Survey of Oyster Grounds in Virginia - Report of J.B. Baylor to the Governor of Virginia

Note: The full Baylor report referenced in this work is located at the Library of Virginia Special Collections (East Side SH365 .V7 1894a) in this document: Wilkins, John T. Oyster Records. Distance and Bearings of Numbered Corners of Public Grounds from Shore Stations, Depth of Water, Descriptions of Shore Stations, &c., &c. ... Richmond: N.p., 1894. Print

Comparing ocean surface boundary vertical mixing schemes including langmuir turbulence

Six recent Langmuir turbulence parameterization schemes and five traditional schemes are implemented in a common single‐column modeling framework and consistently compared. These schemes are tested in scenarios versus matched large eddy simulations, across the globe with realistic forcing (JRA55‐do, WAVEWATCH‐III simulated waves) and initial conditions (Argo), and under realistic conditions as observed at ocean moorings. Traditional non‐Langmuir schemes systematically underpredict large eddy simulation vertical mixing under weak convective forcing, while Langmuir schemes vary in accuracy. Under global, realistic forcing Langmuir schemes produce 6% (−1% to 14% for 90% confidence) or 5.2 m (−0.2 m to 17.4 m for 90% confidence) deeper monthly mean mixed layer depths than their non‐Langmuir counterparts, with the greatest differences in extratropical regions, especially the Southern Ocean in austral summer. Discrepancies among Langmuir schemes are large (15% in mixed layer depth standard deviation over the mean): largest under wave‐driven turbulence with stabilizing buoyancy forcing, next largest under strongly wave‐driven conditions with weak buoyancy forcing, and agreeing during strong convective forcing. Non‐Langmuir schemes disagree with each other to a lesser extent, with a similar ordering. Langmuir discrepancies obscure a cross‐scheme estimate of the Langmuir effect magnitude under realistic forcing, highlighting limited understanding and numerical deficiencies. Maps of the regions and seasons where the greatest discrepancies occur are provided to guide further studies and observations

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease

OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the Ocean Model Intercomparison Project

The Ocean Model Intercomparison Project (OMIP) is an endorsed project in the Coupled Model Intercomparison Project Phase 6 (CMIP6). OMIP addresses CMIP6 science questions, investigating the origins and consequences of systematic model biases. It does so by providing a framework for evaluating (including assessment of systematic biases), understanding, and improving ocean, sea-ice, tracer, and biogeochemical components of climate and earth system models contributing to CMIP6. Among the WCRP Grand Challenges in climate science (GCs), OMIP primarily contributes to the regional sea level change and near-term (climate/decadal) prediction GCs. OMIP provides (a) an experimental protocol for global ocean/sea-ice models run with a prescribed atmospheric forcing; and (b) a protocol for ocean diagnostics to be saved as part of CMIP6. We focus here on the physical component of OMIP, with a companion paper (Orr et al., 2016) detailing methods for the inert chemistry and interactive biogeochemistry. The physical portion of the OMIP experimental protocol follows the interannual Coordinated Ocean-ice Reference Experiments (CORE-II). Since 2009, CORE-I (Normal Year Forcing) and CORE-II (Interannual Forcing) have become the standard methods to evaluate global ocean/sea-ice simulations and to examine mechanisms for forced ocean climate variability. The OMIP diagnostic protocol is relevant for any ocean model component of CMIP6, including the DECK (Diagnostic, Evaluation and Characterization of Klima experiments), historical simulations, FAFMIP (Flux Anomaly Forced MIP), C4MIP (Coupled Carbon Cycle Climate MIP), DAMIP (Detection and Attribution MIP), DCPP (Decadal Climate Prediction Project), ScenarioMIP, HighResMIP (High Resolution MIP), as well as the ocean/sea-ice OMIP simulations

Template bank for compact binary mergers in the fourth observing run of Advanced LIGO, Advanced Virgo, and KAGRA

Template banks containing gravitational wave (GW) waveforms are essential for matched-filtering GW search pipelines. We describe the generation method, the design, and validation of the template bank used by the GstLAL-based inspiral pipeline to analyze data from the fourth observing run of LIGO scientific, Virgo, and KAGRA collaboration. This paper presents a template bank containing $1.8 \times 10^6$ templates that include merging neutron star - neutron star, neutron star - black hole, and black hole - black hole systems up to a total mass of $400$ $M_\odot$. Motivated by observations, component masses below $3$ $M_\odot$ have dimensionless spins ranging between $\pm 0.05$, while component masses between $3$ to $200$ $M_\odot$ have dimensionless spins ranging between $\pm 0.99$, where we assume spin-aligned systems. The low-frequency cutoff is $15$ Hz. The templates are placed in the parameter space according to the metric via a binary tree approach which took $\mathcal{O}\left(10\right)$ minutes when jobs were parallelized. The template bank generated with this method has a $98\%$ match or higher for $90\%$ of the injections, thus being as effective as the template placement method used for the previous observation runs. The volumes of the templates are computed prior to template placement and the nearby templates have similar volumes in the coordinate space, henceforth, enabling a more efficient and less biased implementation of population models. SVD sorting of the O4 template bank has been renewed to use post-Newtonian phase terms, which improved the computational efficiency of SVD by nearly $4 \sim 5$ times as compared to conventional SVD sorting schemes. Template banks and searches focusing on the sub-solar mass parameter space and intermediate-mass black hole parameter space are conducted separately

When to Point Your Telescopes: Gravitational Wave Trigger Classification for Real-Time Multi-Messenger Followup Observations

We develop a robust and self-consistent framework to extract and classify gravitational wave candidates from noisy data, for the purpose of assisting in real-time multi-messenger follow-ups during LIGO-Virgo-KAGRA's fourth observing run~(O4). Our formalism implements several improvements to the low latency calculation of the probability of astrophysical origin~(\PASTRO{}), so as to correctly account for various factors such as the sensitivity change between observing runs, and the deviation of the recovered template waveform from the true gravitational wave signal that can strongly bias said calculation. We demonstrate the high accuracy with which our new formalism recovers and classifies gravitational wave triggers, by analyzing replay data from previous observing runs injected with simulated sources of different categories. We show that these improvements enable the correct identification of the majority of simulated sources, many of which would have otherwise been misclassified. We carry out the aforementioned analysis by implementing our formalism through the \GSTLAL{} search pipeline even though it can be used in conjunction with potentially any matched filtering pipeline. Armed with robust and self-consistent \PASTRO{} values, the \GSTLAL{} pipeline can be expected to provide accurate source classification information for assisting in multi-messenger follow-up observations to gravitational wave alerts sent out during O4.Comment: v2 upload was accidental. revert back to v

Performance of the low-latency GstLAL inspiral search towards LIGO, Virgo, and KAGRA's fourth observing run

GstLAL is a stream-based matched-filtering search pipeline aiming at the prompt discovery of gravitational waves from compact binary coalescences such as the mergers of black holes and neutron stars. Over the past three observation runs by the LIGO, Virgo, and KAGRA (LVK) collaboration, the GstLAL search pipeline has participated in several tens of gravitational wave discoveries. The fourth observing run (O4) is set to begin in May 2023 and is expected to see the discovery of many new and interesting gravitational wave signals which will inform our understanding of astrophysics and cosmology. We describe the current configuration of the GstLAL low-latency search and show its readiness for the upcoming observation run by presenting its performance on a mock data challenge. The mock data challenge includes 40 days of LIGO Hanford, LIGO Livingston, and Virgo strain data along with an injection campaign in order to fully characterize the performance of the search. We find an improved performance in terms of detection rate and significance estimation as compared to that observed in the O3 online analysis. The improvements are attributed to several incremental advances in the likelihood ratio ranking statistic computation and the method of background estimation.Comment: 19 pages, 21 figure

A Positive Feedback Synapse from Retinal Horizontal Cells to Cone Photoreceptors

Cone photoreceptors and horizontal cells (HCs) have a reciprocal synapse that underlies lateral inhibition and establishes the antagonistic center-surround organization of the visual system. Cones transmit to HCs through an excitatory synapse and HCs feed back to cones through an inhibitory synapse. Here we report that HCs also transmit to cone terminals a positive feedback signal that elevates intracellular Ca2+ and accelerates neurotransmitter release. Positive and negative feedback are both initiated by AMPA receptors on HCs, but positive feedback appears to be mediated by a change in HC Ca2+, whereas negative feedback is mediated by a change in HC membrane potential. Local uncaging of AMPA receptor agonists suggests that positive feedback is spatially constrained to active HC-cone synapses, whereas the negative feedback signal spreads through HCs to affect release from surrounding cones. By locally offsetting the effects of negative feedback, positive feedback may amplify photoreceptor synaptic release without sacrificing HC-mediated contrast enhancement

Numerical Analysis of Ca2+ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum

The t-tubules of mammalian ventricular myocytes are invaginations of the cell membrane that occur at each Z-line. These invaginations branch within the cell to form a complex network that allows rapid propagation of the electrical signal, and hence synchronous rise of intracellular calcium (Ca2+). To investigate how the t-tubule microanatomy and the distribution of membrane Ca2+ flux affect cardiac excitation-contraction coupling we developed a 3-D continuum model of Ca2+ signaling, buffering and diffusion in rat ventricular myocytes. The transverse-axial t-tubule geometry was derived from light microscopy structural data. To solve the nonlinear reaction-diffusion system we extended SMOL software tool (http://mccammon.ucsd.edu/smol/). The analysis suggests that the quantitative understanding of the Ca2+ signaling requires more accurate knowledge of the t-tubule ultra-structure and Ca2+ flux distribution along the sarcolemma. The results reveal the important role for mobile and stationary Ca2+ buffers, including the Ca2+ indicator dye. In agreement with experiment, in the presence of fluorescence dye and inhibited sarcoplasmic reticulum, the lack of detectible differences in the depolarization-evoked Ca2+ transients was found when the Ca2+ flux was heterogeneously distributed along the sarcolemma. In the absence of fluorescence dye, strongly non-uniform Ca2+ signals are predicted. Even at modest elevation of Ca2+, reached during Ca2+ influx, large and steep Ca2+ gradients are found in the narrow sub-sarcolemmal space. The model predicts that the branched t-tubule structure and changes in the normal Ca2+ flux density along the cell membrane support initiation and propagation of Ca2+ waves in rat myocytes

Adaptation of pineal expressed teleost exo-rod opsin to non-image forming photoreception through enhanced Meta II decay

Photoreception by vertebrates enables both image-forming vision and non-image-forming responses such as circadian photoentrainment. Over the recent years, distinct non-rod non-cone photopigments have been found to support circadian photoreception in diverse species. By allowing specialization to this sensory task a selective advantage is implied, but the nature of that specialization remains elusive. We have used the presence of distinct rod opsin genes specialized to either image-forming (retinal rod opsin) or non-image-forming (pineal exo-rod opsin) photoreception in ray-finned fish (Actinopterygii) to gain a unique insight into this problem. A comparison of biochemical features for these paralogous opsins in two model teleosts, Fugu pufferfish (Takifugu rubripes) and zebrafish (Danio rerio), reveals striking differences. While spectral sensitivity is largely unaltered by specialization to the pineal environment, in other aspects exo-rod opsins exhibit a behavior that is quite distinct from the cardinal features of the rod opsin family. While they display a similar thermal stability, they show a greater than tenfold reduction in the lifetime of the signaling active Meta II photoproduct. We show that these features reflect structural changes in retinal association domains of helices 3 and 5 but, interestingly, not at either of the two residues known to define these characteristics in cone opsins. Our findings suggest that the requirements of non-image-forming photoreception have lead exo-rod opsin to adopt a characteristic that seemingly favors efficient bleach recovery but not at the expense of absolute sensitivity