Multi-scale trend analysis of water quality using error propagation of generalized additive models.

Effective stewardship of ecosystems to sustain current ecological status or mitigate impacts requires nuanced understanding of how conditions have changed over time in response to anthropogenic pressures and natural variability. Detecting and appropriately characterizing changes requires accurate and flexible trend assessment methods that can be readily applied to environmental monitoring datasets. A key requirement is complete propagation of uncertainty through the analysis. However, this is difficult when there are mismatches between sampling frequency, period of record, and trends of interest. Here, we propose a novel application of generalized additive models (GAMs) for characterizing multi-decadal changes in water quality indicators and demonstrate its utility by analyzing a 30-year record of biweekly-to-monthly chlorophyll-a concentrations in the San Francisco Estuary. GAMs have shown promise in water quality trend analysis to separate long-term (i.e., annual or decadal) trends from seasonal variation. Our proposed methods estimate seasonal averages in a response variable with GAMs, extract uncertainty measures for the seasonal estimates, and then use the uncertainty measures with mixed-effects meta-analysis regression to quantify inter-annual trends that account for full propagation of error across methods. We first demonstrate that nearly identical descriptions of temporal changes can be obtained using different smoothing spline formulations of the original time series. We then extract seasonal averages and their standard errors for an a priori time period within each year from the GAM results. Finally, we demonstrate how across-year trends in seasonal averages can be modeled with mixed-effects meta-analysis regression that propagates uncertainties from the GAM fits to the across-year analysis. Overall, this approach leverages GAMs to smooth data with missing observations or varying sample effort across years to estimate seasonal averages and meta-analysis to estimate trends across years. Methods are provided in the wqtrends R package.

Three dimensional analysis and comparison of human anterior teeth and experimentally created bitemark depressions

A system was proposed to scan dental models to record three-dimensional features seen in the anterior teeth to create a database of dental profiles. Dental casts were randomly selected to create indentations in cowhide leather. Reid Bite Reader was used to measure the bite forces generated by Reynolds Controlled Bite Force Generator to make the teeth impressions. Using the Immersion MicroScribe® 3D, information from the 53 bitemark depressions and 62 sets of dental casts were transferred to an Excel Spreadsheet. Software was developed to perform the 3D comparison using metric and pattern analysis. Statistical analysis showed 100% success when comparing both arches together of the dental casts with the bitemarks or different dental casts.

Intercomparison of In Situ Sensors for Ground-Based Land Surface Temperature Measurements.

Land surface temperature (LST) is a key variable in the determination of land surface energy exchange processes from local to global scales. Accurate ground measurements of LST are necessary for a number of applications including validation of satellite LST products or improvement of both climate and numerical weather prediction models. With the objective of assessing the quality of in situ measurements of LST and to evaluate the quantitative uncertainties in the ground-based LST measurements, intensive field experiments were conducted at NOAA's Air Resources Laboratory (ARL)'s Atmospheric Turbulence and Diffusion Division (ATDD) in Oak Ridge, Tennessee, USA, from October 2015 to January 2016. The results of the comparison of LSTs retrieved by three narrow angle broadband infrared temperature sensors (IRT), hemispherical longwave radiation (LWR) measurements by pyrgeometers, forward looking infrared camera with direct LSTs by multiple thermocouples (TC), and near surface air temperature (AT) are presented here. The brightness temperature (BT) measurements by the IRTs agreed well with a bias of <0.23 °C, and root mean square error (RMSE) of <0.36 °C. The daytime LST(TC) and LST(IRT) showed better agreement (bias = 0.26 °C and RMSE = 0.67 °C) than with LST(LWR) (bias > 1.1 and RMSE > 1.46 °C). In contrast, the difference between nighttime LSTs by IRTs, TCs, and LWR were <0.47 °C, whereas nighttime AT explained >81% of the variance in LST(IRT) with a bias of 2.64 °C and RMSE of 3.6 °C. To evaluate the annual and seasonal differences in LST(IRT), LST(LWR) and AT, the analysis was extended to four grassland sites in the USA. For the annual dataset of LST, the bias between LST (IRT) and LST (LWR) was <0.7 °C, except at the semiarid grassland (1.5 °C), whereas the absolute bias between AT and LST at the four sites were <2 °C. The monthly difference between LST (IRT) and LST (LWR) (or AT) reached up to 2 °C (5 °C), whereas half-hourly differences between LSTs and AT were several degrees in magnitude depending on the site characteristics, time of the day and the season.

Four decades of water quality change in the upper San Francisco Estuary.

Quantitative descriptions of chemical, physical, and biological characteristics of estuaries are critical for developing an ecological understanding of drivers of change. Historical trends and relationships between key species of dissolved inorganic nitrogen (ammonium, nitrate/nitrite, total) from the Delta region of the San Francisco Estuary were modeled with an estuarine adaptation of the Weighted Regressions on Time, Discharge, and Season (WRTDS). Analysis of flow-normalized data revealed trends that were different from those in the observed time-series. Flow-normalized data exhibited changes in magnitude and even reversal of trends relative to the observed data. Modelled trends demonstrated that nutrient concentrations were on average higher in the last twenty years relative to the earlier periods of observation, although concentrations have been slowly declining since the mid-1990s and early 2000s. We further describe mechanisms of change with two case studies that evaluated 1) downstream changes in nitrogen following upgrades at a wastewater treatment plant, and 2) interactions between biological invaders, chlorophyll, macro-nutrients (nitrogen and silica), and flow in Suisun Bay. WRTDS results for ammonium trends showed a distinct signal as a result of upstream wastewater treatment plant upgrades, with specific reductions observed in the winter months during low-flow conditions. Results for Suisun Bay showed that chlorophyll a production in early years was directly stimulated by flow, whereas the relationship with flow in later years was indirect and influenced by grazing pressure. Although these trends and potential causes of change have been described in the literature, results from WRTDS provided an approach to test alternative hypotheses of spatiotemporal drivers of nutrient dynamics in the Delta.

Inflammatory pattern of the infrapatellar fat pad in dogs with canine cruciate ligament disease.

BACKGROUND: Despite the importance of inflammation during the pathogenesis of cranial cruciate ligament disease (CCLD) in dogs and despite the latest knowledge suggesting a significant role of adipose tissue in osteoarthritis, the infrapatellar fat pad (IFP) was up to now mostly disregarded in veterinary investigations. In the present study, the inflammatory activity of the IFP, the main adipose structure within the stifle joint, was thoroughly investigated to evaluate its potential impact in the pathogenesis of this common disease of our canine companions. Samples of IFP, subcutaneous adipose tissue (ScAT) of the thigh and synovial fluid in both diseased (n = 36) and healthy control (n = 23) dogs were tested for their immune cell composition but also for interleukins (IL-1ß, IL-6, IL-8, IL-10), degradative enzymes (MMP-1, MMP-3, MMP-13, TIMP-2, iNOS) and adipokines (leptin and adiponectin). Characterization of the immune cell composition was ascertained by fluorescence activated cell sorting. Gene expression and protein release of the inflammatory markers was determined by real RT-qPCR and ELISA. RESULTS: IFPs of dogs with CCLD had a significantly increased immune cell count with T cells (CD3) as the most abundant immune cells. T cells and macrophages (CD14) were significantly increased compared to healthy controls or corresponding ScAT. In addition, IFPs of dogs with CCLD demonstrated a significant increase on gene as well as protein level of multiple inflammatory indicators (IL-1ß, IL-6, MMP-1, MMP-13) compared to the other tissues. TNFα was only increased on gene expression. Adipokine analysis showed higher secretion of adiponectin and lower leptin secretion in IFP from dogs with CCLD than from controls. In the synovial fluid from dogs with CCLD concentrations of IL-1ß, MMP-1, MMP-13 as well as leptin were significantly increased compared to the synovial fluid from healthy control dogs. CONCLUSIONS: The present study indicates that the IFP is a potential contributory factor in the pathogenesis of CCLD, due to its inflammatory phenotype and the proximity within the stifle joint. To determine the extent of this possible inter-relationship, further studies need to be undertaken.

Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California.

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routine monitoring for either toxin. Dinophysis shellfish toxins (DSTs) and freshwater microcystins are also present within SFB, but not routinely monitored. Acute exposure to any of these toxin groups has severe consequences for marine organisms and humans, but chronic exposure to sub-lethal doses, or synergistic effects from multiple toxins, are poorly understood and rarely addressed. This study documents the occurrence of domoic acid and microcystins in SFB from 2011 to 2016, and identifies domoic acid, microcystins, DSTs, and PSTs in marine mussels within SFB in 2012, 2014, and 2015. At least one toxin was detected in 99% of mussel samples, and all four toxin suites were identified in 37% of mussels. The presence of these toxins in marine mussels indicates that wildlife and humans who consume them are exposed to toxins at both sub-lethal and acute levels. As such, there are potential deleterious impacts for marine organisms and humans and these effects are unlikely to be documented. These results demonstrate the need for regular monitoring of marine and freshwater toxins in SFB, and suggest that co-occurrence of multiple toxins is a potential threat in other ecosystems where freshwater and seawater mix.

Epidermis and Enamel: Insights Into Gnawing Criticisms of Human Bitemark Evidence.

Critics describe forensic dentists' management of bitemark evidence as junk science with poor sensitivity and specificity and state that linkages to a biter are unfounded. Those vocal critics, supported by certain media, characterize odontologists' previous errors as egregious and petition government agencies to render bitemark evidence inadmissible. Odontologists acknowledge that some practitioners have made past mistakes. However, it does not logically follow that the errors of a few identify a systemic failure of bitemark analysis. Scrutiny of the contentious cases shows that most occurred 20 to 40 years ago. Since then, research has been ongoing and more conservative guidelines, standards, and terminology have been adopted so that past errors are no longer reflective of current safeguards. The authors recommend a comprehensive root analysis of problem cases to be used to determine all the factors that contributed to those previous problems. The legal community also shares responsibility for some of the past erroneous convictions. Currently, most proffered bitemark cases referred to odontologists do not reach courts because those forensic dentists dismiss them as unacceptable or insufficient for analysis. Most bitemark evidence cases have been properly managed by odontologists. Bitemark evidence and testimony remain relevant and have made significant contributions in the justice system.

Novel Analyses of Long-Term Data Provide a Scientific Basis for Chlorophyll-a Thresholds in San Francisco Bay.

San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with over-production of phytoplankton. Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll-a (chl-a) and decreases of dissolved oxygen (DO), common occurrences of phytoplankton taxa that can form Harmful Algal Blooms (HAB), and algal toxins in water and mussels reaching levels of concern. As a result, managers now ask: what levels of chl-a in SFB constitute tipping points of phytoplankton biomass beyond which water quality will become degraded, requiring significant nutrient reductions to avoid impairments? We analyzed data for DO, phytoplankton species composition, chl-a, and algal toxins to derive quantitative relationships between three indicators (HAB abundance, toxin concentrations, DO) and chl-a. Quantile regressions relating HAB abundance and DO to chl-a were significant, indicating SFB is at increased risk of adverse HAB and low DO levels if chl-a continues to increase. Conditional probability analysis (CPA) showed chl-a of 13 mg m-3 as a "protective" threshold below which probabilities for exceeding alert levels for HAB abundance and toxins were reduced. This threshold was similar to chl-a of 13 - 16 mg m-3 that would meet a SFB-wide 80 % saturation Water Quality Criterion (WQC) for DO. Higher "at risk" chl-a thresholds from 25 - 40 mg m-3 corresponded to 0.5 probability of exceeding alert levels for HAB abundance, and for DO below a WQC of 5.0 mg L-1 designated for lower South Bay (LSB) and South Bay (SB). We submit these thresholds as a basis to assess eutrophication status of SFB and to inform nutrient management actions. This approach is transferrable to other estuaries to derive chl-a thresholds protective against eutrophication.

Forensic Dental Age Estimation: An Overview.

Forensic age estimation is a scientific process that estimates an individual's true chronologic age by assessing skeletal and dental development and maturation. Although human growth and maturation is unique to each individual, dental techniques for estimating age are currently considered the best in assessing true chronologic age particularly during the age range when the dentition is undergoing morphologic development. This article reviews the principles, methodology and commonly used techniques in forensic age estimation cases.

Sources and fates of heavy metals in a mining-impacted stream: temporal variability and the role of iron oxides.

Heavy metal contamination of surface waters at mining sites often involves complex interactions of multiple sources and varying biogeochemical conditions. We compared surface and subsurface metal loading from mine waste pile runoff and mine drainage discharge and characterized the influence of iron oxides on metal fate along a 0.9-km stretch of Tar Creek (Oklahoma, USA), which drains an abandoned Zn/Pb mining area. The importance of each source varied by metal; mine waste pile runoff contributed 70% of Cd, while mine drainage contributed 90% of Pb, and both sources contributed similarly to Zn loading. Subsurface inputs accounted for 40% of flow and 40-70% of metal loading along this stretch. Streambed iron oxide aggregate material contained highly elevated Zn (up to 27,000 µg g(-1)), Pb (up to 550 µg g(-1)) and Cd (up to 200 µg g(-1)) and was characterized as a heterogeneous mixture of iron oxides, fine-grain mine waste, and organic material. Sequential extractions confirmed preferential sequestration of Pb by iron oxides, as well as substantial concentrations of Zn and Cd in iron oxide fractions, with additional accumulation of Zn, Pb, and Cd during downstream transport. Comparisons with historical data show that while metal concentrations in mine drainage have decreased by more than an order of magnitude in recent decades, the chemical composition of mine waste pile runoff has remained relatively constant, indicating less attenuation and increased relative importance of pile runoff. These results highlight the importance of monitoring temporal changes at contaminated sites associated with evolving speciation and simultaneously addressing surface and subsurface contamination from both mine waste piles and mine drainage.

Analysis of radiocarbon, stable isotopes and DNA in teeth to facilitate identification of unknown decedents.

The characterization of unidentified bodies or suspected human remains is a frequent and important task for forensic investigators. However, any identification method requires clues to the person's identity to allow for comparisons with missing persons. If such clues are lacking, information about the year of birth, sex and geographic origin of the victim, is particularly helpful to aid in the identification casework and limit the search for possible matches. We present here results of stable isotope analysis of (13)C and (18)O, and bomb-pulse (14)C analyses that can help in the casework. The (14)C analysis of enamel provided information of the year of birth with an average absolute error of 1.8±1.3 years. We also found that analysis of enamel and root from the same tooth can be used to determine if the (14)C values match the rising or falling part of the bomb-curve. Enamel laydown times can be used to estimate the date of birth of individuals, but here we show that this detour is unnecessary when using a large set of crude (14)C data of tooth enamel as a reference. The levels of (13)C in tooth enamel were higher in North America than in teeth from Europe and Asia, and Mexican teeth showed even higher levels than those from USA. DNA analysis was performed on 28 teeth, and provided individual-specific profiles in most cases and sex determination in all cases. In conclusion, these analyses can dramatically limit the number of possible matches and hence facilitate person identification work.

Functional characterization of fluorescent hepcidin.

Hepcidin is a peptide hormone that regulates homeostasis in iron metabolism. It binds to the sole known cellular iron exporter ferroportin (Fpn), triggers its internalization, and thereby modulates the efflux of iron from cells. This functional property has been adopted in this study to assess the bioactivity and potency of a range of novel fluorescent hepcidin analogues. Hepcidin was selectively labeled with 6-carboxyfluorescein (CF) and 6-carboxytetramethylrhodamine (TMR) using Fmoc solid phase peptide chemistry. Internalization of Fpn by hepcidin was assessed by high-content microscopic analysis. Both K18- and M21K-labeled hepcidin with TMR and CF exhibited measurable potency when tested in cultured MDCK and T47D cells expressing human ferroportin. The bioactivity of the labeled hepcidin varies with the type of fluorophore and site of attachment of the fluorophores on the hepcidin molecule.

Prioritizing environmental risk of prescription pharmaceuticals.

Low levels of pharmaceutical compounds have been detected in aquatic environments worldwide, but their human and ecological health risks associated with low dose environmental exposure is largely unknown due to the large number of these compounds and a lack of information. Therefore prioritization and ranking methods are needed for screening target compounds for research and risk assessment. Previous efforts to rank pharmaceutical compounds have often focused on occurrence data and have paid less attention to removal mechanisms such as human metabolism. This study proposes a simple prioritization approach based on number of prescriptions and toxicity information, accounting for metabolism and wastewater treatment removal, and can be applied to unmeasured compounds. The approach was performed on the 200 most-prescribed drugs in the US in 2009. Our results showed that under-studied compounds such as levothyroxine and montelukast sodium received the highest scores, suggesting the importance of removal mechanisms in influencing the ranking, and the need for future environmental research to include other less-studied but potentially harmful pharmaceutical compounds.

Spatial heterogeneity of methane ebullition in a large tropical reservoir.

Tropical reservoirs have been identified as important methane (CH(4)) sources to the atmosphere, primarily through turbine and downstream degassing. However, the importance of ebullition (gas bubbling) remains unclear. We hypothesized that ebullition is a disproportionately large CH(4) source from reservoirs with dendritic littoral zones because of ebullition hot spots occurring where rivers supply allochthonous organic material. We explored this hypothesis in Lake Kariba (Zambia/Zimbabwe; surface area >5000 km(2)) by surveying ebullition in bays with and without river inputs using an echosounder and traditional surface chambers. The two techniques yielded similar results, and revealed substantially higher fluxes in river deltas (∼10(3) mg CH(4) m(-2) d(-1)) compared to nonriver bays (<100 mg CH(4) m(-2) d(-1)). Hydroacoustic measurements resolved at 5 m intervals showed that flux events varied over several orders of magnitude (up to 10(5) mg CH(4) m(-2) d(-1)), and also identified strong differences in ebullition frequency. Both factors contributed to emission differences between all sites. A CH(4) mass balance for the deepest basin of Lake Kariba indicated that hot spot ebullition was the largest atmospheric emission pathway, suggesting that future greenhouse gas budgets for tropical reservoirs should include a spatially well-resolved analysis of ebullition hot spots.

Retrospective evaluation of postoperative nasotracheal tubes for oxygen supplementation in dogs following surgery for brachycephalic syndrome: 36 cases (2003-2007).

OBJECTIVE: To assess the utility of nasotracheal tubes in postoperative oxygen supplementation in dogs following corrective surgery for brachycephalic syndrome. DESIGN: Retrospective study 2003-2007. SETTING: University teaching hospital. ANIMALS: Thirty-six client-owned dogs that underwent corrective surgery for brachycephalic syndrome. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Medical records were reviewed for animals that underwent surgical interventions for brachycephalic syndrome including palatoplasty, ventriculectomy, and rhinoplasty. Data collected included signalment, presenting complaints, analgesic and surgical interventions, type of supplemental oxygen therapy, complications and mortality occurring during hospitalization. A nasotracheal tube (NTT) was placed in 20 dogs at the end of surgery; 16 dogs received other forms of oxygen supplementation (8) or no oxygen supplementation (8) during recovery. The total number of postoperative complications was similar in both groups (8/20 dogs with NTTs and 7/16 in those without NTTs). However, respiratory distress was observed in 5 dogs without NTTs but was not observed in any dog while an NTT was in place. One dog in each group died postoperatively. CONCLUSION: Placement of an NTT was found to be easy and may offer benefit in dogs with brachycephalic syndrome as a noninvasive means of delivering oxygen. The use of NTT may minimize severe postoperative morbidity, in particular by reducing postoperative respiratory distress.

Microfenestration using the CUSA Excel ultrasonic aspiration system in chondrodystrophic dogs with thoracolumbar disk extrusion: a descriptive cadaveric and clinical study.

OBJECTIVE: To describe an ultrasonic surgical aspirator assisted disk fenestration technique in dogs. STUDY DESIGN: Descriptive cadaveric and prospective clinical study. ANIMALS: Fresh Beagle cadavers (n=5) and 10 chondrodystrophic dogs with thoracolumbar disk extrusion. METHODS: Cadaveric study: Intervertebral disks T12-L2 were fenestrated with the CUSA Excel in 5 Beagle cadavers, and fenestration efficacy assessed by morphologic examination of the completeness of fenestration and size of annulotomy. Clinical study: the affected intervertebral disk was fenestrated in 10 chondrodystrophic dogs treated by hemilaminectomy for thoracolumbar disk disease. Efficacy of fenestration was evaluated. RESULTS: Mean time necessary to perform CUSA assisted fenestration was 8 minutes (range, 5-10 minutes) for each disk in cadavers and patients. In cadaver spines, removal of the nucleus pulposus was complete in 11/15 disks. In 4 disks, remnants of nucleus pulposus material were observed on the contralateral side. Nuclear material was normal in 9/15 disks and showed evidence of chondroid degeneration on histopathologic examination in the 6 disks. Median annulotomy size was 3 mm. Clinically, no signs of early recurrence were observed and all dogs recovered uneventfully. CONCLUSIONS: CUSA assisted fenestration is a safe and efficient method of fenestration for removal of most of the nucleus pulposus through a limited annulotomy.

Fish consumption and mercury exposure among Louisiana recreational anglers.

BACKGROUND: Methylmercury (MeHg) exposure assessments among average fish consumers in the United States may underestimate exposures among U.S. subpopulations with high intakes of regionally specific fish. OBJECTIVES: We examined relationships among fish consumption, estimated mercury (Hg) intake, and measured Hg exposure within one such potentially highly exposed group, recreational anglers in the state of Louisiana, USA. METHODS: We surveyed 534 anglers in 2006 using interviews at boat launches and fishing tournaments combined with an Internet-based survey method. Hair samples from 402 of these anglers were collected and analyzed for total Hg. Questionnaires provided information on species-specific fish consumption during the 3 months before the survey. RESULTS: Anglers' median hair Hg concentration was 0.81 µg/g (n = 398; range, 0.02-10.7 µg/g); 40% of participants had levels >1 µg/g, which approximately corresponds to the U.S. Environmental Protection Agency's reference dose. Fish consumption and Hg intake were significantly positively associated with hair Hg. Participants reported consuming nearly 80 different fish types, many of which are specific to the region. Unlike the general U.S. population, which acquires most of its Hg from commercial seafood sources, approximately 64% of participants' fish meals and 74% of their estimated Hg intake came from recreationally caught seafood. CONCLUSIONS: Study participants had relatively elevated hair Hg concentrations and reported consumption of a wide variety of fish, particularly locally caught fish. This group represents a highly exposed subpopulation with an exposure profile that differs from fish consumers in other regions of the United States, suggesting a need for more regionally specific exposure estimates and public health advisories.