 4. Synthesis. The smell of predators has the potential to regulate herbivore populations and affect the ecological dynamics of plant biomass and chemical defences

Multiple predator species alter prey behavior, population growth, and a trophic cascade in a model estuarine food web

Predators can influence prey population dynamics by affecting prey behaviors with strong fitness consequences, with cascading effects on lower trophic levels. Here, we demonstrate that multiple predator species can nonconsumptively influence prey population growth and the strength of a trophic cascade in a model marine community. We exposed the herbivorous amphipod Ampithoe longimana to olfactory and visual cues from three common predators (pinfish, mud crabs, brown shrimp) singly and together in a multiple-predator assemblage to quantify the nonconsumptive effects (NCEs) of predator identity and the presence of multiple predators on prey population and community-level metrics. The presence of predator cues, particularly those of the pinfish and the multiple-predator treatments, decreased prey population growth and influenced primary and secondary production. To explore mechanisms underlying the observed NCEs in the experimental communities and their potential influence in the field, we quantified individual prey behavioral responses (changes in grazing rate, diet preference, dispersal, colonization) in the presence of predator cues. Predator cues decreased prey grazing, dispersal, and colonization but did not affect prey diet preference. Given the persistence of NCEs over time and the fact that trophic cascades are common features of marine systems, changes in marine predator communities may have widespread effects on predator-prey behavioral interactions with consequences for ecosystem function even in areas of weak predation pressure

Field experimental evidence that grazers mediate transition between microalgal and seagrass dominance

We tested the relative effects of nutrient loading, reduced predation, and reduced grazing on eelgrass community dynamics in Chesapeake Bay and found evidence supporting the mutualistic mesograzer model in which small invertebrate grazers control accumulation of epiphytic algae, buffer eutrophication effects, and thus facilitate seagrass dominance. Experimental reduction of crustacean grazers in the field stimulated a nearly sixfold increase in epiphytic algae, and reduced seagrass biomass by 65% compared to controls with grazers. Nutrient fertilization generally had much weaker effects, but an interaction with mesograzers was key in changing the sign of fertilization effects on the system: aboveground eelgrass biomass was reduced by fertilization under reduced grazing, but increased by fertilization under ambient grazing. When protected from predators in field cages, these mesograzers limited epiphyte blooms even with nutrient enrichment, and nutrients instead enhanced grazer secondary production. Crustacean mesograzers play a key role in maintaining macrophyte (seagrass) dominance in Chesapeake Bay, in buffering eelgrass against eutrophication, and in efficiently transferring nitrogen to higher trophic levels. Yet, these crustacean grazers are also highly sensitive to predator abundance. Reducing nutrient pollution alone is unlikely to restore seagrass meadows where alterations to food webs have reduced populations of algae-feeding mesograzers. Integration of both water quality and fishery management will be more effective in restoring and maintaining healthy coastal ecosystems

Water dispersible microbicidal cellulose acetate phthalate film

BACKGROUND: Cellulose acetate phthalate (CAP) has been used for several decades in the pharmaceutical industry for enteric film coating of oral tablets and capsules. Micronized CAP, available commercially as "Aquateric" and containing additional ingredients required for micronization, used for tablet coating from water dispersions, was shown to adsorb and inactivate the human immunodeficiency virus (HIV-1), herpesviruses (HSV) and other sexually transmitted disease (STD) pathogens. Earlier studies indicate that a gel formulation of micronized CAP has a potential as a topical microbicide for prevention of STDs including the acquired immunodeficiency syndrome (AIDS). The objective of endeavors described here was to develop a water dispersible CAP film amenable to inexpensive industrial mass production. METHODS: CAP and hydroxypropyl cellulose (HPC) were dissolved in different organic solvent mixtures, poured into dishes, and the solvents evaporated. Graded quantities of a resulting selected film were mixed for 5 min at 37°C with HIV-1, HSV and other STD pathogens, respectively. Residual infectivity of the treated viruses and bacteria was determined. RESULTS: The prerequisites for producing CAP films which are soft, flexible and dispersible in water, resulting in smooth gels, are combining CAP with HPC (other cellulose derivatives are unsuitable), and casting from organic solvent mixtures containing ≈50 to ≈65% ethanol (EtOH). The films are ≈100 µ thick and have a textured surface with alternating protrusions and depressions revealed by scanning electron microscopy. The films, before complete conversion into a gel, rapidly inactivated HIV-1 and HSV and reduced the infectivity of non-viral STD pathogens >1,000-fold. CONCLUSIONS: Soft pliable CAP-HPC composite films can be generated by casting from organic solvent mixtures containing EtOH. The films rapidly reduce the infectivity of several STD pathogens, including HIV-1. They are converted into gels and thus do not have to be removed following application and use. In addition to their potential as topical microbicides, the films have promise for mucosal delivery of pharmaceuticals other than CAP

Hedgehog pathway mutations drive oncogenic transformation in high-risk T-cell acute lymphoblastic leukemia.

The role of Hedgehog signaling in normal and malignant T-cell development is controversial. Recently, Hedgehog pathway mutations have been described in T-ALL, but whether mutational activation of Hedgehog signaling drives T-cell transformation is unknown, hindering the rationale for therapeutic intervention. Here, we show that Hedgehog pathway mutations predict chemotherapy resistance in human T-ALL, and drive oncogenic transformation in a zebrafish model of the disease. We found Hedgehog pathway mutations in 16% of 109 childhood T-ALL cases, most commonly affecting its negative regulator PTCH1. Hedgehog mutations were associated with resistance to induction chemotherapy (P = 0.009). Transduction of wild-type PTCH1 into PTCH1-mutant T-ALL cells induced apoptosis (P = 0.005), a phenotype that was reversed by downstream Hedgehog pathway activation (P = 0.007). Transduction of most mutant PTCH1, SUFU, and GLI alleles into mammalian cells induced aberrant regulation of Hedgehog signaling, indicating that these mutations are pathogenic. Using a CRISPR/Cas9 system for lineage-restricted gene disruption in transgenic zebrafish, we found that ptch1 mutations accelerated the onset of notch1-induced T-ALL (P = 0.0001), and pharmacologic Hedgehog pathway inhibition had therapeutic activity. Thus, Hedgehog-activating mutations are driver oncogenic alterations in high-risk T-ALL, providing a molecular rationale for targeted therapy in this disease

CosMIC: a consistent metric for spike inference from calcium imaging

In recent years, the development of algorithms to detect neuronal spiking activity from two-photon calcium imaging data has received much attention. Meanwhile, few researchers have examined the metrics used to assess the similarity of detected spike trains with the ground truth. We highlight the limitations of the two most commonly used metrics, the spike train correlation and success rate, and propose an alternative, which we refer to as CosMIC. Rather than operating on the true and estimated spike trains directly, the proposed metric assesses the similarity of the pulse trains obtained from convolution of the spike trains with a smoothing pulse. The pulse width, which is derived from the statistics of the imaging data, reflects the temporal tolerance of the metric. The final metric score is the size of the commonalities of the pulse trains as a fraction of their average size. Viewed through the lens of set theory, CosMIC resembles a continuous Sørensen-Dice coefficient — an index commonly used to assess the similarity of discrete, presence/absence data. We demonstrate the ability of the proposed metric to discriminate the precision and recall of spike train estimates. Unlike the spike train correlation, which appears to reward overestimation, the proposed metric score is maximised when the correct number of spikes have been detected. Furthermore, we show that CosMIC is more sensitive to the temporal precision of estimates than the success rate

X-ray emission from isolated neutron stars

X-ray emission is a common feature of all varieties of isolated neutron stars (INS) and, thanks to the advent of sensitive instruments with good spectroscopic, timing, and imaging capabilities, X-ray observations have become an essential tool in the study of these objects. Non-thermal X-rays from young, energetic radio pulsars have been detected since the beginning of X-ray astronomy, and the long-sought thermal emission from cooling neutron star's surfaces can now be studied in detail in many pulsars spanning different ages, magnetic fields, and, possibly, surface compositions. In addition, other different manifestations of INS have been discovered with X-ray observations. These new classes of high-energy sources, comprising the nearby X-ray Dim Isolated Neutron Stars, the Central Compact Objects in supernova remnants, the Anomalous X-ray Pulsars, and the Soft Gamma-ray Repeaters, now add up to several tens of confirmed members, plus many candidates, and allow us to study a variety of phenomena unobservable in "standard'' radio pulsars.Comment: Chapter to be published in the book of proceedings of the 1st Sant Cugat Forum on Astrophysics, "ICREA Workshop on the high-energy emission from pulsars and their systems", held in April, 201

Multiphoton minimal inertia scanning for fast acquisition of neural activity signals

Objective: Multi-photon laser scanning microscopy provides a powerful tool for monitoring the spatiotemporal dynamics of neural circuit activity. It is, however, intrinsically a point scanning technique. Standard raster scanning enables imaging at subcellular resolution; however, acquisition rates are limited by the size of the field of view to be scanned. Recently developed scanning strategies such as Travelling Salesman Scanning (TSS) have been developed to maximize cellular sampling rate by scanning only select regions in the field of view corresponding to locations of interest such as somata. However, such strategies are not optimized for the mechanical properties of galvanometric scanners. We thus aimed to develop a new scanning algorithm which produces minimal inertia trajectories, and compare its performance with existing scanning algorithms. Approach: We describe here the Adaptive Spiral Scanning (SSA) algorithm, which fits a set of near-circular trajectories to the cellular distribution to avoid inertial drifts of galvanometer position. We compare its performance to raster scanning and TSS in terms of cellular sampling frequency and signal-to-noise ratio (SNR). Main Results: Using surrogate neuron spatial position data, we show that SSA acquisition rates are an order of magnitude higher than those for raster scanning and generally exceed those achieved by TSS for neural densities comparable with those found in the cortex. We show that this result also holds true for in vitro hippocampal mouse brain slices bath loaded with the synthetic calcium dye Cal-520 AM. The ability of TSS to "park" the laser on each neuron along the scanning trajectory, however, enables higher SNR than SSA when all targets are precisely scanned. Raster scanning has the highest SNR but at a substantial cost in number of cells scanned. To understand the impact of sampling rate and SNR on functional calcium imaging, we used the Crame ́r-Rao Bound on evoked calcium traces recorded simultaneously with electrophysiology traces to calculate the lower bound estimate of the spike timing occurrence. Significance: The results show that TSS and SSA achieve comparable accuracy in spike time estimates compared to raster scanning, despite lower SNR. SSA is an easily implementable way for standard multi-photon laser scanning systems to gain temporal precision in the detection of action potentials while scanning hundreds of active cells