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Portable smartphone integrated paper sensors for fluorescence detection of As(III) in groundwater

Arsenic contamination in groundwater is a supreme environmental problem, and levels of this toxic metalloid must be strictly monitored by a portable, sensitive and selective analytical device. Herein, a new system of smartphone integrated paper sensors with Cu nanoclusters was established for the effective detection of As(III) in groundwater. For the integration system, the fluorescence emissive peak of Cu nanoclusters at 600 nm decreased gradually with increasing As(III) addition. Meanwhile, the fluorescence color also changed from orange to colorless, and the detection limit was determined as 2.93 nM (0.22 ppb) in a wide detection range. The interfering ions also cannot influence the detection selectivity of As(III). Furthermore, the portable paper sensors based on Cu nanoclusters were fabricated for visual detection of As(III) in groundwater. The quantitative determination of As(III) in natural groundwater has also been accomplished with the aid of a common smartphone. Our work has provided a portable and on-site detection technique toward As(III) in groundwater with high sensitivity and selectivity.

Drought risk of global terrestrial gross primary productivity in recent 40 years detected by a remote sensing-driven process model

Gross primary productivity (GPP) is the largest flux in the global terrestrial carbon cycle and affected by multiple factors. In recent decades, drought has significantly impacted global terrestrial GPP and been projected to occur with increasing frequency and intensity. However, the drought risk of global terrestrial GPP has not been well investigated. In this study, global terrestrial GPP over the period from 1981 to 2016 was simulated with the process-based Boreal Ecosystem Productivity Simulator (BEPS) model. Then, the drought risk of terrestrial GPP was quantified as the product of frequency of drought and reduction of GPP caused by drought, which were determined using the standardized precipitation evapotranspiration index (SPEI). During the study period, the drought risk of terrestrial GPP exhibited detectable spatial heterogeneity, high in southeastern United States, most of South America, southern Europe, central and eastern Africa, eastern and southeastern Asia, and eastern Australia. In these regions, the maximum reduction of GPP might be above 30% in drought years relative to that in normal years. The drought risk of GPP was low at high latitudes of the Northern Hemisphere, in which terrestrial GPP increased slightly in drought years. The spatial pattern of the drought risk of GPP simulated by the BEPS model was close to that of FLUXCOM GPP, which was scaled from tower observations with a machine learning algorithm forced by remote sensing and meteorological data. This study advances our understanding on the impact of drought on terrestrial GPP over the globe.

Dendritic coincidence detection in Purkinje neurons of awake mice

Dendritic coincidence detection is thought fundamental to neuronal processing yet remains largely unexplored in awake animals. Specifically, the underlying dendritic voltage-calcium relationship has not been directly addressed. Here, using simultaneous voltage and calcium two-photon imaging of Purkinje neuron spiny dendrites, we show how coincident synaptic inputs and resulting dendritic spikes modulate dendritic calcium signaling during sensory stimulation in awake mice. Sensory stimulation increased the rate of post-synaptic potentials and dendritic calcium spikes evoked by climbing fiber and parallel fiber synaptic input. These inputs are integrated in a time-dependent and non-linear fashion to enhance the sensory evoked dendritic calcium signal. Intrinsic supralinear dendritic mechanisms, including voltage-gated calcium channels and metabotropic glutamate receptors, are recruited cooperatively to expand the dynamic range of sensory evoked dendritic calcium signals. This establishes how dendrites can use multiple interplaying mechanisms to perform coincidence detection, as a fundamental and ongoing feature of dendritic integration in behaving animals.

Validation of an eDNA-based method for the detection of wildlife pathogens in water

Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in-situ filtration of large volume water samples, developed to detect and quantify aquatic wildlife parasites by qPCR. We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80 %, but detection was not consistent among replicate samples. Within tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable and significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges of eDNA-based methods for detection of parasites in water.

opencc-zeroJan 2021View details →

Nerve ultrasound improves detection of treatment-responsive chronic inflammatory neuropathies

Objective To examine the diagnostic accuracy of nerve ultrasound in a prospective cohort of consecutive patients with a clinical suspicion of chronic inflammatory neuropathies, including chronic inflammatory demyelinating polyneuropathy, Lewis Sumner syndrome and multifocal motor neuropathy, and to determine the added value in the detection of treatment-responsive patients. Methods Between February 2015 and July 2018, we included 100 consecutive incident patients with a clinical suspicion of chronic inflammatory neuropathy. All patients underwent nerve ultrasound, extensive standardized nerve conduction studies (NCS) and other relevant diagnostic investigations. We evaluated treatment response using predefined criteria. A diagnosis of chronic inflammatory neuropathy was established when NCS were abnormal (fulfilling criteria of demyelination of the EFNS/PNS) or when the degree of nerve enlargement detected by sonography was compatible with chronic inflammatory neuropathy and there was response to treatment. Results A diagnosis of chronic inflammatory neuropathy was established in 38 patients. Sensitivity and specificity of nerve ultrasound and NCS were 97.4% and 69.4%, and 78.9% and 93.5%, respectively. The added value of nerve ultrasound in detection of treatment-responsive chronic inflammatory neuropathy patients was 21.1% compared to NCS alone. Conclusions Nerve ultrasound and NCS are complementary techniques with superior sensitivity in the former and specificity in the latter. Addition of nerve ultrasound significantly improves the detection of chronic inflammatory neuropathies. Therefore, it deserves a prominent place in the diagnostic workup of chronic inflammatory neuropathies. Classification of Evidence This study provides Class I evidence that nerve ultrasound is an accurate diagnostic tool to detect chronic inflammatory neuropathies.

opencc-zeroDec 2015View details →

Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.

Data from: Detecting macroevolutionary self-destruction from phylogenies

Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focused on "positive" lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent "negative" lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this article, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. "Self-destructive" traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of "tippiness" as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain, and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work "backwards" to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, color polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self-destruction by considering the number of tips with the trait that arise from each inferred origin, and the degree to which the trait is scattered across the phylogeny. These metrics, and the methods we present, may be useful for testing macroevolutionary hypotheses from phylogenetic patterns.

Data from: Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish

Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 μm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2–0.6 μm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.

opencc-zeroDec 2013View details →

Data from: Detecting cryptic indirect genetic effects

Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the phenotype of an interacting partner. IGEs can dramatically affect the expression and evolution of social traits. However, the interacting phenotype(s) through which they are transmitted are often unknown, or cryptic, and their detection would enhance our ability to accurately predict evolutionary change. To illustrate this challenge and possible solutions to it, we assayed male leg tapping behaviour using inbred lines of Drosophila melanogaster paired with a common focal male strain. The expression of tapping in focal males was dependent on the genotype of their interacting partner, but this strong IGE was cryptic. Using a multiple-regression approach, we identified male startle response as a candidate interacting phenotype: the longer it took interacting males to settle after being startled, the less focal males tapped them. A genome-wide association analysis identified approximately a dozen candidate protein-coding genes potentially underlying the IGE, of which the most significant was slowpoke. Our methodological framework provides information about candidate phenotypes and candidate SNPs that underpin a strong yet cryptic IGE. We discuss how this approach can facilitate the detection of cryptic IGEs contributing to unusual evolutionary dynamics in other study systems.

opencc-zeroDec 2013View details →

Data from: Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.

opencc-zeroDec 2016View details →

Data from: Pregnancy is detected via odour in a wild cooperative breeder

Among mammals, scent has long been known to encode oestrus; however, in many species, detecting pregnancy may also be important in terms of both competition and mate-choice. Here, we show, through odour presentation experiments, that pregnancy is discernible via scent by both sexes in the cooperatively breeding banded mongoose, Mungos mungo. Males spent more time investigating and were more likely to scent mark the odours of non-pregnant females, compared to pregnant females. Females showed increased levels of scent marking when odours were of the same reproductive state as themselves. These results present the first direct demonstration that pregnancy is detectable via scent in wild cooperative breeders. Detecting pregnancy may be particularly important in cooperative breeders as, in addition to the competition between males for receptive mates, there is also intense competition between females for access to alloparental care. Consequently, dominant females benefit from targeting reproductive suppression towards subordinates that represent direct threats, such as pregnant females.

Data from: Detection and polarization of introgression in a five-taxon phylogeny

When multiple speciation events occur rapidly in succession, discordant genealogies due to incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of methods, including the D-statistic (a.k.a. the "ABBA–BABA test"), have been proposed to infer introgression in the presence of ILS for a four-taxon clade. However, no integrated method exists to detect introgression using allelic patterns for more complex phylogenies. Here we explore the issues associated with previous systems of applying D-statistics to a larger tree topology, and propose new DFOIL tests as an integrated framework to infer both the taxa involved in and the direction of introgression for a symmetric five-taxon phylogeny. Using theory and simulations, we show that the DFOIL statistics correctly identify the introgression donor and recipient lineages, even at low rates of introgression. DFOIL is also shown to have extremely low false-positive rates. The DFOIL tests are computationally inexpensive to calculate and can easily be applied to phylogenomic data sets, both genome-wide and in windows of the genome. In addition, we explore both the principles and problems of introgression detection in even more complex phylogenies.

opencc-zeroDec 2017View details →

Data from: Validation of a non-invasive method for the early detection of metabolic syndrome: a diagnostic accuracy test in a working population

Objectives. A non-invasive method for the early detection of Metabolic Syndrome (NIN-MetS) using only Waist to Height Ratio (WHtR) and Blood Pressure (BP) has recently been published, with fixed cut-off values for gender and age. The aim of this study was to validate this method in a large sample of Spanish workers. Design. A diagnostic test accuracy to assess the validity of the method was performed. Setting. Occupational Health Services. Participants. The studies were conducted in 2012-2016 on a sample of 60,799 workers from the Balearic Islands (Spain). Interventions. The NCEP-ATP III criteria were used as the gold standard. NIM-MetS has been devised using classification trees (the CHAID, Chi-squared Automatic Interaction Detection method). Main outcome measures. Anthropometric and biochemical variables to diagnose MetS. Sensitivity, specificity, validity index and Youden Index were determined to analyse the accuracy of the diagnostic test (NIM-MetS). Results. Regarding the validation of the method, sensitivity was 54.7%, specificity 94.9% and validity index 91.2%. The cut-off value for WHtR was 0.54, ranging from 0.51 (lower age group) to 0.56 (higher) in the age groups. Variables more closely associated with MetS were WHtR (AUC=0.85; 95% CI: 0.84-0.86) and Systolic Blood Pressure (AUC=0.79; 95% CI: 0.78-0.80). The final cut-off values for the non-invasive method were WHtR≥0.56 and BP≥128/80 mmHg, which includes four levels of MetS risk (very low, low, moderate and high). Conclusions. The analysed method has shown a high validity index (higher than 91%) for the early detection of MetS. It is a non-invasive method easy to apply and interpret in any health care setting. This method provides a scale of MetS risk which allows a more accurate detection and a more effective intervention.

Data from: Research design considerations to ensure detection of all species in an avian community

1.Recent advances in the estimation of species richness from count data have allowed avian ecologists to incorporate incomplete detectability of species when comparing richness across space or time. Raw counts from single or repeated visits to sample point(s) are nonetheless still used for assessing community composition, and the failure to account for detectability when making these evaluations may lead to incorrect inferences about the community. 2.We estimated detection probabilities (p) for a suite of bird species and used these detection probabilities to determine the minimum number of visits at a single point and the minimum number of points in a grid required to confidently (≥ 90%) detect the full community of birds for rare, moderately rare, and common species. We used occupancy modeling to estimate the detection probabilities for species from two study sites in Nebraska and Saskatchewan. 3.Some common or highly detectable species were confidently detected in a single visit to a point, whereas others with low detection probabilities (p < 0.20) required more than ten visits to be confidently detected at a point. The grid size required to detect a species in an area varied from a single point for a common highly detectable species to over 30 points for a rare species with low detectability. 4.Detection probabilities of the least detectable species in a study area can be used to determine the number of visits to a single point or the number of points in a grid to be confident that the full community is detected. Biologists can conclude that a species is most likely absent from the community if it remains undetected using the appropriate sampling effort.

opencc-zeroDec 2016View details →

Data from: Drosophila increase exploration after visually detecting predators

Novel stimuli elicit behaviors that are collectively known as specific exploration. These behaviors allow the animal to become more familiar with the novel objects within its environment. Specific exploration is frequently suppressed by defensive reactions to predator cues. Herein, we examine if this suppression occurs in Drosophila melanogaster by measuring the response of these flies to wild harvested predators. The flies used in our experiments have been cultured and had not lived under predator threat for multiple decades. In a circular arena with centrally-caged predators, wild type Drosophila actively avoided the pantropical jumping spider, Plexippus paykulli, and the Texas unicorn mantis, Phyllovates chlorophaena, indicating an innate defensive reaction to these predators. Interestingly, wild type Drosophila males also avoided a centrally-caged mock spider, and the avoidance of the mock spider became exaggerated when it was made to move within the cage. Visually impaired Drosophila failed to detect and avoid the Plexippus paykulli and the moving mock spider, while the broadly anosmic orco2 mutants were fully capable of detecting and avoiding Plexippus paykulli, indicating that these flies principally relied upon vison to perceive the predator stimuli. During early exploration of the arena, exploratory activity increased in the presence of Plexippus paykulli and the moving mock spider. The elevated activity induced by Plexippus paykulli disappeared after the fly had finished exploring, suggesting the flies were capable of habituating the predator cues. Taken together, these results indicate that despite being isolated from predators for decades Drosophila will visually detect these predators, retain innate defensive behaviors, respond by increasing exploratory activity in the arena rather than suppressing activity, and may habituate to normal predator cues.

Data from: Allogeneic HY antibodies detected 3 months after female-to-male HCT predict chronic GVHD and nonrelapse mortality in humans

Allogeneic antibodies against minor histocompatibility antigens encoded on the Y chromosome (HY-Abs) develop after hematopoietic cell transplant (HCT) of male recipients with female donors (F→M). However, the temporal association between HY-Ab development and chronic graft-versus-host disease (cGVHD) has yet to be elucidated. We studied 136 adult F→M HCT patients, with plasma prospectively collected through 3 years posttransplant, and measured immunoglobulin G against 6 H-Y antigens. Multiple HY-Abs were frequently detected beginning at 3 months posttransplant: 78 (57%) of F→M patients were seropositive for at least 1 of the 6 HY-Abs, and 3-month seropositivity for each HY-Ab was associated with a persistent seropositive response throughout the posttransplant follow-up period (P < .001 in each). There were no associations between pretransplant features and 3-month overall HY-Ab development. Detection of multiple HY-Abs at 3 months (represented by HY score) was significantly associated with an increased risk of cGVHD (P < .0001) and nonrelapse mortality (P < .01). Compared to clinical factors alone, the addition of HY score to clinical factors improved the predictive potential of cGVHD (P < .01). Monitoring HY-Ab development thus stratifies cGVHD risk in F→M HCT patients and may support preemptive prophylaxis therapy for cGVHD beginning at 3 months posttransplant.

opencc-zeroDec 2013View details →

Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy

RAD-tag is a powerful tool for high-throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome, causing reads to start in the same place, and making it difficult to estimate the extent of PCR duplication. Here, we introduce a slight change to the Illumina sequencing adaptor chemistry, appending a unique four-base tag to the first index read, which allows duplicate discrimination in aligned data. This approach was validated on the Illumina MiSeq platform, using double-digest libraries of ants (Wasmannia auropunctata) and yeast (Saccharomyces cerevisiae) with known genotypes, producing modest though statistically significant gains in the odds of calling a genotype accurately. More importantly, removing duplicates also corrected for strong sample-to-sample variability of genotype calling accuracy seen in the ant samples. For libraries prepared from low-input degraded museum bird samples (Mixornis gularis), which had low complexity, having been generated from relatively few starting molecules, adaptor tags show that virtually all of the genotypes were called with inflated confidence as a result of PCR duplicates. Quantification of library complexity by adaptor tagging does not significantly increase the difficulty of the overall workflow or its cost, but corrects for differences in quality between samples and permits analysis of low-input material.

opencc-zeroDec 2017View details →

Data from: Effect of canine oxytocin receptor gene polymorphism on the successful training of drug detection dogs

Drug detection dogs can be trained to locate various prohibited drugs with targeted odors, and they play an important role in interdiction of drug smuggling in human society. Recent studies provide the interesting hypothesis that the oxytocin system serves as a biological basis for co-evolution between dogs and humans. Here, we offer the new possibility that genetic variation of the canine oxytocin receptor (OXTR) gene may regulate the success of a dog's training to become a drug detection dog. A total of 340 Labrador Retriever dogs that were trained to be drug detection dogs in Japan were analyzed. We genotyped an exonic SNP (rs8679682) in the OXTR gene and compared the training success rate of dogs with different genotypes. We also asked dog trainers in the training facility to evaluate subjective personality assessment scores for each dog, and examined how each dog's training success was related to those scores. A significant effect of the OXTR genotype on the success of the dogs' training was found, with a higher proportion of dogs carrying the C allele (T/C and C/C genotypes) being successful candidates than dogs carrying the T/T genotype. Dog personality scores of Training Focus (Factor 1) were positively correlated with an increased likelihood that a dog would successfully complete training. Although the molecular mechanism of the OXTR gene and its functional pathway related to dog behavior remains unknown, our findings suggest that canine OXTR gene variants may regulate individual differences between dogs in their responsiveness to training for drug detection.