Lateral cavities in streams : flow structure and mean residence times from channel hydraulics, morphology, and computational fluid dynamics

Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and non-transferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widely-recognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor—ratio of the square root of cavity width and depth to the cavity length—represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory

A mean residence time relationship for lateral cavities in gravel-bed rivers and streams: Incorporating streambed roughness and cavity shape

Accurate estimates of mass-exchange parameters in transient storage zones are needed to better understand and quantify solute transport and dispersion in riverine systems. Currently, the predictive mean residence time relies on an empirical entrainment coefficient with a range in variance due to the absence of hydraulic and geomorphic quantities driving mass exchange. Two empirically derived relationships are presented for the mean residence time of lateral cavities-a prevalent and widely recognized type of transient storage-in gravel-bed rivers and streams that incorporates hydraulic and geomorphic parameters. The relationships are applicable for gravel-bed rivers and streams with a range of cavity width to length (W/L) aspect ratios (0.2-0.75), shape, and Reynolds numbers (Re, ranging from 1.0 x 10(4) to 1.0 x 10(7)). The relationships equate normalized mean residence time to nondimensional quantities: Froude number, Re, W/L, depth ratio (ratio of cavity to shear layer depth), roughness factor (ratio of shear to channel velocity), and shape factor (representing degree of cavity equidimensionality). One relationship excludes bed roughness (equation (13)) and the other includes bed roughness (equation (14)). The empirically derived relationships have been verified for conservative tracers (R-2 of 0.83) within a range of flow and geometry conditions. Topics warranting future research are testing the empirical relationship that includes the roughness factor using parameters measured in the vicinity of the cavity to reduce the variance in the correlation, and further development of the relationship for nonconservative transport.This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/.Keywords: transport, Rectangular cavity, Dead zone, Groyne fields, Flow, Groundwater, Transient storage, Channel, Retention, Exchange processe

Defining and measuring the mean residence time of lateral surface transient storage zones in small streams

Surface transient storage (STS) has functional significance in stream ecosystems because it increases solute interaction with sediments. After volume, mean residence time is the most important metric of STS, but it is unclear how this can be measured accurately or related to other timescales and field-measureable parameters. We studied mean residence time of lateral STS in small streams over Reynolds numbers (Re) 5000–200,000 and STS width to length (W/L) aspect ratios between 0.2–0.75. Lateral STS have flow fields characterized by a shear layer spanning the length of the STS entrance, and one primary gyre and one or more secondary gyre(s) in the STS. The study's purpose was to define, measure, and compare residence timescales: volume to discharge ratio (Langmuir timescale); area under normalized concentration curve; and characteristic time of exponential decay, and to compare these timescales to field measureable parameters. The best estimate of STS mean residence time—primary gyre residence time—was determined to be the first characteristic time of exponential decay. An apparent mean residence time can arise, which is considerably larger than other timescales, if probes are placed within secondary gyre(s). The Langmuir timescale is the minimum mean residence time, and is linearly correlated to channel velocity and STS width. The lateral STS mean residence time can be predicted using a physically based hydromorphic timescale derived by Uijttewaal et al. (2001) with an entrainment coefficient of 0.031 ± 0.009 for the Re and W/L studied

Characteristics and Outcomes of US Children and Adolescents With Multisystem Inflammatory Syndrome in Children (MIS-C) Compared With Severe Acute COVID-19

Importance Refinement of criteria for multisystem inflammatory syndrome in children (MIS-C) may inform efforts to improve health outcomes. Objective To compare clinical characteristics and outcomes of children and adolescents with MIS-C vs those with severe coronavirus disease 2019 (COVID-19). Setting, Design, and Participants Case series of 1116 patients aged younger than 21 years hospitalized between March 15 and October 31, 2020, at 66 US hospitals in 31 states. Final date of follow-up was January 5, 2021. Patients with MIS-C had fever, inflammation, multisystem involvement, and positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcriptase–polymerase chain reaction (RT-PCR) or antibody test results or recent exposure with no alternate diagnosis. Patients with COVID-19 had positive RT-PCR test results and severe organ system involvement. Exposure SARS-CoV-2. Main Outcomes and Measures Presenting symptoms, organ system complications, laboratory biomarkers, interventions, and clinical outcomes. Multivariable regression was used to compute adjusted risk ratios (aRRs) of factors associated with MIS-C vs COVID-19. Results Of 1116 patients (median age, 9.7 years; 45% female), 539 (48%) were diagnosed with MIS-C and 577 (52%) with COVID-19. Compared with patients with COVID-19, patients with MIS-C were more likely to be 6 to 12 years old (40.8% vs 19.4%; absolute risk difference [RD], 21.4% [95% CI, 16.1%-26.7%]; aRR, 1.51 [95% CI, 1.33-1.72] vs 0-5 years) and non-Hispanic Black (32.3% vs 21.5%; RD, 10.8% [95% CI, 5.6%-16.0%]; aRR, 1.43 [95% CI, 1.17-1.76] vs White). Compared with patients with COVID-19, patients with MIS-C were more likely to have cardiorespiratory involvement (56.0% vs 8.8%; RD, 47.2% [95% CI, 42.4%-52.0%]; aRR, 2.99 [95% CI, 2.55-3.50] vs respiratory involvement), cardiovascular without respiratory involvement (10.6% vs 2.9%; RD, 7.7% [95% CI, 4.7%-10.6%]; aRR, 2.49 [95% CI, 2.05-3.02] vs respiratory involvement), and mucocutaneous without cardiorespiratory involvement (7.1% vs 2.3%; RD, 4.8% [95% CI, 2.3%-7.3%]; aRR, 2.29 [95% CI, 1.84-2.85] vs respiratory involvement). Patients with MIS-C had higher neutrophil to lymphocyte ratio (median, 6.4 vs 2.7, P < .001), higher C-reactive protein level (median, 152 mg/L vs 33 mg/L; P < .001), and lower platelet count (<150 ×103 cells/μL [212/523 {41%} vs 84/486 {17%}, P < .001]). A total of 398 patients (73.8%) with MIS-C and 253 (43.8%) with COVID-19 were admitted to the intensive care unit, and 10 (1.9%) with MIS-C and 8 (1.4%) with COVID-19 died during hospitalization. Among patients with MIS-C with reduced left ventricular systolic function (172/503, 34.2%) and coronary artery aneurysm (57/424, 13.4%), an estimated 91.0% (95% CI, 86.0%-94.7%) and 79.1% (95% CI, 67.1%-89.1%), respectively, normalized within 30 days. Conclusions and Relevance This case series of patients with MIS-C and with COVID-19 identified patterns of clinical presentation and organ system involvement. These patterns may help differentiate between MIS-C and COVID-19

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

JacksonTracieR2014.pdf

Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and nontransferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widelyrecognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor--ratio of the square root of cavity width and depth to the cavity length--represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory

MicroADV.xlsx

Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and nontransferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widelyrecognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor--ratio of the square root of cavity width and depth to the cavity length--represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory

Bathymetry.xls

Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and nontransferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widelyrecognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor--ratio of the square root of cavity width and depth to the cavity length--represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory

Velocity Profiles and Discharge.xlsx

Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and nontransferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widelyrecognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor--ratio of the square root of cavity width and depth to the cavity length--represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory

Evaluation of the Hydraulic Connection between streams and aquifers at Baker and Snake Creek near Great Basin National Park, Snake Valley, White Pine County, Nevada

Stream channels along Baker and Snake Creek, which drain off the eastern flank of the southern Snake Range in Great Basin National Park and out into Snake Valley, were evaluated to determine their hydraulic connection with their underlying basin-fill and carbonate-rock aquifers. Characterization of this hydraulic connection included: (a) quantifying stream discharge along the creeks and analyzing variations in flow; (b) installing piezometers into the streambeds and measuring vertical head gradients from water-level measurements in both the piezometers and creeks; (c) estimating streambed hydraulic conductivities in piezometers using slug tests; (d) measuring temperature in Baker Creek, a spring, and piezometers, and analyzing variations for gain and loss rates across the streambed; and (e) doing a multiple-well aquifer test along Baker Creek. Stream discharge measurements, vertical head gradients, and streambed hydraulic conductivities were used to map gaining and losing reaches along an 8-kilometer section of Snake Creek that extends from the park boundary to the Nevada-Utah border. Snake Creek has a consistently gaining reach about 300 to 700 meters east of the park boundary where a late-Miocene fault, which juxtaposes Paleozoic footwall limestone against Miocene hanging-wall sedimentary deposits, allows Michaela spring to discharge into the creek from limestone. Snake Creek is disconnected from groundwater about 3 kilometers east of the park boundary. At this location, a recent U.S. Geological Survey monitoring well drilled 2 meters from the stream had a water level of about 60 meters below the streambed elevation, even though the creek exhibits little seepage loss. Groundwater flow models were formulated using MODFLOW-2005 to simulate gaining and losing reaches along Snake Creek and to evaluate aquifer and streambed properties contributing to the hydraulic disconnection. Results from the models suggested that aquifer hydraulic conductivities increase eastward from about 5 meters per day in the Miocene deposits to about 20 meters per day in the Paleozoic limestone and Quaternary deposits, and streambed hydraulic conductivities decrease eastward from approximately 3 meters per day to about 0.0001 meter per day. The low hydraulic conductivity of the streambed near the Utah-Nevada border was needed because of the lack of streamflow loss in a reach where depth to groundwater exceeds 30 meters.At Baker Creek, a second study location farther to the north along the southern Snake Range front, a multiple-well aquifer test was done to estimate streambed and underlying aquifer hydraulic properties over a 400-meter stream section. The test consisted of pumping a well 16 meters away from the creek for 4 days at a rate of 1.64 liters per second and included measurements of water levels and temperature along Baker Creek and in the test and monitoring wells. Water levels in shallow wells next to Baker Creek indicated the creek is losing in the immediate vicinity of the aquifer test. A computer program, SEAWAT, was used to couple MODFLOW-2005 with MT3DMS to estimate streambed and aquifer properties using drawdown and temperature data collected before and during the test with temperature used as a tracer during pumping. Model results suggested that the contact between the Miocene deposits and Quaternary alluvium dips into the alluvium from the north and south of the test site and a megablock is situated within the Miocene deposits immediately south of the pumped well. The initial temperature field had two temperature aureoles, one each around Baker Creek and a spring to the north of the test site that increased in temperature from beneath the creek and spring. The Quaternary alluvium had estimated horizontal and vertical hydraulic conductivities of 8.3 and 0.15 meters per day, respectively. The vertical hydraulic conductivity of the streambed for Baker Creek was 0.5 meter per day. Although the pumping rate was insufficient to produce a measureable decrease in streamflow along Baker Creek, water level declines indicated increased leakage near and downstream of the pumped well. The measured well temperatures during the aquifer test did not improve the estimates of hydraulic properties of the Quaternary alluvium, Miocene deposits, and the streambed beyond what was estimated from the measured drawdown because of uncertainty in knowing the initial distribution of temperature at the test site