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Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Purpose This study aims to explore the authentic questioning practices of English Language Arts teachers. Although language arts (LA) education emphasizes the value of authentic questions in discussions about literature, teachers still tend to ask known-answer questions that guide students toward one literary interpretation. However, outside their classrooms, teachers talk about literary texts from stances of openness and curiosity. Helping teachers recognize and draw on their out-of-school literary practices might help them disrupt entrenched known-answer discourses. The authors studied how the same teachers asked questions about literature in different settings. The authors asked: To what degree and in what ways did teachers’ questions about literature change when they took on different roles in discussions of literature? Design/methodology/approach Drawing on theories of classroom discourses and everyday practices, this study compared and analyzed types of questions asked by high school teachers as they took on three roles: teacher in the high school classroom, discussion leader in a professional development and everyday reader in discussion. Findings Analysis showed that as participants moved further away from their teacher role, they were more likely to ask authentic, curiosity-driven questions that engaged fellow readers in exploratory, dialogic interpretation. They were less likely to attempt to maintain authority over students’ interpretations. Research limitations/implications The authors hope researchers will build on these explorations of teacher stances and language in different roles, so we can work toward disrupt entrenched known-answer discourses in the classroom. Practical implications Drawing on this study’s findings about questioning practices of participants in their role as reader (as opposed to discussion leader or classroom teacher), the authors suggest that teachers and teacher educators consider the following: First, teachers need to understand the power of interpretive authority and known-answer discourses and compare them explicitly to their own everyday practices through rehearsals and reflection. Second, teachers might focus less on theme and more on exploration of individual lines, patterns and unusual authorial moves. Finally, when preparing to teach, if teachers can reconnect with the stance and language of uncertainty and curiosity, they are likely to ask more authentic questions. Social implications These findings suggest both the power of entrenched known-answer discourses to constrain and the potential power of making visible and drawing on teachers’ literary reading practices in out-of-school contexts. Originality/value To the best of the authors’ knowledge, no studies have made an empirical comparison of the relationship between the role a teacher takes on during discussion and the kinds of questions they ask about literature. This study offers insight into the value of everyday curiosity and other out-of-school resources that teachers could – but often do not – bring to their facilitations of classroom discussions. The findings suggest that teachers, teacher educators and researchers must recognize and recruit teachers’ everyday practices to the LA classroom.

Animals (grazing, working, or intrusion) in produce production areas may present a potential contamination source of foodborne pathogens on produce. Cattle grazing on native pecan production orchards, a common practice in the Southern United States, provides a great opportunity to study the impact of grazing practice and waiting periods on contamination rates of foodborne pathogens of tree nuts. Therefore, the objective of this study was to determine the prevalence of Salmonella spp. and Shiga toxin-producing Escherichia coli (STEC), in native pecan production orchards as influenced by waiting periods between grazing cattle and pecan harvest. Soil (10 g), cattle feces (10 g), and in-shell pecans (25 g) were sampled from five cattle-grazed orchards in areas with cattle removed two or four months prior to harvest and not removed. Five non-grazing orchards were sampled at harvest for comparison. Detection and isolation of the pathogens were performed by enrichment, selective isolation, and multiplex PCR. Statistical analyses were performed using contingency tables with Pearson's chi-squared test. The prevalence of STEC (36%) and Salmonella (29%) in cattle-grazed orchards was significantly higher compared to non-grazed orchards (13%; 7%). STEC prevalence in cattle-grazed orchards was higher (38%) in areas with cattle at harvest than in fenced areas where cattle were removed two (29%) and four (27%) months prior to harvest. Salmonella prevalence was similar in areas without fencing (31%), and areas with cattle removed at two (22%) and four months prior to harvest (30%). However, there were not significant differences ( P ≤ 0.05) in contamination rates between waiting periods for either pathogen, suggesting a limited impact of waiting periods on reducing the risk of contamination.

Objective To examine body shape perception in 218 adults without obesity or history of eating disorders during caloric restriction (CR). Methods Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIE) is a 2-year, randomized clinical trial using a 2:1 assignment (CR, 25% reduction in calories; Control, typical diet). For this secondary analysis, we examined perceived body shape using the Body Shape Questionnaire (BSQ). Analyses of BSQ scores are reported by group, over time, by sex, and by BMI. Data for body fat percentage, symptoms of depression, food cravings, maximal oxygen consumption, and stress were analyzed for their association with BSQ scores. Results Compared to control, CR reduced BSQ scores. Women tended to have greater concern with body shape than men across all measurement times. There was no difference in change in BSQ scores at 12 or 24 months between those with a BMI 2 or ≥ 25 kg/m2. Change in body fat percentage was most correlated with change in BSQ score from 0 to 12 (r = 0.39) and 0–24 months (r = 0.38). For change in BSQ score, Akaike/ Bayesian information criterion (AIC/BIC) found that the model of best fit included the following three change predictors: change in body fat percentage, depression symptoms, and food cravings. For 0–12 months, AIC/BIC = 1482.0/1505.6 and for 0–24 months AIC/BIC = 1364.8/1386.5. Conclusions CR is associated with reduced concern for body shape in men and women without obesity and with no history of eating disorders. Body shape perception among this sample was complex and influenced by multiple factors. Level of evidence Level I, randomized controlled trial.

Switchgrass (Panicum virgatum L.) has gained wider attention due to its recognition and use as a model herbaceous crop species for bioenergy production. Genetic diversity information in lowland switchgrass cultivars can help to specify cultivars to be used in the breeding programs aiming for hybrid vigor. The objective of this research was to analyze genetic variation within and among five lowland switchgrass cultivars using amplified fragment length polymorphism (AFLP) markers. AFLP polymorphisms indicated the presence of high genetic variation within lowland switchgrass cultivars with ‘Alamo’ exhibiting the highest genetic variation and ‘Performer’ the lowest. The Nei’s genetic diversity parameters revealed the lowest genetic distance between cultivars ‘Alamo’ and ‘Cimarron’ and the highest value between cultivars ‘Alamo’ and ‘Kanlow’. ‘Alamo’ and ‘Cimarron’ were clustered together while ‘BoMaster’, ‘Kanlow’, and ‘Performer’ were grouped into the other cluster. In addition, there were clusters with mixed genotypes. The findings of this study can be used to select diverse lines as parents for heterosis and inbreeding studies.

Introduction Existing data demonstrate reduced delta power during sleep in chronic pain and depressed patients. However, there has been little examination of the relationship between delta power and next-day reports of pain. We tested the extent to which nocturnal (during the concurrent sleep period) and daytime pain reports are associated with delta power during sleep, as well as the extent to which this association is moderated by depressive symptoms. We hypothesised that reduced delta power and SWS would be associated with increased pain, pain catastrophising, and pain sensitivity. Methods 149 female participants with insomnia and temporomandibular joint pain (TMD) were recruited. We examined nocturnal and daytime measures of pain (pain severity, average pain), pain catastrophizing, and objective pain sensitivity (obtained through quantitative sensory testing (QST)), and calculated relative nocturnal delta (0.5-3.4 Hz) power using polysomnography. We fit linear regression models correcting for depressive symptom severity, age, and total sleep time, and further examined the moderating effect of depression severity on these measures. Results reduced delta power was associated with increased average nocturnal pain (Unstandardized β = -17.67, p= 0.02), morning pain (Unstandardized β = -15.67, p=0.02), and average next-day pain (Unstandardized β = -16.74, p= 0.03). Depression severity did not moderate these relationships. Delta power was not significantly associated with objective pain-sensitivity, nocturnal, or daytime pain catastrophising. However the association between nocturnal pain catastrophising and delta power was moderated by depressive symptom severity (p = 0.04). Simple slopes analysis revealed that when participants had low depressive symptoms ( Discussion These findings demonstrate that delta power during sleep is associated with both nocturnal and daytime experience of pain in patients with TMD. In patients with TMD and low depressive symptoms, reduced delta power was associated with increased nocturnal pain catastrophising.

The purpose of this chapter is to investigate the orientations Jamaican preservice teachers characteristically bring to the diverse youth literature that they read and to examine instructional approaches designed to help student develop a postcolonial orientation that will yield richer insights into their future students. The chapter presents a thematic analysis of extended response survey questions distributed to 86 Jamaican preservice teachers. The results revealed that these preservice teachers primarily sought literature for its ease, enjoyment, escapism, and personal growth, though a minority of students did indicate interest in broader issues of structural inequalities. Unfortunately, such emphases are inadequate to address issues of diversity. Consequently, the chapter proposes three instructional strategies to foster a postcolonial orientation: semantic differential scales, direct instruction in postcolonialism, and the TACT-MR model of writing instruction to develop students' critical empathy.

Purpose Very little research has investigated the effects of ultra-endurance exercise on the bioenergetic status of muscle. The primary objective of this case study was to characterize the changes that occur in skeletal muscle mitochondria in response to a 100-km ultramarathon in monozygotic twins. A second objective was to determine whether mitochondrial function is altered by consuming a periodized low-carbohydrate, high-fat diet (LCHFD) during training compared to a high-carbohydrate diet. Methods One pair of male monozygotic twins ran 100 km on treadmills following 4 weeks of training on either a high carbohydrate or periodized LCHFD. Muscle biopsies were collected 4 weeks prior to the run, as well as 4- and 52-hours post-run. Blood draws were also performed immediately before, as well as 4- and 52-hours post-run. Results Four hours post-run, respiratory capacity, citrate synthase activity and mitochondrial complex protein content were decreased. Two days later, both twins showed signs of rapid recovery in several of these measures. Furthermore, blood levels of creatine phosphokinase, C-reactive protein, and aspartate transaminase were elevated 4 hours after the run, but partially recovered two days later. Conclusion Although there were some differences between the twins, the primary finding is that there is significant mitochondrial impairment induced by running 100 km, which rapidly recovers within 2 days. These results provide ample rationale for future investigations of the effects of ultra-endurance activity on mitochondrial function.

Controlling a medical simulation training exercise, especially one that involves an interactive patient simulator, is a demanding job. It requires monitoring, and sometimes intervening in, technical processes and the learner’s cognitive processes. To explore opportunities for better support for the cognitive demands of simulation directors, we conducted a Work Domain Analysis to generate an Abstraction Hierarchy on the area of management of a simulation training exercise. Our results emphasize the complexity involved, including the management of trade-offs between facilitation of learning and maintenance of the learner’s immersion in the scenario. We identify potential methods of cognitive support for managing these trade-offs. Next steps include analysis of control methods.

High-speed local seeding particle injection for particle image velocimetry has been developed and demonstrated by measuring Mach 3 and Mach 10 turbulent boundary layers. The seeding injectors accel...

Michael Smith,1 Marco Bresolin,1 Rose McCabe2 1Glaucoma Unit, West of England Eye Unit, Exeter, UK; 2School of Health Sciences, City, University of London, London, UKCorrespondence: Michael Smith Email Michael.smith26@nhs.netPurpose: This pilot study was undertaken to examine the feasibility of a larger scale trial examining the effect of interventions to improve patient-clinician collaboration. The primary outcome was the extent of clinician-patient collaboration during glaucoma consultations. The secondary outcomes were the results of the Patient Experience Questionnaire and the patients’ opinion of how involved they were in decisions about their care and how keen they would be to increase this involvement.Methods: This is an observational study of clinician-patient communication involving 9 glaucoma clinicians and 37 patients attending a glaucoma monitoring clinic. Consultations were videotaped and later assessed for the degree of collaboration. Patients completed a validated Patient Experience Questionnaire and a questionnaire designed to collect the patients’ opinion of how involved they were in decisions about their care.Results: The consultations were largely “clinician centred” with clinicians speaking 58% of the sentences and asking a mean of 8.1 questions compared to the patients 2.6. Glaucoma medications were discussed in 97% of consultations. When a treatment change was recommended in 53% of cases different options were discussed. Patients had an overall positive opinion of the consultations. Although 80% of patients indicated they were happy with how involved they were in decisions about their care 44% said they would like to be more involved, and 47% would welcome written information or information sessions on how to be more involved in decisions about their care.Conclusion: Glaucoma consultations remain “clinician-centred” and, in view of the evidence of the benefits of good clinician-patient collaboration, further studies to examine interventions to improve clinician-patient collaboration may be of benefit to glaucoma patients. These interventions could target both clinicians and patients, and many patients in this study indicated they would like to be more involved in decisions about their care and would welcome support in achieving this.Keywords: glaucoma, communication, ophthalmology

Background In human lung transplant recipients, a decline in club cell secretory protein (CCSP) in bronchoalveolar lavage fluid has been associated with chronic lung allograft dysfunction (CLAD) as well as the induction of exosomes and immune responses that lead to CLAD. However, the mechanisms by which CCSP decline contributes to CLAD remain unknown. Methods To define the mechanisms leading to CCSP decline and chronic rejection, we employed two mouse models: 1) chronic rejection after orthotopic single lung transplantation and 2) anti-major histocompatibility complex (MHC) class I-induced obliterative airway disease. Results In the chronic rejection mouse model, we detected circulating exosomes with donor MHC (H2b) and lung self-antigens and also development of antibodies to H2b and lung self-antigens and then a decline in CCSP. Furthermore, DBA2 mice that received injections of these exosomes developed antibodies to donor MHC and lung self-antigens. In the chronic rejection mouse model, natural killer (NK) and CD8 T cells were the predominant graft-infiltrating cells on day 14 of rejection followed by exosomes containing NK cell-associated and cytotoxic molecules on day 14 and 28. When NK cells were depleted, exosomes with NK cell-associated and cytotoxic molecules as well as fibrosis decreased. Conclusions Induction of exosomes led to immune responses to donor MHC and lung self-antigens, resulting in CCSP decline, leading to NK cell infiltration and release of exosomes from NK cells. These results suggest a novel role for exosomes derived from NK cells in the pathogenesis of chronic lung allograft rejection.

A decade (2007–2016) of hourly 6-km-resolution maps of the surface currents across the Mid-Atlantic Bight (MAB) generated by a regional-scale High Frequency Radar network are used to reveal new insights into the spatial patterns of the annual and seasonal mean surface flows. Across the 10-year time series, temporal means and interannual and intra-annual variability are used to quantify the variability of spatial surface current patterns. The 10-year annual mean surface flows are weaker and mostly cross-shelf near the coast, increasing in speed and rotating to more alongshore directions near the shelfbreak, and increasing in speed and rotating to flow off-shelf in the southern MAB. The annual mean surface current pattern is relatively stable year to year compared to the hourly variations within a year. The 10-year seasonal means exhibit similar current patterns, with winter and summer more cross-shore while spring and fall transitions are more alongshore. Fall and winter mean speeds are larger and correspond to when mean winds are stronger and cross-shore. Summer mean currents are weakest and correspond to a time when the mean wind opposes the alongshore flow. Again, intra-annual variability is much greater than interannual, with the fall season exhibiting the most interseasonal variability in the surface current patterns. The extreme fall seasons of 2009 and 2011 are related to extremes in the wind and river discharge events caused by different persistent synoptic meteorological conditions, resulting in more or less rapid fall transitions from stratified summer to well-mixed winter conditions.

Objective This study demonstrates application of human factors methods for understanding causes for lack of timely follow-up of abnormal test results (“missed results”) in outpatient settings. Methods We identified 30 cases of missed test results by querying electronic health record data, developed a critical decision method (CDM)-based interview guide to understand decision-making processes, and interviewed physicians who ordered these tests. We analyzed transcribed responses using a contextual inquiry (CI)-based methodology to identify contextual factors contributing to missed results. We then developed a CI-based flow model and conducted a fault tree analysis (FTA) to identify hierarchical relationships between factors that delayed action. Results The flow model highlighted barriers in information flow and decision making, and the hierarchical model identified relationships between contributing factors for delayed action. Key findings including underdeveloped methods to track follow-up, as well as mismatches, in communication channels, timeframes, and expectations between patients and physicians. Conclusion This case report illustrates how human factors–based approaches can enable analysis of contributing factors that lead to missed results, thus informing development of preventive strategies to address them.

This paper defines a process of predictive approach to evaluate the maintainability of a Commercial Off-the-Shelf (COTS)-based system(CBS) by analyzing the complexity of the deployment of the system. The approach integrates architectural dependencies and the system’s concept of operations to derive a network-based representation of the software system. A greater understanding of the deployment complexity is gained by using a Design Structure Matrix (DSM) to determine the number of architectural dependencies on a COTS product, or in-degree, for each COTS product in the system. The arithmetic mean of the in-degree for all nodes in the system is then compared with the perceived effort to maintain the system. The resultant measure – the in-degree mean – is useful in evaluating the maintainability of the operational system while the system is being designed and throughout its lifetime. Architects can use the approach to assist in COTS product selection and to make product trades to optimize the maintainability of the system. Integrators can use the approach to optimize product deployment and to determine the upgrade strategy for deployment. Finally, maintenance engineers can use the approach to estimate the effort required to maintain the system and to identify areas in which extensive product expertise is required. Because the approach requires only basic information about the system, it can be applied early in the design process and used until the system is decommissioned.

Background The recognition of and response to undertreatment of heart failure (HF) patients can be complicated. A clinical reminder can facilitate use of guideline-concordant β-blocker titration for HF patients with depressed ejection fraction. However, the design must consider the cognitive demands on the providers and the context of the work. Objective This study's purpose is to develop requirements for a clinical decision support tool (a clinical reminder) by analyzing the cognitive demands of the task along with the factors in the Cabana framework of physician adherence to guidelines, the health information technology (HIT) sociotechnical framework, and the Promoting Action on Research Implementation in Health Services (PARIHS) framework of health services implementation. It utilizes a tool that extracts information from medical records (including ejection fraction in free text reports) to identify qualifying patients at risk of undertreatment. Methods We conducted interviews with 17 primary care providers, 5 PharmDs, and 5 Registered Nurses across three Veterans Health Administration outpatient clinics. The interviews were based on cognitive task analysis (CTA) methods and enhanced through the inclusion of the Cabana, HIT sociotechnical, and PARIHS frameworks. The analysis of the interview data led to the development of requirements and a prototype design for a clinical reminder. We conducted a small pilot usability assessment of the clinical reminder using realistic clinical scenarios. Results We identified organizational challenges (such as time pressures and underuse of pharmacists), knowledge issues regarding the guideline, and information needs regarding patient history and treatment status. We based the design of the clinical reminder on how to best address these challenges. The usability assessment indicated the tool could help the decision and titration processes. Conclusion Through the use of CTA methods enhanced with adherence, sociotechnical, and implementation frameworks, we designed a decision support tool that considers important challenges in the decision and execution of β-blocker titration for qualifying HF patients at risk of undertreatment.

Asimina Lazaridou,1 Marc O Martel,1 Christine M Cahalan,1 Marise C Cornelius,1 Olivia Franceschelli,1 Claudia M Campbell,2 Jennifer A Haythornthwaite,2 Michael Smith,2 Joseph Riley,3 Robert R Edwards1 1Department of Anesthesiology, Harvard Medical School, Brigham& Women’s Hospital, Boston, MA, USA; 2Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; 3Department of Community Dentistry and Behavioral Science, College of Dentistry, University of Florida, Gainesville, FL,USA Objective: To examine the influence of anxiety and pain-related catastrophizing on the time course of acute interleukin-6 (IL-6) responses to standardized noxious stimulation among patients with chronic pain.Methods: Data were collected from 48 participants in the following demographically matched groups: patients with chronic pain (n=36) and healthy controls (n=12). Participants underwent a series of Quantitative Sensory Testing (QST) procedures assessing responses to mechanical and thermal stimuli during two separate visits, in a randomized order. One visit consisted of standard, moderately painful QST procedures, while the other visit involved nonpainful analogs to these testing procedures. Blood samples were taken at baseline, and then for up to 2 hours after QST in order to study the time course of IL-6 responses.Results: Results of multilevel analyses revealed that IL-6 responses increased across assessment time points in both visits (p

Scab is the most damaging disease of pecan in the southeastern United States. Pecan trees can attain 44 m in height, so managing disease in the upper canopy is a problem. Fungicide is ordinarily applied using ground-based air-blast sprayers. Although mechanical hedge-pruning and topping of pecan is done for several reasons, improved management of scab is an important reason in the humid, wet Southeast. Resulting shoot growth on cut limbs of susceptible cultivars could lead to more severe scab. In three experiments over three years, we explored the effect of hedge-pruning trees to ∼12 to 14 m compared with non-hedge-pruned trees. All trees received fungicide treatments (air-blast sprays and ≤3 aerial applications). Hedge-pruning either had no effect, or increased or decreased scab severity only slightly on leaflets, immature, or mature fruit (a –9.95 to +14.63% difference in scab severity compared with the control). However, height in the canopy invariably had a large and significant effect on scab severity, and amounted to a 0.05 to 73.77% difference in severity between the lowest and highest sample in the canopy. Fruit weight depended on sample height, with fruit most often weighing less when collected at greater sample heights. A robust relationship between fruit weight and scab severity was found at the highest sample heights where scab was also most often severe (R2 = 0.21 to 0.67, P < 0.0001). Hedge-pruning and topping pecan tree canopies to manage tree size will enable better fungicide coverage, reducing risk of a scab epidemic as more of the canopy is assured efficacious fungicide spray coverage.

The Mid-Atlantic Regional Association Coastal Ocean Observing System (MARACOOS) has undertaken a reprocessing effort for their 6-kilometer gridded surface current product which utilizes data from the network of long-range High Frequency (HF) radar systems. Radar data from January 2017 to December 2017 have been re-examined and reprocessed. It is worthwhile to consider how errors in the real-time processing may be corrected by reprocessing and what improvements may be realized in the total vector map product by such an effort.

Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.

Most individuals with temporomandibular joint disorder (TMD) report experiencing sleep disturbance, which can maintain and exacerbate pain severity. However, the factors underlying the sleep-pain link, especially at the within-person level, have not been fully elucidated. Previous studies suggest that sleep disruption can induce biased attentional and interpretative processes, which can potentially elevate pain expectancy—a potent psychological factor that shapes pain experience. We examined whether morning pain expectancy serves as a mediator in the association between previous night sleep disturbance and pain severity the following evening. The sample included 170 women (mean age=36.3 [SD=11.4]) with co-morbid TMD and insomnia. Sleep was assessed for 14 days using actigraphy. Sleep parameters, including total sleep time (TST), wake after sleep onset (WASO), and sleep onset latency (SOL), were extracted from the data. Subjective reports of previous night sleep and current pain expectancy were measured upon participant's waking, and subsequent pain-related reports were collected at end-of-day during the same 14-day period. Multilevel structural equation modeling was employed to analyze the nested data. The Rmediation software was used to test the significance of the mediated effects. Shorter previous night TST predicted higher pain expectancy (B=-.001, p=.021), such that shorter TST was associated with higher pain expectancy. TST (B=-.002, p=.007) and WASO (B=.002, p=.047) significantly predicted morning pain. Morning pain expectancy (B=.140, p

Temporomandibular joint disorder (TMD) is an idiopathic chronic pain condition and often associated with sleep disturbance. Although racial pain and sleep disparities have been observed in other pain populations, less is known about such disparities in TMD. Given that pain is strongly associated with sleep, Black individuals may experience compounded disparities involving worse pain and sleep outcomes compared to White individuals. Participants (105= White, 26 = Black) completed baseline questionnaires, including the Brief Pain Inventory (BPI), Fear of Pain Questionnaire (FOP), Pain Catastrophizing Scale (PCS), Graded Chronic Pain Scale (GCPS), Jaw Functional Limitation Scale (JFLS), Insomnia Severity Index (ISI), and Dysfunctional Beliefs About Sleep Scale (DBAS). After completing baseline questionnaires, patients completed one night of polysomnography (PSG). Participants completed a 14-day diary assessing sleep continuity which was also objectively measured via actigraphy. Sleep continuity data were aggregated as individual 14-day means. Analyses controlled for age, household income, and education. Black participants reported higher pain severity (p

The U.S. Environmental Protection Agency (USEPA) has restricted concentrated animal feeding operation (CAFO) release of waste products into U.S. waters. These waste products must be disposed of using best management practices. Most of the waste is spread on cropland, but some operations have found other creative uses for waste products. Use of a phosphorus (P) reduction system to remove P from wastewater results in magnesium ammonium phosphate (MAP), a slowly soluble fertilizer. Using a P reduction system will not eliminate the need for land application of manure and wastewater, but it reduces the nutrient load in the waste that is applied thereby making compliance with regulations easier. In the first year of this study, MAP was compared to a controlled release fertilizer (CRF) with a similar nutrient element ratio on plant growth, fruit yield, nitrogen (N), P, potassium (K), calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), and zinc (Zn) concentration in tomato (Solanum lycopersicum L. ‘Mountain Fresh Plus’) plant parts. Plant growth and fruit production were similar with the two fertilizers, but the number of tomato culls was greater with either fertilizer than on control plants. Foliar N, P, Ca, and Mg concentration did not differ regardless of fertilizer treatment. Plants fertilized with CRF had a greater leaf K concentration than those fertilized with MAP, but foliar K concentration did not differ between fertilized and nonfertilized plants. Iron and Mn concentration in above-ground vegetative plant parts (stems and leaves) did not differ regardless of fertilizer treatment, but Zn concentration increased linearly as CRF increased. In the second year, MAP, each of the essential elements contained in MAP separately, and a hand mixture of each of these elements was tested for their effect on tomato plant growth, fruit yield, and tissue N, P, K, Ca, Mg, Fe, Mn, and Zn concentration and content. Magnesium ammonium phosphate and the hand mixture of fertilizer resulted in greater above-ground biomass excluding fruit stem weight and fruit yield than any of the individual nutrient treatments. Calcium sulfate resulted in a greater number and weight of tomatoes harvested than MAP. Nitrogen concentration did not differ among the fertilizer treatments for roots, stems, or leaves, but N content was greater in red fruit with the hand mix of fertilizer than with no fertilizer or with ammonium sulfate or Mg oxide. In immature green fruit at termination of the study, N content was greater with no fertilizer or Ca sulfate than with MAP or triple superphosphate (TSP). Phosphorus, K, and Ca concentrations did not differ among fertilizer treatments for any tissue tested. Magnesium concentration in green tomatoes differed among fertilizer treatments such that Mg concentration of green tomatoes from plants fertilized with TSP was greater than Mg concentration of green tomatoes fertilized with ammonium sulfate or Mg oxide. Phosphorus and K content of green fruit differed among fertilizer treatments with P and K concentration highest in green fruit from plants fertilized with Ca sulfate and lowest in green fruit from plants fertilized with MAP or TSP. Iron and Mn concentrations did not differ among fertilizer treatments for any tissue tested. Zinc concentration in leaves was greater when plants were fertilized with MAP, TSP, Ca sulfate, or Mg oxide than with ammonium sulfate. Zinc concentration of green fruit was greater when fertilized with MAP than with the hand mix, Ca sulfate or Mg oxide. Iron content was highest in green fruit from plants fertilized with TSP and lowest in plants fertilized with ammonium sulfate or control plants. Manganese content of leaves from control plants was greater than that of plants receiving ammonium sulfate while red fruit from plants fertilized with the hand mix had a greater Mn content than red fruit from any other treatment. Foliar Zn content was greater in plants fertilized with Ca sulfate than in those fertilized with the hand mix, ammonium sulfate, or TSP. In contrast, Zn content of red fruit fertilized with the hand mix was greater than for red fruit in any other treatment. Green fruit from control plants and those receiving MAP had a greater Zn content than plants fertilized with the hand mix, TSP, or Mg oxide. Fertilizer application increased Fe, Mn, and Zn content of several plant tissues. None of the labels of fertilizers applied stated that they contained micronutrients; however, small amounts of contamination were possible. Differing micronutrient contents of various plant tissues among fertilizer treatments were probably associated with other elements affecting plant growth or nutrient uptake. The nutrient elements present in the various fertilizers were not always the nutrient elements affected in the plants likely due to another element that may have limited plant growth or nutrient uptake.

High-frequency radar (HFR) surface current data are an increasingly utilized tool for capturing complex dynamics of coastal ocean systems worldwide. The radar is uniquely capable of sampling relevant temporal and spatial scales of nearshore processes that impact event response activities and basic coastal ocean research. HFR is a shore-based remote sensing system and is therefore subject to data gaps, which are predominately due to environmental effects, like increased external noise or low signal due to ocean surface conditions. Many applications of these surface current data require that these gaps be filled, such as Lagrangian numerical models, to estimate material transport and dispersion. This study introduces a new penalized least squares regression method based on a three-dimensional discrete cosine transform method to reconstruct hourly HFR surface current data with a horizontal resolution of 6 km. The method explicitly uses both time and space variability to predict the missing value. Furthermore, the method is fast, robust, and requires relatively low computer memory storage. This paper evaluates the method against two scenarios of common data gaps found in HFR networks currently deployed around the world. The validation is based on observed surface current maps along the mid-Atlantic coast of the United States with specific vectors removed to replicate these common gap scenarios. The evaluation shows that the new method is robust and particularly well suited to fill a more common scenario with complete data coverage surrounding an isolated data gap. It is shown that the real-time application of the method is suitable for filling data gaps in large oceanography datasets with high accuracy.

This paper outlines a diagnostic approach to quantify the maintainability of a Commercial off-the-Shelf (COTS)-based system by analyzing the complexity of the deployment of the system components. Interpretive Structural Modeling (ISM) is used to demonstrate how ISM supports in identifying and understanding interdependencies among COTS components and how they affect the complexity of the maintenance of the COTS Based System (CBS). Through ISM analysis we have determined which components in the CBS contribute most significantly to the complexity of the system. With the ISM, architects, system integrators, and system maintainers can isolate the COTS products that cause the most complexity, and therefore cause the most effort to maintain, and take precautions to only change those products when necessary or during major maintenance efforts. The analysis also clearly shows the components that can be easily replaced or upgraded with very little impact on the rest of the system.

Background A proactive risk assessment using the Healthcare Failure Mode and Effect Analysis (HFMEA) process was completed on the intraocular lens (IOL) selection and implantation process to analyze system vulnerabilities that could cause patient harm. The three largest ophthalmology clinics based on patient surgical volume were studied in the analysis. The analysis included in-clinic eye measurements needed for IOL selection through the actual implantation of the lens in the operating room. Methods The HFMEA process was used for the analysis. A detailed process and subprocess diagram was created through interviews and observations. A multidisciplinary team met 12 times over a 14-week period, evaluating 170 discrete process and subprocess steps and identifying 177 failure modes and 75 failure mode causes for analysis. Results A high degree of process variability and lack of a robust quality assurance process was found. Areas for improvement included reducing variability between and within clinics, reducing variability in processes used by surgeons, modifying equipment and software to better support the work processes, and implementing a quality assurance program requiring observation of staff performing their routine work as opposed to relying on self-reports of quality metrics. Conclusion The HFMEA process provided a more complete understanding of all of the processes associated with cataract surgery. This allowed for the identification of a variety of risk factors to patient safety that had not previously been identified by the more traditional reactive analysis methods, which tend to focus only on vulnerabilities identified by a specific event.

Managing abnormal test results in primary care involves coordination across various settings. This study identifies how primary care teams manage test results in a large, computerized healthcare system in order to inform health information technology requirements for test results management and other distributed healthcare services. At five US Veterans Health Administration facilities, we interviewed 37 primary care team members, including 16 primary care providers, 12 registered nurses, and 9 licensed practical nurses. We performed content analysis using a distributed cognition approach, identifying patterns of information transmission across people and artifacts (e.g. electronic health records). Results illustrate challenges (e.g. information overload) as well as strategies used to overcome challenges. Various communication paths were used. Some team members served as intermediaries, processing information before relaying it. Artifacts were used as memory aids. Health information technology should address the risks of distributed work by supporting awareness of team and task status for reliable management of results.

Pemetrexed has been shown to be effective in the treatment of advanced and metastatic nonsquamous nonsmall cell lung cancer. In this population, renal insufficiency is common; however, pemetrexed is not recommended in patients with a creatinine clearance (CrCl) 45 ml/min due to increased myelosuppression reported in phase I trials. The primary objective of this study is to determine the safety of dose-reduced pemetrexed in patients with a CrCl 45 ml/min.This is a retrospective case series describing the incidence of grade 3 or higher toxicity in patients with CrCl 45 ml/min treated with dose-reduced pemetrexed at The James Cancer Hospital and Solove Research Institute at The Ohio State University.A total of eighteen patients were included. Seven (39%) patients experienced a grade ≥ 3 toxicity. Only 18% of administrations led to a grade ≥ 3 toxicity. Four (22%) patients had grade ≥ 3 hematologic toxicity; three of which were receiving concomitant platinum agents. The fourth patient had a CrCl 30 ml/min. No patients receiving single-agent pemetrexed with a CrCl 30 ml/min experienced grade ≥ 3 hematologic toxicity.Dose-adjusted pemetrexed may be cautiously administered to patients with a CrCl between 30 and 45 ml/min. Extra caution is warranted in patients receiving concomitant chemotherapy with a platinum agent as well as those with a CrCl 30 ml/min. Pemetrexed in combination with a platinum agent should not be routinely recommended for patients with a CrCl 30 ml/min.

We previously investigated the association between single nucleotide polymorphisms (SNPs) in genes related to obesity and inflammation and colorectal cancer in the CLUE II cohort. However, the relationships between these SNPs and colorectal adenomas have not been well evaluated. In a nested case-control study of 135 incident adenoma cases and 269 matched controls in the CLUE II cohort (1989–2000), we genotyped 17 candidate SNPs in 12 genes (PPARG, TCF7L2, ADIPOQ, LEP, IL10, CRP, TLR4, IL6, IL1B, IL8, TNF, RNASEL) and 19 tagSNPs in three genes (IL10, CRP, and TLR4). Conditional logistic regression was used to calculate odds ratios (OR) for adenomas (overall and by size, histology, location, number). Polymorphisms in the inflammatory-related genes CRP, ADIPOQ, IL6, and TLR4 were observed to be associated with adenoma risk. At rs1205 in CRP, T (minor allele) carriers had a higher risk (OR 1.67, 95%CI 1.07–2.60; reference: CC) of adenomas overall and adenomas with aggressive characteristics. At rs1201299 in ADIPOQ, the AC genotype had a higher risk (OR 1.58, 95%CI 1.00–2.49) of adenomas, while the minor AA genotype had a borderline inverse association (OR 0.44, 95%CI 0.18–1.08; reference: CC). At rs1800797 in IL6, the AA genotype had a borderline inverse association (OR 0.53, 95%CI 0.27–1.05; reference: GG). Three TLR4 tagSNPs (rs10116253, rs1927911, rs7873784) were associated with adenomas among obese participants. None of these SNPs were associated with colorectal cancer in our prior study in CLUE II, possibly suggesting a different genetic etiology for early colorectal neoplasia.

Switchgrass (Panicum virgatum L.) has potential to be a major cellulosic bioenergy crop. Selection for late flowering plants will extend the vegetative growth, likely resulting in larger biomass yields. However, the genetic structure for reproductive maturity in switchgrass is undefined. Accordingly, the major objective of this study was to identify genomic regions associated with reproductive development. Two lowland populations, one consisting of 176 progeny from NL94 (♀) × SL93 (♂) and a first-generation self-fertilized population of 265 progeny from NL94, were field established in a randomized complete block design with three replications at two Oklahoma locations in 2011. Phenotypic data of reproductive maturity in the populations were collected in 2012 and 2013. Significant genetic variation for reproductive maturity was observed within the two populations. Broad-sense heritabilities were 0.46 to 0.77 and 0.28 to 0.74 for the hybrid and selfed populations, respectively. A linkage map with 178 simple sequence repeat (SSR) markers of the hybrid population constructed in this study and a pre-existing linkage map of 439 SSR markers in the selfed population were used for quantitative trait loci (QTL) characterization. QTL analyses revealed that reproductive maturity was controlled by multiple genomic regions. The QTL regions between nfsg-125 and PVE-781/782 on linkage group (LG) 2b, between PVGA-1727/1728 and PVGA-1201/1202 on LG 3b, and between PVCAG-2503/2504 and PVAAG-3253/3254 on LG 7a were associated with reproductive maturity in both populations. The markers linked to the significant QTL could be used to accelerate the development of switchgrass germplasm with later flowering to increase biomass yield.