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Respiratory viruses, such as influenza, decrease airway cilia function and expression, which leads to reduced mucociliary clearance and inhibited overall immune defense. Ubiquitination is a posttranslational modification using E3 ligases, which plays a role in the assembly and disassembly of cilia. We examined the role of membrane-associated RING-CH (MARCH) family of E3 ligases during influenza infection and determined that MARCH10, specifically expressed in ciliated epithelial cells, is significantly decreased during influenza infection in mice, human lung epithelial cells, and human lung tissue. Cellular depletion of MARCH10 in differentiated human bronchial epithelial cells (HBECs) using CRISPR/Cas9 showed a decrease in ciliary beat frequency. Furthermore, MARCH10 cellular knockdown in combination with influenza infection selectively decreased immunoreactive levels of the ciliary component, dynein axonemal intermediate chain 1. Cellular overexpression of MARCH10 significantly decreased influenza hemagglutinin protein levels in the differentiated HBECs and knockdown of MARCH10 increased IL-1β cytokine expression, whereas overexpression had the reciprocal effect. These findings suggest that MARCH10 may have a protective role in airway pulmonary host defense and innate immunity during influenza infection.

Hybridization is a complicated, oft-misunderstood process. Once deemed unnatural and uncommon, hybridization is now recognized as ubiquitous among species. But hybridization rates within and among communities are poorly understood despite the relevance to ecology, evolution and conservation. To clarify, we examined hybridization across 75 freshwater fish communities within the Ozarks of the North American Interior Highlands (USA) by single nucleotide polymorphism (SNP) genotyping 33 species ( N = 2865 individuals; double-digest restriction site-associated DNA sequencing (ddRAD)). We found evidence of hybridization (70 putative hybrids; 2.4% of individuals) among 18 species-pairs involving 73% (24/33) of study species, with the majority being concentrated within one family (Leuciscidae/minnows; 15 species; 66 hybrids). Interspecific genetic exchange—or introgression—was evident from 24 backcrossed individuals (10/18 species-pairs). Hybrids occurred within 42 of 75 communities (56%). Four selected environmental variables (species richness, protected area extent, precipitation (May and annually)) exhibited 73–78% accuracy in predicting hybrid occurrence via random forest classification. Our community-level assessment identified hybridization as spatially widespread and environmentally dependent (albeit predominantly within one diverse, omnipresent family). Our approach provides a more holistic survey of natural hybridization by testing a wide range of species-pairs, thus contrasting with more conventional evaluations.

Objective The purpose of this study is to provide Level-1 objective, real-world outcome data for patients with lumbar spinal stenosis suffering from neurogenic claudication secondary to hypertrophic ligamentum flavum. Design The MOTION Study is a prospective, multicenter, randomized controlled trial comparing the mild® Procedure (minimally invasive lumbar decompression; Vertos Medical, Aliso Viejo, CA, USA) as a first-line therapy in combination with nonsurgical conventional medical management (CMM) vs CMM alone as the active control. Methods Patients in the test group received the mild Procedure at baseline. Both the mild+CMM group and the control group were allowed unrestricted access to conventional real-world therapies. Patient-reported outcomes included the Oswestry Disability Index, the Zurich Claudication Questionnaire, and the Numeric Pain Rating Scale. A validated Walking Tolerance Test, the incidence of subsequent lumbar spine interventions, and the occurrence of adverse events were used to measure objective outcomes. Results Sixty-nine patients in each group were analyzed at 1-year follow-up. No device- or procedure-related adverse events were reported in either group. Results from all primary and secondary outcome measures showed statistical significance in favor of mild+CMM. Conclusions One-year results of this Level-1 study demonstrated superiority of mild+CMM over CMM alone for patients with lumbar spinal stenosis who were suffering from neurogenic claudication secondary to hypertrophic ligamentum flavum. Use of the validated Walking Tolerance Test to objectively measure increased ability to walk without severe symptoms provided evidence of statistically significantly better outcomes for mild+CMM than for CMM alone. With no reported device or procedure-related adverse events, the long-standing safety profile of the mild Procedure was reaffirmed. mild is a safe, durable, minimally invasive procedure that has been shown to be effective as an early interventional therapy for patients suffering from symptomatic lumbar spinal stenosis.

Introduction Fungal wound infections (FWI) cause morbidity and increase mortality in burn patients. Our burn center experienced 44 patients with fungal wound colonization (FWC) and/or FWI between JAN 2015 and JAN 2019. In response, we undertook a performance improvement project to prevent and treat FWC and FWI. Methods Members of the multidisciplinary team met to develop a clinical practice guideline (CPG) for the prevention and management of FWC and FWI based on current evidence. We focused on patients with elevated risk, that is, with burns ≥20% total body surface area (TBSA) and in the Burn ICU (BICU). Interventions included: utilizing alternating silver sulfadiazine and mafenide acetate creams upon admission; reducing the use of mafenide acetate solution; utilizing silver nitrate solution post-operatively; and applying topical nystatin cream or powder for suspected FWC or FWI. We educated all staff members and updated order sets and training materials. We collected data on all burn patients who had a wound biopsy out of concern for possible infection. Biopsy results were categorized as FWC or FWI. Retrospective data were collected for MAR 2020 - MAR 2021 (PRE). Post-implementation, prospective data collection began MAR 2022 (POST) and will continue for one year. Adherence to the CPG was assessed by chart review. Mann-Whitney and Fischer Exact tests were performed. Results The PRE (n=15) and POST (n=9) groups were similar in age (43±13 vs. 48±18 years) but differed in TBSA (49±19 vs 28±25%, p< .05). PRE group biopsies showed FWC in 0 patients and FWI in 11 of 15 patients (73%); 8 of these (53%), all with FWI, died. In the POST group, FWC was found in 1 patient (11%) and FWI was found in 2 of 9 patients (22%); one death occurred in the patient with FWC. Adherence to the CPG for admission topical wound care was 7% in the PRE group vs 89% in the POST group (p=0.0001); adherence to the CPG for day-of-biopsy topical wound care was 27% in the PRE group vs 89% in the POST group (p< 0.01). Conclusions Adherence to a CPG for the prevention and treatment of FWC and FWI was associated with a lower (but not statistically significant) prevalence of these complications. Limitations include a difference in the TBSA between the 2 groups and potential concurrent changes in practice. Ongoing data collection includes the evaluation of other potential contributing factors. Applicability of Research to Practice Fungi are common in the environment, and when combined with immunosuppression and extensive open wounds, may cause wound infection in burn patients. More research is needed to further evaluate effective treatments for the prevention and treatment of FWC and FWI in these patients.

Methods, power analysis, and information pertaining to hybrids

Data and SnakeMake workflows used to validate ResistNet. Includes simulations + outputs in "simulation/" subdirectory, and an empirical case study in Speckled Dace in "case_study_spd/"

Genetic differentiation among local groups of individuals, i.e., genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how thisriverscape community genomicsapproach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N=24) were partitioned into discrete sub-populations (K=2–7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x□ =62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the Stream Hierarchy Model. We discuss our conclusions regarding conservation and management and identify the 8-digit Hydrologic Unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.

Phenotypic traits modulate the fate of species interactions with one another and the environment; thus, traits directly shape the past, present, and future evolutionary trajectories of populations. As such, distinct species-specific responses to a shifting environment are widely documented in the form of distinct genetic signatures, i.e., genetic diversity, reflecting differential responses over time. While the link between genetic diversity and phenotypic traits is seemingly fundamental, it has been challenging to establish unequivocally. Across an exemplar freshwater fish metacommunity, we employ phenotypic traits to test if they are significantly related to observed genetic patterns among species. Associated traits were then used to construct trait-based predictive models of genetic diversity. We collected representative constituents of a freshwater fish community (N=31 species) sampled across 75 sites within the White River Basin (Ozark Plateau, USA). For each species, we derived three genetic diversity indices (=HS/HT/G”ST) from SNP data (N=2,000 loci) and assessed 28 phenotypic traits related to morphology, life history, and ecology. We identified a series of traits (N=2–5, depending upon the index) strongly associated with facets of genetic diversity. These were subsequently applied in predictive models that explained 31–68% of the genetic variability across species, suggesting a potential utility as an imputation tactic for data-deficient species. Our approach effectively linked species-specific traits with genetic diversity within and among populations, thereby further clarifying correlations between contemporary ecological processes, as modulated by species traits, and long-term evolutionary trajectories.

Climate change inevitably leaves behind a genetic footprint within phylogeographic legacies of affected species, as individuals are driven to either disperse to track suitable conditions or adaptin situ. One potential consequence is the possibility of hybridization among species, as both geographic ranges and adaptive landscapes shift. The admixture resulting from these newly formed ‘contact zones’ has various outcomes, to include the creation of new lineages. Interpreting these within the context of historic climate change provides clues necessary to predict biotic responses (and thus evolutionary trajectories) as a function of contemporary shifts. Herein, we dissect historic contact zones for Massasaugas (Viperidae;Sistrurusspp.) within two distinct North American regions (southwestern United States and Central Great Plains) using ddRAD sequencing. We identified fine-scale but previously unrecognized population structure within the southwestern contact zone, where we detected contemporary intergradation between Prairie and Desert massasaugas (S. tergeminus tergeminus, andS. t. edwardsii,respectively), with primary divergence indicated by demographic model selection. Within the Central Great Plains, we found evidence for historic secondary contact via Quaternary climatic cycles, subsequently followed by range expansion at the suture zone separatingS. tergeminusandS. catenatus. Extant Missouri populations represent ancestral/relictual vestiges of this earlier hybridization, isolated between the eastern terminus ofS. t. tergeminusand the western edge ofS. catenatus. Our results illustrate how abrupt climate change has driven ancestral hybridization, cryptic diversity, and range dynamism withinSistrurus.

Data repository for: Zbinden ZD, Douglas MR, Chafin TK, Douglas ME. 2022. Trait-based predictors of genomic diversity within freshwater fish communities of the Ozarks. In review.

In progress data repository

Data repository for: Zbinden ZD, Douglas MR, Chafin TK, Douglas ME. 2022. Riverscape community genomics: A comparative analytical framework to identify common drivers of spatial structure. In review.

Data repository for: Zbinden ZD, Douglas MR, Chafin TK, Douglas ME. 2022. A community genomics approach to natural hybridization. In review.

Repository for Frontiers of Biogeography paper "Taxonomic hypotheses and the biogeography of speciation in the Tiger Whiptail complex (Aspidoscelis tigris: Squamata, Teiidae)"

Data repository for: Chafin TK, Zbinden ZD, Douglas MR, Martin BT, Middaugh CR, Gray MC, Ballard JR, Douglas ME. 2021. Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer. Evolutionary Applications. In Press

The large population sizes and high dispersal potential of microbes suggests that a given microbial species should be found in all suitable habitats worldwide. Consequently, microbes should not exhibit the kinds of biogeographic patterns seen in macroorganisms. This paradigm is challenged by a growing list of exotic microbes with biogeographic disjunctions that instead promotes microbial dispersal as inherently limited. We sampled water bodies in the United States and compiled records from the literature and public databases to characterize the distribution of the freshwater planktonic diatom, Discostella asterocostata (Xie, Lin, and Cai) Houk and Klee. Discostella asterocostata was thought to be restricted to the Far East, but we report its presence in ecologically similar water bodies across the eastern United States. Populations from the U.S. and China are indistinguishable morphometrically, suggesting they may be recently separated—a hypothesis supported by paleolimnological data, which support an introduction of D. asterocostata into the U.S. as recently as the mid-1980s. The overlapping distributions of D. asterocostata and invasive carp species, in both their native and nonnative ranges, highlighted Asian carp as a possible vector for introduction of the diatom in the U.S. The existence of exotic diatoms underscores natural constraints on microbial dispersal, resulting in biogeographic distributions that can be upended through human activity.

Being fearful of crime is, unfortunately, a common experience. Research shows that many factors influence a person’s fear of crime, demonstrating that certain groups are generally more fearful than others. Even though they are typically young, college students express being fearful of crime on and off campus. What has yet to be investigated is whether college students who attend school in the United States are fearful at similar levels to their Canadian counterparts. Further, the correlates of fear of crime may also be different. To explore these issues, data from the American College Health Association’s National College Health Assessment II survey of U.S. and Canadian college students are used. Results show that Canadian college students generally perceive their safety as being higher than U.S. college students, even though they face elevated victimization risks. Further, some correlates of fear of crime differ for U.S. and Canadian college students. These findings suggest the need for additional cross-national comparative work to see if patterns generalize across contexts.

Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP data set collected from North American box turtles (Terrapene spp.). Our filtering strategies included: (i) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (= none), and (ii) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (= no filtering). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discordance can seriously impact M-L-classification.

Influenza remains a major public health challenge, as the viral infection activates multiple biological networks linked to altered host innate immunity. Following infection, IFN-λ, a ligand crucial for the resolution of viral infections, is known to bind to its cognate receptor, IFNLR1, in lung epithelia. However, little is known regarding the molecular expression and regulation of IFNLR1. Here, we show that IFNLR1 is a labile protein in human airway epithelia that is rapidly degraded after influenza infection. Using an unbiased proximal ligation biotin screen, we first identified that the Skp-Cullin-F box E3 ligase subunit, FBXO45, binds to IFNLR1. We demonstrate that FBXO45, induced in response to influenza infection, mediates IFNLR1 protein polyubiquitination and degradation through the ubiquitin-proteasome system by docking with its intracellular receptor domain. Furthermore, we found ectopically expressed FBXO45 and its silencing in cells differentially regulated both IFNLR1 protein stability and interferon-stimulated gene expression. Mutagenesis studies also indicated that expression of a K319R/K320R IFNLR1 variant in cells exhibited reduced polyubiquitination, yet greater stability and proteolytic resistance to FBXO45 and influenza-mediated receptor degradation. These results indicate that the IFN-λ-IFNLR1 receptor axis is tightly regulated by the Skp-Cullin-F box ubiquitin machinery, a pathway that may be exploited by influenza infection as a means to limit antiviral responses.

STUDY OBJECTIVES: We investigated whether patient adherence to positive airway pressure (PAP) therapy was significantly different between groups whose PAP machines were dispensed by a traditional durable medical equipment (DME) supplier (DME group) versus those provided directly by an integrated sleep practice (ISP group). METHODS: This was a retrospective cohort study that analyzed 3884 patients (ages 18-64) who were set up with a new PAP machine for sleep-disordered breathing. The channel through which PAP therapy was dispensed (DME vs ISP) was chosen as part of the natural course of treatment, making patient choice and third-party payor likely important selection factors. We analyzed whether the groups had significant differences in adherence rates and nightly usage duration after 30 days, 90 days, and 1 year of therapy. RESULTS: The ISP group had a significantly higher rate of PAP adherence at 30 days (71% vs 66%; P = .004), 90 days (66% vs 56%; P < .00001), and 1 year (52% vs 33%; P < .00001) following initiation of PAP therapy, relative to the DME group. There was a significantly higher duration of PAP use among the ISP group at 30 days (357 vs 345 minutes; P = .002), 90 days (348 vs 319 minutes; P < .00001), and 1 year (312 vs 164 minutes; P < .00001). CONCLUSIONS: This study suggests improved short- and long-term PAP adherence rates among patients who received PAP therapy through an ISP. As current health care trends drive sleep medicine practices to adopt chronic care management models, further studies are needed to better understand the tradeoffs of receiving PAP through traditional DME providers. CITATION: Andry JM Jr, Toban G, Chafin C, Noah W. Positive airway pressure therapy supplied by an integrated sleep practice associated with greater adherence among pre–Medicare-aged patients with sleep-disordered breathing. J Clin Sleep Med. 2021;17(1):31–36.

Ideonella sakaiensis produces an enzyme, PETase, that is capable of hydrolyzing polyethylene terephthalate (PET) plastic. We demonstrate that although I. sakaiensis can grow on amorphous plastic, it does not grow on highly crystalline plastic under otherwise identical conditions. Both amorphous film and amorphous plastic obtained from commercial food containers support the growth of the bacteria, whereas highly crystalline film and the highly crystalline body of a plastic water bottle do not support growth. Highly crystalline PET can be melted and rapidly cooled to make amorphous plastic which then supports bacterial growth, whereas the same plastic can be melted and slowly cooled to make crystalline plastic which does not support growth. We further subject a plastic water bottle to a top-to-bottom analysis, finding that only amorphous sections are degraded, namely the finish (threading), the topmost portion of the shoulder which connects to the finish, and the area immediately surrounding the centre of the base. Finally, we use these results to estimate that the percentage of non-degradable plastic in plastic water bottles ranges from 52% to 82% (depending on size), demonstrating that most of the plastic found in PET water bottles will not be degraded by I. sakaiensis.

Resveratrol is a sustainable and versatile bio-derived phenolic compound that has shown promise as a high glass-transition temperature (Tg), flame-resistant building block for thermoset networks. In this study, three components of epoxy thermoset resins were synthesized from resveratrol: trans-resveratrol trisepoxy (1), dihydroresveratrol trisepoxy (2), and a trifunctional amine, 4,4′-((5-(4-(4-aminophenoxy)phenethyl)-1,3-phenylene)bis(oxy))dianiline (4). The epoxy monomers were low melting solids (mp 2000 mg/L, and no cytotoxicity up to its solubility limit. The epoxy monomers were cured with 4,4′-methylenedianiline (3) and 4 to produce four epoxy–amine networks (A–D). Networks C and D, prepared with the resveratrol-derived aniline, contained up to 52.6% bio-based material. The moisture uptake, thermal stability, and dry/wet thermomechanical properties of the networks were measured. The networks had Tg’s as high as 285 °C, approximately 110 °C higher than networks based on petroleum-derived bisphenol A (BPA). In addition, the resveratrol networks had char yields as high as 51 and 46% in nitrogen and air, respectively, compared to ca. 15 and 5%, respectively, for BPA-based networks. Overall, this study shows the advantages of resveratrol-based epoxy and amine monomers as components of sustainable, low-toxicity, high-temperature resin systems.

To relate maxillary and lingual frenulum configuration to breastfeeding success.Cross-sectional study.Newborn nursery in tertiary care academic hospital.Newborns were observed between 24 and 72 hours after birth. Mothers were asked a series of questions relating to their breastfeeding experience. The maxillary and lingual frenula were examined and scored. Corresponding LATCH scores were recorded.A total of 161 mothers with newborns participated. The mean gestational age of newborns was 38.81 weeks (95% CI, 38.65-38.98); 82 (50.9%) male and 79 (49.1%) female newborns were included. In sum, 70.8% had the maxillary frenulum attached to the edge of the alveolar ridge; 28.6%, attached to the fixed gingiva; and 0.6%, attached to mobile gingiva. In addition, 3.7% had anterior ankyloglossia, and 96.3% had no obvious anterior ankyloglossia. There was no significant correlation between maxillary frenulum scores or lingual frenulum scores and LATCH scores (We did not find that maxillary frenulum configuration correlated with LATCH scores. Mothers experienced with breastfeeding had better LATCH scores. Attention toward breastfeeding education, particularly in new mothers, should precede maxillary frenotomy in neonates with breastfeeding difficulties.

Salivary gland disease in the pediatric population is rare, yet it encompasses a wide spectrum of disease. It is estimated that 4.3% of salivary gland disease occurs in the pediatric population, with most classified as nonneoplastic. Further extrapolation reveals that 5% of salivary gland neoplastic diseases occur in patients younger than 20 years. Moreover, salivary gland tumors represent 1% of all head and neck tumors across all ages. Regardless, clinicians across all fields should be familiar with the workup of various pediatric salivary gland diseases and appropriate referral to a pediatric otolaryngologist.

Accurate calibration of polarization dependent optical elements is often necessary in optical experiments. A versatile polarimeter device to measure the polarization state of light is a valuable tool in these experiments. Here we report a rotating waveplate-based polarimeter capable of complete Stokes vector analysis of collimated light. Calibration of the device allows accurate measurements over a range of wavelengths, with a bandwidth of >30 nm in this implementation. A photo-interrupter trigger system supplies the phase information necessary for full determination of the Stokes vector. An Arduino microcontroller performs rapid analysis and displays the results on a liquid crystal display. The polarimeter is compact and can be placed anywhere on an optical table on a single standard post. The components to construct the device are only a fraction of the cost of commercially available devices while the accuracy and precision of the measurements are of the same order of magnitude., 4 pages, 3 figures

Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed “threatened” status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (n = 387 and >22 k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the “anomaly zone” of tree space producing ambiguities that served to confound prior studies. Our results not only support the resurrection of the three species as distinct entities but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species level.

The purpose of this article is to review the symbolic-experiential family therapy model of Carl Whitaker and apply it specifically to recent neuroscience findings. The article concludes that symbolic-experiential family therapy reflects many of the recent findings in neuroscience including the role of implicit learning and memory formation, the importance of the relationship between the couple or family and the therapist, increasing stress and anxiety in order to facilitate change, which activates the right brain, and unstructured and spontaneous interaction, which promotes brain reorganization.

Precision tissue diagnostics rely on high quality input specimens so that assay results are not affected by artifact, but advances in collection and processing of tissue specimens have lagged behind innovations in diagnostic assay development. Therefore, we have designed and evaluated a novel surgical tissue collection device that maintains and monitors sample temperature and motion throughout transport so that the major preanalytical variable of tissue temperature can be controlled and measured. This device, in combination with an improved cold–hot tissue fixation protocol affords optimal biomarker preservation in less overall time, thereby simultaneously improving diagnostic quality and turnaround time. We collected 50 primary and metastatic liver tumors using a novel transport device. Tissue was fixed using a rapid cold–hot fixation protocol and immunohistochemical assays were used to assess the performance of the device, in comparison to control tissue preserved using standard clinical fixation protocol. Two pathologists evaluated the IHC studies in a blinded fashion to determine the immunophenotype of each tumor. The observed IHC staining intensities and the clinical impressions of the immunophenotypes did not differ between tissue collected with the novel device and control tissue, while improvements in processing time were achieved. The novel cold transport device and rapid fixation protocol can be successfully and safely combined and used to monitor specimen conditions, thus preserving the diagnostic utility of specimens and improving the overall turn-around time of the diagnostic process. Electronic supplementary material The online version of this article (10.1007/s10561-019-09800-8) contains supplementary material, which is available to authorized users.

The development of precision testing for disease diagnosis has advanced medicine by specifically matching patients with drugs to treat specific diseases. High-quality diagnostics start with high-quality tissue specimens. The development and optimization of tissue handling and processing have lagged behind bioassay development. Ultrasound time-of-flight (TOF) technology has been successfully used to monitor the critical processing step of tissue fixation with formalin. In this study, we expand the use of this technology to monitor tissue dehydration and clearing by analyzing TOF signals from 270 different specimens, representing 13 different tissue types obtained through surgical resections. We determined the time constant τ90 for each tissue type for the following tissue processing solvents: 70% ethanol, 90% ethanol, 100% ethanol, and xylene. The TOF signals were correlated with tissue morphology to ensure that high-quality tissue was produced. Tissues can be grouped into those exhibiting fast and slow reagent diffusion. We monitored incomplete dehydration of tissue by skipping a key processing step, dehydration in absolute ethanol, and then correlated the τ90 with poor histomorphology, demonstrating that the technique can detect significant processing errors. Ultrasound TOF technology can therefore be used to monitor all phases of tissue processing cycle and yields an important preanalytical quality metric.

PurposeIt is well established that partnerships between universities and community organizations can serve to enhance student learning and employability (Anderson et al., 2011; Arantes do Amaral and Matsusaki, 2017; Jones and Sherr, 2014; Voss et al., 2015). Within this context, the purpose of this paper is to explore how one such partnership has resulted in the successful implementation of three pedagogical methodologies, which individually and collectively promote student-centered learning and employability skills through an experiential learning framework.Design/methodology/approachUsing this methodological case study approach where the pedagogies of internships, service-learning opportunities, and project-based learning are critically evaluated, the research reveals only positive benefits for students, faculty, and the community organization(s). These benefits center on improved employability skills, the development of social skills and societal contribution for students.FindingsParticipating students also noted the development of their confidence and the importance of feedback from both peers and assigned staff. Members of faculty considered the opportunity for students to put theory into practice, enhanced employability skills and the collective nature of the methodologies as the main benefits with The center echoing the sentiments of other stakeholders. The center considered the workplace preparedness, the development of soft skills and confidence and the collective nature of the methodologies as the main benefits of the partnership.Originality/valueThe insight provided by the research contributes to existing literature through examining the relationship between an academic institution and its community, providing a practical framework and guidelines for the implementation of student-centered pedagogical methods.

ObjectiveTo present the appropriate medical care standards for organizations that sponsor athletic activities for secondary school–aged athletes.Data SourcesTo develop the current standards and identify current best-practices evidence, the task force used a multistep process that included reviewing the existing 2004 Appropriate Medical Care for Secondary School–Aged Athletes consensus points and cross-referencing of National Athletic Trainers' Association (NATA) statements and official documents from the strategic alliance (the NATA, NATA Foundation, Board of Certification, and Commission on Accreditation of Athletic Training Education). Gaps in the recommendations from the 2004 Appropriate Medical Care for Secondary School–Aged Athletes document were identified by the task force, and the new appropriate medical care standards were developed and refined.Conclusions and RecommendationsTwelve standards, with supporting substandards, were developed that encompassed readiness to participate in activity; facilities; equipment; protective materials; environmental policies; nutrition, hydration, and dietary supplementation; wellness and long-term health; comprehensive emergency action plans; on-site immediate care; on-site therapeutic interventions; psychological concerns; and athletic health care administration. Collectively, these standards describe a comprehensive approach to providing appropriate health care to secondary school–aged athletes and should serve as a framework with which organizations can evaluate and improve the medical care supplied to adolescent athletes.

Interferon lambda (IFNλ) signaling is a promising therapeutic target against viral infection in murine models, yet little is known about its molecular regulation and its cognate receptor, interferon lambda receptor 1 (IFNLR1) in human lung. We hypothesized that the IFNλ signaling axis was active in human lung macrophages. In human alveolar macrophages (HAMs), we observed increased IFNLR1 expression and robust increase in interferon-stimulated gene (ISG) expression in response to IFNλ ligand. While human monocytes express minimal IFNLR1, differentiation of monocytes into macrophages with macrophage colony-stimulating factor (M-CSF) or granulocyte-macrophage colony-stimulating factor (GM-CSF) increased IFNLR1 mRNA, IFNLR1 protein expression, and cellular response to IFNλ ligation. Conversely, in mice, M-CSF or GM-CSF stimulated macrophages failed to produce ISGs in response to related ligands, IFNL2 or IFNL3, suggesting that IFNLR1 signaling in macrophages is species-specific. We next hypothesized that IFNλ signaling was critical in influenza antiviral responses. In primary human airway epithelial cells and precision-cut human lung slices, influenza infection substantially increased IFNλ levels. Pretreatment of both HAMs and differentiated human monocytes with IFNL1 significantly inhibited influenza infection. IFNLR1 knockout in the myeloid cell line, THP-1, exhibited reduced interferon responses to either direct or indirect exposure to influenza infection suggesting the indispensability of IFNLR1 for antiviral responses. These data demonstrate the presence of IFNλ - IFNLR1 signaling axis in human lung macrophages and a critical role of IFNλ signaling in combating influenza infection.

(225)Biodiversity in southwestern North America has a complex biogeographic history involving tectonism interspersed with climatic fluctuations. This yields a contemporary pattern replete with historic idiosyncrasies often difficult to interpret when viewed from through the lens of modern ecology. TheAspidoscelis tigris(Tiger Whiptail) complex (Squamata: Teiidae) is one such group in which potential taxonomic boundaries have been confounded by a series of complex biogeographic processes that have defined the evolution of the clade. To clarify this situation, we first generated multiple taxonomic hypotheses, which were subsequently tested using mitochondrial DNA sequences (ATPase 8 and 6) evaluated across 239 individuals representing five continental members of this complex. To do so, we evaluated the manner by which our models parsed phylogenetic and biogeographic patterns. We found considerable variation among species ‘hypotheses’, which we suggest in part reflects inflated levels of inter-population genetic divergence caused by historical demographic expansion and contraction cycles. Inter-specific boundaries withA. marmoratusjuxtaposed topographically with the Cochise Filter Barrier that separates Sonoran and Chihuahuan deserts (interpreted herein as case of ‘soft’ allopatry). Patterns of genetic divergence were consistent across the Cochise Filter Barrier, regardless of sample proximity. Surprisingly, this also held true for intraspecific comparisons that spanned the Colorado River. These in turn suggest geomorphic processes as a driver of speciation in thetigriscomplex, with intraspecific units governed locally by demographic processes.HIGHLIGHTSPhylogeographies of vertebrates within the southwestern deserts of North America have been shaped by climatic fluctuations imbedded within broad geomorphic processes.The resulting synergism drives evolutionary processes, such as an expansion of within-species genetic divergence over time. Taxonomic inflation often results (i.e., an increase in recognized taxa due to arbitrary delineations), such as when morphological divergences fail to juxtapose with biogeographic hypotheses.However, isolated groups can be discriminated within-species by mapping genetic variability onto geographic distances. This approach can often diagnose ‘hard’ barriers to dispersal, or alternatively, strong selection acting against hybridization. On the other hand, elevated genetic divergences among groups less-isolated would underscore isolation-by-distance (i.e., an increase in genetic differentiation concomitant with geographic distance).The biogeographic patterns we identified in Tiger Whiptail are largely synonymous with those found in other regional species, particularly given the geomorphic separation of Mohave and Sonoran deserts by the Colorado River, and Sonoran/ Chihuahuan deserts by the Cochise Filter Barrier.Our results for the Tiger Whiptail complex broaden and extend the context within which polytypic species are conserved and managed, particularly those that reflect an incongruence among molecular and morphological standards.

The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological ‘ecotypes’ observed in polyploid snowtrout (Cyprinidae: Schizothorax ). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq ( N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples ( N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational ‘ecotypes’ were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively ‘masks’ previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.

Genetic screens provide a mechanism to identify genes involved with different cellular and organismal processes. Using a Flp/FRT screen in the Drosophila eye we identified mutations that result in alterations and de-regulation of cell growth and division. From this screen a group of undergraduate researchers part of the Fly-CURE consortium mapped and characterized a new allele of the gene Hippo, HpoN.1.2.

Statistical methods that quantify individual movements have limited applicability within dendritic ecological networks (DENs), to include riverscapes. We promote an approach herein by deriving an analytical framework (=DistNet and ResistNet) that more appropriately quantifies differentiation by meshing individual DEN segments with fitted distances and annotated environmental features. We first explored the spatial arrangement of diversity in a river network by fitting pairwise distances against graph edges. We then derived effective resistance models (e.g., as a composite of an array of possible environmental covariates) by using a genetic algorithm for heuristic model selection, invoking circuit theory (CircuitScape) to form a graph-based complement to ResistanceGA (a landscape ecology package). Although numerous pairwise distance metrics can be employed, we utilized genetic distances encompassing 13,218 ddRAD loci from N=762 Speckled Dace (Cyprinidae: Rhinichthys osculus) sampled at 78 Colorado River localities (µ=9.77/site). When distances for each locus were fitted into the network, we found intraspecific divergences due to stream reaches were greater than expected when distances alone. In fitting model-averaged ‘effective resistance’ models to the same network, we showed the manner by which a host of anthropogenic and environmental variables contribute to patterns of connectivity underlying riverscape genetic differentiation. Our framework represents a contemporary approach to deriving metapopulation/ metacommunity structure within DENs, in that it allows: (a) The extension of projections into unsampled temporal/spatial components; (b) Comparisons to be made among species and/or drainages, both of which benefit multi-species management; and (c) the quantification of locus-specific patterns, from which adaptive hypotheses could then be derived. “The intimate relation of hydrological conditions to fish life is proverbial; to be hopelessly or dangerously maladjusted to one’s environment is to be a ‘fish out of water’” (Hubbs 1941).

Identifying protein-protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity-dependent biotinylation method that uses an "abortive" biotin ligase to detect proximal interactions in cells in a highly reproducible manner. Recent advancements in proximity-dependent biotinylation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However, issues of size, stability, and background labeling of these constructs persist. Here we modified the structure of BioID2, derived from Aquifex aeolicus BirA, to create a smaller, highly active, biotin ligase that we named MicroID2. Truncation of the C terrminus of BioID2 and addition of mutations to alleviate blockage of biotin/ATP binding at the active site of BioID2 resulted in a smaller and highly active construct with lower background labeling. Several additional point mutations improved the function of our modified MicroID2 construct compared with BioID2 and other biotin ligases, including TurboID and miniTurbo. MicroID2 is the smallest biotin ligase reported so far (180 amino acids [AAs] for MicroID2 versus 257 AAs for miniTurbo and 338 AAs for TurboID), yet it demonstrates only slightly less labeling activity than TurboID and outperforms miniTurbo. MicroID2 also had lower background labeling than TurboID. For experiments where precise temporal control of labeling is essential, we in addition developed a MicroID2 mutant, termed lbMicroID2 (low background MicroID2), that has lower labeling efficiency but significantly reduced biotin scavenging compared with BioID2. Finally, we demonstrate utility of MicroID2 in mass spectrometry experiments by localizing MicroID2 constructs to subcellular organelles and measuring proximal interactions.

Microcystins are natural hepatotoxic metabolites secreted by cyanobacteria in aquatic ecosystems. When present at elevated concentrations, microcystins can affect water quality aesthetics; contaminate drinking water reservoirs and recreational waters; disrupt normal ecosystem functioning; and cause health hazards to animals, plants, and humans. Animal and human exposures to microcystins generally result from ingesting contaminated drinking water or physically contacting tainted water. Much research has identified a multitude of liver problems from oral exposure to microcystins, varying from hepatocellular damage to primary liver cancer. Provisional guidelines for microcystins in drinking and recreational water have been established to prevent toxic exposures and protect public health. With increasing occurrences of eutrophication in freshwater systems, microcystin contamination in groundwater and surface waters is growing, posing threats to aquatic and terrestrial plants and agricultural soils used for crop production. These microcystins are often transferred to crops via irrigation with local sources of water, such as bloom-forming lakes and ponds. Microcystins can survive in high quantities in various parts of plants (roots, stems, and leaves) due to their high chemical stability and low molecular weight, increasing health risks for consumers of agricultural products. Studies have indicated potential health risks associated with contaminated fruits and vegetables sourced from irrigated water containing microcystins. This review considers the exposure risk to humans, plants, and the environment due to the presence of microcystins in local water reservoirs used for drinking and irrigation. Additional studies are needed to understand the specific health impacts associated with the consumption of microcystin-contaminated agricultural plants.