bluuebunny/crossref_metadata_2025 huggingface dataset:
The Methodology of Political Theory
Authors: List Christian , Valentini Laura
Published: September 2016

This article examines the methodology of a core branch of contemporary political theory or philosophy: “analytic” political theory. After distinguishing political theory from related fields, such as political science, moral philosophy, and legal theory, the article discusses the analysis of political concepts. It then turns to the notions of principles and theories, as distinct from concepts, and reviews the methods of assessing such principles and theories (e.g. the reflective-equilibrium method), for the purpose of justifying or criticizing them. Finally, it looks at a recent debate on how abstract and idealized political theory should be, and assesses the significance of disagreement in political theory. The discussion is carried out from an angle inspired by the philosophy of science.
Methodology in Nineteenth-and Early Twentieth-Century Analytic Philosophy
Authors: Soames Scott
Published: September 2016

Early analytic philosophical methodology was dominated by two paradigms. The first, arising from the logicism of Frege and Russell, held that linguistic and logical analyses are tools for answering traditional philosophical questions—for example, What are numbers, material objects, and other minds? and How do we know about them? The answers were that these things are whatever they have to be to explain our knowledge of them. For Russell, this inspired a conception of logical analysis that led to revisionary metaphysical minimalism in the service of an unexamined conception of knowledge. The second paradigm, stemming from Wittgenstein and Carnap, was based on philosophical theories of the limits of meaningful discourse that excluded most traditional philosophy. G. E. Moore, whose starting point was common-sense knowledge, offered a partial corrective to both paradigms. The era’s most important achievements were the foundations it laid for genuine sciences of language, logic, and information.
Philosophical Heuristics and Philosophical Methodology
Authors: Hájek Alan
Published: September 2016

Philosophy has a wealth of heuristics—philosophical heuristics—although they have not been well documented or studied. Sometimes they draw attention to a problem with a philosophical position—for example, it involves a problematic definite description, or it has to make a choice that seems arbitrary. Sometimes they provide solutions to a problem—for example, there are many techniques for handling arbitrariness. Sometimes they suggest ways of replacing hard problems with easier ones, with strategies for approaching the latter—for example, replacing intensional notions with extensional surrogates, and then perhaps diagramming the latter. Sometimes they appeal to fertile modes of thinking more generally—for example, continuity reasoning. Philosophers have been becoming increasingly self-conscious of their methodology, yet I believe that the study of such heuristics has been surprisingly neglected. This chapter highlights the importance of philosophical heuristics to philosophical methodology. It considers especially a cluster involving the notion of resemblance.
Logic and Philosophical Methodology
Authors: Burgess John P.
Published: September 2016

This article explores the role of logic in philosophical methodology, as well as its application in philosophy. The discussion gives a roughly equal coverage to the seven branches of logic: elementary logic, set theory, model theory, recursion theory, proof theory, extraclassical logics, and anticlassical logics. Mathematical logic comprises set theory, model theory, recursion theory, and proof theory. Philosophical logic in the relevant sense is divided into the study of extensions of classical logic, such as modal or temporal or deontic or conditional logics, and the study of alternatives to classical logic, such as intuitionistic or quantum or partial or paraconsistent logics. The nonclassical consists of the extraclassical and the anticlassical, although the distinction is not clearcut.
Phenomenology
Authors: Carman Taylor
Published: September 2016

This article explores the role of phenomenology in philosophical inquiry. It begins by discussing Edmund Husserl’s phenomenological reductions (the “transcendental” and the “eidetic”), the sharp distinction he draws between consciousness and reality, and his intuitive claims about intentionality. It then considers Martin Heidegger’s conceptions of phenomenon and phenomenology in relation to hermeneutics before returning to Husserl’s argument that we have a direct intuition, not just of entities, but of the phenomenal appearance of their being (and nonbeing). It also examines Heidegger’s claim that “ontology is possible only as phenomenology” and concludes by assessing phenomenology’s legacy and relevance to philosophy.
Reflective Equilibrium
Authors: Cath Yuri
Published: September 2016

This article examines the method of reflective equilibrium (RE), most closely associated with John Rawls, and its role in philosophical inquiry. It begins with an overview of RE before discussing some of the subtleties involved in its interpretation, including challenges to the standard assumption that RE is committed to a coherentist rather than foundationalist view of justification. It then evaluates some of the main objections to RE, including objections that this method is too conservative, objections that appeal to the possibility of disagreements between people that employ this method, and objections that this method generates unreasonable beliefs. It concludes by considering how RE relates to recent debates about the role of intuitions in philosophy, suggesting the relationship is more complex and interesting than it is usually assumed to be.
What is Philosophical Methodology?
Authors: Dever Josh
Published: September 2016

This article discusses what kind of thing a philosophical methodology (good or not) is or would be, and what kind of questions would count as methodological. The primary focus is on a “higher-order” reading, on which admissible answers are the epistemological methods that distinguish philosophy from the natural sciences and the humanities, or the pursuit of a description of reality at the most fundamental level. The article uses the term “Philosophical Methodology” to pick out questions of the higher order, and “philosophical methodology” for questions of the lower order. To provide a robust data pool, it takes all occurrences of the word “methodological” in entries of the Stanford Encyclopedia of Philosophynford Encyclopedia of Philosophy, and considers what plausible theories of Philosophical Methodology can be fitted into that range of usage. It also discusses seven hypotheses that account for the nature of Philosophical Methodology: Eliminativism, Working-Hypothesism, Epistemologism, Theory Selectionism, Necessary Preconditionalism, Hierarchicalism, and Eliminatedivism.
Wittgenstein’s Global Deflationism
Authors: Horwich Paul
Published: September 2016

This article explores Ludwig Wittgenstein’s ideas about the nature of philosophy, with particular emphasis on his rejection of “T-philosophy”—a traditionally dominant form of philosophy that, although self-consciosly a priori, is shaped by theoretical goals and methods of reasoning that closely resemble those of the sciences. After discussing the goals and methods that characterize T-philosophy, the article presents a formidable Wittgensteinian argument against that practice. It proceeds to describe the sort of treatment of particular philosophical problems that is called for by this argument; and it assesses the common complaint against Wittgenstein that his overall position is self-undermining—an anti-theoretical theory. It goes on to consider whether Wittgenstein’s perspective involves an objectionable prioritization of language over reality, that is, an objectionable “linguistic turn”. Finally, it compares Wittgenstein’s arguments with the Oxonian “ordinary language philosophy” of philosophers such as Austin, Ryle, and Strawson.
Conceivability and Possibility
Authors: Hill Christopher S.
Published: September 2016

This article examines some philosophical questions about knowledge of modality, including how we determine whether a proposition is necessary or contingent and what procedures to use for recognizing possibility. It maintains that virtually anything is conceivable, and that conceivability is therefore incapable of providing a reliable test for possibility. Whether a conceivable state of affairs is genuinely possible depends on whether it is compatible with the class of necessary truths. But this means that we must have some independent way of recognizing necessity. The article explains that independent access to necessity in terms of the hypothesis that various modal truths constitute an implicit definition of necessity. To a large extent, our knowledge of necessity derives from our grasp of this definition. The article also criticizes Cartesian modal arguments for dualism, and raises an objection to the view that metaphysical necessity can be reductively explained in terms of subjunctive conditionals.
Philosophical Naturalism
Authors: Kornblith Hilary
Published: September 2016

This article focuses on naturalistic approaches to philosophical methodology. It begins with an overview of naturalism, its relationship with views about the a priori, and the implications of a philosopher’s commitment to naturalism for proper method in philosophy. It then considers the disagreement among naturalists about the tenability of the a priori/a posteriori distinction with respect to naturalism, before turning to a discussion of the use of science to address philosophical questions. It also looks at work in epistemology which draws on results in the cognitive sciences as a way of understanding the nature of knowledge, with particular emphasis on the role of Alvin Goldman in getting epistemologists to pay attention to the import of empirical work for understanding epistemological issues. Finally, it explores experimental philosophy as a methodological approach to philosophical questions and comments on the debate over the legitimacy of armchair methods in philosophy.
Before the Spring
Authors: Saad Reem
Published: September 2016

This chapter focuses on the rural preludes to the Egyptian uprising in 2011 and examines two instances of conflict that correspond to two different phases of rural protest. The first instance concerns farmers’ responses to the 1992 tenancy law, fully implemented in 1997. The law deprived almost one million families of their main source of work and food security. Despite the devastating impact on their livelihoods, tenants mostly resorted either to coping with the new conditions or to age-old sporadic protest activities that were, ultimately, not effective. The second instance of protest activity concerns spectacular forms of rural protest that intensified during the latter half of the decade preceding the Egyptian uprising. Here we see a qualitative shift in the types and scope of rural resistance in an especially illuminating moment that sheds light on the subsequent events. The chapter concludes that a significant shift in types of resistance may have to do with social and spatial factors rather than traditional concerns over farming and agricultural land.
Aristotle on Practical Reason
Authors: Taylor Christopher C. W.
Published: September 2016

For Aristotle,phronēsis, the excellence of the practical intellect, is two-fold, consisting of a true conception of the end to be achieved by action and correct deliberation about the means to achieve that end. Three accounts have been given as to how that true conception of the end is acquired: i) by virtue of character, ii) by dialectic, i.e. critical reasoning concerning authoritative beliefs, and iii) by induction from data of experience. Virtue of character is the proper responsiveness of the appetitive element in the soul to reason; it is itself a rational state, presupposing a prior grasp of the end by the intellect. Dialectic and experience are each required for the attainment of that grasp, the role of the former being apparently to formulate more or less indeterminate principles that it is the task of moral experience to make determinate.
Holistic Review in Medical School Admissions and Selection: A Strategic, Mission-Driven Response to Shifting Societal Needs
Authors: Conrad Sarah S. , Addams Amy N. , Young Geoffrey H.
Published: September 2016

Medical schools and residency programs have always sought excellence in the areas of education, research, and clinical care. However, these pursuits are not accomplished within a vacuum—rather, they are continually and necessarily influenced by social, cultural, political, legal, and economic forces. Persistent demographic inequalities coupled with rapidly evolving biomedical research and a complex legal landscape heighten our collective awareness and emphasize the continued need to consider medicine’s social contract when selecting, educating, and developing physicians and physician–scientists.

Selection—who gains access to a medical education and to a career as a physician, researcher, and/or faculty member—is as much art as science. Quantitative assessments of applicants yield valuable information but fail to convey the full story of an applicant and the paths they have taken. Human judgment and evidence-based practice remain critical parts of implementing selection processes that yield the desired outcomes. Holistic review, in promoting the use of strategically designed, evidence-driven, mission-based, diversity-aware processes, provides a conceptual and practical framework for marrying the art with the science without sacrificing the unique value that each brings.

In this Commentary, the authors situate medical student selection as both responsive to and informed by broader social context, health and health care needs, educational research and evidence, and state and federal law and policy. They propose that holistic review is a strategic, mission-driven, evidence-based process that recognizes diversity as critical to excellence, offers a flexible framework for selecting future physicians, and facilitates achieving institutional mission and addressing societal needs.
Median Effective Dose of Intranasal Dexmedetomidine for Rescue Sedation in Pediatric Patients Undergoing Magnetic Resonance Imaging
Authors: Zhang Wenhua , Fan Yanting , Zhao Tianyun , Chen Jinghui , Zhang Gaolong , Song Xingrong
Published: September 2016

Background

The median effective dose (ED50) of intranasal dexmedetomidine after failed chloral hydrate sedation has not been described for children. This study aims to determine the ED50 of intranasal dexmedetomidine for rescue sedation in children aged 1 to 36 months, who were inadequately sedated by chloral hydrate administration during magnetic resonance imaging (MRI).

Methods

This study was performed on 120 children, who were 1 to 36 months old and underwent MRI scanning. Intranasal dexmedetomidine was administered as a rescue sedative to children not adequately sedated after the initial oral dose of chloral hydrate (50 mg/kg). Children were stratified into four age groups. ED50 values were estimated from the up-and-down method of Dixon and Massey and probit regression. Other variables included induction time, time to wake up, vital signs, oxygen saturation, MRI scanning time, and recovery characteristics.

Results

ED50 of intranasal dexmedetomidine for rescue sedation was 0.4 μg/kg (95% CI, 0.34 to 0.50) in children aged 1 to 6 months, 0.5 μg/kg (95% CI, 0.48 to 0.56) in children aged 7 to 12 months, 0.9 μg/kg (95% CI, 0.83 to 0.89) in children aged 13 to 24 months, and 1.0 μg/kg (95% CI, 0.94 to 1.07) in children aged 25 to 36 months. There were no significant differences in sedation induction time or time to wake up between the different age groups. Additionally, no significant adverse hemodynamic or hypoxemic effects were noted.

Conclusions

The authors determined the ED50 for rescue sedation using intranasal dexmedetomidine after failed chloral hydrate sedation in children. It was found that ED50 increases with advancing age during the first 3 yr of life.
Parenting Intervention for Prevention of Behavioral Problems in Elementary School-Age Filipino-American Children: A Pilot Study in Churches
Authors: Javier Joyce R. , Coffey Dean M. , Schrager Sheree M. , Palinkas Lawrence A. , Miranda Jeanne
Published: September 2016

Objective:

This study aims to test an evidence-based parenting program offered in churches among Filipino-American parents and estimate effect size for a fully powered trial.

Methods:

Twenty-two parents of children aged 6 to 12 years were randomly assigned to either an intervention or a waiting-list control group. Parents' perceptions of child behavior, parenting practices, and parenting stress were obtained at baseline. Parents in the experimental group attended The Incredible Years School Age Program, which consisted of 12 weekly 2-hour sessions. A follow-up assessment was performed after the intervention and 12 weeks later. The intervention was subsequently repeated with the control group. Satisfaction was assessed with a 40-item measure. Analysis of covariance was used to compare the intervention group postintervention versus the control group. Paired t-tests compared mean parenting practices, parenting stress, and child behavior outcomes. Satisfaction was assessed descriptively.

Results:

Twenty-two parents completed all assessments and the intervention. Analysis of variance comparing intervention and control groups with repeated measures (pre- and post-test measures) revealed that the program has a positive impact on parenting stress, parenting practices (physical punishment, positive verbal discipline), and parent's perception of their child's behavior (internalizing symptoms, externalizing symptoms, and number of problematic behaviors). Analyses of all participants comparing pre- and post intervention revealed improvements in parenting stress, positive verbal discipline, and child externalizing and total problem behaviors. Families reported high satisfaction with the content and format of the intervention.

Conclusion:

Results support the feasibility of providing an evidence-based parenting program to Filipino parents in churches to prevent future behavioral health problems.
Collaborative Learning in the Texas Medicaid 1115 Waiver Program
Authors: Revere Lee , Semaan Adele , Lievsay Nicole , Hall Jessica , Wang Zheng M. , Begley Charles
Published: September 2016

The Texas Medicaid 1115 Transformation Waiver reforms the state's safety net systems by creating a Delivery System Reform Incentive Payment incentive pool for innovative healthcare delivery. The Waiver supports the design and implementation of transformative projects. As part of the Waiver requirements, regions created Learning Collaboratives to collaborate on project implementation and outcomes. This paper describes the experience of one region in adapting the Institute for Healthcare Improvement Breakthrough Series (IHI BTS) model, as a framework for their Learning Collaborative. Implementation of the Learning Collaborative was systematic, multidimensional, and regularly evaluated. Some features of the IHI model were adapted, specifically longer Plan-Do-Check-Act cycles and the lack of a single clinical focus. This experience demonstrates the ability of a region to improve health from a more diverse perspective than the traditional IHI BTS Collaboratives. Within the region, organizations are connecting, agencies are building continuums of care, and stakeholders are involved in healthcare delivery. The initial stages show a remarkable increase in communication and enhanced relationships between providers. At the end of the 5-year Waiver, evaluation of the impact of the regional and cohort Learning Collaboratives will determine how well the adapted IHI BTS model facilitated improvements in the community's health.
Using Nurse Practitioner Co-Management to Reduce Hospitalizations and Readmissions Within a Home-Based Primary Care Program
Authors: Jones Masha G. , DeCherrie Linda V. , Meah Yasmin S. , Hernandez Cameron R. , Lee Eric J. , Skovran David M. , Soriano Theresa A. , Ornstein Katherine A.
Published: September 2016

Nurse practitioner (NP) co-management involves an NP and physician sharing responsibility for the care of a patient. This study evaluates the impact of NP co-management for clinically complex patients in a home-based primary care program on hospitalizations, 30-day hospital readmissions, and provider satisfaction. We compared preenrollment and postenrollment hospitalization and 30-day readmission rates of home-bound patients active in the Nurse Practitioner Co-Management Program within the Mount Sinai Visiting Doctors Program (MSVD) (n = 87) between January 1, 2012, and July 1, 2013. Data were collected from electronic medical records. An anonymous online survey was administered to all physicians active in the MSVD in July 2013 (n = 13).

After enrollment in co-management, patients have lower annual hospitalization rates (1.26 vs. 2.27, p = .005) and fewer patients have 30-day readmissions (5.8% vs. 17.2%, p = .004). Eight of 13 physicians feel “much” or “somewhat” less burned out by their work after implementation of co-management. The high level of provider satisfaction and reductions in annual hospitalization and readmission rates among high-risk home-bound patients associated with NP co-management may yield not only benefits for patients, caregivers, and providers but also cost savings for institutions.
Negative Association of Hospital Efficiency Under Increasing Geographic Elevation on Acute Myocardial Infarction In-Patient Mortality
Authors: Devaraj Srikant , Patel Pankaj C.
Published: September 2016

Although variation in-patient outcomes based on hospitals' geographic location has been studied, altitude of hospitals above sea level may also affect patient outcomes. Possibly, because of negative physical and psychological effects of altitude on hospital employees, hospital efficiency may decline at higher altitudes. Greater focus on hospital efficiency, despite decreasing efficiency at higher altitudes, could increase demands on hospital employees and further deteriorate patient outcomes. Using data envelopment analysis on a sample of 840 hospital-year observations representing 95,504 patients with acute myocardial infarction (AMI) in the United States, and controlling for patient, hospital, and county characteristics and controlling for hospital, state, and year fixed effects, we find support for the negative association between hospital altitude and efficiency; for 1 percentage point increase in efficiency and every 1,000 feet increase in altitude above the sea level, the mortality of patients with AMI increases by 0.66 percentage points. The findings have implications for hospital performance at increasing geographic elevation and introduces to the literature the notion of “health economics of elevation,” to suggest that elevation of a hospital may be an important criterion for consideration for policy makers and insurance firms.
Transection of Radioactive Seeds in Breast Specimens
Authors: Gilcrease Michael Z. , Dogan Basak E. , Black Dalliah M. , Contreras Alejandro , Dryden Mark J. , Jimenez Sandra M.
Published: September 2016

Radioactive seed localization is a new procedure for localizing breast lesions that has several advantages over the standard wire-localization procedure. It is reported to be safe for both patients and medical personnel. Although it is theoretically possible to transect the titanium-encapsulated seed while processing the breast specimen in the pathology laboratory, the likelihood of such an event is thought to be exceedingly low. In fact, there are no previous reports of such an event in the literature to date. We recently encountered 2 cases in which a radioactive seed was inadvertently transected while slicing a breast specimen at the grossing bench. In this report, we describe each case and offer recommendations for minimizing radioactive exposure to personnel and for preventing radioactive contamination of laboratory equipment.
Risk Factor Analysis for Capsular Contracture, Malposition, and Late Seroma in Subjects Receiving Natrelle 410 Form-Stable Silicone Breast Implants
Authors: McGuire Patricia , Reisman Neal R. , Murphy Diane K.
Published: September 2016

Background:

Natrelle 410 silicone breast implants are approved in the United States for breast augmentation, reconstruction, and revision.

Methods:

In two ongoing, prospective, multicenter 10-year studies, 17,656 subjects received Natrelle 410 implants for augmentation (n = 5059), revision-augmentation (n = 2632), reconstruction (n = 7502), or revision-reconstruction (n = 2463). Capsular contracture, implant malposition, and late seroma were documented. Cox proportional hazards regression analyses evaluated potential associations between subject-, implant-, and surgery-related factors and these complications.

Results:

Median follow-up was 4.1, 2.6, 2.1, and 2.3 years in the augmentation, revision-augmentation, reconstruction, and revision-reconstruction cohorts, respectively. Incidence of capsular contracture across cohorts ranged from 2.3 to 4.1 percent; malposition, 1.5 to 2.7 percent; and late seroma, 0.1 to 0.2 percent. Significant risk factors for capsular contracture were subglandular implant placement, periareolar incision site, and older device age in the augmentation cohort (p < 0.0001), older subject age in the revision-augmentation cohort (p < 0.0001), and higher body mass index (p = 0.0026) and no povidone-iodine pocket irrigation (p = 0.0006) in the reconstruction cohort. Significant risk factors for malposition were longer incision size in the augmentation cohort (p = 0.0003), capsulectomy at the time of implantation in the reconstruction cohort (p = 0.0028), and implantations performed in physicians’ offices versus hospitals or standalone surgical facilities in both revision cohorts (p < 0.0001). The incidence of late seroma was too low to perform risk factor analysis.

Conclusions:

These data reaffirm the safety of Natrelle 410 implants. Knowledge of risk factors for capsular contracture and implant malposition offers guidance for reducing complications and optimizing outcomes.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, II.
Platysma Bands: Is a Change Needed in the Surgical Paradigm?
Authors: Trévidic Patrick , Criollo-Lamilla Gisella
Published: September 2016

Background:

Platysma bands are one of the first signs of aging of the neck. Current theories suggest that these bands develop because of skin sagging followed by loss of muscle tone. Treatment strategies therefore aim to tighten skin and muscle. The aim of the present study was to demonstrate that platysma bands are caused by muscular activity during the aging process and are not secondary to skin sagging. This suggests a new approach to managing platysma bands.

Methods:

The authors conducted a descriptive, prospective clinical study of 25 patients who presented with definitive, unilateral, facial palsy following otoneurosurgical treatment. The authors targeted their observations on anterior neck bands. Patients were followed for up to 10 years.

Results:

Of the 25 patients, 76 percent had visible platysma bands on the healthy side, but not on the paralyzed side, of their face. Platysma bands were present on both sides in the 12 percent of patients who had a spastic form of facial paralysis. There was no worsening of the platysma band appearance in any patient. No ptosis of the neck skin on the paralyzed side was observed.

Conclusions:

This study demonstrated that platysma bands are not related to relaxation of the platysma and skin laxity, but are caused by activity of the platysma muscle. The skin follows the muscle. These observations support a change in surgical management of the aging neck, moving from tightening the skin to denervating the platysma muscle. Further studies need to fully characterize the efficacy and safety of platysma muscle denervation in this indication.
Sex Related Differences in the Risk of Antibody-Mediated Rejection and Subsequent Allograft Vasculopathy Post-Heart Transplantation: A Single-Center Experience
Authors: Grupper Avishay , Nestorovic Emilija M. , Daly Richard C. , Milic Natasa M. , Joyce Lyle D. , Stulak John M. , Joyce David L. , Edwards Brooks S. , Pereira Naveen L. , Kushwaha Sudhir S.
Published: September 2016

Background

Pregnancies may result in antibodies against HLA, a risk factor for antibody-mediated rejection (AMR) and subsequent cardiac allograft vasculopathy (CAV) after heart transplantation (HTx). The aim of this study was to evaluate sex differences in the incidence of AMR events and subsequent risk of CAV among HTx recipients.

Methods

The study comprised 160 patients (51 [32%] women) who underwent HTx in 2008 to 2014. The cumulative effect of AMR events was calculated by AMR score (sum of myocardial biopsy grading divided by number of biopsies taken during 3 years post-HTx).

Results

Females had higher levels of anti-HLA I antibodies pre-HTx compared to males which was associated with a history of pregnancies, total number of children and with a higher AMR score at 6 months post-HTx (P < 0.05). Women demonstrated a significant increase in the total incidence of AMR events (27 vs. 7%, P = 0.001) and in AMR scores at 6, 12, 24 and 36 months post-HTx compared to men (P < 0.05). There were no differences in cellular rejection between the groups. A history of AMR events was associated with a significantly increased risk of severe CAV onset (hazard ratio, 7.0; 95% confidence interval, 1.5-31.5; P = 0.012).

Conclusions

Women are at higher risk for AMR post-HTx which subsequently increases their risk for CAV. Females recipients may benefit from closer surveillance to identify AMR at an earlier stage post-HTx, and targeted immunosuppressive therapy to attenuate the development of CAV.
Meniscus ascent by thrips (Thysanoptera)
Authors: Ortega-Jiménez Victor Manuel , Arriaga-Ramirez Sarahi , Dudley Robert
Published: September 2016

Meniscus climbing using a fixed body posture has been well documented for various aquatic and neustonic insects, but is not known from small flying insects that inadvertently become trapped on water surfaces. Here, we show that thrips (order Thysanoptera) can ascend a meniscus by arching their non-wetting bodies to translate head-first and upward along a water surface; if initially oriented backwards, they can turn by 180° to ascend head-first, and climb upward on a surrounding boundary. Using variable-concentration sucrose solutions, we show that translational and climbing speeds during meniscus ascent vary inversely with fluid viscosity. Becoming trapped in water is a frequent event for flying insects, and given that most of them are very small, dedicated behaviours to escape water may be commonplace among pterygotes.
A hybrid algorithm for coupling partial differential equation and compartment-based dynamics
Authors: Harrison Jonathan U. , Yates Christian A.
Published: September 2016

Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction–diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing particle numbers. An alternative description of many of these systems can be derived in the diffusive limit as a deterministic, continuum system of partial differential equations (PDEs). Although the numerical solution of such PDEs is, in general, much more efficient than the full stochastic simulation, the deterministic continuum description is generally not valid when copy numbers are low and stochastic effects dominate. Therefore, to take advantage of the benefits of both of these types of models, each of which may be appropriate in different parts of a spatial domain, we have developed an algorithm that can be used to couple these two types of model together. This hybrid coupling algorithm uses an overlap region between the two modelling regimes. By coupling fluxes at one end of the interface and using a concentration-matching condition at the other end, we ensure that mass is appropriately transferred between PDE- and compartment-based regimes. Our methodology gives notable reductions in simulation time in comparison with using a fully stochastic model, while maintaining the important stochastic features of the system and providing detail in appropriate areas of the domain. We test our hybrid methodology robustly by applying it to several biologically motivated problems including diffusion and morphogen gradient formation. Our analysis shows that the resulting error is small, unbiased and does not grow over time.
Automated multi-objective calibration of biological agent-based simulations
Authors: Read Mark N. , Alden Kieran , Rose Louis M. , Timmis Jon
Published: September 2016

Computational agent-based simulation (ABS) is increasingly used to complement laboratory techniques in advancing our understanding of biological systems. Calibration, the identification of parameter values that align simulation with biological behaviours, becomes challenging as increasingly complex biological domains are simulated. Complex domains cannot be characterized by single metrics alone, rendering simulation calibration a fundamentally multi-metric optimization problem that typical calibration techniques cannot handle. Yet calibration is an essential activity in simulation-based science; the baseline calibration forms a control for subsequent experimentation and hence is fundamental in the interpretation of results. Here, we develop and showcase a method, built around multi-objective optimization, for calibrating ABSs against complex target behaviours requiring several metrics (termedobjectives) to characterize. Multi-objective calibration (MOC) delivers those sets of parameter values representing optimal trade-offs in simulation performance against each metric, in the form of a Pareto front. We use MOC to calibrate a well-understood immunological simulation against both establisheda prioriand previously unestablished target behaviours. Furthermore, we show that simulation-borne conclusions are broadly, but not entirely, robust to adopting baseline parameter values from different extremes of the Pareto front, highlighting the importance of MOC's identification of numerous calibration solutions. We devise a method for detecting overfitting in a multi-objective context, not previously possible, used to save computational effort by terminating MOC when no improved solutions will be found. MOC can significantly impact biological simulation, adding rigour to and speeding up an otherwise time-consuming calibration process and highlighting inappropriate biological capture by simulations that cannot be well calibrated. As such, it produces more accurate simulations that generate more informative biological predictions.
Different modes of variation for each BG lineage suggest different functions
Authors: Chattaway John , Ramirez-Valdez R. Andrei , Chappell Paul E. , Caesar Joseph J. E. , Lea Susan M. , Kaufman Jim
Published: September 2016

Mammalian butyrophilins have various important functions, one for lipid binding but others as ligands for co-inhibition of αβ T cells or for stimulation of γδ T cells in the immune system. The chicken BG homologues are dimers, with extracellular immunoglobulin variable (V) domains joined by cysteines in the loop equivalent to complementarity-determining region 1 (CDR1). BG genes are found in three genomic locations: BG0 on chromosome 2, BG1 in the classical MHC (the BF-BL region) and many BG genes in the BG region just outside the MHC. Here, we show that BG0 is virtually monomorphic, suggesting housekeeping function(s) consonant with the ubiquitous tissue distribution. BG1 has allelic polymorphism but minimal sequence diversity, with the few polymorphic residues at the interface of the two V domains, suggesting that BG1 is recognized by receptors in a conserved fashion. Any phenotypic variation should be due to the intracellular region, with differential exon usage between alleles. BG genes in the BG region can generate diversity by exchange of sequence cassettes located in loops equivalent to CDR1 and CDR2, consonant with recognition of many ligands or antigens for immune defence. Unlike the mammalian butyrophilins, there are at least three modes by which BG genes evolve.
A modified predator–prey model for the interaction of police and gangs
Authors: Sooknanan J. , Bhatt B. , Comissiong D. M. G.
Published: September 2016

A modified predator–prey model with transmissible disease in both the predator and prey species is proposed and analysed, with infected prey being more vulnerable to predation and infected predators hunting at a reduced rate. Here, the predators are the police and the prey the gang members. In this system, we examine whether police control of gangs is possible. The system is analysed with the help of stability analyses and numerical simulations. The system has five steady states—four of which involve no core gang members and one in which all the populations coexist. Thresholds are identified which determine when the predator and prey populations survive and when the disease remains endemic. For parameter values where the spread of disease among the police officers is greater than the death of the police officers, the diseased predator population survives, when it would otherwise become extinct.
On the integral representations for the confluent hypergeometric function
Authors: Fejzullahu Bujar Xh.
Published: September 2016

In this paper, we derive a new contour integral representation for the confluent hypergeometric function as well as for its various special cases. Consequently, we derive expansions of the confluent hypergeometric function in terms of functions of the same kind. Furthermore, we obtain a new identity involving integrals and sums of confluent hypergeometric functions. Our results generalized several well-known results in the literature.
Brain evolution and development: adaptation, allometry and constraint
Authors: Montgomery Stephen H. , Mundy Nicholas I. , Barton Robert A.
Published: September 2016

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns.
DNA methylation mediates genetic variation for adaptive transgenerational plasticity
Authors: Herman Jacob J. , Sultan Sonia E.
Published: September 2016

Environmental stresses experienced by individual parents can influence offspring phenotypes in ways that enhance survival under similar conditions. Although such adaptive transgenerational plasticity is well documented, its transmission mechanisms are generally unknown. One possible mechanism is environmentally induced DNA methylation changes. We tested this hypothesis in the annual plantPolygonum persicaria, a species known to express adaptive transgenerational plasticity in response to parental drought stress. Replicate plants of 12 genetic lines (sampled from natural populations) were grown in dry versus moist soil. Their offspring were exposed to the demethylating agent zebularine or to control conditions during germination and then grown in dry soil. Under control germination conditions, the offspring of drought-stressed parents grew longer root systems and attained greater biomass compared with offspring of well-watered parents of the same genetic lines. Demethylation removed these adaptive developmental effects of parental drought, but did not significantly alter phenotypic expression in offspring of well-watered parents. The effect of demethylation on the expression of the parental drought effect varied among genetic lines. Differential seed provisioning did not contribute to the effect of parental drought on offspring phenotypes. These results demonstrate that DNA methylation can mediate adaptive, genotype-specific effects of parental stress on offspring phenotypes.
Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation
Authors: Higham Timothy E. , Rogers Sean M. , Langerhans R. Brian , Jamniczky Heather A. , Lauder George V. , Stewart William J. , Martin Christopher H. , Reznick David N.
Published: September 2016

Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator–prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process.
Explaining the geographical origins of seasonal influenza A (H3N2)
Authors: Wen Frank , Bedford Trevor , Cobey Sarah
Published: September 2016

Most antigenically novel and evolutionarily successful strains of seasonal influenza A (H3N2) originate in East, South and Southeast Asia. To understand this pattern, we simulated the ecological and evolutionary dynamics of influenza in a host metapopulation representing the temperate north, tropics and temperate south. Although seasonality and air traffic are frequently used to explain global migratory patterns of influenza, we find that other factors may have a comparable or greater impact. Notably, a region's basic reproductive number (
R
0
) strongly affects the antigenic evolution of its viral population and the probability that its strains will spread and fix globally: a 17–28% higher
R
0
in one region can explain the observed patterns. Seasonality, in contrast, increases the probability that a tropical (less seasonal) population will export evolutionarily successful strains but alone does not predict that these strains will be antigenically advanced. The relative sizes of different host populations, their birth and death rates, and the region in which H3N2 first appears affect influenza's phylogeography in different but relatively minor ways. These results suggest general principles that dictate the spatial dynamics of antigenically evolving pathogens and offer predictions for how changes in human ecology might affect influenza evolution.
Always chew your food: freshwater stingrays use mastication to process tough insect prey
Authors: Kolmann Matthew A. , Welch Kenneth C. , Summers Adam P. , Lovejoy Nathan R.
Published: September 2016

Chewing, characterized by shearing jaw motions and high-crowned molar teeth, is considered an evolutionary innovation that spurred dietary diversification and evolutionary radiation of mammals. Complex prey-processing behaviours have been thought to be lacking in fishes and other vertebrates, despite the fact that many of these animals feed on tough prey, like insects or even grasses. We investigated prey capture and processing in the insect-feeding freshwater stingrayPotamotrygon motorousing high-speed videography. We find thatPotamotrygon motorouses asymmetrical motion of the jaws, effectively chewing, to dismantle insect prey. However, CT scanning suggests that this species has simple teeth. These findings suggest that in contrast to mammalian chewing, asymmetrical jaw action is sufficient for mastication in other vertebrates. We also determined that prey capture in these rays occurs through rapid uplift of the pectoral fins, sucking prey beneath the ray's body, thereby dissociating the jaws from a prey capture role. We suggest that the decoupling of prey capture and processing facilitated the evolution of a highly kinetic feeding apparatus in batoid fishes, giving these animals an ability to consume a wide variety of prey, including molluscs, fishes, aquatic insect larvae and crustaceans. We proposePotamotrygonas a model system for understanding evolutionary convergence of prey processing and chewing in vertebrates.
Selfish evolution of cytonuclear hybrid incompatibility inMimulus
Authors: Case Andrea L. , Finseth Findley R. , Barr Camille M. , Fishman Lila
Published: September 2016

Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility inMimulus. In hybrids between Iron Mountain (IM)Mimulus guttatus×Mimulus nasutus, two tightly linkedM. guttatusalleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that theRfalleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation inRfat IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, theRfregion shows elevatedFST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations,Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility.