High resolution assessment of commercial fisheries activity along the US West Coast using Vessel Monitoring System data with a case study using California groundfish fisheries.

Commercial fisheries along the US West Coast are important components of local and regional economies. They use various fishing gear, target a high diversity of species, and are highly spatially heterogeneous, making it challenging to generate a synoptic picture of fisheries activity in the region. Still, understanding the spatial and temporal dynamics of US West Coast fisheries is critical to meet the US legal mandate to manage fisheries sustainably and to better coordinate activities among a growing number of users of ocean space, including offshore renewable energy, aquaculture, shipping, and interactions with habitats and key non-fishery species such as seabirds and marine mammals. We analyzed vessel tracking data from Vessel Monitoring System (VMS) from 2010 to 2017 to generate high-resolution spatio-temporal estimates of contemporary fishing effort across a wide range of commercial fisheries along the entire US West Coast. We identified over 247,000 fishing trips across the entire VMS data, covering over 25 different fisheries. We validated the spatial accuracy of our analyses using independent estimates of spatial groundfish fisheries effort generated through the NOAA's National Marine Fisheries Service Observer Program. Additionally, for commercial groundfish fisheries operating in federal waters in California, we combined the VMS data with landings and ex-vessel value data from California commercial fisheries landings receipts to generate highly resolved estimates of landings and ex-vessel value, matching over 38,000 fish tickets with VMS data that included 87% of the landings and 76% of the ex-vessel value for groundfish. We highlight fisheries-specific and spatially-resolved patterns of effort, landings, and ex-vessel value, a bimodal distribution of fishing effort with respect to depth, and variable and generally declining effort over eight years. The information generated by our study can help inform future sustainable spatial fisheries management and other activities in the marine environment including offshore renewable energy planning.

Posterior Shoulder Instability and Glenoid Bone Loss: A Review and a Free Bone Graft Technique.

Posterior glenoid bone loss (pGBL) is frequently associated with posterior shoulder instability. Posterior glenohumeral instability accounts for a small percentage of shoulder pathologies, and critical bone loss in posterior instability has not been well defined in the literature. Younger patient populations who participate in activities that repetitively stress the posterior stabilizing structures of the shoulder are more prone to developing posterior shoulder instability. A variety of surgical options have been described, ranging from isolated capsulolabral repair to glenoid osteotomy. Soft-tissue repair alone may be an inadequate treatment in cases of pGBL and places patients at a high risk of recurrence. Our preferred technique for posterior glenoid reconstruction in cases of pGBL involves the transfer of a free iliac crest bone graft onto the native glenoid. The graft is contoured to fit the osseous defect and secured to provide an extension of the glenoid track. In this study, we review pGBL in the setting of posterior instability and describe our technique in detail. Further long-term studies are needed to refine the indications for glenoid bone graft procedures and quantify what constitutes a critical pGBL.

Effects of basin-scale climate modes and upwelling on nearshore marine heatwaves and cold spells in the California Current.

Marine heatwaves and cold spells (MHWs/MCSs) have been observed to be increasing globally in frequency and intensity based on satellite remote sensing and continue to pose a major threat to marine ecosystems worldwide. Despite this, there are limited in-situ based observational studies in the very shallow nearshore region, particularly in Eastern Boundary Current Upwelling Systems (EBUS). We analyzed a unique dataset collected in shallow waters along central California spanning more than four decades (1978-2020) and assessed links with basin-scale climate modes [Pacific Decadal Oscillation (PDO) and El Niño (MEI)] and regional-scale wind-driven upwelling. We found no significant increase/decrease in MHW/MCS frequency, duration, or intensity over the last four decades, but did observe considerable interannual variability linked with basin-scale climate modes. Additionally, there was a decrease in both MHW/MCS occurrence during the upwelling season, and the initiation of individual MHWs/MCSs coincided with anomalous upwelling. Most notably, the co-occurrence of warm (cold) phases of the PDO and MEI with negative (positive) upwelling anomalies strongly enhanced the relative frequency of positive (negative) temperature anomalies and MHW (MCS) days. Collectively, both basin-scale variability and upwelling forcing play a key role in predicting extreme events and shaping nearshore resilience in EBUS.

NFκB and Cyclic AMP Response Element Sites Mediate the Valproic Acid and UL138 Responsiveness of the Human Cytomegalovirus Major Immediate Early Enhancer and Promoter.

The major immediate early enhancer and promoter (MIEP) of human cytomegalovirus (HCMV) drives the transcription of the immediate early one (IE1) and IE2 genes, whose encoded proteins stimulate productive, lytic replication. The MIEP is activated by the virally encoded and tegument-delivered pp71 protein at the start of de novo lytic infections of fully differentiated cells. Conversely, the MIEP is silenced at the start of de novo latent infections within incompletely differentiated myeloid cells in part because tegument-delivered pp71 is sequestered in the cytoplasm in these cells, but also by viral factors that repress transcription from this locus, including the UL138 protein. During both modes of infection, MIEP activity can be increased by the histone deacetylase inhibitor valproic acid (VPA); however, UL138 inhibits the VPA-responsiveness of the MIEP. Here, we show that two families of cellular transcription factors, NF-κB and cAMP response element-binding protein (CREB), together control the VPA-mediated activation and UL138-mediated repression of the HCMV MIEP. IMPORTANCE Artificial regulation of the HCMV MIEP, either activation or repression, is an attractive potential means to target the latent reservoirs of virus for which there is currently no available intervention. The MIEP could be repressed to prevent latency reactivation or induced to drive the virus into the lytic stage that is visible to the immune system and inhibited by multiple small-molecule antiviral drugs. Understanding how the MIEP is regulated is a critical part of designing and implementing either strategy. Our revelation here that NF-κB and CREB control the responsiveness of the MIEP to the viral UL138 protein and the FDA-approved drug VPA could help in the formulation and execution of promoter regulatory strategies against latent HCMV.

Molecular ecology of the sleeper shark subgenus Somniosus (Somniosus) reveals genetic homogeneity within species and lack of support for S. antarcticus.

Inferences made from molecular data support regional stock assessment goals by providing insights into the genetic population dynamics of enigmatic species. Population genomics metrics, such as genetic diversity and population connectivity, serve as useful proxies for species health and stability. Sleeper sharks (genus Somniosus) are ecologically important deep-sea predators, estimated to reach ages of 250 to 300 yr and taking decades to reach sexual maturity. The subgenus Somniosus (Somniosus) is comprised of 3 species: S. pacificus, S. microcephalus, and S. antarcticus. Given the life history strategy of somniosids, they are vulnerable to overfishing and population declines. Further, data to assess the stocks of these species are limited. To address this deficiency, we used the reduced representation library method Restriction-site Associated DNA sequencing (RADseq) to conduct phylogenomic and population genomics analyses, providing novel information for use in stock assessments. Our results strongly support the species status of S. microcephalus (N = 79), but recover S. antarcticus (N = 2) intermixed within the S. pacificus (N = 170) clade. Population genomics analyses reveal genetic homogeneity within S. pacificus and S. microcephalus, and estimates of effective population size were in the hundreds for both species. Kinship analysis identified 2 first-degree relative pairs within our dataset (1 within each species). Our results contribute new information for stock assessments of these uniquely long-lived species by providing the strongest molecular evidence to date for the synonymization of S. antarcticus and S. pacificus, as well as estimating population genomic metrics for each supported species within the Somniosus (Somniosus) subgenus.

Conservation implications of revised genetic structure resulting from new population discovery: the threatened eastern sand darter (Ammocrypta pellucida) in Canada.

Human activity can put non-game fishes at higher risk of extinction because of inappropriate management action. Eastern sand darter (Ammocrypta pellucida), a small benthic fish classified as threatened across much of its northern range, inhabits increasingly fragmented sandy habitats and, as a non-game fish, may be easily overlooked in conservation efforts. In this study, the authors use genotype data from nine microsatellite loci and cytochrome oxidase I (COI) sequencing data across its northern native range to re-assess genetic structure and to characterize a newly discovered, geographically disjunct population. Previous microsatellite marker analyses had identified seven distinct population genetic clusters across the region sampled; the analysis of this study showed that the newly discovered population (West Lake, Ontario) exhibits a divergent structure. COI haplotype analysis suggests that a single haplotype recolonized the Great Lakes and surrounding water bodies after the Wisconsinan glacial period, and subsequent fluctuation in water levels and habitat fragmentation resulted in divergence of genetic clusters. Although the novel West Lake population has a common ancestral source with other populations in the broader region, its divergent genetic signature merits its consideration as a separate conservation unit. The analyses of this study highlight the potential conservation implications of the discovery of new populations, particularly those of at-risk species, even within a region that has been genetically well characterized.

Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure.

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.

Development and characterization of thirteen novel microsatellite markers for use in Greenland sharks (Somniosus microcephalus), with cross-amplification in Pacific sleeper sharks (Somniosus pacificus).

OBJECTIVE: The objectives of this work are to isolate, develop, and characterize polymorphic microsatellite markers for use in Greenland sharks (Somniosus microcephalus). RESULTS: Thirteen microsatellite loci were successfully amplified and yielded multi-locus genotypes for 36 S. microcephalus individuals from Grise Fjord (n = 16) and Svalbard (n = 20). Each locus yielded between 2 and 9 alleles and observed heterozygosity ranged from 0.11 to 0.70 when estimated across both sites. One locus and three loci deviated from HWE following Bonferroni correction, for individuals sampled from Grise Fjord and Svalbard, respectively. Cross-amplification was successful at every locus for five of the ten S. pacificus individuals.

Vaginal Cuff Closure with Dual-Arm Robot and Near-Infrared Fluorescent Sutures.

This paper presents a dual-arm suturing robot. We extend the Smart Tissue Autonomous Robot (STAR) with a second robot manipulator, whose purpose is to manage loose suture thread, a task that was previously executed by a human assistant. We also introduce novel near-infrared fluorescent (NIRF) sutures that are automatically segmented and delimit the boundaries of the suturing task. During ex-vivo experiments of porcine models, our results demonstrate that this new system is capable of outperforming human surgeons in all but one metric for the task of vaginal cuff closure (porcine model) and is more consistent in every aspect of the task. We also present results to demonstrate that the system can perform a vaginal cuff closure during an in-vivo experiment (porcine model).

Scale performance and composition in a small Amazonian armored catfish, Corydoras trilineatus.

The cory catfishes (Callichthyidae) are small, South American armored catfishes with a series of dermal scutes that run the length of the fish from posterior to the parieto-supraoccipital down to the caudal peduncle. In this study, we explore the anatomy and functional performance of the armored scutes in the three-striped cory catfish, Corydoras trilineatus. The lateral surface has a dorsal and a ventral row of scutes that interact at the horizontal septum. The scutes have little overlap with sequential posterior scutes (~33% overlap) and a deep ridge in the internal surface that connects to the underlying soft tissue. The internal surface of C. trilineatus scutes is stiffer than the external surface, contrary to the findings in a related species of cory catfish, C. aeneus, which documented a hypermineralized, enamel-like, non-collagenous, hyaloine layer along the external surface of the scute. Clearing and staining of C. trilineatus scutes revealed that the scutes have highly mineralized (~50% mineralization) regions embedded in between areas of low mineralization along the posterior margin. Puncture tests showed that posterior scutes were weaker than both anterior and middle scutes, and scutes attached to the body required 50% more energy to puncture than isolated scutes. Corydoras trilineatus has the strongest armor in areas critical for protecting vital organs and the external armored scute receives synergistic benefits from interactions to the soft underlying tissue, which combine to provide a tough protective armor that still allows for flexible mobility.

Proximity of the Carotid Bifurcation to the Laryngeal Prominence: Results of a Cadaver Study and Recommendations for Safe Pulse Palpation.

BACKGROUND/PURPOSE: The carotid bifurcation (CB) is the location of the carotid sinus and the baroreceptors and is also a major site for atherosclerotic plaque formation. Health care providers have therefore been cautioned to avoid the CB during carotid pulse palpation (CPP) to prevent triggering the baroreflex, occluding an artery, or propagating a thrombus. Potential risks of adverse events during CPP may be greater for older adults due to age-related vascular changes and increased risk of baroreceptor hypersensitivity. The exact location of the CB relative to easily identifiable landmarks has, however, not been well-studied. The purpose of this descriptive study was to identify the location of the CB relative to key landmarks in a cadaver sample and to make recommendations allowing clinicians to avoid the CB during CPP. METHODS: The CB and other regional landmarks in 17 male and 20 female cadavers were exposed by dissection and pins were placed at all landmarks. Digital calipers were then used to measure the distance between the CB and all landmarks. RESULTS AND DISCUSSION: The mean vertical distance from the laryngeal prominence (LP) to the CB was 25.14 mm for females and 36.13 mm for males. No CBs were located below the LP. Ninety-four percent of female CBs and 100% of male CBs were located above the LP, and 74% of female subjects and 87% of male subjects had CBs greater than 20.00 mm superior to the LP. No clinically relevant relationships were found between the CB and any of the other measured landmarks. CONCLUSIONS: Based on this cadaver sample, CPP below the level of the LP in a supine individual would be unlikely to compress the CB and thus unlikely to trigger the baroreflex or occlude the region of greatest atherosclerotic buildup. If a pulse is not palpable below the LP, moving vertically up to 1 cm above the LP in a supine individual would be likely to compress the CB in only a small number of cases.

Functional cross talk between the Fanconi anemia and ATRX/DAXX histone chaperone pathways promotes replication fork recovery.

Fanconi anemia (FA) is a chromosome instability syndrome characterized by increased cancer predisposition. Specifically, the FA pathway functions to protect genome stability during DNA replication. The central FA pathway protein, FANCD2, locates to stalled replication forks and recruits homologous recombination (HR) factors such as CtBP interacting protein (CtIP) to promote replication fork restart while suppressing new origin firing. Here, we identify alpha-thalassemia retardation syndrome X-linked (ATRX) as a novel physical and functional interaction partner of FANCD2. ATRX is a chromatin remodeler that forms a complex with Death domain-associated protein 6 (DAXX) to deposit the histone variant H3.3 into specific genomic regions. Intriguingly, ATRX was recently implicated in replication fork recovery; however, the underlying mechanism(s) remained incompletely understood. Our findings demonstrate that ATRX forms a constitutive protein complex with FANCD2 and protects FANCD2 from proteasomal degradation. ATRX and FANCD2 localize to stalled replication forks where they cooperate to recruit CtIP and promote MRE11 exonuclease-dependent fork restart while suppressing the firing of new replication origins. Remarkably, replication restart requires the concerted histone H3 chaperone activities of ATRX/DAXX and FANCD2, demonstrating that coordinated histone H3 variant deposition is a crucial event during the reinitiation of replicative DNA synthesis. Lastly, ATRX also cooperates with FANCD2 to promote the HR-dependent repair of directly induced DNA double-stranded breaks. We propose that ATRX is a novel functional partner of FANCD2 to promote histone deposition-dependent HR mechanisms in S-phase.

Defending Political Theory After Burke: Stewart's Intellectual Disciplines and the Demotion of Practice.

To subject politics to "theory," "metaphysics," or "speculation" was disreputable in 1790s Britain, owing largely to the success of Edmund Burke's Reflections on the Revolution in France (1790), which linked these practices with enthusiasm. This fact is well established, but less studied are the means by which those committed to these forms of inquiry defended their intellectual conduct. Dugald Stewart's Elements of the Philosophy of the Human Mind (1792) was a pedagogical text that instructed the Scottish elite on how to govern their faculties; it was also a riposte to Burkean prudence, portraying the veneration of practice as theoretically naive.

Feature identification in time series data sets.

We present a computationally inexpensive, flexible feature identification method which uses a comparison of time series to identify a rank-ordered set of features in geophysically-sourced data sets. Many physical phenomena perturb multiple physical variables nearly simultaneously, and so features are identified as time periods in which there are local maxima of absolute deviation in all time series. Unlike other available methods, this method allows the analyst to tune the method using their knowledge of the physical context. The method is applied to a data set from a moored array of instruments deployed in the coastal environment of Monterey Bay, California, and a data set from sensors placed within the submerged Yax Chen Cave System in Tulum, Quintana Roo, Mexico. These example data sets demonstrate that the method allows for the automated identification of features which are worthy of further study.

Proteomic changes across a natural temperature gradient in a marine gastropod.

Responses of marine ectotherms to variable environmental temperature often entails maintanence of cellular homeostasis and physiological function through temperature compensation and physiological changes. We investigated the physiological response to thermal stress by examining proteomic changes in the marine kelp forest gastropod and emerging fisheries species Kellet's whelk (Kelletia kelletii) across a naturally-existing thermal gradient that ranges from a warmer-water site inside the species' native range and extends to the northern, cold-water edge of the range. We hypothesized that abundance of cellular stress response and energy metabolism proteins would increase with decreasing temperature in support of cold-compensation. Our exploratory proteomic analysis of whelk gill tissue (N = 6 whelks) from each of the four California Channel Island sites revealed protein abundance changes related to the cytoskeleton, energy metabolism/oxidative stress, and cell signaling. The changes did not correlate consistently with temperature. Nonetheless, whelks from the coldest island site showed increased abundance of energy metabolism and oxidative stress proteins, possibly suggesting oxidative damage of lipid membranes that is ameliorated by antioxidants and may aid in their cold stress response. Similarly, our exploratory analysis revealed abundances of cell signaling proteins that were higher at the coldest site compared to the warmest site, possibly indicating an importance for cell signaling regulation in relatively cooler environments. This study provides protein targets for future studies related to thermal effects in marine animals and may contribute to understanding the physiological response of marine organisms to future ocean conditions.

Parallel evolutionary forces influence the evolution of male and female songs in a tropical songbird.

Given the important role that animal vocalizations play in mate attraction and resource defence, acoustic signals are expected to play a significant role in speciation. Most studies, however, have focused on the acoustic traits of male animals living in the temperate zone. In contrast to temperate environments, in the tropics, it is commonplace for both sexes to produce complex acoustic signals. Therefore, tropical birds offer the opportunity to compare the sexes and provide a more comprehensive understanding of the evolution of animal signals. In this study, we quantified patterns of acoustic variation in Rufous-and-white Wrens (Thryophilus rufalbus) from five populations in Central America. We quantified similarities and differences between male and female songs by comparing the role that acoustic adaptation, cultural isolation and neutral genetic divergence have played in shaping acoustic divergence. We found that males and females showed considerable acoustic variation across populations, although females exhibited greater population divergence than males. Redundancy analysis and partial-redundancy analysis revealed significant relationships between acoustic variation and ecological variables, genetic distance, and geographic distance. Both ambient background noise and geographic distance explained a high proportion of variance for both males and females, suggesting that both acoustic adaptation and cultural isolation influence song. Overall, our results indicate that parallel evolutionary forces act on male and female acoustic signals and highlight the important role that cultural drift and selection play in the evolution of both male and female songs.

Nanotechnology in orthopedics: a clinically oriented review.

The utility of nanotechnology in medicine, specifically within the field of orthopedics, is a topic of extensive research. Our review provides a unique comprehensive overview of the current and potential future uses of nanotechnology with respect to orthopedic sub-specialties. Nanotechnology offers an immense assortment of novel applications, most notably the use of nanomaterials as scaffolds to induce a more favorable interaction between orthopedic implants and native bone. Nanotechnology has the capability to revolutionize the diagnostics and treatment of orthopedic surgery, however the long-term health effects of nanomaterials are poorly understood and extensive research is needed regarding clinical safety.

Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries.

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom-designed group-specific primer set and next-generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.

Origins of the Greenland shark (Somniosus microcephalus): Impacts of ice-olation and introgression.

Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub-Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial-interglacial cycles. We propose that the initial S. microcephalus-S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period-which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale.