Asymmetric discrimination of non-speech tonal analogues of vowels

Published in final edited form as: J Exp Psychol Hum Percept Perform. 2019 February ; 45(2): 285–300. doi:10.1037/xhp0000603.Directional asymmetries reveal a universal bias in vowel perception favoring extreme vocalic articulations, which lead to acoustic vowel signals with dynamic formant trajectories and well-defined spectral prominences due to the convergence of adjacent formants. The present experiments investigated whether this bias reflects speech-specific processes or general properties of spectral processing in the auditory system. Toward this end, we examined whether analogous asymmetries in perception arise with non-speech tonal analogues that approximate some of the dynamic and static spectral characteristics of naturally-produced /u/ vowels executed with more versus less extreme lip gestures. We found a qualitatively similar but weaker directional effect with two-component tones varying in both the dynamic changes and proximity of their spectral energies. In subsequent experiments, we pinned down the phenomenon using tones that varied in one or both of these two acoustic characteristics. We found comparable asymmetries with tones that differed exclusively in their spectral dynamics, and no asymmetries with tones that differed exclusively in their spectral proximity or both spectral features. We interpret these findings as evidence that dynamic spectral changes are a critical cue for eliciting asymmetries in non-speech tone perception, but that the potential contribution of general auditory processes to asymmetries in vowel perception is limited.Accepted manuscrip

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization.

Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Author Video: An author video summary of this article is available

The Tully-Fisher Relation of Barred Galaxies

We present new data exploring the scaling relations, such as the Tully-Fisher relation (TFR), of bright barred and unbarred galaxies. A primary motivation for this study is to establish whether barredness correlates with, and is a consequence of, virial properties of galaxies. Various lines of evidence suggest that dark matter is dominant in disks of bright unbarred galaxies at 2.2 disk scale lengths, the point of peak rotation for a pure exponential disk. We test the hypothesis that the TF plane of barred high surface brightness galaxies is offset from the mean TFR of unbarred galaxies, as might be expected if barred galaxies are ``maximal'' in their inner parts. We use existing and new TF data to search for basic structural differences between barred and unbarred galaxies. Our new data consist of 2-dimensional Halpha velocity fields derived from SparsePak integral field spectroscopy (IFS) and V,I-band CCD images collected at the WIYN Observatory for 14 strongly barred galaxies. We use WIYN/SparsePak (2-D) velocity fields to show that long-slit (1-D) spectra yield reliable circular speed measurements at or beyond 2.2 disk scale lengths, far from any influence of the bar. This enables us to consider line width measurements from extensive TF surveys which include barred and nonbarred disks and derive detailed scaling relation comparisons. We find that for a given luminosity, barred and unbarred galaxies have comparable structural and dynamical parameters, such as peak velocities, scale lengths, or colors. In particular, the location of a galaxy in the TF plane is independent of barredness. In a global dynamical sense, barred and unbarred galaxies behave similarly and are likely to have, on average, comparable fractions of luminous and dark matter at a given radius. (abridged)Comment: Accepted for publication in the ApJ (September 1, 2003 issue, v594). Appendix figures with I-band image and superimposed 2-D velocity field plus rotation curves must be downloaded separately (due to size constraints) from http://www.astro.ubc.ca/people/courteau/public/courteau03_TFbars.ps.g

Clathrin exchange during clathrin-mediated endocytosis

During clathrin-mediated endocytosis, clathrin-coated pits invaginate to form clathrin-coated vesicles (CVs). Since clathrin-coated pits are planar structures, whereas CVs are spherical, there must be a structural rearrangement of clathrin as invagination occurs. This could occur through simple addition of clathrin triskelions to the edges of growing clathrin-coated pits with very little exchange occurring between clathrin in the pits and free clathrin in the cytosol, or it could occur through large scale exchange of free and bound clathrin. In the present study, we investigated this question by studying clathrin exchange both in vitro and in vivo. We found that in vitro clathrin in CVs and clathrin baskets do not exchange with free clathrin even in the presence of Hsc70 and ATP where partial uncoating occurs. However, surprisingly FRAP studies on clathrin-coated pits labeled with green fluorescent protein–clathrin light chains in HeLa cells show that even when endocytosis is blocked by expression of a dynamin mutant or depletion of cholesterol from the membrane, replacement of photobleached clathrin in coated pits on the membrane occurs at almost the same rate and magnitude as when endocytosis is occurring. Furthermore, very little of this replacement is due to dissolution of old pits and reformation of new ones; rather, it is caused by a rapid ATP-dependent exchange of clathrin in the pits with free clathrin in the cytosol. On the other hand, consistent with the in vitro data both potassium depletion and hypertonic sucrose, which have been reported to transform clathrin-coated pits into clathrin cages just below the surface of the plasma membrane, not only block endocytosis but also block exchange of clathrin. Taken together, these data show that ATP-dependent exchange of free and bound clathrin is a fundamental property of clathrin-coated pits, but not clathrin baskets, and may be involved in a structural rearrangement of clathrin as clathrin-coated pits invaginate

Crizanlizumab and comparators for adults with sickle-cell disease:a systematic review and network meta-analysis

Objectives Treatment options for preventing vaso-occlusive crises (VOC) among patients with sickle cell disease (SCD) are limited, especially if hydroxyurea treatment has failed or is contraindicated. A systematic literature review (SLR) and network meta-analysis (NMA) were conducted to evaluate the efficacy and safety of crizanlizumab for older adolescent and adult (≥16 years old) SCD patients.Methods The SLR included randomised controlled trials (RCTs) and uncontrolled studies. Bayesian NMA of VOC, all-cause hospitalisation days and adverse events were conducted.Results The SLR identified 51 studies and 9 RCTs on 14 treatments that met the NMA inclusion criteria. The NMA found that crizanlizumab 5.0 mg/kg was associated with a reduction in VOC (HR 0.55, 95% credible interval (0.43, 0.69); Bayesian probability of superiority >0.99), all-cause hospitalisation days (0.58 (0.50, 0.68); >0.99) and no evidence of difference on adverse events (0.91 (0.59, 1.43) 0.66) or serious adverse events (0.93 (0.47, 1.87); 0.59) compared with placebo. The HR for reduction in VOC for crizanlizumab relative to L-glutamine was (0.67 (0.50, 0.88); >0.99). These results were sensitive to assumptions regarding whether patient age is an effect modifier.Conclusions This NMA provides preliminary evidence comparing the efficacy of crizanlizumab with other treatments for VOC prevention

A new variance ratio metric to detect the timescale of compensatory dynamics

Understanding the mechanisms governing ecological stability—why a property such as primary productivity is stable in some communities and variable in others—has long been a focus of ecology. Compensatory dynamics, in which anti-synchronous fluctuations between populations buffer against fluctuations at the community level, are a key theoretical mechanism of stability. Classically, compensatory dynamics have been quantified using a variance ratio approach that compares the ratio between community variance and aggregate population variance, such that a lower ratio indicates compensation and a higher ratio indicates synchrony among species fluctuations. However, population dynamics may be influenced by different drivers that operate on different timescales, and evidence from aquatic systems indicates that communities can be compensatory on some timescales and synchronous on others. The variance ratio and related metrics cannot reflect this timescale specificity, yet have remained popular, especially in terrestrial systems. Here, we develop a timescale-specific variance ratio approach that formally decomposes the classical variance ratio according to the timescales of distinct contributions. The approach is implemented in a new R package, called tsvr, that accompanies this paper. We apply our approach to a long-term, multisite grassland community dataset. Our approach demonstrates that the degree of compensation vs. synchrony in community dynamics can vary by timescale. Across sites, population variability was typically greater over longer compared to shorter timescales. At some sites, minimal timescale specificity in compensatory dynamics translated this pattern of population variability into a similar pattern of greater community variability on longer compared to shorter timescales. But at other sites, differentially stronger compensatory dynamics at longer compared to shorter timescales produced lower-than-expected community variability on longer timescales. Within every site, there were plots that exhibited shifts in the strength of compensation between timescales. Our results highlight that compensatory vs. synchronous dynamics are intrinsically timescale-dependent concepts, and our timescale-specific variance ratio provides a metric to quantify timescale specificity and relate it back to the classic variance ratio

Chemoselective Alteration of Fluorophore Scaffolds as a Strategy for the Development of Ratiometric Chemodosimeters

Ratiometric sensors generally couple binding events or chemical reactions at a distal site to changes in the fluorescence of a core fluorophore scaffold. However, such approaches are often hindered by spectral overlap of the product and reactant species. We provide a strategy to design ratiometric sensors that display dramatic spectral shifts by leveraging the chemoselective reactivity of novel functional groups inserted within fluorophore scaffolds. As a proof-of-principle, fluorophores containing a borinate (RF620) or silanediol (SiOH2R) functionality at the bridging position of the xanthene ring system are developed as endogenous H2O2 sensors. Both these fluorophores display far-red to near-infrared excitation and emission prior to reaction. Upon oxidation by H2O2 both sensors are chemically converted to tetramethylrhodamine, producing significant (≥66 nm) blue-shifts in excitation and emission maxima. This work provides a new concept for the development of ratiometric probes

py4DSTEM: a software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full 2D image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields and other sample-dependent properties. However, extracting this information requires complex analysis pipelines, from data wrangling to calibration to analysis to visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail, and present results from several experimental datasets. We have also implemented a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open source HDF5 standard. We hope this tool will benefit the research community, helps to move the developing standards for data and computational methods in electron microscopy, and invite the community to contribute to this ongoing, fully open-source project

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling