We track and analyze the re-situation of scientific knowledge in the field of human population genomics ancestry studies. We understand re-situation as a process of accommodating the direct or indirect transfer of objects of knowledge from one site/situation to (one or many) other sites/situations. Our take on the concept borrows from Mary S. Morgan's work on facts traveling while expanding it to include other objects of knowledge such as models, data, software, findings, and visualizations. We structure a specific case study by tracking the re-situation of these objects between three research projects studying human population diversity reported in three articles in Science, Genome Research and PLoS Genetics between 2002 and 2005. We characterize these three engagements as a unit of analysis, a "skirmish," in order to compare: (a) the divergence of interests in how life-scientists answer similar research questions and (b) to track the challenging transformation of workflows in research laboratories as these scientific objects are re-situated individually or in bundles. Our analysis of the case study shows that an accurate understanding of re-situation requires tracking the whole bundle of objects in a project because they interact in particular key ways. The absence or dismissal of these interactions opens the door to unforeseen trade-offs, misunderstandings and misrepresentations about research design(s) and workflow(s) and what these say about the questions asked and the findings produced.

Recent outbreaks of chytridiomycosis, the disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have contributed to population declines of numerous amphibian species worldwide. The devastating impacts of this disease have led researchers to attempt drastic conservation measures to prevent further extinctions and loss of biodiversity. The conservation measures can be labour-intensive or expensive, and in many cases have been unsuccessful. We developed a mathematical model of Bd outbreaks that includes the effects of demographic stochasticity and within-host fungal load dynamics. We investigated the impacts of one-time treatment conservation strategies during the disease outbreak that occurs following the initial arrival of Bd into a previously uninfected frog population. We found that for all versions of the model, for a large fraction of parameter space, none of the one-time treatment strategies are effective at preventing disease-induced extinction of the amphibian population. Of the strategies considered, treating frogs with antifungal agents to reduce their fungal load had the greatest likelihood of a beneficial outcome and the lowest risk of decreasing the persistence of the frog population, suggesting that this disease mitigation strategy should be prioritized over disinfecting the environment or reducing host density.

© 2016 The Author(s). Larvae of intertidal species develop at sea and must return to adult habitats to replenish populations. Similarly, nutrients, detritus and plankton provide important subsidies spurring growth and reproduction of macroalgae and filter-feeding invertebrates that form the foundation of intertidal communities. Together, these factors determine the density and intensity of interactions among community members. We hypothesized that spatial variation in surfzone hydrodynamics affects the delivery of plankton subsidies. We compared entire zooplankton communities inside and outside the surf zone daily while monitoring physical conditions for one month each at two shores with different surfzone characteristics. Opposite cross-shore distributions of larvae and other zooplankters occurred at the two sites: zooplankton was much more abundant inside the mildly sloping dissipative surf zone (DSZ) with rip currents and was more abundant outside the steep reflective surf zone (RSZ). Biophysical numerical simulations demonstrated that zooplankters were concentrated in rip channels of the DSZ and were mostly unable to enter the RSZ, indicating the hydrodynamic processes behind the observed spatial variation of zooplankters in the surf zone. Differences in the concentration of larvae and other zooplankters between the inner shelf and surf zone may be an underappreciated, key determinant of spatial variation in inshore communities.

Larvae of many intertidal species develop offshore and must cross the surf zone to complete their onshore migration to adult habitats. Depending on hydrodynamics, the surf zone may limit this migration, especially on reflective rocky shores. As a logistically tractable analog of a rocky shore environment, we carried out a comprehensive biological and physical study of the hydrodynamics of a steep reflective sandy beach. Holoplankton and precompetent larval invertebrates were much less abundant within the surf zone than offshore, and their concentrations inside and outside the surf zone were not significantly correlated, suggesting that they were not entering the surf zone. Persistent offshore flow throughout the water column at the outer edge of the surf zone may prevent these organisms from entering the surf zone. In contrast, the concentrations of detritus and a competent larval invertebrate (i.e. cyprids), while also not significantly correlated with concentrations offshore, were frequently more concentrated in the surf zone than offshore. Within the surf zone, the concentration of detritus was significantly correlated with concentrations of competent larval invertebrates (barnacles, gastropods, polychaetes, and bopyrid amphipod) and organisms that may be associated with detritus (amphipods and harpacticoid copepods). These concentrations were significantly negatively correlated with average daily wave height. We hypothesize that detritus and larvae enter the surf zone near the bottom during calm wave conditions by a process of near-bottom streaming. Near-bottom streaming is associated with all surf zones and may be a general mechanism for onshore transport of larvae close to the coast.

The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.

Identifying biophysical mechanisms of larval transport is essential to understanding the delivery of larvae to adult habitats. In addition, harmful algal blooms (HABs) can be transported onshore from populations that form offshore. In summer 2011, we measured sea surface and bottom temperatures and daily phytoplankton abundance and intertidal cyprid (barnacle post larvae) settlement at Carmel River State Beach, California, USA. Using time-series analysis, we compared the abundance of Pseudo-nitzschia spp. and daily cyprid settlement to physical forcing mechanisms (e.g. internal tides and upwelling-relaxation events) that could generate onshore delivery. Minimum bottom water temperature was significantly cross-correlated with the spring-neap tidal cycle; minimum temperatures occurred between neap and spring tides, and maximum temperatures were recorded around neap tides. When the temperature data were transformed to remove the relationship between tides and temperature, we found significantly higher maximum sea surface temperatures during upwelling-relaxation events. We observed 4 pulses in Pseudo-nitzschia spp. abundance. Pseudo-nitzschia spp. chains were longest at the start of pulses and then decreased, suggesting that they had been transported to shore from a more productive site offshore, likely the upwelling front. Pulses occurred during periods of maximum sea surface temperature associated with upwelling-relaxation events. In contrast, cyprid settlement was significantly cross-correlated with the spring-neap tidal cycle, with settlement peaks occurring during fortnightly periods of cold bottom temperatures; onshore transport of cyprids appears to have been due to the internal tides. © Inter-Research 2014.

Surf zone hydrodynamics vary along shorelines potentially affecting the delivery of larvae and zooplankton subsidies to intertidal communities, and, hence, the intensity of postsettlement interactions, growth and reproduction of filter-feeding foundation species and planktivorous fishes. We investigated the ability of zooplankton assemblages to enter the wide surf zone of the rip-channeled, more dissipative beach at Sand City, California, and the narrow surf zone of the steep reflective beach at nearby Carmel River State Beach. Every day for a month, we surveyed zooplankton inside and outside the surf zone and concomitant larval settlement of the dominant invertebrate onshore at each site in this upwelling regime. At the more dissipative surf zone, all zooplankters were far more concentrated inside than outside the surf zone. Many taxa increased in the surf zone and the predominant invertebrate on beaches, Emerita analoga, settled abundantly when prevailing northwesterly winds relaxed and waves were small. At the reflective surf zone, concentrations of zooplankters of most taxa were far greater outside than inside the surf zone, and many taxa increased in the surf zone when waves were small. Twice as many taxa were positively correlated inside and outside the surf zone at the dissipative than the reflective surf zone, indicating that zooplankters were more freely exchanged although behavior also played a role. Thus, spatial and temporal variation in surf zone hydrodynamics may regulate subsidies of zooplankton food and larval recruits to nearshore communities with potential cascading effects on community dynamics and structure.

Most harmful algal blooms (HAB) originate away from the shore and, for them to endanger human health, they must be first transported to shore after which they must enter the surf zone where they can be feed upon by filter feeders. The last step in this sequence, entrance into the surf zone, depends on surf zone hydrodynamics. During two 30-day periods, we sampled Pseudo-nitzschia and particulate domoic acid (pDA) in and offshore of a more dissipative surf zone at Sand City, California (2010) and sampled Pseudo-nitzschia in and out of reflective surf zones at a beach and rocky shores at Carmel River State Beach, California (2011). At Sand City, we measured domoic acid in sand crabs, Emerita analoga. In the more dissipative surf zone, concentrations of Pseudo-nitzschia and pDA were an order of magnitude higher in samples from a rip current than in samples collected just seaward of the surf zone and were 1000 times more abundant than in samples from the shoals separating rip currents. Domoic acid was present in all the Emerita samples and varied directly with the concentration of pDA and Pseudo-nitzschia in the rip current. In the more reflective surf zones, Pseudo-nitzschia concentrations were 1-2 orders of magnitude lower than in samples from 125 and 20m from shore. Surf zone hydrodynamics affects the ingress of Pseudo-nitzschia into surf zones and the exposure of intertidal organisms to HABs on the inner shelf.

BACKGROUND: 1.8 million Veterans are estimated to need legal services, such as for housing eviction prevention, discharge upgrades, and state and federal Veterans benefits. While having ones legal needs met is known to improve ones health and its social determinants, many Veterans legal needs remain unmet. Public Law 116-315 enacted in 2021 authorizes VA to fund legal services for Veterans (LSV) by awarding grants to legal service providers including nonprofit organizations and law schools legal assistance programs. This congressionally mandated LSV initiative will award grants to about 75 competitively selected entities providing legal services. This paper describes the protocol for evaluating the initiative. The evaluation will fulfill congressional reporting requirements, and inform continued implementation and sustainment of LSV over time. METHODS: Our protocol calls for a prospective, mixed-methods observational study with a repeated measures design, aligning to the Reach Effectiveness Adoption Implementation Maintenance (RE-AIM) and Integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) frameworks. In 2023, competitively selected legal services-providing organizations will be awarded grants to implement LSV. The primary outcome will be the number of Veterans served by LSV in the 12 months after the awarding of the grant. The evaluation has three Aims. Aim 1 will focus on measuring primary and secondary LSV implementation outcomes aligned to RE-AIM. Aim 2 will apply the mixed quantitative-qualitative Matrixed Multiple Case Study method to identify patterns in implementation barriers, enablers, and other i-PARIHS-aligned factors that relate to observed outcomes. Aim 3 involves a mixed-methods economic evaluation to understand the costs and benefits of LSV implementation. DISCUSSION: The LSV initiative is a new program that VA is implementing to help Veterans who need legal assistance. To optimize ongoing and future implementation of this program, it is important to rigorously evaluate LSVs outcomes, barriers and enablers, and costs and benefits. We have outlined the protocol for such an evaluation, which will lead to recommending strategies and resource allocation for VAs LSV implementation.

Surf zones, regions of breaking waves, are at the interface between the shore and coastal ocean. Surf zone hydrodynamics may affect delivery of phytoplankton subsidies to the intertidal zone. Over a month of daily sampling at an intermediate surf zone with bathymetric rip currents and a reflective surf zone, we measured surf zone hydrodynamics and compared concentrations of coastal phytoplankton taxa in the surf zones to concentrations offshore. At the intermediate surf zone, ~80% of the variability in the concentration of coastal phytoplankton taxa within the surf zone was explained by their variation offshore; however, concentrations were much higher and lower than those offshore in samples from a bathymetric rip current and over the adjacent shoal, respectively. Hydrodynamics at this intermediate surf zone did not hinder the delivery of coastal phytoplankton to the surf zone, but the bathymetric rip current system appeared to redistribute phytoplankton concentrating them within eddies. At the reflective shore, we sampled surf zones at a beach and two adjacent rocky intertidal sites. Concentrations of typical coastal phytoplankton taxa were usually an order of magnitude or more lower than those offshore, even when offshore samples were collected just 20 m beyond the breakers. The phytoplankton assemblages inside and outside the surf zone often appeared to be disconnected. Surf zone hydrodynamics at the steep, reflective shore coupled with low phytoplankton concentrations in near-surface water appeared to limit delivery of phytoplankton subsidies to the surf zone. Surf zone hydrodynamics may be a key factor in the alongshore variation in phytoplankton subsidies to coastal communities.