A low-rank ensemble Kalman filter for elliptic observations

We propose a regularization method for ensemble Kalman filtering (EnKF) with elliptic observation operators. Commonly used EnKF regularization methods suppress state correlations at long distances. For observations described by elliptic partial differential equations, such as the pressure Poisson equation (PPE) in incompressible fluid flows, distance localization should be used cautiously, as we cannot disentangle slowly decaying physical interactions from spurious long-range correlations. This is particularly true for the PPE, in which distant vortex elements couple nonlinearly to induce pressure. Instead, these inverse problems have a low effective dimension: low-dimensional projections of the observations strongly inform a low-dimensional subspace of the state space. We derive a low-rank factorization of the Kalman gain based on the spectrum of the Jacobian of the observation operator. The identified eigenvectors generalize the source and target modes of the multipole expansion, independently of the underlying spatial distribution of the problem. Given rapid spectral decay, inference can be performed in the low-dimensional subspace spanned by the dominant eigenvectors. This low-rank EnKF is assessed on dynamical systems with Poisson observation operators, where we seek to estimate the positions and strengths of point singularities over time from potential or pressure observations. We also comment on the broader applicability of this approach to elliptic inverse problems outside the context of filtering.

A simplified computational model of possible hydrodynamic interactions between respiratory and swimming-related water flows in labriform-swimming fishes

Hydrodynamic interactions in bony fishes between respiratory fluid flows leaving the opercular openings and simultaneous flows generated by movements of downstream pectoral fins are both poorly understood and likely to be complex. Labriform-swimming fishes that swim primarily by moving only their pectoral fins are good subjects for these studies. We performed a computational fluid dynamics investigation of a simplified 2D model of these interactions based on previously published experimental observations of both respiratory and pectoral fin movements under both resting and slow, steady swimming conditions in two similar labriform swimmers: the bluegill sunfish (L. macrochirus) and the largemouth bass (M. salmoides). We carried out a parametric study investigating the effects that swimming speed, strength of opercular flow and phase difference between the pectoral fin motion and the opercular opening and closing have on the thrust and sideslip forces generated by the pectoral fins during both the abduction and adduction portions of the fin movement cycle. We analyzed pressure distributions on the fin surface to determine physical differences in flows with and without opercular jets. The modeling indicates that complex flow structures emerge from the coupling between the opercular jets and vortex shedding from pectoral fins. The jets from the opercular openings appear to exert significant influence on the forces generated by the fins; they are potentially significant in the maneuverability of at least some labriform swimmers. The numerical simulations and the analysis establish a framework for the study of these interactions in various labriform swimmers in a variety of flow regimes. Similar situations in groups of fishes using other swimming modes should also be investigated.

Smoothed particle hydrodynamics simulation of biphasic soft tissue and its medical applications

Modeling the coupled fluid and elastic mechanics of blood perfused soft tissues is important for medical applications. In particular, the current study aims to capture the effect of tissue swelling and the transport of blood through damaged tissue under bleeding or hemorrhaging conditions. The soft tissue is considered a dynamic poro-hyperelastic material with blood-filled voids. A biphasic formulation-effectively, a generalization of Darcy's law-is utilized, treating the phases as occupying fractions of the same volume. A Stokes-like friction force and a pressure that penalizes deviations from volume fractions summing to unity serve as the interaction force between solid and liquid phases. The resulting equations for both phases are discretized with the method of smoothed particle hydrodynamics (SPH). The solver is validated separately on each phase and demonstrates good agreement with exact solutions in test problems. Simulations of oozing, hysteresis, swelling, drying and shrinkage, and tissue fracturing and hemorrhage are shown in the paper. Graphical Abstract In the paper, a new methodology for the numerical simulation of the full dynamic response of blood-perfused soft tissues was developed.

Model of Left Ventricular Contraction: Validation Criteria and Boundary Conditions

Computational models of cardiac contraction can provide critical insight into cardiac function and dysfunction. A necessary step before employing these computational models is their validation. Here we propose a series of validation criteria based on left ventricular (LV) global (ejection fraction and twist) and local (strains in a cylindrical coordinate system, aggregate cardiomyocyte shortening, and low myocardial compressibility) MRI measures to characterize LV motion and deformation during contraction. These validation criteria are used to evaluate an LV finite element model built from subject-specific anatomy and aggregate cardiomyocyte orientations reconstructed from diffusion tensor MRI. We emphasize the key role of the simulation boundary conditions in approaching the physiologically correct motion and strains during contraction. We conclude by comparing the global and local validation criteria measures obtained using two different boundary conditions: the first constraining the LV base and the second taking into account the presence of the pericardium, which leads to greatly improved motion and deformation.

A regulated multiscale closed-loop cardiovascular model, with applications to hemorrhage and hypertension

A computational tool is developed for simulating the dynamic response of the human cardiovascular system to various stressors and injuries. The tool couples 0-dimensional models of the heart, pulmonary vasculature, and peripheral vasculature to 1-dimensional models of the major systemic arteries. To simulate autonomic response, this multiscale circulatory model is integrated with a feedback model of the baroreflex, allowing control of heart rate, cardiac contractility, and peripheral impedance. The performance of the tool is demonstrated in 2 scenarios: neurogenic hypertension by sustained stimulation of the sympathetic nervous system and an acute 10% hemorrhage from the left femoral artery.

Theoretical and experimental study of the dynamic response of absorber-based, micro-scale, oscillatory probes for contact sensing applications

This paper presents two models for predicting the frequency response of micro-scale oscillatory probes. These probes are manufactured by attaching a thin fiber to the free end of one tine of a quartz tuning fork oscillator. In these studies, the attached fibers were either 75 μm diameter tungsten or 7 μm diameter carbon with lengths ranging from around 1 to 15 mm. The oscillators used in these studies were commercial 32.7 kHz quartz tuning forks. The first theoretical model considers lateral vibration of two beams serially connected and provides a characteristic equation from which the roots (eigenvalues) are extracted to determine the natural frequencies of the probe. A second, lumped model approximation is used to derive an approximate frequency response function for prediction of tine displacements as a function of a modal force excitation corresponding to the first mode of the tine in the absence of a fiber. These models are used to evaluate the effect of changes in both length and diameter of the attached fibers. Theoretical values of the natural frequencies of different modes show an asymptotic relationship with the length and a linear relationship with the diameter of the attached fiber. Similar results are observed from experiment, one with a tungsten probe having an initial fiber length of 14.11 mm incrementally etched down to 0.83 mm, and another tungsten probe of length 8.16 mm incrementally etched in diameter, in both cases using chronocoulometry to determine incremental volumetric material removal. The lumped model is used to provide a frequency response again reveals poles and zeros that are consistent with experimental measurements. Finite element analysis shows mode shapes similar to experimental microscope observations of the resonating carbon probes. This model provides a means of interpreting measured responses in terms of the relative motion of the tine and attached fibers. Of particular relevance is that, when a "zero" is observed in the response of the tine, one mode of the fiber is matched to the tine frequency and is acting as an absorber. This represents an optimal condition for contact sensing and for transferring energy to the fiber for fluid mixing, touch sensing, and surface modification applications.

Transport of inertial particles by viscous streaming in arrays of oscillating probes

A mechanism for the transport of microscale particles in viscous fluids is demonstrated. The mechanism exploits the trapping of such particles by rotational streaming cells established in the vicinity of an oscillating cylinder, recently analyzed in previous work. The present work explores a strategy of transporting particles between the trapping points established by multiple cylinders undergoing oscillations in sequential intervals. It is demonstrated that, by controlling the sequence of oscillation intervals, an inertial particle is effectively and predictably transported between the stable trapping points. Arrays of cylinders in various arrangements are investigated, revealing a technique for constructing arbitrary particle trajectories. It is found that the domain from which particles can be transported and trapped by an oscillator is extended, even to regions in which particles are shielded, by the presence of other stationary cylinders. The timescales for transport are examined, as are the mechanisms by which particles are drawn away from an obstacle toward the trapping point of an oscillator.

Evaluation of the Upper Airway Morphology: The Role of Cone Beam Computed Tomography

Cone beam computed tomography (CBCT) has several applications in dentomaxillofacial diagnosis. Frequently, the imaged volume encompasses the upper airway. This article provides a systematic approach to airway analysis and the implications of the anatomic and pathologic alterations. It discusses the role of CBCT in management of obstructive sleep apnea (OSA) patients. This paper also highlights technological advances that combine CBCT imaging with computational modeling of the airway and the potential clinical applications of such technologies.

A Computational Study of the Flow Through a Vitreous Cutter

Vitrectomy is an ophthalmic microsurgical procedure that removes part or all of the vitreous humor from the eye. The procedure uses a vitreous cutter consisting of a narrow shaft with a small orifice at the end through which the humor is aspirated by an applied suction. An internal guillotine oscillates back and forth across the orifice to alter the local shear response of the humor. In this work, a computational study of the flow in a vitreous cutter is conducted in order to gain better understanding of the vitreous behavior and provide guidelines for a new vitreous cutter design. The flow of a Newtonian surrogate of vitreous in a two-dimensional analog geometry is investigated using a finite difference-based immersed boundary method with an algebraically formulated fractional-step method. A series of numerical experiments is performed to evaluate the impact of cutting rate, aspiration pressure, and opening/closing transition on the vitreous cutter flow rate and transorifice pressure variation during vitrectomy. The mean flow rate is observed to increase approximately linearly with aspiration pressure and also increase nearly linearly with duty cycle. A study of time-varying flow rate, velocity field, and vorticity illuminates the flow behavior during each phase of the cutting cycle and shows that the opening/closing transition plays a key role in improving the vitreous cutter’s efficacy and minimizing the potential damage to surrounding tissue. The numerical results show similar trend in flow rate as previous in vitro experiments using water and balanced saline solution and also demonstrate that high duty cycle and slow opening/closing phases lead to high flow rate and minor disturbance to the eye during vitrectomy, which are the design requirements of an ideal vitreous cutter.

Fluid transport and coherent structures of translating and flapping wings

The Lagrangian coherent structures (LCSs) of simple wing cross sections in various low Reynolds number motions are extracted from high-fidelity numerical simulation data and examined in detail. The entrainment process in the wake of a translating ellipse is revealed by studying the relationship between attracting structures in the wake and upstream repelling structures, with the help of blocks of tracer particles. It is shown that a series of slender lobes in the repelling LCS project upstream from the front of the ellipse and "pull" fluid into the wake. Each lobe is paired with a corresponding wake vortex, into which the constituent fluid particles are folded. Flexible and rigid foils in flapping motion are studied, and the resulting differences in coherent structures are used to elucidate their differences in force generation. The clarity with which these flow structures are revealed, compared to the vorticity or velocity fields, provides new insight into the vortex shedding mechanisms that play an important role in unsteady aerodynamics.

Lagrangian coherent structures in low Reynolds number swimming

This work explores the utility of the finite-time Lyapunov exponent (FTLE) field for revealing flow structures in low Reynolds number biological locomotion. Previous studies of high Reynolds number unsteady flows have demonstrated that ridges of the FTLE field coincide with transport barriers within the flow, which are not shown by a more classical quantity such as vorticity. In low Reynolds number locomotion (O(1)-O(100)), in which viscous diffusion rapidly smears the vorticity in the wake, the FTLE field has the potential to add new insight to locomotion mechanics. The target of study is an articulated two-dimensional model for jellyfish-like locomotion, with swimming Reynolds number of order 1. The self-propulsion of the model is numerically simulated with a viscous vortex particle method, using kinematics adapted from previous experimental measurements on a live medusan swimmer. The roles of the ridges of the computed forward- and backward-time FTLE fields are clarified by tracking clusters of particles both backward and forward in time. It is shown that a series of ridges in front of the jellyfish in the forward-time FTLE field transport slender fingers of fluid toward the lip of the bell orifice, which are pulled once per contraction cycle into the wake of the jellyfish, where the fluid remains partitioned. A strong ridge in the backward-time FTLE field reveals a persistent barrier between fluid inside and outside the subumbrellar cavity. The system is also analyzed in a body-fixed frame subject to a steady free stream, and the FTLE field is used to highlight differences in these frames of reference.

Numerical simulations of undulatory swimming at moderate Reynolds number

We perform numerical simulations of the swimming of a three-linkage articulated system in a moderately viscous regime. The computational methodology focuses on the creation, diffusion and transport of vorticity from the surface of the bodies into the fluid. The simulations are dynamically coupled, in that the motion of the three-linkage swimmer is computed simultaneously with the dynamics of the fluid. The novel coupling scheme presented in this work is the first to exploit the relationship between vorticity creation and body dynamics. The locomotion of the system, when subject to undulatory inputs of the hinges, is computed at Reynolds numbers of 200 and 1000. It is found that the forward swimming speed increases with the Reynolds number, and that in both cases the swimming is slower than in an inviscid medium. The vortex shedding is examined, and found to exhibit behavior consistent with experimental flow visualizations of fish.

Evidence-based librarianship: an overview

OBJECTIVE

To demonstrate how the core characteristics of both evidence-based medicine (EBM) and evidence-based health care (EBHC) can be adapted to health sciences librarianship.

METHOD

Narrative review essay involving development of a conceptual framework. The author describes the central features of EBM and EBHC. Following each description of a central feature, the author then suggests ways that this feature applies to health sciences librarianship.

RESULTS

First, the decision-making processes of EBM and EBHC are compatible with health sciences librarianship. Second, the EBM and EBHC values of favoring rigorously produced scientific evidence in decision making are congruent with the core values of librarianship. Third, the hierarchical levels of evidence can be applied to librarianship with some modifications. Library researchers currently favor descriptive-survey and case-study methods over systematic reviews, randomized controlled trials, or other higher levels of evidence. The library literature nevertheless contains diverse examples of randomized controlled trials, controlled-comparison studies, and cohort studies conducted by health sciences librarians.

CONCLUSIONS

Health sciences librarians are confronted with making many practical decisions. Evidence-based librarianship offers a decision-making framework, which integrates the best available research evidence. By employing this framework and the higher levels of research evidence it promotes, health sciences librarians can lay the foundation for more collaborative and scientific endeavors.

Evidence-based librarianship: searching for the needed EBL evidence

This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

The vital few meet the trivial many: unexpected use patterns in a monographs collection

PURPOSE

To test three related hypotheses about monographs circulation at academic health sciences libraries: (1) Juran's "Vital Few" Principle, sometimes incorrectly referred to as the "Pareto Principle"; (2) most (> 30%) new monographs will not circulate within four years; and, (3) Trueswell's 20/80 rule concerning intensity of monographs circulation.

METHODS

Retrospective circulation study conducted at a major academic health sciences library in November 1997 on monographs acquired during 1993, utilizing an online review file.

RESULTS

Unexpectedly, most monographs (84%) had circulated at least once in the four years following acquisition. Combining circulation and in-house data revealed that 90.7% of the monographs acquired in 1993 had been used at least once. Small percentages of these monographs produced disproportionately high circulation levels.

CONCLUSION

Monographs circulation rates confirm Juran's Vital Few principle. Most monographs circulated at least once in contrast to results reported by the Pittsburgh Study or other studies reported by Hardesty and Fenske. The results do not comply with Trueswell's 20/80 ratio rule. Further research needs to investigate the effects of low students to books ratios and problem-based learning (PBL) curricula upon monographs utilization.

The roles of library liaisons in a problem-based learning (PBL) medical school curriculum: a case study from University of New Mexico

The relationships between problem-based learning (PBL) curricula and libraries have generated a substantial number of journal articles, but few have addressed the importance of the interaction between health science libraries and PBL curricula. This article attempts to contribute to this dimension through a description of the roles of library liaisons. First we describe the evolution of the liaison roles beginning 2 years prior to the implementation of a PBL curriculum. We then describe the core responsibilities of liaisons at the University of New Mexico (UNM) with mention of other innovative roles developed by some liaisons.

Identifying peer-reviewed journals in clinical medicine

BACKGROUND

Two directories that contain information about serials also offer lists of thousands of journals identified as peer-reviewed. Librarians generally regard these lists as authoritative.

OBJECTIVE

To identify clinical medicine journals on both peer-reviewed lists, measure the extent of discrepancies between these two lists, and determine the cause for these discrepancies.

DESIGN

Comparison study.

MEASUREMENTS

The extent of the discrepancies were tallied once the author had attempted to control for all extraneous variables. Interviews with the editorial staffs of each directory in regard to procedures for compiling the directories did not produce an explanation for these discrepancies.

RESULTS

Nearly half (46%) of the 784 clinical medicine journals were unique to either one directory's list of peer-reviewed journals or the other's, indicating significant discrepancies between the two directories. Specifically, The Serials Directory listed 211 (27%) unique titles and Ulrich's International Periodicals Directory listed 150 (19%) unique titles (total unique titles = 46%). Both directories listed 423 of the same titles (54%).

CONCLUSION

Widespread confusion about the actual identities of peer reviewed clinical medicine journals appears to explain the discrepancies between lists in these two periodical directories.

Accuracy of indexing coverage information as reported by serials sources

This article reports on the accuracy of indexing service coverage information listed in three serials sources: Ulrich's International Periodicals Directory, SERLINE, and The Serials Directory. The titles studied were randomly selected journals that began publication in either 1981 or 1986. Aggregate results reveal that these serials sources perform at 92%, 97%, and 95% levels of accuracy respectively. When the results are analyzed by specific indexing services by year, the performance scores ranged from 80% to 100%. All three serials sources tend to underreport index coverage. The author advances five recommendations for improving index coverage accuracy and four specific proposals for future research. The results suggest that, for the immediate future, librarians should treat index coverage information reported in these three serials sources with some skepticism.

A problem-based learning curriculum in transition: the emerging role of the library

This case study describes library education programs that serve the University of New Mexico School of Medicine, known for its innovative problem-based learning (PBL) curricular track. The paper outlines the specific library instruction techniques that are integrated into the curriculum. The adaptation of library instruction to a PBL mode of medical education, including the use of case studies, is discussed in detail. Also addressed are the planning processes for the new PBL curriculum scheduled for implementation in 1993, including the activities of library faculty and staff and the probable new role of the library in the new curriculum.