Evaluating the Suitability of Linear and Nonlinear Regression Approaches for the Langmuir Adsorption Model as Applied toward Biomass-Based Adsorbents: Testing Residuals and Assessing Model Validity.

Regression analysis is a powerful tool in adsorption studies. Researchers often favor linear regression for its simplicity when fitting isotherm models, such as the Langmuir equation. Validating regression assumptions is crucial to ensure that the model accurately represents the data and allows appropriate inferences. This study provides a detailed examination of assumption checking in the context of adsorption studies while simultaneously evaluating the robustness of linear regression methods for fitting the Langmuir equation to isotherm data from 2,4-dichlorophenol (DCP) adsorption onto various biomass-based adsorbents and activated carbon. Different linearized Langmuir equations (Hanes-Woolf, Lineweaver-Burk, Eadie-Hofstee, and Scatchard) were compared to nonlinear regression, and each method was validated by rigorous residual checking. This included visual plots of residuals as well as statistical tests, including the Durbin-Watson test for autocorrelation (independence), the Shapiro-Wilk test for normality, and the White test for homoscedasticity. Key findings indicate that the Hanes-Woolf (type 1) and Lineweaver-Burk (type 2) linearizations were the best for most biomass adsorbents studied and that Eadie-Hofstee (type 3) and Scatchard (type 4) were generally invalid due to the negative parameters or assumption violations. For activated carbon, all linearization methods were unsuitable due to independence violations. In the case of nonlinear regression, there were no major assumption violations for all of the adsorbents. Symbolic regression identified the Langmuir equation only for activated carbon (AC). This study revealed shortcomings in relying solely on linearized Langmuir models. A proposed workflow recommends using nonlinear or weighted nonlinear regression, starting with Hanes-Woolf or Lineweaver-Burk linearization results as initial values for parameter estimation. If assumptions remain violated with nonlinear techniques, novel methods such as symbolic regression should be employed. This advanced regression technique can improve adsorption models' accuracy and predictive behavior without the stringent need for assumption checking. Symbolic regression can also aid in understanding mechanisms of novel adsorbents.

The Interplay of Binary and Quantitative Structure on the Stability of Mutualistic Networks.

Understanding how the structure of biological systems impacts their resilience (broadly defined) is a recurring question across multiple levels of biological organization. In ecology, considerable effort has been devoted to understanding how the structure of interactions between species in ecological networks is linked to different broad resilience outcomes, especially local stability. Still, nearly all of that work has focused on interaction structure in presence-absence terms, and has not investigated quantitative structure, i.e., the arrangement of interaction strengths in ecological networks. We investigated how the interplay between binary and quantitative structure impacts stability in mutualistic interaction networks (those in which species interactions are mutually beneficial), using community matrix approaches. We additionally examined the effects of network complexity and within-guild competition for context. In terms of structure, we focused on understanding the stability impacts of nestedness, a structure in which more-specialized species interact with smaller subsets of the same species that more-generalized species interact with. Most mutualistic networks in nature display binary nestedness, which is puzzling because both binary and quantitative nestedness are known to be destabilizing on their own. We found that quantitative network structure has important consequences for local stability. In more-complex networks, binary-nested structures were the most stable configurations, depending on the quantitative structures; but which quantitative structure was stabilizing depended on network complexity and competitive context. As complexity increases, and in the absence of within-guild competition, the most stable configurations have a nested binary structure with a complementary (i.e., anti-nested) quantitative structure. In the presence of within-guild competition, however, the most stable networks are those with a nested binary structure and a nested quantitative structure. In other words, the impact of interaction-overlap on community persistence is dependent on the competitive context. These results help to explain the prevalence of binary nested structures in nature and underscore the need for future empirical work on quantitative structure.

Faster-growing parasites threaten host populations via patch-level population dynamics and higher virulence; a case study in Varroa mites (Mesostigmata: Varroidae) and honey bees (Hymenoptera: Apidae).

Honey bee parasites remain a critical challenge to management and conservation. Because managed honey bees are maintained in colonies kept in apiaries across landscapes, the study of honey bee parasites allows the investigation of spatial principles in parasite ecology and evolution. We used a controlled field experiment to study the relationship between population growth rate and virulence (colony survival) of the parasite Varroa destructor (Anderson and Trueman). We used a nested design of 10 patches (apiaries) of 14 colonies to examine the spatial scale at which Varroa population growth matters for colony survival. We tracked Varroa population size and colony survival across a full year and found that Varroa populations that grow faster in their host colonies during the spring and summer led to larger Varroa populations across the whole apiary (patch) and higher rates of neighboring colony loss. Crucially, this increased colony loss risk manifested at the patch scale, with mortality risk being related to spatial adjacency to colonies with fast-growing Varroa strains rather than with Varroa growth rate in the colony itself. Thus, within-colony population growth predicts whole-apiary virulence, demonstrating the need to consider multiple scales when investigating parasite growth-virulence relationships.

Validity of the brief executive-function assessment tool in an outpatient substance use disorder setting.

The Brief Executive-function Assessment Tool (BEAT) was developed and validated for use in residential substance use disorder treatment settings, where participants are mostly abstinent. It is therefore unclear whether the BEAT is valid for use in outpatient settings, where participants may be actively using substances. The effects of acute intoxication and withdrawal have the potential to alter the results of the BEAT. The current study sought to establish construct and criterion validity of the BEAT in an outpatient substance use disorder sample and to detect its sensitivity to substance use over the previous 24 hours and also over the past month. A total of 74 clients of a New South Wales-based outpatient substance use disorder service participated in the current study. Construct validity was demonstrated by significant correlations between the BEAT and three performance-based tests of executive functioning. Criterion validity was established in that the BEAT discriminated between those deemed impaired or not on a criterion composite measure of executive functioning. Test operating characteristics (88% sensitivity, 69% specificity, 44% PPV, and 95% NPV) were also established relative to this composite measure as a reference standard. The BEAT was insensitive to use/abstinence over the previous 24 hours and the past month.

Prevalence, Laterality, and Classification of Ossified Petroclival Ligaments: An Anatomical and Histological Study With Application to Skull Base Surgery.

Background The petroclival ligament (PL) forms the roof of Dorello's canal (DC). In humans, partial and complete ossification of this ligament have been reported. When completely ossified, DC is transformed into a bony foramen for the abducens nerve and accompanying vascular structures. As this osteological finding might have an impact on skull base surgery, this anatomical study was performed. Methodology Using 100 adult human skulls, the presence of an ossified PL was noted and classified. The diameter of the resultant bony foramen and laterality were documented. Additionally, PL was evaluated histologically in 10 heads. Results Overall, 8% of the sides were found to have partial or complete ossification of the PL. Partial ossification (type I) was noted on 3% of the sides. Completely ossified PL was identified on 5% of the sides. Some ossified ligaments (2.5%) were seen as an ossified bridge (type II), and others (2.5%) were converted into small foramina (type III). Three skulls (3%) were found to have a completely ossified ligament bilaterally. The mean diameter of the underlying DC was 0.8 mm. Partially ossified ligaments were statistically more likely to be on the right sides, and the diameter of the underlying DC was statistically smaller in type III. Histologically, the PL was found to have bone within it on three skull sides. Conclusions An ossified ligament can be found on imaging of the skull base. Moreover, during surgical approaches to the petroclival region and, specifically, DC, skull base surgeons should be cognizant of this anatomical variation.

Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.

Differences in individual flowering time change pollen limitation and seed set in three montane wildflowers.

PREMISE: Changes to flowering time caused by climate change could affects plant fecundity, but studies that compare the individual-level responses of phenologically distinct, co-occurring species are lacking. We assessed how variation in floral phenology affects the fecundity of individuals from three montane species with different seasonal flowering times, including in snowmelt acceleration treatments to increase variability in phenology. METHODS: We collected floral phenology and seed set data for individuals of three montane plant species (Mertensia fusiformis, Delphinium nuttallianum, Potentilla pulcherrima). To examine the drivers of seed set, we measured conspecific floral density and conducted pollen limitation experiments to isolate pollination function. We advanced the phenology of plant communities in a controlled large-scale snowmelt acceleration experiment. RESULTS: Differences in individual phenology relative to the rest of the population affected fecundity in our focal species, but effects were species-specific. For our early-season species, individuals that bloomed later than the population peak bloom had increased fecundity, while for our midseason species, simply blooming before or after the population peak increased individual fecundity. For our late-season species, blooming earlier than the population peak increased fecundity. The early and midseason species were pollen-limited, and conspecific density affected seed set only for our early-season species. CONCLUSIONS: Our study shows that variation in individual phenology affects fecundity in three phenologically distinct montane species, and that pollen limitation may be more influential than conspecific density. Our results suggest that individual-level changes in phenology are important to consider for understanding plant reproductive success.

Loss of endangered frugivores from seed dispersal networks generates severe mutualism disruption.

Many tropical seed-dispersing frugivores are facing extinction, but the consequences of the loss of endangered frugivores for seed dispersal is not well understood. We investigated the role of frugivore endangerment status via robustness-to-coextinction simulations (in this context, more accurately described as robustness-to-partner-loss simulations) using data from the Brazilian Atlantic Forest biodiversity hotspot. By simulating the extinction of endangered frugivores, we found a rapid and disproportionate loss of tree species with dispersal partners in the network, and this surprisingly surpassed any other frugivore extinction scenario, including the loss of the most generalist frugivores first. A key driver of this pattern is that many specialist plants rely on at-risk frugivores as seed-dispersal partners. Moreover, interaction compensation in the absence of endangered frugivores may be unlikely because frugivores with growing populations forage on fewer plant species than frugivores with declining populations. Therefore, protecting endangered frugivores could be critical for maintaining tropical forest seed dispersal, and their loss may have higher-than-expected functional consequences for tropical forests, their regeneration processes, and the maintenance of tropical plant diversity.

Toxicity of perfluoroalkyl substances (PFAS) toward embryonic stages of mahi-mahi (Coryphaena hippurus).

Perfluoroalkyl substances (PFAS) are highly persistent organic pollutants that have been detected in a wide array of environmental matrices and, in turn, diverse biota including humans and wildlife wherein they have been associated with a multitude of toxic, and otherwise adverse effects, including ecosystem impacts. In the present study, we developed a toxicity assay for embryonic stages of mahi-mahi (Coryphaena hippurus), as an environmentally relevant pelagic fish species, and applied this assay to the evaluation of the toxicity of "legacy" and "next-generation" PFAS including, respectively, perfluorooctanoic acid (PFOA) and several perfluoroethercarboxylic acids (PFECA). Acute embryotoxicity, in the form of lethality, was measured for all five PFAS toward mahi-mahi embryos with median lethal concentrations (LC50) in the micromolar range. Consistent with studies in other similar model systems, and specifically the zebrafish, embryotoxicity in mahi-mahi generally (1) correlated with fluoroalkyl/fluoroether chain length and hydrophobicity, i.e., log P, of PFAS, and thus, aligned with a role of uptake in the relative toxicity; and (2) increased with continuous exposure, suggesting a possible role of development stage specifically including a contribution of hatching (and loss of protective chorion) and/or differentiation of target systems (e.g., liver). Compared to prior studies in the zebrafish embryo model, mahi-mahi was significantly more sensitive to PFAS which may be related to differences in either exposure conditions (e.g., salinity) and uptake, or possibly differential susceptibility of relevant targets, for the two species. Moreover, when considered in the context of the previously reported concentration of PFAS within upper sea surface layers, and co-localization of buoyant eggs (i.e., embryos) and other early development stages (i.e., larvae, juveniles) of pelagic fish species to the sea surface, the observed toxicity potentially aligns with environmentally relevant concentrations in these marine systems. Thus, impacts on ecosystems including, in particular, population recruitment are a possibility. The present study is the first to demonstrate embryotoxicity of PFAS in a pelagic marine fish species, and suggests that mahi-mahi represents a potentially informative, and moreover, environmentally relevant, ecotoxicological model for PFAS in marine systems.

Upper-limit agricultural dietary exposure to streptomycin in the laboratory reduces learning and foraging in bumblebees.

In the past decade, the broadcast-spray application of antibiotics in US crops has increased exponentially in response to bacterial crop pathogens, but little is known about the sublethal impacts on beneficial organisms in agroecosystems. This is concerning given the key roles that microbes play in modulating insect fitness. A growing body of evidence suggests that insect gut microbiomes may play a role in learning and behaviour, which are key for the survival of pollinators and for their pollination efficacy, and which in turn could be disrupted by dietary antibiotic exposure. In the laboratory, we tested the effects of an upper-limit dietary exposure to streptomycin (200 ppm)-an antibiotic widely used to treat bacterial pathogens in crops-on bumblebee (Bombus impatiens) associative learning, foraging and stimulus avoidance behaviour. We used two operant conditioning assays: a free movement proboscis extension reflex protocol focused on short-term memory formation, and an automated radio-frequency identification tracking system focused on foraging. We show that upper-limit dietary streptomycin exposure slowed training, decreased foraging choice accuracy, increased avoidance behaviour and was associated with reduced foraging on sucrose-rewarding artificial flowers flowers. This work underscores the need to further study the impacts of antibiotic use on beneficial insects in agricultural systems.

The effects of pollinator diversity on pollination function.

Pollination is a key ecological function of most terrestrial ecosystems. Decades of research on single-trophic-level communities, particularly plant communities, have helped to build the foundation of diversity-function theory. Yet as it stands, this theory appears to be less useful for intertrophic-level functions such as pollination, as evidenced by empirical findings that are often inconsistent with theoretical expectations. In this review, we evaluate how canonical diversity-function theory has been applied to pollination function, focusing on empirical studies of the mechanisms that drive pollinator diversity-function relationships. We first identified key features of pollination function that have hampered reconciliation with current theory. We then examined terminology for mechanisms used to discuss the findings from pollinator diversity-function studies that are sometimes inconsistent with established ecological concepts. We propose a revised diversity-function framework and describe two non-canonical diversity-function mechanisms that are particularly applicable to pollination. The first, "interactive functional complementarity," was identified previously but remains overlooked. The second, a new diversity-function mechanism, "functional enhancement," occurs when pollinator diversity increases within-niche activity. Finally, we discuss experimental approaches necessary to detect diversity-function effects in pollination.

Brief executive-function assessment tool: A new cognitive impairment screening tool for alcohol and other drug services.

Accurate screening for cognitive impairment in alcohol and other drug (AOD) services would help to identify individuals who may need supports to obtain the greatest benefit from substance use disorder (SUD) treatment. At present there is no screening measure that has been developed specifically to detect cognitive impairment in a SUD population. This study examines the psychometric properties of the Brief Executive-function Assessment Tool (BEAT), which was specifically designed for this purpose. This study involving 501 individuals with SUD and 145 normal control participants established internal consistency (n = 646; 0.734), interrater (n = 60; 0.994), and test-retest reliability (n = 177; 0.845), and construct (all correlations p ≤ 0.05), and criterion (n = 467; ANCOVA p < 0.001) validity. Test operating characteristics (n = 500; 87% sensitivity, 71% specificity, 21% PPP, and 99% NPP) were also established relative to an independent criterion variable made up of three established performance-based neuropsychological tests. Findings support the reliability and validity of the BEAT as a screening measure of executive function impairment with high sensitivity and a low rate of false negatives.

Trade-offs Among Resilience, Robustness, Stability, and Performance and How We Might Study Them.

Biological systems are likely to be constrained by trade-offs among robustness, resilience, and performance. A better understanding of these trade-offs is important for basic biology, as well as applications where biological systems can be designed for different goals. We focus on redundancy and plasticity as mechanisms governing some types of trade-offs, but mention others as well. Whether trade-offs are due to resource constraints or "design" constraints (i.e., structure of nodes and links within a network) will also affect the types of trade-offs that are important. Identifying common themes across scales of biological organization will require that researchers use similar approaches to quantifying robustness, resilience, and performance, using units that can be compared across systems.

Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures.

Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.

Yield of clinically reportable genetic variants in unselected cerebral palsy by whole genome sequencing.

Cerebral palsy (CP) is the most common cause of childhood physical disability, with incidence between 1/500 and 1/700 births in the developed world. Despite increasing evidence for a major contribution of genetics to CP aetiology, genetic testing is currently not performed systematically. We assessed the diagnostic rate of genome sequencing (GS) in a clinically unselected cohort of 150 singleton CP patients, with CP confirmed at >4 years of age. Clinical grade GS was performed on the proband and variants were filtered, and classified according to American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines. Variants classified as pathogenic or likely pathogenic (P/LP) were further assessed for their contribution to CP. In total, 24.7% of individuals carried a P/LP variant(s) causing or increasing risk of CP, with 4.7% resolved by copy number variant analysis and 20% carrying single nucleotide or indel variants. A further 34.7% carried one or more rare, high impact variants of uncertain significance (VUS) in variation intolerant genes. Variants were identified in a heterogeneous group of genes, including genes associated with hereditary spastic paraplegia, clotting and thrombophilic disorders, small vessel disease, and other neurodevelopmental disorders. Approximately 1/2 of individuals were classified as likely to benefit from changed clinical management as a result of genetic findings. In addition, no significant association between genetic findings and clinical factors was detectable in this cohort, suggesting that systematic sequencing of CP will be required to avoid missed diagnoses.

Increased oscillatory power in a computational model of the olfactory bulb due to synaptic degeneration.

Several neurodegenerative diseases impact the olfactory system, and in particular the olfactory bulb, early in disease progression. One mechanism by which damage occurs is via synaptic dysfunction. Here, we implement a computational model of the olfactory bulb and investigate the effect of weakened connection weights on network oscillatory behavior. Olfactory bulb network activity can be modeled by a system of equations that describes a set of coupled nonlinear oscillators. In this modeling framework, we propagate damage to synaptic weights using several strategies, varying from localized to global. Damage propagated in a dispersed or spreading manner leads to greater oscillatory power at moderate levels of damage. This increase arises from a higher average level of mitral cell activity due to a shift in the balance between excitation and inhibition. That this shift leads to greater oscillations depends critically on the nonlinearity of the activation function. Linearized analysis of the network dynamics predicts when this shift leads to loss of oscillatory activity. We thus demonstrate one potential mechanism involved in the increased gamma oscillations seen in some animal models of Alzheimer's disease, and we highlight the potential that pathological olfactory bulb behavior presents as an early biomarker of disease.

Plant-pollinator interaction niche broadens in response to severe drought perturbations.

The composition of plant-pollinator interactions-i.e., who interacts with whom in diverse communities-is highly dynamic, and we have a very limited understanding of how interaction identities change in response to perturbations in nature. One prediction from niche and diet theory is that resource niches will broaden to compensate for resource reductions driven by perturbations, yet this has not been empirically tested in plant-pollinator systems in response to real-world perturbations in the field. Here, we use a long-term dataset of floral visitation to Ipomopsis aggregata, a montane perennial herb, to test whether the breadth of its floral visitation niche (i.e., flower visitor richness) changed in response to naturally occurring drought perturbations. Fewer floral resources are available in drought years, which could drive pollinators to expand their foraging niches, thereby expanding plants' floral visitation niches. We compared two drought years to three non-drought years to analyze changes in niche breadth and community composition of floral visitors to I. aggregata, predicting broadened niche breadth and distinct visitor community composition in drought years compared to non-drought years. We found statistically significant increases in niche breadth in drought years as compared to non-drought conditions, but no statistically distinguishable changes in community composition of flower visitors. Our findings suggest that plants' floral visitation niches may exhibit considerable plasticity in response to disturbance. This may have widespread consequences for community-level stability as well as functional consequences if increased niche overlap affects pollination services.

DCTN1-ALK gene fusion in inflammatory myofibroblastic tumor (IMT) of the CNS.

PURPOSE: Inflammatory myofibroblastic tumor (IMT) is a rare neoplastic tumor type of intermediate biological potential, only recently distinguished from the non-neoplastic category of inflammatory pseudotumor (IP). The literature describes very few cases of IMTs arising in the central nervous system (CNS), and the distinguishing clinical, pathological, and molecular features of IMT-CNS are not well understood. Our purpose is to publish a case of an IMT-CNS with a novel DCTN1-ALK gene fusion, furthering in the literature's characterization of a rare tumor type. METHODS: Review of the literature included a PubMed Database search of articles found by the following searches: "Inflammatory myofibroblastic tumor;" "Inflammatory myofibroblastic tumor central nervous system;" "ALK gene fusion;" and "DCTN1-ALK gene fusion." Inclusion of articles discovered by these search terms was determined through critical appraisal of article relevance, number of citations, cross-citation within articles of interest, and rare findings with conflicting conclusions in an effort to reduce publication bias. RESULTS: We present a case of IMT-CNS with several distinctive molecular features including a DCTN1-ALK gene fusion, the first of its kind described in an intracranial IMT. CONCLUSION: IMT is an infrequent tumor type and its presentation within the CNS is exceedingly rare. The paucity of cases, along with the ambiguity of terminology in the literature, has stunted accurate clinical, pathological, and molecular characterization of IMT-CNS. Our case report improves the characterization of the recently appreciated category of IMT-CNS so that connections between phenotype and prognosis, and between genotype and treatment, can eventually be made.