Salt marshes are delicate landforms at the boundary between the sea and land. These ecosystems support a diverse biota that modifies the erosive characteristics of the substrate and mediates sediment ...transport processes. Here we present a broad overview of recent numerical models that quantify the formation and evolution of salt marshes under different physical and ecological drivers. In particular, we focus on the coupling between geomorphological and ecological processes and on how these feedbacks are included in predictive models of landform evolution. We describe in detail models that simulate fluxes of water, organic matter, and sediments in salt marshes. The interplay between biological and morphological processes often produces a distinct scarp between salt marshes and tidal flats. Numerical models can capture the dynamics of this boundary and the progradation or regression of the marsh in time. Tidal channels are also key features of the marsh landscape, flooding and draining the marsh platform and providing a source of sediments and nutrients to the marsh ecosystem. In recent years, several numerical models have been developed to describe the morphogenesis and long‐term dynamics of salt marsh channels. Finally, salt marshes are highly sensitive to the effects of long‐term climatic change. We therefore discuss in detail how numerical models have been used to determine salt marsh survival under different scenarios of sea level rise.
Key Points
Coupling between geomorphology and ecology is critical in salt marshes
Need to quantify the feedbacks between vegetation and sediment transport
Numerical models can predict the survival of salt marshes under sea level rise
Surgical skin flaps are frequently used in plastic and reconstructive surgery to repair acquired or congenital defects. Necrosis is a common complication associated with these flaps postoperatively ...as a result of inadequate blood supply. Stem cells are precursor cells with the potential to differentiate into more specialized cells. Angiogenic factors act to direct cellular differentiation and organization to form new vascular elements. Our theory was that the combination of angiogenic growth factors with stem cells derived from the subject preoperatively would augment neovascularization, thereby increasing blood supply to the flap, which may ultimately improve flap survival. In phase I, 40 Lewis rats were randomized into 4 groups of 10. Random dorsal skin flaps were elevated and treated at the same time. The first group was injected with only medium, the second with stem cells, the third with stem cells and angiogenic factors, and the fourth with angiogenic growth factors. Millimetric measurements of flap viability at 7 and 14 days did not show any statistically significant differences between the studied groups. In phase II, 24 rats were also randomized into 4 groups of 6, but this time were treated 1 week before flap elevation. The viability measurements showed an increased rate of viability in the group in which stem cells and the angiogenic factors were administered simultaneously (84.5% +/- 3.2%) as compared with the unmodified control group (62.6% +/- 7.3%) or to the groups in which only precursor cells (60.4% +/- 7.9%) or angiogenic factors (62.3%+/- 10.1%). Increased blood supply brought by these manipulations is believed translated to increased tissue flap survival. Punch biopsies showed that "green fluorescent protein"-labeled precursor cells was noted to form luminal structures in the treated flaps. The vascular cast of all flaps was filled with Mercox plastic resin. After euthanasia, the soft tissues of the harvested flaps were dissolved and the remaining vascular cast was weighted. The weight-based ratio of the vascular composition was determined. The flaps injected with both stem cells and angiogenic factors showed higher values. We conclude that the administration of bone marrow stem cells with angiogenic factors 1 week before flap creation improves the survival of ischemic random skin flaps.
We surveyed male breeding birds in five habitats (bottomland forest, maritime oak Quercus spp., pine Pinus spp. forest, maritime shrub, saltmarsh) of coastal Georgia, USA using distance-sampling ...methods to estimate population densities. We examined species-habitat relationships using indicator species analysis (ISA). Acadian Flycatcher (Empidonax virescens) in bottomland forest, Northern Parula (Parula americana) in maritime oak, Brown-headed Nuthatch (Sitta pusilla) in pine forest, Clapper Rail (Rallus longirostris) in saltmarsh, and White-eyed Vireo (Vireo griseus) in shrub habitat ranked highest for Partners in Flight (PIF) priority species by densities. The ISA indicated fewer PIF priority species were associated with saltmarsh, but more species (6) were unique to saltmarsh than any other habitat. Indicator species occurred more often in maritime oak than bottomland forest (8 vs. 6), but both habitats had similar numbers of PIF priority species (4). Shrub habitat covered the smallest area (∼0.2%) and had three PIF priority species, including Painted Bunting (Passerina ciris), the only PIF species with extremely high priority in this study.
Abstract
Background
We aimed to evaluate a testing program to facilitate control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission at a large university and measure spread ...in the university community using viral genome sequencing.
Methods
Our prospective longitudinal study used remote contactless enrollment, daily mobile symptom and exposure tracking, and self-swab sample collection. Individuals were tested if the participant was exposed to a known SARS-CoV-2-infected person, developed new symptoms, or reported high-risk behavior (such as attending an indoor gathering without masking or social distancing), if a member of a group experiencing an outbreak, or at enrollment. Study participants included students, staff, and faculty at an urban public university during the Autumn quarter of 2020.
Results
We enrolled 16 476 individuals, performed 29 783 SARS-CoV-2 tests, and detected 236 infections. Seventy-five percent of positive cases reported at least 1 of the following: symptoms (60.8%), exposure (34.7%), or high-risk behaviors (21.5%). Greek community affiliation was the strongest risk factor for testing positive, and molecular epidemiology results suggest that specific large gatherings were responsible for several outbreaks.
Conclusions
A testing program focused on individuals with symptoms and unvaccinated persons who participate in large campus gatherings may be effective as part of a comprehensive university-wide mitigation strategy to control the spread of SARS-CoV-2.
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage ...genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.
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•More than 40,000 small gene families predicted in phages from diverse environments•More than 5,000 small gene families predicted to encode anti-CRISPR proteins•More than 9,000 small gene families predicted to encode secreted or transmembrane proteins•Identified novel core phage proteins like baseplate proteins and phage tail proteins
Fremin et al. use comparative genomics to predict more than 40,000 small-gene families in phage from diverse environments. Small genes are approximately 3-fold more prevalent in phage than prokaryotic genomes. This resource includes more than 5,000 anti-CRISPR small-gene families and more than 9,000 secreted or transmembrane small-gene families.
Many wetland restoration projects occur on former agricultural soils that have a history of disturbance and fertilization, making them prone to phosphorus (P) release upon flooding. To study the ...relationship between P release and hydrologic regime, we collected soil cores from three restoration wetlands and three undisturbed wetlands around Upper Klamath Lake in southern Oregon, U.S.A. Soil cores were subjected to one of three hydrologic regimes—flooded, moist, and dry—for 7.5 weeks, and P fluxes were measured upon reflooding. Soils from restoration wetlands released P upon reflooding regardless of the hydrologic regime, with the greatest releases coming from soils that had been flooded or dried. Undisturbed wetland soils released P only after drying. Patterns in P release can be explained by a combination of physical and biological processes, including the release of iron‐bound P due to anoxia in the flooded treatment and the mineralization of organic P under aerobic conditions in the dry treatment. Higher rates of soil P release from restoration wetland soils, particularly under flooded conditions, were associated with higher total P concentrations compared with undisturbed wetland soils. We conclude that maintaining moist soil is the means to minimize P release from recently flooded wetland soils. Alternatively, prolonged flooding provides a means of liberating excess labile P from former agricultural soils while minimizing continued organic P mineralization and soil subsidence.
Elevated mercury concentrations have been reported in fish and wildlife from the Everglades in recent years. The hypothesis that eutrophication caused by the impact of phosphorous- (P) rich ...agricultural runoff stimulated methylmercury accumulation was put forward because eutrophication had been shown to be a cause for methylmercury accumulation in other ecosystems. We tested this hypothesis by obtaining total mercury (HgT) concentrations and accumulation rates and estimating the potential for microbial methylation and methylmercury degradation in peat soils collected along a P gradient in water conservation area 2A (WCA-2A). A negative correlation observed between HgT and P concentrations in soils (r 2 = 0.64) was explained by increased peat accretion rates in a nutrient-enriched area (7.1−7.5 mm yr-1) as compared to an unenriched area (1.92−2.50 mm yr-1), estimated using lead-210 and cesium-137 dating. Total Hg accumulation rates (post-1964) were comparable for the enriched and unenriched sites (29−30 and 29−37 μg m-2 yr-1, respectively). Thus, calculations of HgT accumulation rates are confounded by differences in peat accretion rates in the Everglades. Potential rates for both methylation (2.3−48.6 ng g-1 day-1) and demethylation (6.5−113.2 ng g-1 day-1) were higher in samples from WCA-2A than in samples collected in an area of the Everglades that had never been exposed to nutrients. However, trends suggesting the relationships of these activities to the P gradient in WCA-2A were not detected, and methylation to demethylation ratios did not correlate with soil P concentrations. The results suggest that (i) nutrient-enriched agricultural runoff originating upstream of WCA-2A did not contribute significantly to HgT built up in the northern Everglades and (ii) eutrophication did not affect the potential for net methylmercury formation in peat soils.
Home electronic incarceration, otherwise known as HEI, is an alternative to traditional incarceration. HEI allows inmates who meet certain qualifications, including stable residency, employment, and ...nonviolent offenses, to serve their sentence from their residence rather than in jail. Before the onset of the COVID-19 pandemic in 2020, the Albemarle-Charlottesville Regional Jail (ACRJ) maintained a restricted capacity for HEI, primarily extending this opportunity to frequent offenders who met the qualifications above (Dornfeld et al., 2023). At the advent of COVID-19, ACRJ increased their capacity and use of HEI to reduce the number of occupants in the jail and, as a result, mitigate contagion risk (Kumer, 2023). Following the expansion of the HEI program, (Dornfeld et al., 2023) discovered that HEI participants had lower reoffense rates than jail-sentenced counterparts who committed similar crimes. Currently, HEI participants are determined from information gleaned from their files or by court order (Kumer, 2023). To streamline this selection process and increase the participation of inmates benefitting from HEI, factors were investigated that correlate with HEI's success. This research will assist jail administration in identifying candidates who will gain the most from HEI and recommend those offenders to the program.The methods consist of quantitative analysis of booking data acquired from ACRJ along with insight and guidance from contacts at Region Ten Community Services, an organization dedicated to working with those affected by mental illnesses, substance abuse, and/or developmental disabilities. Additionally, Offender and Aid Restoration- Jefferson Area Community Corrections (OAR-JACC) provided a meaningful understanding of the project. The quantitative analysis focuses on factors that may correlate with HEI violations and changes in recidivism rates including criminal history, current charge, mental health, employment, and gender.Factors were identified and analyzed that increase the likelihood of an inmate successfully completing their HEI sentence without violation, using the improved stability provided by HEI to prevent recidivism. These factors formulate sentencing recommendations for ACRJ's decision-making process.
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