Issues in Reproducible Simulation Research.

In recent years, serious concerns have arisen about reproducibility in science. Estimates of the cost of irreproducible preclinical studies range from 28 billion USD per year in the USA alone (Freedman et al. in PLoS Biol 13(6):e1002165, 2015) to over 200 billion USD per year worldwide (Chalmers and Glasziou in Lancet 374:86-89, 2009). The situation in the social sciences is not very different: Reproducibility in psychological research, for example, has been estimated to be below 50% as well (Open Science Collaboration in Science 349:6251, 2015). Less well studied is the issue of reproducibility of simulation research. A few replication studies of agent-based models, however, suggest the problem for computational modeling may be more severe than for laboratory experiments (Willensky and Rand in JASSS 10(4):2, 2007; Donkin et al. in Environ Model Softw 92:142-151, 2017; Bajracharya and Duboz in: Proceedings of the symposium on theory of modeling and simulation-DEVS integrative M&S symposium, pp 6-11, 2013). In this perspective, we discuss problems of reproducibility in agent-based simulations of life and social science problems, drawing on best practices research in computer science and in wet-lab experiment design and execution to suggest some ways to improve simulation research practice.

Optimization and Control of Agent-Based Models in Biology: A Perspective.

Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of analyzing and using ABMs, due to the lack of the type of mathematical tools available for more traditional models, which leaves simulation as the primary approach. As models become large, simulation becomes challenging. This paper proposes a novel approach to two mathematical aspects of ABMs, optimization and control, and it presents a few first steps outlining how one might carry out this approach. Rather than viewing the ABM as a model, it is to be viewed as a surrogate for the actual system. For a given optimization or control problem (which may change over time), the surrogate system is modeled instead, using data from the ABM and a modeling framework for which ready-made mathematical tools exist, such as differential equations, or for which control strategies can explored more easily. Once the optimization problem is solved for the model of the surrogate, it is then lifted to the surrogate and tested. The final step is to lift the optimization solution from the surrogate system to the actual system. This program is illustrated with published work, using two relatively simple ABMs as a demonstration, Sugarscape and a consumer-resource ABM. Specific techniques discussed include dimension reduction and approximation of an ABM by difference equations as well systems of PDEs, related to certain specific control objectives. This demonstration illustrates the very challenging mathematical problems that need to be solved before this approach can be realistically applied to complex and large ABMs, current and future. The paper outlines a research program to address them.

Exercise training comprising of single 20-s cycle sprints does not provide a sufficient stimulus for improving maximal aerobic capacity in sedentary individuals.

PURPOSE: Sprint interval training (SIT) provides a potent stimulus for improving maximal aerobic capacity ([Formula: see text]), which is among the strongest markers for future cardiovascular health and premature mortality. Cycling-based SIT protocols involving six or more 'all-out' 30-s Wingate sprints per training session improve [Formula: see text], but we have recently demonstrated that similar improvements in [Formula: see text] can be achieved with as few as two 20-s sprints. This suggests that the volume of sprint exercise has limited influence on subsequent training adaptations. Therefore, the aim of the present study was to examine whether a single 20-s cycle sprint per training session can provide a sufficient stimulus for improving [Formula: see text]. METHODS: Thirty sedentary or recreationally active participants (10 men/20 women; mean ± SD age: 24 ± 6 years, BMI: 22.6 ± 4.0 kg m(-2), [Formula: see text]: 33 ± 7 mL kg(-1) min(-1)) were randomised to a training group or a no-intervention control group. Training involved three exercise sessions per week for 4 weeks, consisting of a single 20-s Wingate sprint (no warm-up or cool-down). [Formula: see text] was determined prior to training and 3 days following the final training session. RESULTS: Mean [Formula: see text] did not significantly change in the training group (2.15 ± 0.62 vs. 2.22 ± 0.64 L min(-1)) or the control group (2.07 ± 0.69 vs. 2.08 ± 0.68 L min(-1); effect of time: P = 0.17; group × time interaction effect: P = 0.26). CONCLUSION: Although we have previously demonstrated that regularly performing two repeated 20-s 'all-out' cycle sprints provides a sufficient training stimulus for a robust increase in [Formula: see text], our present study suggests that this is not the case when training sessions are limited to a single sprint.

Effects of a 12-month moderate weight loss intervention on insulin sensitivity and inflammation status in nondiabetic overweight and obese subjects.

Weight loss intervention is the principal non-pharmacological method for prevention and treatment of type 2 diabetes. However, little is known whether it influences insulin sensitivity directly or via its anti-inflammatory effect. The aim of this study was to assess the independent role of changes in inflammation status and weight loss on insulin sensitivity in this population.Overweight and obese nondiabetic participants without co-morbidities underwent a one-year weight loss intervention focused on caloric restriction and behavioral support. Markers of inflammation, body composition, anthropometric para-meters, and insulin sensitivity were recorded at baseline, 6, and 12 months. Insulin sensitivity was assessed with frequently sampled intravenous glucose tolerance test and Minimal Model. Twenty-eight participants (F: 15, M: 13, age 39±5 years, BMI 33.2±4.6 kg/m(2)) completed the study, achieving 9.4±6.9% weight loss, which was predominantly fat mass (7.7±5.6 kg, p<0.0001). Dietary intervention resulted in significant decrease in leptin, leptin-to-adiponectin ratio, hs-CRP, and IL-6 (all p<0.02), and improvement in HOMA-IR and Insulin Sensitivity Index (SI) (both p<0.001). In response to weight loss IL-1ß, IL-2, leptin, and resistin were significantly associated with insulin, sensitivity, whereas sICAM-1 had only marginal additive effect. Moderate weight loss in otherwise healthy overweight and obese individuals resulted in an improvement in insulin sensitivity and in the overall inflammation state; the latter played only a minimal independent role in modulating insulin sensitivity.

The Big Impact of Small Groups on College Drinking.

College drinking is a problem with severe academic, health, and safety consequences. The underlying social processes that lead to increased drinking activity are not well understood. Social Norms Theory is an approach to analysis and intervention based on the notion that students' misperceptions about the drinking culture on campus lead to increases in alcohol use. In this paper we develop an agent-based simulation model, implemented in MATLAB, to examine college drinking. Students' drinking behaviors are governed by their identity (and how others perceive it) as well as peer influences, as they interact in small groups over the course of a drinking event. Our simulation results provide some insight into the potential effectiveness of interventions such as social norms marketing campaigns.

Patterns of differential introgression in a salamander hybrid zone: inferences from genetic data and ecological niche modelling.

Hybrid zones have yielded considerable insight into many evolutionary processes, including speciation and the maintenance of species boundaries. Presented here are analyses from a hybrid zone that occurs among three salamanders -Plethodon jordani, Plethodon metcalfi and Plethodon teyahalee- from the southern Appalachian Mountains. Using a novel statistical approach for analysis of non-clinal, multispecies hybrid zones, we examined spatial patterns of variation at four markers: single-nucleotide polymorphisms (SNPs) located in the mtDNA ND2 gene and the nuclear DNA ILF3 gene, and the morphological markers of red cheek pigmentation and white flecks. Concordance of the ILF3 marker and both morphological markers across four transects is observed. In three of the four transects, however, the pattern of mtDNA is discordant from all other markers, with a higher representation of P. metcalfi mtDNA in the northern and lower elevation localities than is expected given the ILF3 marker and morphology. To explore whether climate plays a role in the position of the hybrid zone, we created ecological niche models for P. jordani and P. metcalfi. Modelling results suggest that hybrid zone position is not determined by steep gradients in climatic suitability for either species. Instead, the hybrid zone lies in a climatically homogenous region that is broadly suitable for both P. jordani and P. metcalfi. We discuss various selective (natural selection associated with climate) and behavioural processes (sex-biased dispersal, asymmetric reproductive isolation) that might explain the discordance in the extent to which mtDNA and nuclear DNA and colour-pattern traits have moved across this hybrid zone.

Analysis of genetic diversity in flowering dogwood natural stands using microsatellites: the effects of dogwood anthracnose.

Flowering dogwood (Cornus florida L.) populations recently have experienced severe declines caused by dogwood anthracnose. Mortality has ranged from 48 to 98%, raising the concern that genetic diversity has been reduced significantly. Microsatellite data were used to evaluate the level and distribution of genetic variation throughout much of the native range of the tree. Genetic variation in areas affected by anthracnose was as high as or higher than areas without die-offs. We found evidence of four widespread, spatially contiguous genetic clusters. However, there was little relationship between geographic distance and genetic difference. These observations suggest that high dispersal rates and large effective population sizes have so far prevented rapid loss of genetic diversity. The effects of anthracnose on demography and community structure are likely to be far more consequential than short-term genetic effects.

Pattern, process and geographic modes of speciation.

The tradition of classifying cases of speciation into discrete geographic categories (allopatric, parapatric and sympatric) fuelled decades of fruitful research and debate. Not surprisingly, as the science has become more sophisticated, this simplistic taxonomy has become increasingly obsolete. Geographic patterns are now reasonably well understood. Sister species are rarely sympatric, implying that sympatric speciation, it its most general sense, is rare. However, sympatric speciation, even in its most restricted population genetic sense, is possible. Several case studies have demonstrated that divergence has occurred in nature without geographic barriers to gene flow. Obviously, different sets of criteria for sympatric speciation will lead to different numbers of qualifying cases. But changing the rules of nomenclature to make 'sympatric speciation' more or less common does not constitute scientific progress. Advances in the study of speciation have come from studies of the processes that constrain or promote divergence, and how they are affected by geography.

Leadership in an academic discipline.

Leading an academic discipline poses moral and ethical challenges, requiring a special set of capabilities. Leadership in a clinical academic discipline involves leading the transformation of education, research, leadership and patient care. Daily struggles within strategic, political and cultural milieu are the norm and effective leaders are able to navigate through these struggles and see opportunities for growth.

Dobzhansky-Muller model of hybrid dysfunction supported by poor burst-speed performance in hybrid tiger salamanders.

Speciation may result from 'complementary' genetic differences that cause dysfunction when brought together in hybrids despite having no deleterious effects within pure species genomes. The theory of complementary genes, independently proposed by Dobzhansky and Muller, yields specific predictions about the genetics of hybrid fitness. Here, I show how alternative models of hybrid dysfunction can be compared using a simple multivariate analysis of hybrid indices calculated from molecular markers. I use the approach to fit models of hybrid dysfunction to swimming performance in hybrid tiger salamander larvae. Poor burst-speed performance is a dysfunction suggesting low vigour and could translate directly into low survival. My analyses show that the Dobzhansky-Muller model fits these data better than heterozygote disadvantage. The approach demonstrated here can be applied to a broad array of nonmodel species, potentially leading to important generalizations about the genetics of hybrid dysfunction.

What, if anything, is sympatric speciation?

Sympatric speciation has always fascinated evolutionary biologists, and for good reason; it pits diversifying selection directly against the tendency of sexual reproduction to homogenize populations. However, different investigators have used different definitions of sympatric speciation and different criteria for diagnosing cases of sympatric speciation. Here, we explore some of the definitions that have been used in empirical and theoretical studies. Definitions based on biogeography do not always produce the same conclusions as definitions based on population genetics. The most precise definitions make sympatric speciation an infinitesimal end point of a continuum. Because it is virtually impossible to demonstrate the occurrence of such a theoretical extreme, we argue that testing whether a case fits a particular definition is less informative than evaluating the biological processes affecting divergence. We do not deny the importance of geographical context for understanding divergence. Rather, we believe this context can be better understood by modelling and measuring quantities, such as gene flow and selection, rather than assigning cases to discrete categories like sympatric and allopatric speciation.

Correlation between visual clues, objective architectural features, and interobserver agreement in prostate cancer.

Three pathologists evaluated a number of designated architectural features to assign grades to 41 cases of well- to moderately differentiated adenocarcinoma, and their opinions were compared. The consensus opinion was obtained and evaluated against objective measurements of glandular architecture that were obtained by morphometric techniques. The observers agreed on gland size, gland uniformity, and the number of glands per field in only 49%, 31%, and 39% of cases, respectively. There were significant differences in the Gleason grades assigned by observers. Paired matching of individual Gleason grades showed agreement among observers in 44% (18 of 41), 56% (23 of 41), and 75% (31 of 41) of cases, respectively. This level of interobserver disagreement occurred even though cases with predominant patterns were selected carefully and those with variable patterns were excluded. A direct relationship appears to exist between increasing Gleason grade and increasing glandular variability, and there is an inverse relationship between Gleason grade, gland lumen area, and the number of glandular nuclei, as assessed by a group of pathologists.

The use of regenerable, affinity ligand-based surfaces for immunosensor applications.

The regeneration of antibody-binding surfaces is of major importance for re-usable sensor formats such as required for direct 'real-time' biosensing technologies and is often difficult to achieve. Antibodies commonly bind the antigen with high avidity and may themselves be sensitive to regeneration conditions. The interaction of polyclonal anti-chlorpyriphos antibody with an immobilised chlorpyriphos-ovalbumin (chlor-oval) conjugate and the interaction of soluble recombinant CD4 with covalently immobilised anti-CD4 IgG are presented in order to highlight these difficulties. Affinity-capture is suggested as an alternative format as it facilitates surface regeneration, directed immobilisation and the attainment of interaction progress curves that conform to the ideal pseudo-first-order kinetic interaction model. Protein A, protein G and polyclonal anti-mouse Fe-coated surfaces were used to observe the interaction of captured anti-GST monoclonal antibody with glutathione-s-transferase (GST). It was shown that a protein A affinity-capture surface produced ideal interaction progress curves while both protein G and polyclonal anti-mouse Fe resulted in systemic deviations.

Out-of-hospital cardiac arrest due to coronary heart disease: a comparison of survival before and after the introduction of defribrillators in ambulances.

OBJECTIVE: To assess the actual impact on coronary mortality of equipping ambulances with defibrillators. DESIGN: Retrospective analysis of routine medical and legal records of all those who had a cardiac arrest attributed to coronary heart disease occurring outside hospital in a defined population before and after the introduction of Heartstart. SETTING: City of Glasgow, North of the River Clyde, 1984 and 1990. PATIENTS: 296 and 267 men and women aged 25-64 inclusive in 1984 and 1990 respectively who had a cardiac arrest outside hospital which was attributed to coronary heart disease (International Classification of Diseases codes 410-414, ninth revision). RESULTS: The impact on coronary mortality in 1990 of equipping ambulances with defibrillators concurred with the earlier prediction of less than 1% of all coronary deaths. The circumstances of cardiac arrest were largely unchanged; most occurred outside hospital in the victim's home and the principal witnesses were members of the victim's family. A call for help before cardiac arrest was made in very few cases and cardiopulmonary resuscitation was attempted by laypersons in less than a third of the deaths they witnessed. There was a significant increase in the number of cardiopulmonary resuscitation attempts made by ambulance crews (16% v 32%, P < 0.01). Ambulance crews, however, still attended less than half of all cases (44% and 47%). CONCLUSION: The impact of equipping ambulances with defibrillators will remain small unless strategies are introduced that focus on improving the public's response to coronary emergencies by calling for help promptly and initiating cardiopulmonary resuscitation before the arrival of the emergency services.

A comparative evaluation of moxalactam: antimicrobial activity, pharmacokinetics, adverse reactions, and clinical efficacy.

Although moxalactam is not, technically speaking, a cephalosporin it is chemically and microbiologically so closely related to those compounds that it can be viewed as a member of the cephalosporin family. Moxalactam has a spectrum of activity that includes both gram positive and gram negative bacteria. Its gram positive activity is less than earlier cephalosporins, but its activity against the Enterobacteriaceae is similar to that of the aminoglycoside family of antibiotics in most comparative studies. Although moxalactam is considerably less active against gram positive bacteria than cefotaxime, another third generation cephalosporin, its higher and more prolonged serum levels probably offset this disadvantage. Compared to cefoperazone, the stability of moxalactam to many types of beta lactamases produced by gram negative bacteria may be advantageous in the therapy of infections caused by hospital-acquired pathogens. Clinical studies suggest that moxalactam can be used for empiric therapy of suspected gram negative infections when Pseudomonas and other non-fermentative bacteria, such as Acinetobacter, are not suspected. Impressive improvements in the survival of patients with gram negative enteric bacillary meningitis have been reported. Although moxalactam, cefotaxime, and cefoperazone have activity against Pseudomonas aeruginosa, none of these antibiotics should be used alone as therapy for suspected or proven severe systemic infections caused by this pathogen. Cost is a major problem with all of the new cephalosporin-like antibiotics. While this high cost may be partially balanced by the use of a single agent compared to an antibiotic combination for therapy in some situations, these antibiotics are not cost effective for prophylactic use. Superinfection with fungi, such as Candida, and Streptococcus faecalis have occurred, and toxicities, such as bleeding due to vitamin K deficiency and disulfuram-like reactions, have also been reported. Reports of resistance to moxalactam and the other third generation cephalosporins are of major concern and indicate the need to closely monitor antibiotic susceptibility patterns of hospital acquired organisms if these antibiotics are to be used for empiric therapy of suspected gram negative non-pseudomonas sepsis.

Facet fracture-dislocation injuries of the cervical spine.

Sixty-eight patients with acute traumatic cervical facet fracture-dislocation injuries are presented. These patients represented 6.7% of all cervical spine fractures identified over a 12-year period. Thirty-one patients had unilateral facet injuries and 37 had bilateral facet injuries. Neurological morbidity was 90% and was most severe among bilateral facet injury patients (84% complete injuries). Spinal shock was identified in 13 patients and was a poor prognostic indicator for the subsequent recovery of associated neurological deficits. Closed reduction was attempted in 66 of 68 patients and was successful in 58% of the patients. Seven patients deteriorated. Open reduction-internal fixation was successful in 83% of 24 patients with a 4% morbidity. Seventy-eight percent of patients improved with rapid closed reduction, and 60% improved with open reduction-internal fixation; however, only 10 patients of the entire 68 made significant neurological recoveries. In these 10 patients, the timing of decompression-realignment appeared to be more important than the means of reduction.

Cervical-to-petrous internal carotid artery bypass procedure. Technical note.

The technique for cervical-to-petrous internal carotid artery saphenous vein bypass is described. This procedure was used in the treatment of three patients with high cervical or skull base vascular injuries. All grafts were patent on follow-up angiography.

Clinical use of a frameless stereotactic arm: results of 325 cases.

The viewing wand is a frameless stereotactic arm that can be used in conjunction with computerized tomography (CT) or magnetic resonance (MR) imaging to provide image-based intraoperative navigation. The authors report a series of 325 cases in which the viewing wand was used and evaluated for its utility, ease of integration into the standard surgical setup, reliability, and real-world accuracy. The use of the system was associated with minimal additional effort or time spent in setting up the procedure as long as a trained technician performed the data transfer and reconstruction. The viewing wand was used in 165 cases in conjunction with CT and 145 cases with MR imaging. The system was reliable, achieving a useful registration in 310 of 325 cases (95.4%). Fiducial-based registration was more accurate than an anatomical landmark-surface fit algorithm method of registration (mean 2.8 vs. 5.6 mm error, respectively, for CT; and mean 3.0 vs. 6.2 mm for MR imaging). The actual error of the system in estimating the position of the probe tip just after registration was judged by the operating surgeon to be less than 2 mm in 92% of MR imaging cases and in 82% of CT cases, between 2 and 5 mm in 7% of MR imaging and 17% of CT cases, and greater than 5 mm in less than 1% of MR imaging and 1.2% of CT cases. The accuracy of the system degraded during the operation, so that by the third evaluation the error was estimated to be less than 2 mm in 77% of MR imaging and 62% of CT cases. Overall, the viewing wand was found to be reliable and accurate. This real-world accuracy was sufficient for a broad range of applications including glioma resection, cerebrospinal fluid shunting procedures, resection of small subcortical masses, and temporal lobe resection. The system is a useful navigational aid that allows a direct approach to intracranial pathology without the drawbacks of application and the limitations of a stereotactic frame.

Superficial fine needle aspiration by clinicians: a survey of utilization.

Quality assurance is as much concerned with cost, turnaround time, and use of resources as with test reliability and outcome. The cytopathologist needs to be aware of the knowledge base and expectations of clinicians who perform fine needle aspiration (FNA) biopsies of superficial lesions without technical assistance. To this end, a single correct answer multiple choice questionnaire was sent to 82 procedure-oriented clinical faculty members. Completed answer sheets from 35 faculty members were analyzed. The score for fee and turnaround time was 63.2 per cent and for knowledge of technique 70.6 per cent. The overall score for use of FNA was 64.7 per cent and for specimen handling was 45.6 per cent. Of those 65 per cent of participants who made comments, 30 per cent stressed importance of shorter turnaround time and 27 per cent emphasized the need for training in this area of endeavor. It is concluded that the quality of diagnosis can be improved by placing greater emphasis on training and education, the provision of written material, courses or tutorials in technique, written and verbal feedback regarding specimen adequacy, and by making more extensive use of electronic transmission of results.