Permutation inference for the general linear model Winkler, Anderson M.; Ridgway, Gerard R.; Webster, Matthew A. ...
NeuroImage (Orlando, Fla.),
05/2014, Letnik:
92, Številka:
100
Journal Article, Web Resource
Recenzirano
Odprti dostop
Permutation methods can provide exact control of false positives and allow the use of non-standard statistics, making only weak assumptions about the data. With the availability of fast and ...inexpensive computing, their main limitation would be some lack of flexibility to work with arbitrary experimental designs. In this paper we report on results on approximate permutation methods that are more flexible with respect to the experimental design and nuisance variables, and conduct detailed simulations to identify the best method for settings that are typical for imaging research scenarios. We present a generic framework for permutation inference for complex general linear models (glms) when the errors are exchangeable and/or have a symmetric distribution, and show that, even in the presence of nuisance effects, these permutation inferences are powerful while providing excellent control of false positives in a wide range of common and relevant imaging research scenarios. We also demonstrate how the inference on glm parameters, originally intended for independent data, can be used in certain special but useful cases in which independence is violated. Detailed examples of common neuroimaging applications are provided, as well as a complete algorithm – the “randomise” algorithm – for permutation inference with the glm.
•Permutation for the GLM in the presence of nuisance or non-independence.•A generalised statistic that performs well even under heteroscedasticity.•Permutation and/or sign-flipping, exchangeability blocks and variance groups.•The “randomise” algorithm, as well as various practical examples.
There is a growing interest in controlling the synthesis of colloidal metal nanocrystals and thus tailoring their properties toward various applications. In this context, choosing an appropriate ...combination of reagents (e.g., salt precursor, reductant, capping agent, and stabilizer) plays a pivotal role in enabling the synthesis of metal nanocrystals with diversified sizes, shapes, and structures. Here we present a comprehensive review that highlights one of the key reagents for the synthesis of metal nanocrystals via chemical reduction: the reductants. We start with a brief introduction to the compounds commonly employed as reductants in the colloidal synthesis of metal nanocrystals by showing their oxidation half‐reactions and the corresponding oxidation potentials. Then we offer specific examples pertaining to the controlled synthesis of metal nanocrystals, followed by some fundamental aspects covering the general mechanisms of metal ion reduction based on the Marcus Theory. Afterwards, we present a case‐by‐case discussion on a wide variety of reductants, including their major properties, reduction mechanisms, and additional effects on the final products. We illustrate these aspects by selecting key examples from the literature and paying close attention to the underlying mechanism in each case. At the end, we conclude by summarizing the highlights of the review and providing some perspectives on future directions.
Reductants play a pivotal role in controlling the shapes and surface structures of noble‐metal nanocrystals, which affect both the reaction kinetics and thermodynamics significantly. By choosing an appropriate reductant, one is able to produce various noble metal nanocrystals with a variety of shapes, with typical examples including Pd, Pt, Au, Ag, and Rh.
A fundamental understanding of the in vivo biodegradation phenomenon as well as an appreciation of cellular and tissue responses which determine the biocompatibility of biodegradable PLA and PLGA ...microspheres are important components in the design and development of biodegradable microspheres containing bioactive agents for therapeutic application. This chapter is a critical review of biodegradation, biocompatibility and tissue/material interactions, and selected examples of PLA and PLGA microsphere controlled release systems. Emphasis is placed on polymer and microsphere characteristics which modulate the degradation behaviour and the foreign body reaction to the microspheres. Selected examples presented in the chapter include microspheres incorporating bone morphogenetic protein (BMP) and leuprorelin acetate as well as applications or interactions with the eye, central nervous system, and lymphoid tissue and their relevance to vaccine development. A subsection on nanoparticles and nanospheres is also included. The chapter emphasizes biodegradation and biocompatibility; bioactive agent release characteristics of various systems have not been included except where significant biodegradation and biocompatibility information have been provided.
Despite their recognized limitations, bibliometric assessments of scientific productivity have been widely adopted. We describe here an improved method to quantify the influence of a research article ...by making novel use of its co-citation network to field-normalize the number of citations it has received. Article citation rates are divided by an expected citation rate that is derived from performance of articles in the same field and benchmarked to a peer comparison group. The resulting Relative Citation Ratio is article level and field independent and provides an alternative to the invalid practice of using journal impact factors to identify influential papers. To illustrate one application of our method, we analyzed 88,835 articles published between 2003 and 2010 and found that the National Institutes of Health awardees who authored those papers occupy relatively stable positions of influence across all disciplines. We demonstrate that the values generated by this method strongly correlate with the opinions of subject matter experts in biomedical research and suggest that the same approach should be generally applicable to articles published in all areas of science. A beta version of iCite, our web tool for calculating Relative Citation Ratios of articles listed in PubMed, is available at https://icite.od.nih.gov.
Physiology and function of the tight junction Anderson, James M; Van Itallie, Christina M
Cold Spring Harbor perspectives in biology,
08/2009, Letnik:
1, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Understanding of tight junctions has evolved from their historical perception as inert solute barriers to recognition of their physiological and biochemical complexity. Many proteins are specifically ...localized to tight junctions, including cytoplasmic actin-binding proteins and adhesive transmembrane proteins. Among the latter are claudins, which are critical barrier proteins. Current information suggests that the paracellular barrier is most usefully modeled as having two physiologic components: a system of charge-selective small pores, 4 A in radius, and a second pathway created by larger discontinuities in the barrier, lacking charge or size discrimination. The first pathway is influenced by claudin expression patterns and the second is likely controlled by different proteins and signals. Recent information on claudin function and disease-causing mutations have led to a more complete understanding of their role in barrier formation, but progress is impeded by lack of high resolution structural information.
Robust yet simple remote sensing methodologies for mapping instantaneous land-surface fluxes of water, energy and CO
2 exchange within a coupled framework add significant value to large-scale ...monitoring networks like FLUXNET, facilitating upscaling of tower flux observations to address questions of regional carbon cycling and water availability. This study investigates the implementation of an analytical, light-use efficiency (LUE) based model of canopy resistance within a Two-Source Energy Balance (TSEB) scheme driven primarily by thermal remote sensing inputs. The LUE model computes coupled canopy-scale carbon assimilation and transpiration fluxes, and replaces a Priestley–Taylor (PT) based transpiration estimate used in the original form of the TSEB model. In turn, the thermal remote sensing data provide valuable diagnostic information about the sub-surface moisture status, obviating the need for precipitation input data and prognostic modeling of the soil water balance. Both the LUE and PT forms of the model are compared with eddy covariance tower measurements acquired in rangeland near El Reno, OK. The LUE method resulted in improved partitioning of the surface energy budget, capturing effects of midday stomatal closure in response to increased vapor pressure deficit and reducing errors in half-hourly flux predictions from 16 to 12%. The spatial distribution of CO
2 flux was mapped over the El Reno study area using data from an airborne thermal imaging system and compared to fluxes measured by an aircraft flying a transect over rangeland, riparian areas, and harvested winter wheat. Soil respiration contributions to the net carbon flux were modeled spatially using remotely sensed estimates of soil surface temperature, soil moisture, and leaf area index. Modeled carbon and water fluxes from this heterogeneous landscape compared well in magnitude and spatial pattern to the aircraft fluxes. The thermal inputs proved to be valuable in modifying the effective LUE from a nominal species-dependent value. The model associates cooler canopy temperatures with enhanced transpiration, indicating higher canopy conductance and carbon assimilation rates. The surface energy balance constraint in this modeling approach provides a useful and physically intuitive mechanism for incorporating subtle signatures of soil moisture deficiencies and reduced stomatal aperture, manifest in the thermal band signal, into the coupled carbon and water flux estimates.
We investigated the relationship between individual subjects' functional connectomes and 280 behavioral and demographic measures in a single holistic multivariate analysis relating imaging to ...non-imaging data from 461 subjects in the Human Connectome Project. We identified one strong mode of population co-variation: subjects were predominantly spread along a single 'positive-negative' axis linking lifestyle, demographic and psychometric measures to each other and to a specific pattern of brain connectivity.
Traditional sociodemographic disparities in adolescent vaccination initiation for the HPV, Tdap, and MenACWY vaccines have declined in the United States of America. This decline raises the question ...of whether inequities in access have been successfully addressed. This paper synthesizes research on the resource barriers that inhibit vaccination alongside research on vaccine hesitancy where parents actively refuse vaccination. To do so, I classify the primary reason why teens are unvaccinated in the National Immunization Survey-Teen 2012-2022 into three categories: resource failure, agentic refusal, and other reasons. I use three non-exclusive subsamples of teens who are unvaccinated against the HPV (N = 87,163), MenACWY (N = 54,726), and Tdap (N = 10,947) vaccines to examine the relative importance of resource failure reasons and agentic refusal reasons for non-vaccination across time and teens' sociodemographic characteristics. Results indicate that resource failure reasons continue to explain a substantial portion of the reasons why teens are unvaccinated and disproportionately affect racially/ethnically and economically marginalized teens. Thus, even as sociodemographic inequalities in rates of vaccination have declined, inequities in access remain consequential.
Despite antiretroviral therapy, proviral latency of human immunodeficiency virus type 1 (HIV-1) remains a principal obstacle to curing the infection. Inducing the expression of latent genomes within ...resting CD4(+) T cells is the primary strategy to clear this reservoir. Although histone deacetylase inhibitors such as suberoylanilide hydroxamic acid (also known as vorinostat, VOR) can disrupt HIV-1 latency in vitro, the utility of this approach has never been directly proven in a translational clinical study of HIV-infected patients. Here we isolated the circulating resting CD4(+) T cells of patients in whom viraemia was fully suppressed by antiretroviral therapy, and directly studied the effect of VOR on this latent reservoir. In each of eight patients, a single dose of VOR increased both biomarkers of cellular acetylation, and simultaneously induced an increase in HIV RNA expression in resting CD4(+) cells (mean increase, 4.8-fold). This demonstrates that a molecular mechanism known to enforce HIV latency can be therapeutically targeted in humans, provides proof-of-concept for histone deacetylase inhibitors as a therapeutic class, and defines a precise approach to test novel strategies to attack and eradicate latent HIV infection directly.
Maltreatment-related childhood adversity is the leading preventable risk factor for mental illness and substance abuse. Although the association between maltreatment and psychopathology is ...compelling, there is a pressing need to understand how maltreatment increases the risk of psychiatric disorders. Emerging evidence suggests that maltreatment alters trajectories of brain development to affect sensory systems, network architecture and circuits involved in threat detection, emotional regulation and reward anticipation. This Review explores whether these alterations reflect toxic effects of early-life stress or potentially adaptive modifications, the relationship between psychopathology and brain changes, and the distinction between resilience, susceptibility and compensation.
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