COMPARATIVE PERFORMANCE OF TWO AUTOMATED MACHINE LEARNING PLATFORMS FOR COVID-19 DETECTION BY MALDI-TOF-MS

The 2019 novel coronavirus infectious disease (COVID-19) pandemic has resulted in an unsustainable need for diagnostic tests. Currently, molecular tests are the accepted standard for the detection of SARS-CoV-2. Mass spectrometry (MS) enhanced by machine learning (ML) has recently been postulated to serve as a rapid, high-throughput, and low-cost alternative to molecular methods. Automated ML is a novel approach that could move mass spectrometry techniques beyond the confines of traditional laboratory settings. However, it remains unknown how different automated ML platforms perform for COVID-19 MS analysis. To this end, the goal of our study is to compare algorithms produced by two commercial automated ML platforms (Platforms A and B). Our study consisted of MS data derived from 361 subjects with molecular confirmation of COVID-19 status including SARS-CoV-2 variants. The top optimized ML model with respect to positive percent agreement (PPA) within Platforms A and B exhibited an accuracy of 94.9%, PPA of 100%, negative percent agreement (NPA) of 93%, and an accuracy of 91.8%, PPA of 100%, and NPA of 89%, respectively. These results illustrate the MS methods robustness against SARS-CoV-2 variants and highlight similarities and differences in automated ML platforms in producing optimal predictive algorithms for a given dataset.

Smart allocation of restoration funds over space and time.

A challenge for natural area managers is to ensure that public expenditure on land restoration is cost effective, efficient and transparent but this is difficult to achieve in practice, especially when there are many possible projects across multiple years. Here we develop a "roadmap" for investment in land restoration. It explicitly considers space, time and their interaction, in relation to ecological outcomes and restoration costs (and their variation in time and space). Using integer linear programming optimization in a benefit-cost accounting framework, the roadmap incorporates: transitions between different stages of ecological recovery in a spatial mosaic of multiple ecosystem types; cost schedules associated with managing those transitions over time; time lags between beginning management and achieving outcomes; variations to constraints and goals associated with various factors including site accessibility, specific conservation priorities (such as threatened species or ecosystems); and background environmental trends. This approach enables land managers to: (1) forecast landscape-scale outcomes of management strategies over long timeframes; (2) address the question of how long it will take and how much it will cost to achieve specific outcomes; and (3) explore potential trade-offs in outcomes among alternative management strategies. We illustrate its application using a case study of forest restoration in Australia by a local government authority across a public conservation estate comprising 765 land units of varying size, totaling ˜13,000 ha, across five different floristic vegetation types, with an annual budget of ˜AU$5M, projected over a 50-yr timeframe. These simulations revealed a trade-off between management strategies that seek to increase either the total cover of native forest or the amount of high quality forest: quality-based strategies were favored in scenarios in which shorter term (20-30 yr) timeframes were chosen at the outset, but cover-based strategies were favored if longer time horizons were initially targeted. Projected outcomes were also strongly influenced by assumed background rates of vegetation decline or recovery. Many of the issues in this restoration roadmap are generalizable (even though specific outcomes and trade-offs are likely to vary among case studies), and the approach is both scalable and transferable to other regions and ecosystems.

Stabilization of cultural innovations depends on population density: Testing an epidemiological model of cultural evolution against a global dataset of rock art sites and climate-based estimates of ancient population densities.

Demographic models of human cultural evolution have high explanatory potential but weak empirical support. Here we use a global dataset of rock art sites and climate and genetics-based estimates of ancient population densities to test a new model based on epidemiological principles. The model focuses on the process whereby a cultural innovation becomes endemic in a population, predicting that this cannot occur unless population density exceeds a critical threshold. Analysis of the data, using a Bayesian statistical framework, shows that the model has stronger empirical support than a proportional model, where detection is directly proportional to population density, or a null model, where rock art detection ratios and population density are independent. Results for different geographical areas and periods are compatible with the predictions of the model and confirm its superiority with respect to the null model. Re-analysis of the rock art data, using a second set of independent population estimates, again supports the superiority of the model. Although the available data is sparse and the analysis cannot exclude all possible sources of bias, this is evidence that population density above a critical threshold may be a necessary condition for the maintenance of rock art as a stable part of a population's cultural repertoire. Methods similar to those described can be used to test the model for other classes of archaeological artifact and to compare it against other models.

Violence prevention accelerators for children and adolescents in South Africa: A path analysis using two pooled cohorts.

BACKGROUND: The INSPIRE framework was developed by 10 global agencies as the first global package for preventing and responding to violence against children. The framework includes seven complementary strategies. Delivering all seven strategies is a challenge in resource-limited contexts. Consequently, governments are requesting additional evidence to inform which 'accelerator' provisions can simultaneously reduce multiple types of violence against children. METHODS AND FINDINGS: We pooled data from two prospective South African adolescent cohorts including Young Carers (2010-2012) and Mzantsi Wakho (2014-2017). The combined sample size was 5,034 adolescents. Each cohort measured six self-reported violence outcomes (sexual abuse, transactional sexual exploitation, physical abuse, emotional abuse, community violence victimisation, and youth lawbreaking) and seven self-reported INSPIRE-aligned protective factors (positive parenting, parental monitoring and supervision, food security at home, basic economic security at home, free schooling, free school meals, and abuse response services). Associations between hypothesised protective factors and violence outcomes were estimated jointly in a sex-stratified multivariate path model, controlling for baseline outcomes and socio-demographics and correcting for multiple-hypothesis testing using the Benjamini-Hochberg procedure. We calculated adjusted probability estimates conditional on the presence of no, one, or all protective factors significantly associated with reduced odds of at least three forms of violence in the path model. Adjusted risk differences (ARDs) and adjusted risk ratios (ARRs) with 95% confidence intervals (CIs) were also calculated. The sample mean age was 13.54 years, and 56.62% were female. There was 4% loss to follow-up. Positive parenting, parental monitoring and supervision, and food security at home were each associated with lower odds of three or more violence outcomes (p < 0.05). For girls, the adjusted probability of violence outcomes was estimated to be lower if all three of these factors were present, as compared to none of them: sexual abuse, 5.38% and 1.64% (ARD: -3.74% points, 95% CI -5.31 to -2.16, p < 0.001); transactional sexual exploitation, 10.07% and 4.84% (ARD: -5.23% points, 95% CI -7.26 to -3.20, p < 0.001); physical abuse, 38.58% and 23.85% (ARD: -14.72% points, 95% CI -19.11 to -10.33, p < 0.001); emotional abuse, 25.39% and 12.98% (ARD: -12.41% points, 95% CI -16.00 to -8.83, p < 0.001); community violence victimisation, 36.25% and 28.37% (ARD: -7.87% points, 95% CI -11.98 to -3.76, p < 0.001); and youth lawbreaking, 18.90% and 11.61% (ARD: -7.30% points, 95% CI -10.50 to -4.09, p < 0.001). For boys, the adjusted probability of violence outcomes was also estimated to be lower if all three factors were present, as compared to none of them: sexual abuse, 2.39% to 1.80% (ARD: -0.59% points, 95% CI -2.24 to 1.05, p = 0.482); transactional sexual exploitation, 6.97% to 4.55% (ARD: -2.42% points, 95% CI -4.77 to -0.08, p = 0.043); physical abuse from 37.19% to 25.44% (ARD: -11.74% points, 95% CI -16.91 to -6.58, p < 0.001); emotional abuse from 23.72% to 10.72% (ARD: -13.00% points, 95% CI -17.04 to -8.95, p < 0.001); community violence victimisation from 41.28% to 35.41% (ARD: -5.87% points, 95% CI -10.98 to -0.75, p = 0.025); and youth lawbreaking from 22.44% to 14.98% (ARD -7.46% points, 95% CI -11.57 to -3.35, p < 0.001). Key limitations were risk of residual confounding and not having information on protective factors related to all seven INSPIRE strategies. CONCLUSION: In this cohort study, we found that positive and supervisory caregiving and food security at home are associated with reduced risk of multiple forms of violence against children. The presence of all three of these factors may be linked to greater risk reduction as compared to the presence of one or none of these factors. Policies promoting action on positive and supervisory caregiving and food security at home are likely to support further efficiencies in the delivery of INSPIRE.

The nature and treatment of phonological text agraphia.

Phonological alexia and agraphia are written language disorders characterised by disproportionate difficulty reading and spelling nonwords in comparison to real words. In phonological alexia, it has been shown that, despite relatively accurate reading of words in isolation, text-level reading deficits are often marked and persistent. Specifically, some individuals demonstrate difficulty reading functors and affixes in sentences, a profile referred to as phonological text alexia. In this paper, we demonstrate an analogous manifestation of the phonological impairment on text-level writing and suggest the term "phonological text agraphia". We examined four individuals with phonological alexia/agraphia who also showed disproportionate difficulty writing well-formed sentences in comparison to their grammatical competence in spoken utterances. Implementation of a phonological treatment protocol resulted in significantly improved sublexical phonology skills as well as improvements in grammatical accuracy of written narratives. These findings support the notion of a common phonological impairment underlying nonword reading/spelling deficits and sentence-level difficulties.

A millennial-scale record of Pb and Hg contamination in peatlands of the Sacramento-San Joaquin Delta of California, USA.

In this paper, we provide the first record of millennial patterns of Pb and Hg concentrations on the west coast of the United States. Peat cores were collected from two micro-tidal marshes in the Sacramento-San Joaquin Delta of California. Core samples were analyzed for Pb, Hg, and Ti concentrations and dated using radiocarbon and (210)Pb. Pre-anthropogenic concentrations of Pb and Hg in peat ranged from 0.60 to 13.0µgg(-1)and from 6.9 to 71ngg(-1), respectively. For much of the past 6000+ years, the Delta was free from anthropogenic pollution, however, beginning in ~1425CE, Hg and Pb concentrations, Pb/Ti ratios, Pb enrichment factors (EFs), and HgEFs all increased. Pb isotope compositions of the peat suggest that this uptick was likely caused by smelting activities originating in Asia. The next increases in Pb and Hg contamination occurred during the California Gold Rush (beginning ~1850CE), when concentrations reached their highest levels (74µgg(-1) Pb, 990ngg(-1) Hg; PbEF=12 and HgEF=28). Lead concentrations increased again beginning in the ~1920s with the incorporation of Pb additives in gasoline. The phase-out of lead additives in the late 1980s was reflected in changes in Pb isotope ratios and reductions in Pb concentrations in the surface layers of the peat. The rise and subsequent fall of Hg contamination was also tracked by the peat archive, with the highest Hg concentrations occurring just before 1963CE and then decreasing during the post-1963 period. Overall, the results show that the Delta was a pristine region for most of its ~6700-year existence; however, since ~1425CE, it has received Pb and Hg contamination from both global and regional sources.

Mercury cycling in agricultural and managed wetlands, Yolo Bypass, California: spatial and seasonal variations in water quality.

The seasonal and spatial variability of water quality, including mercury species, was evaluated in agricultural and managed, non-agricultural wetlands in the Yolo Bypass Wildlife Area, an area managed for multiple beneficial uses including bird habitat and rice farming. The study was conducted during an 11-month period (June 2007 to April 2008) that included a summer growing season and flooded conditions during winter. Methylmercury (MeHg) concentrations in surface water varied over a wide range (0.1 to 37ngL(-1) unfiltered; 0.04 to 7.3ngL(-1) filtered). Maximum MeHg values are among the highest ever recorded in wetlands. Highest MeHg concentrations in unfiltered surface water were observed in drainage from wild rice fields during harvest (September 2007), and in white rice fields with decomposing rice straw during regional flooding (February 2008). The ratio of MeHg to total mercury (MeHg/THg) increased about 20-fold in both unfiltered and filtered water during the growing season (June to August 2007) in the white and wild rice fields, and about 5-fold in fallow fields (July to August 2007), while there was little to no change in MeHg/THg in the permanent wetland. Sulfate-bearing fertilizer had no effect on Hg(II) methylation, as sulfate-reducing bacteria were not sulfate-limited in these agricultural wetlands. Concentrations of MeHg in filtered and unfiltered water correlated with filtered Fe, filtered Mn, DOC, and two indicators of sulfate reduction: the SO4(2-)/Cl(-) ratio, and δ(34)S in aqueous sulfate. These relationships suggest that microbial reduction of SO4(2-), Fe(III), and possibly Mn(IV) may contribute to net Hg(II)-methylation in this setting.

Lagrangian mass-flow investigations of inorganic contaminants in wastewater-impacted streams.

Understanding the potential effects of increased reliance on wastewater treatment plant (WWTP) effluents to meet municipal, agricultural, and environmental flow requires an understanding of the complex chemical loading characteristics of the WWTPs and the assimilative capacity of receiving waters. Stream ecosystem effects are linked to proportions of WWTP effluent under low-flow conditions as well as the nature of the effluent chemical mixtures. This study quantifies the loading of 58 inorganic constituents (nutrients to rare earth elements) from WWTP discharges relative to upstream landscape-based sources. Stream assimilation capacity was evaluated by Lagrangian sampling, using flow velocities determined from tracer experiments to track the same parcel of water as it moved downstream. Boulder Creek, Colorado and Fourmile Creek, Iowa, representing two different geologic and hydrologic landscapes, were sampled under low-flow conditions in the summer and spring. One-half of the constituents had greater loads from the WWTP effluents than the upstream drainages, and once introduced into the streams, dilution was the predominant assimilation mechanism. Only ammonium and bismuth had significant decreases in mass load downstream from the WWTPs during all samplings. The link between hydrology and water chemistry inherent in Lagrangian sampling allows quantitative assessment of chemical fate across different landscapes.

Anthropogenic tracers, endocrine disrupting chemicals, and endocrine disruption in Minnesota lakes.

Concentrations of endocrine disrupting chemicals and endocrine disruption in fish were determined in 11 lakes across Minnesota that represent a range of trophic conditions and land uses (urban, agricultural, residential, and forested) and in which wastewater treatment plant discharges were absent. Water, sediment, and passive polar organic integrative samplers (POCIS) were analyzed for steroidal hormones, alkylphenols, bisphenol A, and other organic and inorganic molecular tracers to evaluate potential non-point source inputs into the lakes. Resident fish from the lakes were collected, and caged male fathead minnows were deployed to evaluate endocrine disruption, as indicated by the biological endpoints of plasma vitellogenin and gonadal histology. Endocrine disrupting chemicals, including bisphenol A, 17ß-estradiol, estrone, and 4-nonylphenol were detected in 90% of the lakes at part per trillion concentrations. Endocrine disruption was observed in caged fathead minnows and resident fish in 90% of the lakes. The widespread but variable occurrence of anthropogenic chemicals in the lakes and endocrine disruption in fish indicates that potential sources are diverse, not limited to wastewater treatment plant discharges, and not entirely predictable based on trophic status and land use.

The Fock space method of vibrational analysis.

A reformulation of a semiclassical theory that presently seems uniquely capable of interpreting generic complex multiresonant vibrational spectra is presented. Once given the spectroscopic Hamiltonian which reveals the set of possible resonant couplings and its eigenstates, the new and old formulations both yield without any further computation level by level dynamical assignments for the spectra. Computing a simple trajectory in phase space reveals the motions that when quantized yield the assigned levels. The reformulation introduces two new projected representations of the wave functions. The first is in action space and the second in angle space. The projected representations often allow the reduced angle space, where nodal searches are made, to be of lower dimension than formally occurred. In addition the action representation is a similarly lower dimension lattice representation whose discreteness and regularity allow higher reduced dimensions to be studied. The lattice representation is used to produce a significantly more complete and detailed assignment of the thiophosgene spectrum than previously published.

Evaluation of statistical treatments of left-censored environmental data using coincident uncensored data sets: I. Summary statistics.

The main classes of statistical treatment of below-detection limit (left-censored) environmental data for the determination of basic statistics that have been used in the literature are substitution methods, maximum likelihood, regression on order statistics (ROS), and nonparametric techniques. These treatments, along with using all instrument-generated data (even those below detection), were evaluated by examining data sets in which the true values of the censored data were known. It was found that for data sets with less than 70% censored data, the best technique overall for determination of summary statistics was the nonparametric Kaplan-Meier technique. ROS and the two substitution methods of assigning one-half the detection limit value to censored data or assigning a random number between zero and the detection limitto censored data were adequate alternatives. The use of these two substitution methods, however, requires a thorough understanding of how the laboratory censored the data. The technique of employing all instrument-generated data--including numbers below the detection limit--was found to be less adequate than the above techniques. At high degrees of censoring (greater than 70% censored data), no technique provided good estimates of summary statistics. Maximum likelihood techniques were found to be far inferior to all other treatments except substituting zero or the detection limit value to censored data.

Assignment and extracting dynamics from experimentally and theoretically obtained spectroscopic hamiltonians in the complex spectral and classically chaotic regions.

An analysis of existing algebraic multiresonance spectroscopic Hamiltonians, derived by fitting to experimental data or from classical canonical or quantum Van Vleck perturbation theory, allows without any significant further classical or quantum calculation the assignment of quantum numbers and motions to states observed in spectra that were previously thought to be irregular or just unassignable. In such cases, inspection of the amplitude and phase of eigenfunctions previously calculated in the Hamiltonians derivation process but now transformed to a reduced dimension semiclassical action-angle representation reveals extremely simple albeit unfamiliar topologies that give quantum numbers by simply counting nodes and phase advances. The topology allows these simple wave functions to be sorted into dynamically different excitation ladders or classes of states which are associated with different regions of phase space. The rungs of these ladders or the states in the classes intersperse in energy causing the spectral complexity. No experimental procedure allows such sorting. The success of the work stems from (1) the qualitative insights of nonlinear dynamics, (2) the conversion of the quantum problem in full dimension to a semiclassical one in reduced dimension by use of a canonical transform that takes advantage of the polyad and other constants of the motion, and (3) the judicious choice of the reduced angle variables to reflect rational ratio resonance frequency conditions. This leads to localization of those semiclassical wave functions, which are affected by the particular resonance. In reverse, the localized appearance of the reduced dimension wave function reveals which resonances govern it and makes sorting visually simple. The success of the work also stems from (4) the revealing use of plots of phase advances as well as the usual densities of the eigenstates for sorting and assignment purposes. Even in classically chaotic regions, organizing trajectories, which correspond to averages over regional phase space structures that need not be computed, can easily be drawn as the structure about which eigenfunction localization takes place. The organizing trajectories when transformed back to the full dimensional configuration space reveal the internal molecular motions. The complexity of the usual quantum stationary and propagated wave functions and associated classical trajectories forbids most often such assignments and sorting. This procedure brings the ability to interpret complex vibrational spectra to a degree previously thought possible only for lower excitations. The new methodology replaces and extends the computationally more difficult parts of a procedure used by the authors that was applied successfully to several molecules during the past few years. The new methodology is applied to DCO, CHBrClF, and the bending of acetylene.

Assignment and extraction of dynamics of a small molecule with a complex vibrational spectrum: thiophosgene.

The dispersed fluorescence spectrum of the ground electronic state of thiophosgene, SCCl2, is analyzed in a very complex region of vibrational excitation, 7000-9000 cm(-1). The final result is that most of the inferred excited vibrational levels are assigned in terms of approximate constants of the motion. Furthermore, each level is associated with a rung on a ladder of quantum states on the basis of common reduced dimension fundamental motions. The resulting ladders cannot be identified by any experimental means, and it is the interspersing in energy of their rungs that makes the spectrum complex even after the process of level separation into polyads. Van Vleck perturbation theory is used to create polyad constants of the motion and a spectroscopic Hamiltonian from a potential fitted to experimental data. The eigen functions of this spectroscopic Hamiltonian are rewritten as semiclassical wave functions and transformed to a representation that allows us to analyze and assign the spectra with no other work other than to utilize concepts from nonlinear dynamics.

Chemical loading into surface water along a hydrological, biogeochemical, and land use gradient: a holistic watershed approach.

Identifying the sources and impacts of organic and inorganic contaminants at the watershed scale is a complex challenge because of the multitude of processes occurring in time and space. Investigation of geochemical transformations requires a systematic evaluation of hydrologic, landscape, and anthropogenic factors. The 1160 km2 Boulder Creek Watershed in the Colorado Front Range encompasses a gradient of geology, ecotypes, climate, and urbanization. Streamflow originates primarily as snowmelt and shows substantial annual variation. Water samples were collected along a 70-km transect during spring-runoff and base-flow conditions, and analyzed for major elements, trace elements, bulk organics, organic wastewater contaminants (OWCs), and pesticides. Major-element and trace-element concentrations were low in the headwaters, increased through the urban corridor, and had a step increase downstream from the first major wastewater treatment plant (WWTP). Boron, gadolinium, and lithium were useful inorganic tracers of anthropogenic inputs. Effluent from the WWTP accounted for as much as 75% of the flow in Boulder Creek and was the largest chemical input. Under both hydrological conditions, OWCs and pesticides were detected in Boulder Creek downstream from the WWTP outfall as well as in the headwater region, and loads of anthropogenic-derived contaminants increased as basin population density increased. This report documents a suite of potential endocrine-disrupting chemicals in a reach of stream with native fish populations showing indication of endocrine disruption.

Accumulation of contaminants in fish from wastewater treatment wetlands.

Increasing demands on water resources in arid environments make reclamation and reuse of municipal wastewater an important component of the water budget. Treatment wetlands can be an integral part of the water-reuse cycle providing both water-quality enhancement and habitat functions. When used for habitat, the bioaccumulation potential of contaminants in the wastewater is a critical consideration. Water and fish samples collected from the Tres Rios Demonstration Constructed Wetlands near Phoenix, Arizona, which uses secondary-treated wastewater to maintain an aquatic ecosystem in a desert environment, were analyzed for hydrophobic organic compounds (HOC) and trace elements. Semipermeable membrane devices (SPMD) were deployed to investigate uptake of HOC. The wetlands effectively removed HOC, and concentrations of herbicides, pesticides, and organic wastewater contaminants decreased 40-99% between inlet and outlet. Analysis of Tilapia mossambica and Gambusia affinis indicated accumulation of HOC, including p,p'-DDE and trans-nonachlor. The SPMD accumulated the HOC detected in the fish tissue as well as additional compounds. Trace-element concentrations in whole-fish tissue were highly variable, but were similar between the two species. Concentrations of HOC and trace elements varied in different fish tissue compartments, and concentrations in Tilapia liver tissue were greater than those in the whole organism or filet tissue. Bioconcentration factors for the trace elements ranged from 5 to 58,000 and for the HOC ranged from 530 to 150,000.