Overview: Computer vision and machine learning for microstructural characterization and analysis

The characterization and analysis of microstructure is the foundation of microstructural science, connecting the materials structure to its composition, process history, and properties. Microstructural quantification traditionally involves a human deciding a priori what to measure and then devising a purpose-built method for doing so. However, recent advances in data science, including computer vision (CV) and machine learning (ML) offer new approaches to extracting information from microstructural images. This overview surveys CV approaches to numerically encode the visual information contained in a microstructural image, which then provides input to supervised or unsupervised ML algorithms that find associations and trends in the high-dimensional image representation. CV/ML systems for microstructural characterization and analysis span the taxonomy of image analysis tasks, including image classification, semantic segmentation, object detection, and instance segmentation. These tools enable new approaches to microstructural analysis, including the development of new, rich visual metrics and the discovery of processing-microstructure-property relationships.Comment: submitted to Materials and Metallurgical Transactions

Geostationary Coastal and Air Pollution Events (GeoCAPE) Wide Angle Spectrometer (WAS)

The GeoCAPE Wide Angle Spectrometer (WAS) Study was a revisit of the COEDI Study from 2012. The customer primary goals were to keep mass, volume and cost to a minimum while meeting the science objectives and maximizing flight opportunities by fitting on the largest number of GEO accommodations possible. Riding on a commercial GEO satellite minimizes total mission costs. For this study, it is desired to increase the coverage rate,km2min, while maintaining ground sample size, 375m, and spectral resolution, 0.4-0.5nm native resolution. To be able to do this, the IFOV was significantly increased, hence the wide angle moniker. The field of view for COEDI was +0.6 degrees or (2048) 375m ground pixels. The WAS Threshold (the IDL study baseline design) is +2.4 degrees IDL study baseline design) is +2.4 degrees

High-Frequency Dynamics of Ocean pH: A Multi-Ecosystem Comparison

The effect of Ocean Acidification (OA) on marine biota is quasi-predictable at best. While perturbation studies, in the form of incubations under elevated pCO2, reveal sensitivities and responses of individual species, one missing link in the OA story results from a chronic lack of pH data specific to a given species' natural habitat. Here, we present a compilation of continuous, high-resolution time series of upper ocean pH, collected using autonomous sensors, over a variety of ecosystems ranging from polar to tropical, open-ocean to coastal, kelp forest to coral reef. These observations reveal a continuum of month-long pH variability with standard deviations from 0.004 to 0.277 and ranges spanning 0.024 to 1.430 pH units. The nature of the observed variability was also highly site-dependent, with characteristic diel, semi-diurnal, and stochastic patterns of varying amplitudes. These biome-specific pH signatures disclose current levels of exposure to both high and low dissolved CO2, often demonstrating that resident organisms are already experiencing pH regimes that are not predicted until 2100. Our data provide a first step toward crystallizing the biophysical link between environmental history of pH exposure and physiological resilience of marine organisms to fluctuations in seawater CO2. Knowledge of this spatial and temporal variation in seawater chemistry allows us to improve the design of OA experiments: we can test organisms with a priori expectations of their tolerance guardrails, based on their natural range of exposure. Such hypothesis-testing will provide a deeper understanding of the effects of OA. Both intuitively simple to understand and powerfully informative, these and similar comparative time series can help guide management efforts to identify areas of marine habitat that can serve as refugia to acidification as well as areas that are particularly vulnerable to future ocean change

Young low‐income ethnic minority children watch less television when their mothers regulate what they are viewing

AimParenting practices can reduce how much television (TV) children watch. This study evaluated the longitudinal association between maternal regulation of TV content and the amount of TV watched by low-income ethnic minority children.MethodsThis was a secondary data analysis of the Welfare, Children & Families: A Three City Study. Data were used from ethnic minority mothers with a child from birth to 4 years old, collected over two waves approximately 16 months apart. The dependent variable was the amount of TV watched by the child (wave two). The main independent variable was the maternal regulation of TV content (wave one). Using multiple linear regression, we evaluated the relationship between maternal regulation of TV content and the amount of TV watched by the child, adjusting for covariates.ResultsOf the 835 mothers, 71% were high content regulators and 8% reported no content regulation. Children whose mothers reported no regulation watched more TV approximately 16 months later than those whose mothers reported high regulation of content (β = 0.91, 95% CI: 0.09-1.73).ConclusionOur findings suggest that regulating content influences viewing amounts in young children approximately 16 months later. Interventions focused on heightening parental regulation of content may improve content and diminish viewing amounts

Psychosis in a 12-year-old HIV-positive girl with an increased serum concentration of efavirenz

Clearance and adverse effects of efavirenz are associated with CYP2B6-G516T polymorphism. Little is known about the prevalence of genotypes and implications for screening in children. We report (to our knowledge, for the first time in a child) the emergence of psychosis in a 12-year old white girl with an increased efavirenz concentration and heterozygous gene polymorphism of the CYP2B6-G516T. © 2007 by the Infectious Diseases Society of America. All rights reserved

Activating hidden signals by mimicking cryptic sites in a synthetic extracellular matrix

Abstract Cryptic sites are short signaling peptides buried within the native extracellular matrix (ECM). Enzymatic cleavage of an ECM protein reveals these hidden peptide sequences, which interact with surface receptors to control cell behavior. Materials that mimic this dynamic interplay between cells and their surroundings via cryptic sites could enable application of this endogenous signaling phenomenon in synthetic ECM hydrogels. We demonstrate that depsipeptides (“switch peptides”) can undergo enzyme-triggered changes in their primary sequence, with proof-of-principle studies showing how trypsin-triggered primary sequence rearrangement forms the bioadhesive pentapeptide YIGSR. We then engineered cryptic site-mimetic synthetic ECM hydrogels that experienced a cell-initiated gain of bioactivity. Responding to the endothelial cell surface enzyme aminopeptidase N, the inert matrix transformed into an adhesive synthetic ECM capable of supporting endothelial cell growth. This modular system enables dynamic reciprocity in synthetic ECMs, reproducing the natural symbiosis between cells and their matrix through inclusion of tunable hidden signals

Evaluation of accuracy and precision in an amplicon sequencing workflow for marine protist communities

Advances in high-throughput DNA sequencing methods reveal the vast diversity of marine protists. Amplicon sequencing of “barcode” genes, such as the 18S small subunit ribosomal RNA gene (henceforth, 18S gene), is a cost-effective and widely used genetic method for assessing the composition of marine protist communities. This method is now being applied from local to global scales to interrogate the causes and consequences of protist community variations. Significant efforts have been made to validate amplicon methods targeting prokaryotes, but the precision, accuracy, and quantitative potential of 18S gene amplicon sequencing methods for marine protists remain unclear. Here, we use artificial (mock) communities and environmental samples collected from the Santa Barbara Channel, CA to evaluate the precision and accuracy in an amplicon workflow targeting the V9 hypervariable region of the 18S gene for marine protists. Overall, we find that this amplicon workflow has high precision and reasonable accuracy, but the magnitude of analytical uncertainty can increase significantly unless certain procedural issues are avoided. Finally, we demonstrate the value of positive and negative controls in, and the quantitative potential of, amplicon sequencing assessments of marine protist communities

Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis

<p><b>Objectives:</b> To define gut microbial patterns in preterm infants with and without necrotizing enterocolitis (NEC) and to characterize clinical factors related to the composition of the preterm intestinal microbiome.</p> <p><b>Methods:</b> Fecal samples were collected at one-week intervals from infants with gestational ages <30 weeks at a single level IV neonatal intensive care unit. Using 16S rRNA gene sequencing, the composition and diversity of microbiota were determined in samples collected from five NEC infants and five matched controls. Hierarchical linear regression was used to identify clinical factors related to microbial diversity and specific bacterial signatures.</p> <p><b>Results:</b> Low levels of diversity were demonstrated in samples obtained from all preterm infants and antibiotic exposure further decreased diversity among both NEC cases and controls. Fecal microbial composition differed between NEC cases and controls, with a greater abundance of <i>Proteobacteria</i> and bacteria belonging to the class <i>Gammaproteobacteria</i> among NEC infants. Control infants demonstrated a greater abundance of bacteria belonging to the phylum <i>Firmicutes</i>.</p> <p><b>Conclusion:</b> These findings indicate that an association exists between intestinal <i>Proteobacteria</i> and NEC, and strengthens the notion that an overly exuberant response to Gram-negative products, particularly lipopolysaccharide, in the preterm intestine is involved in NEC pathogenesis. Cumulative exposure to antibiotics corresponded to a reduction in microbial diversity in both NEC cases and controls.</p

DMRT5 together with DMRT3 directly controls hippocampus development and neocortical area map formation

Mice that are constitutively null for the zinc finger doublesex and mab-3 related (Dmrt) gene, Dmrt5/Dmrta2, show a variety of patterning abnormalities in the cerebral cortex, including the loss of the cortical hem, a powerful cortical signaling center. In conditional Dmrt5 gain of function and loss of function mouse models, we generated bidirectional changes in the neocortical area map without affecting the hem. Analysis indicated that DMRT5, independent of the hem, directs the rostral-to-caudal pattern of the neocortical area map. Thus, DMRT5 joins a small number of transcription factors shown to control directly area size and position in the neocortex. Dmrt5 deletion after hem formation also reduced hippocampal size and shifted the position of the neocortical/paleocortical boundary. Dmrt3, like Dmrt5, is expressed in a gradient across the cortical primordium. Mice lacking Dmrt3 show cortical patterning defects akin to but milder than those in Dmrt5 mutants, perhaps in part because Dmrt5 expression increases in the absence of Dmrt3 DMRT5 upregulates Dmrt3 expression and negatively regulates its own expression, which may stabilize the level of DMRT5. Together, our findings indicate that finely tuned levels of DMRT5, together with DMRT3, regulate patterning of the cerebral cortex