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Data associated with publication “Walking dynamics are symmetric (enough)”
No full textData files and source code associated with the statistical methods and plots from the publication. From the publication abstract: Many biological phenomena such as locomotion, circadian cycles and breathing are rhythmic in nature and can be modelled as rhythmic dynamical systems. Dynamical systems modelling often involves neglecting certain characteristics of a physical system as a modelling convenience. For example, human locomotion is frequently treated as symmetric about the sagittal plane. In this work, we test this assumption by examining human walking dynamics around the steady state (limit-cycle). Here, we adapt statistical cross-validation in order to examine whether there are statistically significant asymmetries and, even if so, test the consequences of assuming bilateral symmetry anyway. Indeed, we identify significant asymmetries in the dynamics of human walking, but nevertheless show that ignoring these asymmetries results in a more consistent and predictive model. In general, neglecting evident characteristics of a system can be more than a modelling convenience—it can produce a better model
Data associated with the publication: Integrated Community Case Management of childhood illness (iCCM) project
No full textAs a part of the Catalytic Initiative to Save a Million Lives, the Integrated Community Case Management of Childhood Illness (iCCM) project sought to demonstrate that rapid scale-ups in coverage for proven interventions would lead to reductions in under-five mortality in Burkina Faso, Malawi, and Ethiopia
Data associated with the Real-Time Monitoring of Under-Five Mortality (RMM) project
No full textThe Real-Time Monitoring of Under-Five Mortality (RMM) project aimed to develop and test methods for producing estimates of child mortality for recent periods of one year or less. Three broad approaches were assessed: 1) community-based reporting of vital events; 2) calibration of facility data to represent deaths in the population; and 3) rapid survey methods. Between 2008 and 2013, we applied and rigorously evaluated at least two of these approaches in each of five countries in sub-Saharan Africa: Ethiopia, Ghana, Malawi, Mali, and Niger. The RMM project has generated an important body of evidence that can inform efforts to strengthen civil registration and vital statistics systems in low-income countries
Immigrant Incorporation in East Asian Democracies (IIEAD) Project: Focus Group Interviews in South Korea [collection]
No full textImmigrant Incorporation in East Asian Democracies (Cambridge University Press, 2020) is based on 31 months of fieldwork conducted in Japan, South Korea, and Taiwan from 2009 to 2016. This book examines how the civic legacies of past struggles for democracy shape current movements for immigrant rights. Examining three industrial democracies in Northeast Asia with overlapping immigration and citizenship policies, immigrant populations, and immigration histories, this book offers insights into the gaps between state policies and immigrant political behavior across similarly situated countries. In addition to comparing policy reforms, state-institutionalized rights for migrants, and immigrant incorporation policies, programs, and services, this project seeks to better understand the process of political incorporation through the lens of migrants themselves. In order to understand the incentives and disincentives for particular forms of political engagement as well as immigrant strategies for political empowerment, the methods employed must allow the respondents to generate their own questions, concepts, and categorizations. In addition to Japanese, South Korean, and Taiwanese government publications and archival materials, the project relies on a combination of questionnaires, over 150 in-depth interviews with immigrants, pro-immigrant activists, and government officials, and 28 focus groups with immigrant communities in the three countries. The Immigrant Incorporation in East Asian Democracies (IIEAD) Project contains the focus group data associated with this book. In Japan, the focus groups consisted of migrants from the Korean peninsula, mainland China, the Philippines, Brazil, Peru, Bangladesh, and Ethiopia; in Korea, participants were nationals of mainland China, Taiwan, Vietnam, the Philippines, Mongolia, and Myanmar; and, in Taiwan, participants consisted of migrants from Vietnam, Indonesia, Thailand, and the Philippines. The IIEAD collection contains transcripts and English translations of 16 focus groups from the study: eight conducted in Japan and eight in South Korea. The focus group transcripts from Taiwan are not included in the IIEAD collection due to their sensitive nature. In order to ensure the confidentiality of the focus group participants, all personal identifiers have been removed from the transcripts in the IIEAD collection, including participants’ names, self-introductions at the beginning of the focus groups, and informal conversations that either contained personal information or that were between participants and not meant to be directed at the group. This study collection includes the South Korea focus group data
Data associated with: Controlling Colloidal Particles with Electric Fields
No full textIn this instructional review, we discuss how to control individual colloids and ensembles of colloids using electric fields. We provide background on the electrokinetic transport mechanisms and kT-scale equilibrium colloidal interactions that enable such control. We also describe the experimental configurations, microscopy methods, image analyses, and material systems for which these mechanisms have been successfully employed. Methods are presented for creating various structures including colloidal chains, quasi-2D colloidal crystals, and 3D colloidal crystals. We also describe electric-field-mediated feedback control of the colloidal crystal size as well as colloidal crystal assembly and disassembly. Finally, we discuss future extensions of these methods that aim to incorporate accurate colloidal crystallization dynamic models into electric-field-mediated feedback control to allow rapid assembly, disassembly, and repair of defect-free colloidal structures
Data associated with: Size dependent thermodynamics and kinetics in electric field mediated colloidal crystal assembly.
No full text From the study abstract We compare measurements and models of the system size dependent assembly of quasi-two dimensional (2D) colloidal crystals within interfacial quadrupole electrodes. Perturbation theory (PT) and Monte Carlo (MC) simulations are used to make thermodynamic predictions of the voltages required to obtain all particles within a crystalline phase for different system sizes. These results show good agreement with video microscopy (VM) measurements of colloidal crystals contain
ing 75–300 particles. Colloidal assembly kinetic trajectories for the same system sizes are quantified from VM experiments using order parameters (reaction coordinates) to capture real-space local and global hexagonal ordering. These trajectories are fit with a Smoluchowski model to extract configuration dependent free energy and diffusivity landscapes (FEL, DL) that capture the microscopic details of assembly dynamics. Landscape features, such as the number and heights of barriers and local gradients, capture the formation, diffusion, and migration of grain boundaries in polycrystalline states, which are increasingly prevalent for n
> 200 but vanish for n < 150. These results demonstrate the importance of system size effects in the formation and annealing of polycrystalline states in colloidal crystallization processes. The data in this study are organized in zip files, with each zip file representing a key step in the research process. NOTE: Fortran 90 code used for MC simulations and to extract FEL and DL are available by request to Dr. Michael Bevan. </p
Data associated with the publication: Long-term trends of nutrients and sediment from the nontidal Chesapeake watershed: an assessment of progress by river and season
No full textFrom the study abstract: To assess historical loads of nitrogen (N), phosphorus (P), and suspended sediment (SS) from the nontidal Chesapeake Bay watershed (NTCBW), we analyzed decadal seasonal trends of flow-normalized loads at the fall-line of nine major rivers that account for >90% of NTCBW flow. Evaluations of loads by season revealed N, P, and SS load magnitudes have been highest in January-March and lowest in July-September, but the temporal trends have followed similar decadal-scale patterns in all seasons, with notable exceptions. Generally, total N (TN) load has dropped since the late 1980s, but particulate nutrients and SS have risen since the mid-1990s. The majority of these rises were from Susquehanna River and relate to diminished net trapping at the Conowingo Reservoir. Substantial rises in SS were also observed, however, in other rivers. Moreover, the summed rise in particulate P load from other rivers is of similar magnitude as from Susquehanna. Dissolved nutrient loads have dropped in the upland (Piedmont and above) rivers, but risen in two small rivers in the Coastal Plain affected by lagged groundwater input. In addition, analysis of fractional contributions revealed consistent N trends across the upland watersheds. Finally, total N:total P ratios have declined in most rivers, suggesting the potential for changes in nutrient limitation. Overall, this integrated study of historical data highlights the value of maintaining long-term monitoring at multiple watershed locations
Data associated with: Endothelial cell responses to micropillar substrates of varying dimensions and stiffness
No full textData files associated with seleted figures from the title publication. From the abstract: In the vascular niche, the extracellular matrix (ECM) provides a structural scaffold with a rich ligand landscape of essential matrix proteins that supports the organization and stabilization of endothelial cells (ECs) into functional blood vessels. Many of the physical interactions between ECs and macromolecular components of the ECM occur at both the micron and submicron scale. In addition, the elasticity of the ECM has been shown to be a critical factor in the progress of the angiogenic cascade.
Here, we sought to determine the effect of substrate topography and elasticity (stiffness) on EC behavior. Utilizing a unique SiO2 substrate with an array of micropillars, we first demonstrate that micropillars with heights >3 μm significantly decrease EC adhesion and spreading. Fibronectin (Fn) patterning of 1 μm high micropillars enabled EC adhesion onto the micropillars and promoted alignment in a single-cell chain manner. We then developed a robust method to generate a soft micropillar substrate array made of polydimethylsiloxane (PDMS), similar to the SiO2 substrate. Finally, we examined the kinetics of EC adhesion and spreading on the soft PDMS substrates compared to the stiff SiO2 substrates. Culturing cells on the PDMS substrates demonstrated an enhanced EC elongation and alignment when compared to stiff SiO2 with similar topographical features. We conclude that the elongation and alignment of ECs is coregulated by substrate topography and stiffness and can be harnessed to guide vascular organization
Data associated with: Smooth-Muscle-Like cells derived from human embryonic stem cells support and augment cord-like structures in vitro
No full textFrom the publication abstract: Engineering vascularized tissue is crucial for its successful implantation, survival, and integration with the host tissue. Vascular smooth muscle cells (v-SMCs) provide physical support to the vasculature and aid in maintaining endothelial viability. In this study, we show an efficient derivation of v-SMCs from human embryonic stem cells (hESCs), and demonstrate their functionality and ability to support the vasculature in vitro. Human ESCs were differentiated in monolayers and supplemented with platelet-derived growth factor-BB (PDGF-BB) and transforming growth factor-beta 1 (TGF-β1). Human ESC-derived smooth-muscle-like cells (SMLCs) were found to highly express specific smooth muscle cell (SMC) markers—including α-smooth muscle actin, calponin, SM22, and smooth muscle myosin heavy chain—to produce and secrete fibronectin and collagen, and to contract in response to carbachol. In vitro tubulogenesis assays revealed that these hESC-derived SMLCs interacted with human endothelial progenitor cell (EPCs) to form longer and thicker cord-like structures in vitro. We have demonstrated a simple protocol for the efficient derivation of highly purified SMLCs from hESCs. These in vitro functional SMLCs interacted with EPCs to support and augment capillary-like structures (CLSs), demonstrating the potential of hESCs as a cell source for therapeutic vascular tissue engineering
Data associated with: Vascular endothelial growth factor and substrate mechanics regulate in vitro tubulogenesis of endothelial progenitor cells.
No full textEndothelial progenitor cells (EPCs) in the circulatory system have been suggested to maintain vascular homeostasis and contribute to adult vascular regeneration and repair. These processes require that EPCs break down the extracellular matrix (ECM), migrate, differentiate and undergo tube morphogenesis. Evidently, the ECM plays a critical role by providing biochemical and biophysical cues that regulate cellular behaviour. Using a chemically and mechanically tunable hydrogel to study tube morphogenesis
in vitro, we show that vascular endothelial growth factor (VEGF) and substrate mechanics co-regulate tubulogenesis of EPCs. High levels of VEGF are required to initiate tube morphogenesis and activate matrix metalloproteinases (MMPs), which enable EPC migration. Under these conditions, the elasticity of the substrate affects the progression of tube morphogenesis. With decreases in substrate stiffness, we observe decreased MMP expression while increased cellular elongation, with intracel
lular vacuole extension and coalescence to open lumen compartments. RNAi studies demonstrate that membrane type 1-MMP (MT1-MMP) is required to enable the movement of EPCs on the matrix and that EPCs sense matrix stiffness through signalling cascades leading to the activation of the RhoGTPase Cdc42. Collectively, these results suggest that coupled responses for VEGF stimulation and modulation of substrate stiffness are required to regulate tube morphogenesis of EPCs. The data in this study are organized by major steps in the research process: viscoelasticity measurements of hydrogels, capillary like structure (CLS) formation, quantification of the CLSs, and the effects of suppression of MT1-MMP and Cdc42 on tube formation