Dam builders and their works: Beaver influences on the structure and function of river corridor hydrology, geomorphology, biogeochemistry and ecosystems

Beavers (Castor fiber, Castor canadensis) are one of the most influential mammalian ecosystem engineers, heavily modifying river corridor hydrology, geomorphology, nutrient cycling, and ecosystems. As an agent of disturbance, they achieve this first and foremost through dam construction, which impounds flow and increases the extent of open water, and from which all other landscape and ecosystem impacts follow. After a long period of local and regional eradication, beaver populations have been recovering and expanding throughout Europe and North America, as well as an introduced species in South America, prompting a need to comprehensively review the current state of knowledge on how beavers influence the structure and function of river corridors. Here, we synthesize the overall impacts on hydrology, geomorphology, biogeochemistry, and aquatic and terrestrial ecosystems. Our key findings are that a complex of beaver dams can increase surface and subsurface water storage, modify the reach scale partitioning of water budgets, allow site specific flood attenuation, alter low flow hydrology, increase evaporation, increase water and nutrient residence times, increase geomorphic heterogeneity, delay sediment transport, increase carbon, nutrient and sediment storage, expand the extent of anaerobic conditions and interfaces, increase the downstream export of dissolved organic carbon and ammonium, decrease the downstream export of nitrate, increase lotic to lentic habitat transitions and aquatic primary production, induce ‘reverse’ succession in riparian vegetation assemblages, and increase habitat complexity and biodiversity on reach scales. We then examine the key feedbacks and overlaps between these changes caused by beavers, where the decrease in longitudinal hydrologic connectivity create ponds and wetlands, transitions between lentic to lotic ecosystems, increase vertical hydraulic exchange gradients, and biogeochemical cycling per unit stream length, while increased lateral connectivity will determine the extent of open water area and wetland and littoral zone habitats, and induce changes in aquatic and terrestrial ecosystem assemblages. However, the extent of these impacts depends firstly on the hydro-geomorphic landscape context, which determines the extent of floodplain inundation, a key driver of subsequent changes to hydrologic, geomorphic, biogeochemical, and ecosystem dynamics. Secondly, it depends on the length of time beavers can sustain disturbance at a given site, which is constrained by top down (e.g. predation) and bottom up (e.g. competition) feedbacks, and ultimately determines the pathways of river corridor landscape and ecosystem succession following beaver abandonment. This outsized influence of beavers on river corridor processes and feedbacks is also fundamentally distinct from what occurs in their absence. Current river management and restoration practices are therefore open to re-examination in order to account for the impacts of beavers, both positive and negative, such that they can potentially accommodate and enhance the ecosystem engineering services they provide. It is hoped that our synthesis and holistic framework for evaluating beaver impacts can be used in this endeavor by river scientists and managers into the future as beaver populations continue to expand in both numbers and range

How Best to Hunt a Mammoth - Toward Automated Knowledge Extraction From Graphical Research Models

In the Information Systems (IS) discipline, central contributions of research projects are often represented in graphical research models, clearly illustrating constructs and their relationships. Although thousands of such representations exist, methods for extracting this source of knowledge are still in an early stage. We present a method for (1) extracting graphical research models from articles, (2) generating synthetic training data for (3) performing object detection with a neural network, and (4) a graph reconstruction algorithm to (5) storing results into a designated research model format. We trained YOLOv7 on 20,000 generated diagrams and evaluated its performance on 100 manually reconstructed diagrams from the Senior Scholars\u27 Basket. The results for extracting graphical research models show a F1-score of 0.82 for nodes, 0.72 for links, and an accuracy of 0.72 for labels, indicating the applicability for supporting the population of knowledge repositories contributing to knowledge synthesi

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways—at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75–79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology

Recent changes in extreme floods across multiple continents

Analyses of trends in observed floods often focus on relatively frequent events, whereas changes in rare floods are only studied for a small number of locations that have exceptionally long observational records. Understanding changes in rare floods is especially relevant as these events are often most damaging and influence the design of major structures. Here, we provide an assessment of changes in the largest flood events (similar to 0.033 annual exceedance probability) observed during the period 1980-2009 for 1744 catchments located in Australia, Brazil, Europe and the United States. The occurrence of rare floods in spatial aggregate shows strong temporal variability and peaked around 1995. During the 30 year period, there are overall increases in both the frequency and magnitude of extreme floods. These increases are strongest in Europe and the United States, and weakest in Brazil and Australia. Physical causes of the reported short-term variability and longer-term changes in extreme floods currently remain elusive, because the key drivers vary between catchments. Nonetheless, this approach provides the basis for a more spatially representative assessment of changes in extreme flood occurrence

A Cationic Peptide, TAT-Cd 0 , Inhibits Herpes Simplex Virus Type 1 Ocular Infection In Vivo

PURPOSE. To test the in vivo activity of a peptide derived from the protein transducing domain of the human immunodeficiency virus (HIV) Tat protein, TAT-Cd 0 , in a murine herpes simplex type 1 (HSV-1) keratitis model. METHODS. The efficacy of TAT-Cd 0 was assessed in a postinfection treatment model with different concentrations (1 mg/mL, 0.1 mg/mL, 0.01 mg/mL) of the peptide in one of four delivery vehicles: artificial tears, PBS, methylcellulose, and aquaphor cream. Treatment began within 4 or 24 hours postinfection. Viral titers in the tear film were determined by plaque assay. RESULTS. TAT-Cd 0 reduced the severity of keratitis in all of the delivery vehicles tested when treatment started, 4 hours postinfection. Peptide in the tears or PBS delivery vehicle had the most significant reduction in disease severity and delayed the onset of vascularization and stromal keratitis. The percentage of mice presenting with disease was also significantly reduced and viral titers were reduced by 1 log at 24 hours postinfection in mice treated with 1 mg/mL TAT-Cd 0 , suggesting that inhibiting replication early is sufficient to achieve clinical effects. Lower concentrations were not effective and delaying treatment by 24 hours was also not effective. CONCLUSIONS. This study shows that TAT-Cd 0 is an effective antiviral against HSV-1 strain KOS when applied shortly postinfection and that aqueous-based formulations are more suitable. (Invest Ophthalmol Vis Sci

Particle Production in Matrix Cosmology

We consider cosmological particle production in 1+1 dimensional string theory. The process is described most efficiently in terms of anomalies, but we also discuss the explicit mode expansions. In matrix cosmology the usual vacuum ambiguity of quantum fields in time-dependent backgrounds is resolved by the underlying matrix model. This leads to a finite energy density for the "in" state which cancels the effect of anomalous particle production.Comment: 24 pages, 1 figure; v2: references added, minor change

String Theory Effects on Five-Dimensional Black Hole Physics

We review recent developments in understanding quantum/string corrections to BPS black holes and strings in five-dimensional supergravity. These objects are solutions to the effective action obtained from M-theory compactified on a Calabi-Yau threefold, including the one-loop corrections determined by anomaly cancellation and supersymmetry. We introduce the off-shell formulation of this theory obtained through the conformal supergravity method and review the methods for investigating supersymmetric solutions. This leads to quantum/string corrected attractor geometries, as well as asymptotically flat black strings and spinning black holes. With these solutions in hand, we compare our results with analogous studies in four-dimensional string-corrected supergravity, emphasizing the distinctions between the four and five dimensional theories.Comment: 85 pages; uses ws-ijmpa-mod.cls article class; Invited review for IJMP

Inverse relationship between oligoclonal expanded CD69- TTE and CD69+ TTE cells in bone marrow of multiple myeloma patients.

CD8+CD57+ terminal effector T (TTE) cells are a component of marrow-infiltrating lymphocytes and may contribute to the altered immune responses in multiple myeloma (MM) patients. We analyzed TTE cells in the bone marrow (BM) and peripheral blood (PB) of age-matched controls and patients with monoclonal gammopathy of undetermined significance (MGUS), smoldering MM (SMM), and newly diagnosed (ND) MM using flow cytometry, mass cytometry, and FlowSOM clustering. TTE cells are heterogeneous in all subjects, with BM containing both CD69- and CD69+ subsets, while only CD69- cells are found in PB. Within the BM-TTE compartment, CD69- and CD69+ cells are found in comparable proportions in controls, while CD69- cells are dominant in MGUS and SMM and predominantly either CD69- or CD69+ cells in NDMM. A positive relationship between CD69+TTE and CD69-TTE cells is observed in the BM of controls, lost in MGUS, and converted to an inverse relationship in NDMM. CD69-TTE cells include multiple oligoclonal expansions of T-cell receptor/Vβ families shared between BM and PB of NDMM. Oligoclonal expanded CD69-TTE cells from the PB include myeloma-reactive cells capable of killing autologous CD38hi plasma cells in vitro, involving degranulation and high expression of perforin and granzyme. In contrast to CD69-TTE cells, oligoclonal expansions are not evident within CD69+TTE cells, which possess low perforin and granzyme expression and high inhibitory checkpoint expression and resemble T resident memory cells. Both CD69-TTE and CD69+TTE cells from the BM of NDMM produce large amounts of the inflammatory cytokines interferon-γ and tumor necrosis factor α. The balance between CD69- and CD69+ cells within the BM-TTE compartment may regulate immune responses in NDMM and contribute to the clinical heterogeneity of the disease

Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy

DNA repair enzymes are essential for maintaining the integrity of the DNA sequence. Unfortunately, very little is known about how these enzymes recognize damaged regions along the helix. Structural analysis of cellular repair enzymes bound to DNA reveals that these enzymes are able to recognize DNA in a variety of conformations. However, the prevalence of these deformations in the absence of enzymes remains unclear, as small populations of DNA conformations are often difficult to detect by NMR and X-ray crystallography. Here, we used time-resolved fluorescence spectroscopy to examine the conformational dynamics of linear, nicked, gapped, and bulged DNA in the absence of protein enzymes. This analysis reveals that damaged DNA is polymorphic in nature and able to adopt multiple individual conformations. We show that DNA repair intermediates that contain a one-nucleotide gap and bulge have a significant propensity to adopt conformations in which the orphan base resides outside the DNA helix, while DNA structures damaged by a nick or two-nucleotide gap favor intrahelical conformations. Because changes in DNA conformation appear to guide the recognition of DNA repair enzymes, we suggest that the current approach could be used to study the mechanism of DNA repair. Structural analyses of many DNA-enzyme complexes reveal that cellular repair enzymes recognize DNA in a variety o