2,405 research outputs found
Larval rockfish diversity abundance dynamics in association with a marine protected area in the Southern California Bight
Marine protected areas (MPAs) are areas aimed at protecting natural and cultural resources that are often proposed as a way to alleviate the effects of overfishing on populations of targeted species; these areas have varying degrees of fishing and recreational use restrictions. In order to assess MPA efficacy, it is important to determine the mechanisms by which the presence of MPAs affect reproductive output within and potentially even beyond their boundaries. I attempted to address this through studying the responses of rockfish (Sebastes spp.) larval abundances to the presence of the Cowcod Conservation Areas (CCAs) located within the Southern California Bight region. Rockfish larvae were collected from mesozooplankton samples obtained during winter survey cruises by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program and identified by sequencing the cytochrome b gene. I constructed time-series of rockfish larval abundances within the Southern California Bight from 1998 to 2013.
I found that, not only have delta mean larval abundances of multiple rockfish species increased throughout the period, three historically-targeted species’ delta mean larval abundances—Bank Rockfish (S. rufus), Speckled Rockfish (S. ovalis), and Olive Rockfish (S. serranoides)—increased at a greater rate within the CCAs compared to locations with similar environmental parameters outside of the CCAs. This is the first decadal-scale study that explicitly demonstrates an increase in reproductive output from an MPA in the form of increased larval 2 abundances, thus contributing crucial information to the understanding of MPA efficacy.
Additionally, the dataset created during this study will become the basis for several future studies that will further elucidate the spatiotemporal dynamics of rockfish larvae within CCAs and in the Southern California Bight region as a whole. These studies will further contribute to understanding the efficacy of the CCAs in their facilitation of rockfish species recovery, as well as provide important information for rockfish fisheries management in the region
Phase retrieval from power spectra of masked signals
In diffraction imaging, one is tasked with reconstructing a signal from its
power spectrum. To resolve the ambiguity in this inverse problem, one might
invoke prior knowledge about the signal, but phase retrieval algorithms in this
vein have found limited success. One alternative is to create redundancy in the
measurement process by illuminating the signal multiple times, distorting the
signal each time with a different mask. Despite several recent advances in
phase retrieval, the community has yet to construct an ensemble of masks which
uniquely determines all signals and admits an efficient reconstruction
algorithm. In this paper, we leverage the recently proposed polarization method
to construct such an ensemble. We also present numerical simulations to
illustrate the stability of the polarization method in this setting. In
comparison to a state-of-the-art phase retrieval algorithm known as PhaseLift,
we find that polarization is much faster with comparable stability.Comment: 18 pages, 3 figure
Adaptive Mantel Test for AssociationTesting in Imaging Genetics Data
Mantel's test (MT) for association is conducted by testing the linear
relationship of similarity of all pairs of subjects between two observational
domains. Motivated by applications to neuroimaging and genetics data, and
following the succes of shrinkage and kernel methods for prediction with
high-dimensional data, we here introduce the adaptive Mantel test as an
extension of the MT. By utilizing kernels and penalized similarity measures,
the adaptive Mantel test is able to achieve higher statistical power relative
to the classical MT in many settings. Furthermore, the adaptive Mantel test is
designed to simultaneously test over multiple similarity measures such that the
correct type I error rate under the null hypothesis is maintained without the
need to directly adjust the significance threshold for multiple testing. The
performance of the adaptive Mantel test is evaluated on simulated data, and is
used to investigate associations between genetics markers related to
Alzheimer's Disease and heatlhy brain physiology with data from a working
memory study of 350 college students from Beijing Normal University
The Gerby Gopakumar-Mari\~no-Vafa Formula
We prove a formula for certain cubic -Hodge integrals in terms of loop
Schur functions. We use this identity to prove the
Gromov-Witten/Donaldson-Thomas correspondence for local -gerbes over
\proj^1.Comment: 43 pages, Published Versio
Genome-wide screen for genes involved in Caenorhabditis elegans developmentally timed sleep
In Caenorhabditis elegans, Notch signaling regulates developmentally timed sleep during the transition from L4 larval stage to adulthood (L4/A) . To identify core sleep pathways and to find genes acting downstream of Notch signaling, we undertook the first genome-wide, classical genetic screen focused on C. elegans developmentally timed sleep. To increase screen efficiency, we first looked for mutations that suppressed inappropriate anachronistic sleep in adult hsp::osm-11 animals overexpressing the Notch coligand OSM-11 after heat shock. We retained suppressor lines that also had defects in L4/A developmentally timed sleep, without heat shock overexpression of the Notch coligand. Sixteen suppressor lines with defects in developmentally timed sleep were identified. One line carried a new allele of goa-1; loss of GOA-1 Gαo decreased C. elegans sleep. Another line carried a new allele of gpb-2, encoding a Gβ5 protein; Gβ5 proteins have not been previously implicated in sleep. In other scenarios, Gβ5 GPB-2 acts with regulators of G protein signaling (RGS proteins) EAT-16 and EGL-10 to terminate either EGL-30 Gαq signaling or GOA-1 Gαo signaling, respectively. We found that loss of Gβ5 GPB-2 or RGS EAT-16 decreased L4/A sleep. By contrast, EGL-10 loss had no impact. Instead, loss of RGS-1 and RGS-2 increased sleep. Combined, our results suggest that, in the context of L4/A sleep, GPB-2 predominantly acts with EAT-16 RGS to inhibit EGL-30 Gαq signaling. These results confirm the importance of G protein signaling in sleep and demonstrate that these core sleep pathways function genetically downstream of the Notch signaling events promoting sleep
Mechanisms of pattern formation during T cell adhesion
T cells form intriguing patterns during adhesion to antigen-presenting cells.
The patterns at the cell-cell contact zone are composed of two types of
domains, which either contain short TCR/MHCp receptor-ligand complexes or the
longer LFA-1/ICAM-1 complexes. The final pattern consists of a central TCR/MHCp
domain surrounded by a ring-shaped LFA-1/ICAM-1 domain, while the
characteristic pattern formed at intermediate times is inverted with TCR/MHCp
complexes at the periphery of the contact zone and LFA-1/ICAM-1 complexes in
the center. In this article, we present a statistical-mechanical model of cell
adhesion and propose a novel mechanism for the T cell pattern formation. Our
mechanism for the formation of the intermediate inverted pattern is based (i)
on the initial nucleation of numerous TCR/MHCp microdomains, and (ii) on the
diffusion of free receptors and ligands into the contact zone. Due to this
inward diffusion, TCR/MHCp microdomains at the rim of the contact zone grow
faster and form an intermediate peripheral ring for sufficiently large TCR/MHCp
concentrations. In agreement with experiments, we find that the formation of
the final pattern with a central TCR/MHCp domain requires active cytoskeletal
transport processes. Without active transport, the intermediate inverted
pattern seems to be metastable in our model, which might explain patterns
observed during natural killer (NK) cell adhesion. At smaller TCR/MHCp complex
concentrations, we observe a different regime of pattern formation with
intermediate multifocal TCR/MHCp patterns which resemble experimental patterns
found during thymozyte adhesion.Comment: 12 pages, 8 figure
Binding cooperativity of membrane adhesion receptors
The adhesion of cells is mediated by receptors and ligands anchored in
apposing membranes. A central question is how to characterize the binding
affinity of these membrane-anchored molecules. For soluble molecules, the
binding affinity is typically quantified by the binding equilibrium constant
K3D in the linear relation [RL] = K3D [R][L] between the volume concentration
[RL] of bound complexes and the volume concentrations [R] and [L] of unbound
molecules. For membrane-anchored molecules, it is often assumed by analogy that
the area concentration of bound complexes [RL] is proportional to the product
[R][L] of the area concentrations for the unbound receptor and ligand
molecules. We show here (i) that this analogy is only valid for two planar
membranes immobilized on rigid surfaces, and (ii) that the thermal roughness of
flexible membranes leads to cooperative binding of receptors and ligands. In
the case of flexible membranes, the area concentration [RL] of receptor-ligand
bonds is proportional to the square of [R][L] for typical lengths and
concentrations of receptors and ligands in cell adhesion zones. The cooperative
binding helps to understand why different experimental methods for measuring
the binding affinity of membrane-anchored molecules have led to values
differing by several orders of magnitude.Comment: 9 pages, 4 figures; to appear in Soft Matte
Intrinsically stretchable and transparent thin-film transistors based on printable silver nanowires, carbon nanotubes and an elastomeric dielectric.
Thin-film field-effect transistor is a fundamental component behind various mordern electronics. The development of stretchable electronics poses fundamental challenges in developing new electronic materials for stretchable thin-film transistors that are mechanically compliant and solution processable. Here we report the fabrication of transparent thin-film transistors that behave like an elastomer film. The entire fabrication is carried out by solution-based techniques, and the resulting devices exhibit a mobility of ∼30 cm(2) V(-1) s(-1), on/off ratio of 10(3)-10(4), switching current >100 μA, transconductance >50 μS and relative low operating voltages. The devices can be stretched by up to 50% strain and subjected to 500 cycles of repeated stretching to 20% strain without significant loss in electrical property. The thin-film transistors are also used to drive organic light-emitting diodes. The approach and results represent an important progress toward the development of stretchable active-matrix displays
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