Metrics reloaded: Pitfalls and recommendations for image analysis validation

The field of automatic biomedical image analysis crucially depends on robust and meaningful performance metrics for algorithm validation. Current metric usage, however, is often ill-informed and does not reflect the underlying domain interest. Here, we present a comprehensive framework that guides researchers towards choosing performance metrics in a problem-aware manner. Specifically, we focus on biomedical image analysis problems that can be interpreted as a classification task at image, object or pixel level. The framework first compiles domain interest-, target structure-, data set- and algorithm output-related properties of a given problem into a problem fingerprint, while also mapping it to the appropriate problem category, namely image-level classification, semantic segmentation, instance segmentation, or object detection. It then guides users through the process of selecting and applying a set of appropriate validation metrics while making them aware of potential pitfalls related to individual choices. In this paper, we describe the current status of the Metrics Reloaded recommendation framework, with the goal of obtaining constructive feedback from the image analysis community. The current version has been developed within an international consortium of more than 60 image analysis experts and will be made openly available as a user-friendly toolkit after community-driven optimization

Shoreline Dynamics Along a Developed River Mouth Barrier Island: Multi-Decadal Cycles of Erosion and Event-Driven Mitigation

Human modifications in response to erosion have altered the natural transport of sediment to and across the coastal zone, thereby potentially exacerbating the impacts of future erosive events. Using a combination of historical shoreline-change mapping, sediment sampling, three-dimensional beach surveys, and hydrodynamic modeling of nearshore and inlet processes, this study explored the feedbacks between periodic coastal erosion patterns and associated mitigation responses, focusing on the open-ocean and inner-inlet beaches of Plum Island and the Merrimack River Inlet, Massachusetts, United States. Installation of river-mouth jetties in the early 20th century stabilized the inlet, allowing residential development in northern Plum Island, but triggering successive, multi-decadal cycles of alternating beach erosion and accretion along the inner-inlet and oceanfront beaches. At a finer spatial scale, the formation and southerly migration of an erosion “hotspot” (a setback of the high-water line by ∼100 m) occurs regularly (every 25–40 years) in response to the refraction of northeast storm waves around the ebb-tidal delta. Growth of the delta progressively shifts the focus of storm wave energy further down-shore, replenishing updrift segments with sand through the detachment, landward migration, and shoreline-welding of swash bars. Monitoring recent hotspot migration (2008–2014) demonstrates erosion (\u3e30,000 m3 of sand) along a 350-m section of beach in 6 months, followed by recovery, as the hotspot migrated further south. In response to these erosion cycles, local residents and governmental agencies attempted to protect shorefront properties with a variety of soft and hard structures. The latter have provided protection to some homes, but enhanced erosion elsewhere. Although the local community is in broad agreement about the need to plan for long-term coastal changes associated with sea-level rise and increased storminess, real-time responses have involved reactions mainly to short-term (years) erosion threats. A collective consensus for sustainable management of this area is lacking and the development of a longer-term adaptive perspective needed for proper planning has been elusive. With a deepening understanding of multi-decadal coastal dynamics, including a characterization of the relative contributions of both nature and humans, we can be more optimistic that adaptations beyond mere reactions to shoreline change are achievable

Understanding Refugees\u27 Perspectives on Health Care

Introduction. Burlington, Vermont accepts refugees from around the world. These individuals face unique barriers to accessing healthcare due to language, culture and finances. Research suggests that cultural beliefs about healthcare can affect ability or willingness to seek medical care. Gaining a better understanding of refugee perspectives of the healthcare system may offer insight into how to rectify this issue. Objectives. The goal of this study was to learn about refugee perspectives of the healthcare system and assess their use of services. Methods. We surveyed a convenience sample of 24 refugees to learn more about thoughts and practices surrounding healthcare and the use of the medical system. Results. Survey findings suggested that refugees who had been living in the US for longer than one year access healthcare resources differently from more recent arrivals. Most respondents agreed that reasons for going to a healthcare provider revolved around the diagnosis and treatment of current ailments. Regardless of time spent in the U.S., most respondents were unlikely to seek out preventive care. Refugees who had been in the U.S. longer than one year were less likely to seek out emergency services for acute symptoms that would be better served by a visit with their PCP. Conclusions. Recent arrivals used the emergency room for primary care needs more than those living in the U.S. longer than one year, suggesting the efficacy of provided health education. Study data suggests an important area for improvement may be increased education for refugees about the importance of preventive care.https://scholarworks.uvm.edu/comphp_gallery/1250/thumbnail.jp

Overcoming early career barriers to interdisciplinary climate change research

Climate-change impacts are among the most serious and complex challenges facing society, affecting both natural and social systems. Addressing these requires a new paradigm of interdisciplinary collaboration which incorporates tools, techniques, and insights from across the social, natural, and engineering sciences. Yet, a wide range of intrinsic and extrinsic hurdles need to be overcome to conduct successful, integrated interdisciplinary research. The results of a bibliometric analysis and survey of early to mid-career scientists from 56 countries who were involved with the interdisciplinary DISsertations initiative for the advancement of Climate Change ReSearch (DISCCRS) emphasize the particular challenges faced by early career researchers. Survey respondents perceive conflict between the need for interdisciplinary climate-change research and its potential detriment to career advancement. However, participation in interventions for early career scientists, such as networking and training symposia, had both perceived and measurable impacts on the likelihood of engagement in climate-centric interdisciplinary research. Respondents also ranked alternative mechanisms for encouraging incorporation of interdisciplinary science at early career stages, prioritizing funding of interdisciplinary seed grants, fellowships, and junior faculty networks, interdisciplinary teamwork and communication training, and interdepartmental symposia. To this we add the suggestion that interdisciplinarity be incorporated into tenure and promotion evaluations through the use of exploratory science mapping tools. Despite the need to foster interdisciplinary research and the availability of multiple prospective solutions, there remain expansive structural challenges to its promotion and recognition which, unless collectively addressed, will continue to hinder its potential growth and application to climate-change science

Tidal erosion and upstream sediment trapping modulate records of land-use change in a formerly glaciated New England estuary

Land clearing, river impoundments, and other human modifications to theupland landscape and within estuarine systems can drive coastal change at local to regionalscales. However, as compared with mid-latitude coasts, the impacts of human modificationsalong sediment-starved formerly glaciated coastal landscapes are relatively understudied.To address this gap, we present a late-Holocene record of changing sediment accumulationrates and sediment sources from sediment cores collected across a tidal flat in theMerrimack River estuary (Mass., USA). We pairsedimentology, geochronology, bulk- andstable-isotope organic geochemistry, and hydrodynamic simulations with historical datato evaluate human and natural impacts on coastal sediment fluxes. During the 17th to19th centuries, accumulation rates increased by an order of magnitude in the central tidalflat, likely in response to enhanced delivery of terrestrial sediment resulting from uplanddeforestation. However, the overall increase in accumulation (0.56–2.6 mm/year) withinthe estuary is subtle and spatially variableacross the tidal flats because of coincidentanthropogenic land clearing and dam building, upland sediment storage, and estuarinehydrodynamics. This study provides insight into the response of formerly glaciated fluvial-coastal systems to human modifications, and underscores the role of estuarine environmen-tal conditions in modifying upland signals of land-use change

Following the Sand Grains

When longshore transport systems encounter tidal inlets, complex mechanisms are involved in bypassing sand to downdrift barriers. Here, this process is examined at Plum Island Sound and Essex Inlets, Massachusetts, USA. One major finding from this study is that sand is transferred along the coast—especially at tidal inlets—by parcels, in discrete steps, and over decadal-scale periods. The southerly orientation of the main-ebb channel at Plum Island Sound, coupled with the landward migration of bars from the ebb delta to the central portion of the downdrift Castle Neck barrier island, have formed a beach protuberance. During the constructional phase, sand is sequestered at the protuberance and the spit-end of the barrier becomes sediment starved, leading to shoreline retreat and a broadening of the spit platform at the mouth to Essex Bay (downdrift side of Castle Neck). Storm-induced sand transport from erosion of the spit and across the spit platform is washed into Essex Bay, filling channels and enlarging flood deltas. This study illustrates the pathways and processes of sand transfer along the shoreline of a barrier-island/tidal-inlet system and provides an important example of the processes that future hydrodynamic and sediment-transport modeling should strive to replicate

Complex coastal change in response to autogenic basin infilling: An example from a sub-tropical Holocene strandplain

Thick bay-fill sequences that often culminate in strandplain development serve as important sedimentary archives of land-ocean interaction, although distinguishing between internal and external forcings is an ongoing challenge. This study employs sediment cores, ground-penetrating radar surveys, radiocarbon dates, palaeogeographic reconstructions and hydrodynamic modelling to explore the role of autogenic processes - notably a reduction in wave energy in response to coastal embayment infilling - in coastal evolution and shoreline morphodynamics. Following a regional 2 to 4m highstand at ca 58ka, the 75km(2) Tijucas Strandplain in southern Brazil built from fluvial sediments deposited into a semi-enclosed bay. Holocene regressive deposits are underlain by fluvial sands and a Pleistocene transgressive-regressive sequence, and backed by a highstand barrier-island. The strandplain is immediately underlain by 5 to 16m of seaward-thickening, fluvially derived, Holocene-age, basin-fill mud. Several trends are observed from the landward (oldest) to the seaward (youngest) sections of the strandplain: (i) the upper shoreface and foreshore become finer and thinner and shift from sand-dominated to mud-dominated; (ii) beachface slopes decrease from \u3e11 degrees to ca 7 degrees; and (iii) progradation rates increase from 04 to 18myr(-1). Hydrodynamic modelling demonstrates a correlation between progressive shoaling of Tijucas Bay driven by sea-level fall and sediment infilling and a decrease in onshore wave-energy transport from 18 to 4kWm(-1). The combination of allogenic (sediment supply, falling relative sea-level and geology) and autogenic (decrease in wave energy due to bay shoaling) processes drove the development of a regressive system with characteristics that are rare, if not unique, in the Holocene and rock records. These findings demonstrate the complexities in architecture styles of highstand and regressive systems tracts. Furthermore, this article highlights the diverse internal and external processes and feedbacks responsible for the development of these intricate marginal marine sedimentary systems

Climate-induced variability in South Atlantic wave direction over the past three millennia

Through alteration of wave-generating atmospheric systems, global climate changes play a fundamental role in regional wave climate. However, long-term wave-climate cycles and their associated forcing mechanisms remain poorly constrained, in part due to a relative dearth of highly resolved archives. Here we use the morphology of former shorelines preserved in beach-foredune ridges (BFR) within a protected embayment to reconstruct changes in predominant wave directions in the Subtropical South Atlantic during the last ~ 3000 years. These analyses reveal multi-centennial cycles of oscillation in predominant wave direction in accordance with stronger (weaker) South Atlantic mid- to high-latitudes mean sea-level pressure gradient and zonal westerly winds, favouring wave generation zones in higher (lower) latitudes and consequent southerly (easterly) wave components. We identify the Southern Annular Mode as the primary climate driver responsible for these changes. Long-term variations in interhemispheric surface temperature anomalies coexist with oscillations in wave direction, which indicates the influence of temperature-driven atmospheric teleconnections on wave-generation cycles. These results provide a novel geomorphic proxy for paleoenvironmental reconstructions and present new insights into the role of global multi-decadal to multi-centennial climate variability in controlling coastal-ocean wave climate

High-frequency ultrasonic speckle velocimetry in sheared complex fluids

High-frequency ultrasonic pulses at 36 MHz are used to measure velocity profiles in a complex fluid sheared in the Couette geometry. Our technique is based on time-domain cross-correlation of ultrasonic speckle signals backscattered by the moving medium. Post-processing of acoustic data allows us to record a velocity profile in 0.02--2 s with a spatial resolution of 40 $\mu$m over 1 mm. After a careful calibration using a Newtonian suspension, the technique is applied to a sheared lyotropic lamellar phase seeded with polystyrene spheres of diameter 3--10 $\mu$m. Time-averaged velocity profiles reveal the existence of inhomogeneous flows, with both wall slip and shear bands, in the vicinity of a shear-induced ``layering'' transition. Slow transient regimes and/or temporal fluctuations can also be resolved and exhibit complex spatio-temporal flow behaviors with sometimes more than two shear bands.Comment: 15 pages, 18 figures, submitted to Eur. Phys. J. A