Showing papers by "University of Nevada, Reno published in 2016"
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
5,187 citations
TL;DR: The open-source FALCON and FALcon-Unzip algorithms are introduced to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes.
Abstract: While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short- or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.
1,490 citations
06 Oct 2016
TL;DR: Gunstone et al. as discussed by the authors reviewed recent research on self-regulated learning and discuss the implications of this research for science education, focusing on three components of selfregulated learning including cognition, metacognition, and motivation.
Abstract: The purpose of this article is to review recent research on self-regulated learning and discuss the implications of this research for science education. We draw on examples of self-regulated learning from the science education literature to summarise and illustrate effective instructional methods and the development of metacognitive understanding (Gunstone; 1999a; Rickey & Stacy, 2000; White & Mitchell, 1994). We also focus on the crucial role that metacognition plays in self-regulation (Baird & White, 1996; Nichols, Tippins, & Wieseman, 1997; White, 1998). We divide our discussion into two main parts. The first focuses on three components of selfregulated learning, including cognition, metacognition, and motivation. We relate these aspects of self-regulation to current practices in science education. The second section focuses on six general instructional strategies for improving self-regulation in the science classroom. We focus on the use of inquiry based learning, the role of collaborative support, strategy and problem solving instruction, the construction of mental models, the use of technology to support learning, and the role of personal beliefs such as self-efficacy and epistemological world views. These instructional strategies are selected because they reflect extensive research agendas over the last decade within the science education literature and are essential to metacognition and self-regulation (Butler & Winne, 1995; Gunstone, 1999b).
1,073 citations
TL;DR: In a paternal mouse model given a high-fat diet, a subset of sperm transfer RNA–derived small RNAs (tsRNAs), mainly from 5′ transfer RNA halves and ranging in size from 30 to 34 nucleotides, exhibited changes in expression profiles and RNA modifications.
Abstract: Increasing evidence indicates that metabolic disorders in offspring can result from the father's diet, but the mechanism remains unclear. In a paternal mouse model given a high-fat diet (HFD), we showed that a subset of sperm transfer RNA-derived small RNAs (tsRNAs), mainly from 5' transfer RNA halves and ranging in size from 30 to 34 nucleotides, exhibited changes in expression profiles and RNA modifications. Injection of sperm tsRNA fractions from HFD males into normal zygotes generated metabolic disorders in the F1 offspring and altered gene expression of metabolic pathways in early embryos and islets of F1 offspring, which was unrelated to DNA methylation at CpG-enriched regions. Hence, sperm tsRNAs represent a paternal epigenetic factor that may mediate intergenerational inheritance of diet-induced metabolic disorders.
969 citations
TL;DR: A survey of original evidence shows that histological data always supported a 1:1 ratio of glia to neurons in the entire human brain, and a range of 40–130 billion glial cells, and the current status of knowledge about the number of cells is reviewed.
Abstract: For half a century, the human brain was believed to contain about 100 billion neurons and one trillion glial cells, with a glia:neuron ratio of 10:1. A new counting method, the isotropic fractionator, has challenged the notion that glia outnumber neurons and revived a question that was widely thought to have been resolved. The recently validated isotropic fractionator demonstrates a glia:neuron ratio of less than 1:1 and a total number of less than 100 billion glial cells in the human brain. A survey of original evidence shows that histological data always supported a 1:1 ratio of glia to neurons in the entire human brain, and a range of 40-130 billion glial cells. We review how the claim of one trillion glial cells originated, was perpetuated, and eventually refuted. We compile how numbers of neurons and glial cells in the adult human brain were reported and we examine the reasons for an erroneous consensus about the relative abundance of glial cells in human brains that persisted for half a century. Our review includes a brief history of cell counting in human brains, types of counting methods that were and are employed, ranges of previous estimates, and the current status of knowledge about the number of cells. We also discuss implications and consequences of the new insights into true numbers of glial cells in the human brain, and the promise and potential impact of the newly validated isotropic fractionator for reliable quantification of glia and neurons in neurological and psychiatric diseases. J. Comp. Neurol. 524:3865-3895, 2016. © 2016 Wiley Periodicals, Inc.
683 citations
Smithsonian Tropical Research Institute1, Texas A&M University at Galveston2, National University of Colombia3, University of Florida4, Florida International University5, University of Nevada, Reno6, Florida State University7, Scripps Institution of Oceanography8, United States Geological Survey9, University of California, Riverside10, Federal Fluminense University11, Rutgers University12, University of Iowa13, Universidade Federal de Minas Gerais14, Hamilton College15, University of California, Berkeley16, Texas A&M University17, Natural History Museum18, Woods Hole Oceanographic Institution19, National Museum of Natural History20, Washington and Lee University21, University of California, Davis22
TL;DR: An exhaustive review and reanalysis of geological, paleontological, and molecular records converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma.
Abstract: The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.
595 citations
TL;DR: The third-wave treatments are characterized by openness to older clinical traditions, a focus on second order and contextual change, an emphasis of function over form, and the construction of flexible and effective repertoires, among other features.
442 citations
16 May 2016
TL;DR: A novel path planning algorithm for the autonomous exploration of unknown space using aerial robotic platforms that employs a receding horizon “next-best-view” scheme and its good scaling properties enable the handling of large scale and complex problem setups.
Abstract: This paper presents a novel path planning algorithm for the autonomous exploration of unknown space using aerial robotic platforms The proposed planner employs a receding horizon “next-best-view” scheme: In an online computed random tree it finds the best branch, the quality of which is determined by the amount of unmapped space that can be explored Only the first edge of this branch is executed at every planning step, while repetition of this procedure leads to complete exploration results The proposed planner is capable of running online, onboard a robot with limited resources Its high performance is evaluated in detailed simulation studies as well as in a challenging real world experiment using a rotorcraft micro aerial vehicle Analysis on the computational complexity of the algorithm is provided and its good scaling properties enable the handling of large scale and complex problem setups
427 citations
Purdue University1, University of Nevada, Reno2, Monsanto3, Old Dominion University4, North Carolina State University5, University College London6, Oklahoma State University–Stillwater7, Spanish National Research Council8, National Institutes of Health9, Wellcome Trust10, University of Cambridge11, J. Craig Venter Institute12, Leidos13, Broad Institute14, University of Notre Dame15, University of Nevada, Las Vegas16, University of Barcelona17, Carlos III Health Institute18, University of Massachusetts Medical School19, University of Connecticut20, University of Lausanne21, University of Oxford22, West Virginia University23, Virginia Tech24, Indiana University25, University of Maryland, Baltimore26, Kansas State University27, Texas A&M University28, University of Minnesota29, National University of Singapore30, University of Manchester31, University of California, San Francisco32, Iowa State University33, Colorado State University34, Pennsylvania State University35, Max Planck Society36, University of California, Riverside37, ANSES38, University of Santiago de Compostela39, Pompeu Fabra University40, California State Polytechnic University, Pomona41, University of Queensland42, University of the Sunshine Coast43, Swiss Institute of Bioinformatics44, University of Geneva45, University of Copenhagen46, University of Tennessee Health Science Center47, Wellcome Trust Sanger Institute48, University of Vigo49, University of Illinois at Urbana–Champaign50, Quinnipiac University51, International Livestock Research Institute52
TL;DR: Insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival are reported.
Abstract: Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
406 citations
TL;DR: In this paper, the authors demonstrate measurement times exceeding 10 − 5 s and zeptonewton force sensitivity with laser-cooled silica nanospheres trapped in an optical lattice, which enables a variety of applications including electric-field sensing, inertial sensing, and gravimetry.
Abstract: Optically trapped nanospheres in high vacuum experience little friction and hence are promising for ultrasensitive force detection. Here we demonstrate measurement times exceeding ${10}^{5}$ s and zeptonewton force sensitivity with laser-cooled silica nanospheres trapped in an optical lattice. The sensitivity achieved exceeds that of conventional room-temperature solid-state force sensors by over an order of magnitude, and enables a variety of applications including electric-field sensing, inertial sensing, and gravimetry. The particle is confined at the antinodes of the optical standing wave, and by studying the motion of a particle which has been moved to an adjacent trapping site, the known spacing of the antinodes can be used to calibrate the displacement spectrum of the particle. Finally, we study the dependence of the trap stability and lifetime on the laser intensity and gas pressure, and examine the heating rate of the particle in vacuum without feedback cooling.
293 citations
TL;DR: A novel automated crack detection algorithm, the STRUM (spatially tuned robust multifeature) classifier, is presented, and results on real bridge data using a state-of-the-art robotic bridge scanning system are demonstrated.
Abstract: Detection of cracks on bridge decks is a vital task for maintaining the structural health and reliability of concrete bridges. Robotic imaging can be used to obtain bridge surface image sets for automated on-site analysis. We present a novel automated crack detection algorithm, the STRUM (spatially tuned robust multifeature) classifier, and demonstrate results on real bridge data using a state-of-the-art robotic bridge scanning system. By using machine learning classification, we eliminate the need for manually tuning threshold parameters. The algorithm uses robust curve fitting to spatially localize potential crack regions even in the presence of noise. Multiple visual features that are spatially tuned to these regions are computed. Feature computation includes examining the scale-space of the local feature in order to represent the information and the unknown salient scale of the crack. The classification results are obtained with real bridge data from hundreds of crack regions over two bridges. This comprehensive analysis shows a peak STRUM classifier performance of 95% compared with 69% accuracy from a more typical image-based approach. In order to create a composite global view of a large bridge span, an image sequence from the robot is aligned computationally to create a continuous mosaic. A crack density map for the bridge mosaic provides a computational description as well as a global view of the spatial patterns of bridge deck cracking. The bridges surveyed for data collection and testing include Long-Term Bridge Performance program's (LTBP) pilot project bridges at Haymarket, VA, USA, and Sacramento, CA, USA.
TL;DR: In this article, the authors examined 2010 mortality data obtained from the World Health Organization for populous, high-income countries (n = 23) and calculated death rates per 100,000 population for each country and for the aggregation of all non-US countries overall and by age and sex.
TL;DR: Age-accumulation of circ RNAs in brain tissues was found to be largely independent from linear RNA expression of host genes, suggesting that circRNAs might play biological roles relevant to the aging nervous system.
Abstract: Circular RNAs (circRNAs) are a newly appreciated class of RNAs expressed across diverse phyla. These enigmatic transcripts are most commonly generated by back-splicing events from exons of protein-coding genes. This results in highly stable RNAs due to the lack of free 5' and 3' ends. CircRNAs are enriched in neural tissues, suggesting that they might have neural functions. Here, we sought to determine whether circRNA accumulation occurs during aging in mice. Total RNA-seq profiling of young (1 month old) and aged (22 month old) cortex, hippocampus and heart samples was performed. This led to the confident detection of 6,791 distinct circRNAs across these samples, including 675 novel circRNAs. Analysis uncovered a strong bias for circRNA upregulation during aging in neural tissues. These age-accumulation trends were verified for individual circRNAs by RT-qPCR and Northern analysis. In contrast, comparison of aged versus young hearts failed to reveal a global trend for circRNA upregulation. Age-accumulation of circRNAs in brain tissues was found to be largely independent from linear RNA expression of host genes. These findings suggest that circRNAs might play biological roles relevant to the aging nervous system.
TL;DR: Evidence is provided of a cuticular mechanism that slows the uptake of pyrethroids, contributing to the resistance phenotype and potentially broadening resistance to multiple insecticide classes, thus providing additional challenges to resistance management.
Abstract: The role of cuticle changes in insecticide resistance in the major malaria vector Anopheles gambiae was assessed. The rate of internalization of (14)C deltamethrin was significantly slower in a resistant strain than in a susceptible strain. Topical application of an acetone insecticide formulation to circumvent lipid-based uptake barriers decreased the resistance ratio by ∼50%. Cuticle analysis by electron microscopy and characterization of lipid extracts indicated that resistant mosquitoes had a thicker epicuticular layer and a significant increase in cuticular hydrocarbon (CHC) content (∼29%). However, the CHC profile and relative distribution were similar in resistant and susceptible insects. The cellular localization and in vitro activity of two P450 enzymes, CYP4G16 and CYP4G17, whose genes are frequently overexpressed in resistant Anopheles mosquitoes, were analyzed. These enzymes are potential orthologs of the CYP4G1/2 enzymes that catalyze the final step of CHC biosynthesis in Drosophila and Musca domestica, respectively. Immunostaining indicated that both CYP4G16 and CYP4G17 are highly abundant in oenocytes, the insect cell type thought to secrete hydrocarbons. However, an intriguing difference was indicated; CYP4G17 occurs throughout the cell, as expected for a microsomal P450, but CYP4G16 localizes to the periphery of the cell and lies on the cytoplasmic side of the cell membrane, a unique position for a P450 enzyme. CYP4G16 and CYP4G17 were functionally expressed in insect cells. CYP4G16 produced hydrocarbons from a C18 aldehyde substrate and thus has bona fide decarbonylase activity similar to that of dmCYP4G1/2. The data support the hypothesis that the coevolution of multiple mechanisms, including cuticular barriers, has occurred in highly pyrethroid-resistant An gambiae.
TL;DR: In this article, a bibliographic review is presented to demonstrate the tribological behavior of natural fiber reinforced composites and find a knowledge about their usability for various applications that tribology plays a dominant role.
TL;DR: The CLIP staging system is stable and consistently the best prognostic model in all patients and in patients with different viral etiology and treatment strategy.
TL;DR: Development here of Median Interannual Difference Adjusted for Skewness (MIDAS), a variant of the Theil‐Sen median trend estimator, which computes a robust and realistic estimate of trend uncertainty and has the potential for broader application in the geosciences.
Abstract: Automatic estimation of velocities from GPS coordinate time series is becoming required to cope with the exponentially increasing flood of available data, but problems detectable to the human eye are often overlooked. This motivates us to find an automatic and accurate estimator of trend that is resistant to common problems such as step discontinuities, outliers, seasonality, skewness, and heteroscedasticity. Developed here, Median Interannual Difference Adjusted for Skewness (MIDAS) is a variant of the Theil-Sen median trend estimator, for which the ordinary version is the median of slopes vij = (xj-xi )/(tj-ti ) computed between all data pairs i > j. For normally distributed data, Theil-Sen and least squares trend estimates are statistically identical, but unlike least squares, Theil-Sen is resistant to undetected data problems. To mitigate both seasonality and step discontinuities, MIDAS selects data pairs separated by 1 year. This condition is relaxed for time series with gaps so that all data are used. Slopes from data pairs spanning a step function produce one-sided outliers that can bias the median. To reduce bias, MIDAS removes outliers and recomputes the median. MIDAS also computes a robust and realistic estimate of trend uncertainty. Statistical tests using GPS data in the rigid North American plate interior show ±0.23 mm/yr root-mean-square (RMS) accuracy in horizontal velocity. In blind tests using synthetic data, MIDAS velocities have an RMS accuracy of ±0.33 mm/yr horizontal, ±1.1 mm/yr up, with a 5th percentile range smaller than all 20 automatic estimators tested. Considering its general nature, MIDAS has the potential for broader application in the geosciences.
TL;DR: In this paper, the authors presented a possible mechanism linking snowmelt rate and streamflow generation using a gridded implementation of the Budyko framework. But, they did not consider the effect of seasonal changes in regional air temperature on streamflow.
Abstract: Declining mountain snowpack and earlier snowmelt across the western United States has implications for downstream communities. We present a possible mechanism linking snowmelt rate and streamflow generation using a gridded implementation of the Budyko framework. We computed an ensemble of Budyko streamflow anomalies (BSA) using Variable Infiltration Capacity model-simulated evapotranspiration, potential evapotranspiration, and estimated precipitation at 1/16° resolution from 1950-2013. BSA was correlated with simulated baseflow efficiency (r2 = 0.64) and simulated snowmelt rate (r2 = 0.42). The strong correlation between snowmelt rate and baseflow efficiency (r2 = 0.73) links these relationships and supports a possible streamflow generation mechanism wherein greater snowmelt rates increase subsurface flow. Rapid snowmelt may thus bring the soil to field capacity, facilitating below-root-zone percolation, streamflow, and a positive BSA. Previous works have shown that future increases in regional air temperature may lead to earlier, slower snowmelt, and hence, decreased streamflow production via the mechanism proposed by this work.
TL;DR: The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches, and enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.
Abstract: While genome assembly projects have been successful in a number of haploid or inbred species, one of the current main challenges is assembling non-inbred or rearranged heterozygous genomes. To address this critical need, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble Single Molecule Real-Time (SMRT(R)) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We demonstrate the quality of this approach by assembling new reference sequences for three heterozygous samples, including an F1 hybrid of the model species Arabidopsis thaliana, the widely cultivated V. vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata that have challenged short-read assembly approaches. The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches. The phased diploid assembly enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.
TL;DR: The status of the Zika virus outbreak is reviewed, with a focus on how the epidemiology, insect vectors, neuropathology, virology and immunology inform options and strategies available for medical countermeasure development and deployment.
Abstract: Introduction Reports of high rates of primary microcephaly and Guillain-Barre syndrome associated with Zika virus infection in French Polynesia and Brazil have raised concerns that the virus circulating in these regions is a rapidly developing neuropathic, teratogenic, emerging infectious public health threat. There are no licensed medical countermeasures (vaccines, therapies or preventive drugs) available for Zika virus infection and disease. The Pan American Health Organization (PAHO) predicts that Zika virus will continue to spread and eventually reach all countries and territories in the Americas with endemic Aedes mosquitoes. This paper reviews the status of the Zika virus outbreak, including medical countermeasure options, with a focus on how the epidemiology, insect vectors, neuropathology, virology and immunology inform options and strategies available for medical countermeasure development and deployment. Methods Multiple information sources were employed to support the review. These included publically available literature, patents, official communications, English and Lusophone lay press. Online surveys were distributed to physicians in the US, Mexico and Argentina and responses analyzed. Computational epitope analysis as well as infectious disease outbreak modeling and forecasting were implemented. Field observations in Brazil were compiled and interviews conducted with public health officials.
Journal Article•
TL;DR: The recent progress made in understanding the biogenesis and regulation of circRNAs are highlighted, newly uncovered circRNA functions are discussed, and the methodological approaches that could reveal more exciting and unexpected roles for these RNAs are explained.
Abstract: Many thousands of Circular RNAs (circRNAs) have recently been identified in metazoan genomes by transcriptome-wide sequencing. Most circRNAs are generated by back-splicing events from exons of protein-coding genes. A great deal of progress has recently been made in understanding the genome-wide expression patterns, biogenesis, and regulation of circRNAs. To date, however, few functions of circRNAs have been identified. CircRNAs are preferentially expressed in neural tissues and some are found at synapses, suggesting possible functions in the nervous system. Several circRNAs have been shown to function as microRNA "sponges" to counteract microRNA mediated repression of mRNA. New functions for circRNAs are arising, including protein sequestration, transcriptional regulation, and potential functions in cancer. Here, we highlight the recent progress made in understanding the biogenesis and regulation of circRNAs, discuss newly uncovered circRNA functions, and explain the methodological approaches that could reveal more exciting and unexpected roles for these RNAs.
TL;DR: In this paper, the authors review the processes and physics that control precipitation phase as relevant to hydrologists, focusing on the importance of processes occurring aloft, and conclude that current PPMs are too simple to capture important processes and are not well validated for most locations.
Abstract: . The phase of precipitation when it reaches the ground is a first-order driver of hydrologic processes in a watershed. The presence of snow, rain, or mixed-phase precipitation affects the initial and boundary conditions that drive hydrological models. Despite their foundational importance to terrestrial hydrology, typical phase partitioning methods (PPMs) specify the phase based on near-surface air temperature only. Our review conveys the diversity of tools available for PPMs in hydrological modeling and the advancements needed to improve predictions in complex terrain with large spatiotemporal variations in precipitation phase. Initially, we review the processes and physics that control precipitation phase as relevant to hydrologists, focusing on the importance of processes occurring aloft. There is a wide range of options for field observations of precipitation phase, but there is a lack of a robust observation networks in complex terrain. New remote sensing observations have the potential to increase PPM fidelity, but generally require assumptions typical of other PPMs and field validation before they are operational. We review common PPMs and find that accuracy is generally increased at finer measurement intervals and by including humidity information. One important tool for PPM development is atmospheric modeling, which includes microphysical schemes that have not been effectively linked to hydrological models or validated against near-surface precipitation-phase observations. The review concludes by describing key research gaps and recommendations to improve PPMs, including better incorporation of atmospheric information, improved validation datasets, and regional-scale gridded data products. Two key points emerge from this synthesis for the hydrologic community: (1) current PPMs are too simple to capture important processes and are not well validated for most locations, (2) lack of sophisticated PPMs increases the uncertainty in estimation of hydrological sensitivity to changes in precipitation phase at local to regional scales. The advancement of PPMs is a critical research frontier in hydrology that requires scientific cooperation between hydrological and atmospheric modelers and field scientists.
TL;DR: This feature paper aims at discussing the concept of these novel macromolecules from a topological viewpoint, spotlighting the expected behavior of 2D polymers in the context of polymer physics and polymer chemistry and highlighting the potential of these sheet-like macromolescules for application purposes.
TL;DR: In this paper, the effect of reinforcement, volume fraction, normal load, and sliding velocity on the tribological performance of aluminum matrix composites reinforced by graphene nanoplatelets and pure aluminum was investigated.
TL;DR: This paper presents a new algorithm capable of computing short inspection paths via an alternating two-step optimization algorithm according to which at every iteration it attempts to find a new and improved set of viewpoints that together provide full coverage with decreased path cost.
Abstract: This paper presents a new algorithm for three-dimensional coverage path planning for autonomous structural inspection operations using aerial robots. The proposed approach is capable of computing short inspection paths via an alternating two-step optimization algorithm according to which at every iteration it attempts to find a new and improved set of viewpoints that together provide full coverage with decreased path cost. The algorithm supports the integration of multiple sensors with different fields of view, the limitations of which are respected. Both fixed-wing as well as rotorcraft aerial robot configurations are supported and their motion constraints are respected at all optimization steps, while the algorithm operates on both mesh- and occupancy map-based representations of the environment. To thoroughly evaluate this new path planning strategy, a set of large-scale simulation scenarios was considered, followed by multiple real-life experimental test-cases using both vehicle configurations.
TL;DR: Fibroblast strains had a similar morphology to MSCs, expressed the same cell surface markers as MSCS and could also differentiate into adipocytes, chondrocytes and osteoblasts, and express FSP1 in patterns similar to fibroblasts.
Abstract: Background/Aims: Human mesenchymal stromal/stem cells (MSCs), derived from many different tissues, are characterized by a fibroblast-like morphology, the expression of certain cell surface markers and their ability to differentiate into adipocytes, chondrocytes and osteoblasts. A number of studies have shown that MSCs share many characteristics with fibroblasts; however, there is no well-defined set of phenotypic characteristics that could distinguish between these 2 types of cells. Methods: We used 4 well-established human fibroblast strains from 3 different tissue sources and several human MSC strains from 2 different tissue sources to compare the phenotypic and immunological characteristics of these cells. Results: Fibroblast strains had a similar morphology to MSCs, expressed the same cell surface markers as MSCs and could also differentiate into adipocytes, chondrocytes and osteoblasts. Also, similar to MSCs, these fibroblasts were capable of suppressing T cell proliferation and modulating the immunophenotype of macrophages. We also show that MSCs deposit extracellular matrices of collagen type I and fibronectin, and express FSP1 in patterns similar to fibroblasts. Conclusions: Based on currently accepted definitions for cultured human MSCs and fibroblasts, we could not find any immunophenotypic property that could make a characteristic distinction between MSCs and fibroblasts.
Cornell University1, University of Notre Dame2, Loyola University Chicago3, University of Toledo4, University of Nevada, Reno5, University of Georgia6, National Oceanic and Atmospheric Administration7, Texas Tech University8, The Nature Conservancy9, Colorado State University10, University of Michigan11, Resources For The Future12, Rice University13, University of Wyoming14, Governors State University15, United States Fish and Wildlife Service16, University of Alabama17, Illinois Natural History Survey18, University of Toronto19, Michigan Department of Community Health20, United States Department of Agriculture21
TL;DR: Improvements have come from species-specific trait-based risk assessments, of estimates of introduction, establishment, spread, and impact probabilities, especially from pathways of commerce in living organisms, and spatially explicit dispersal models.
Abstract: Risk analysis of species invasions links biology and economics, is increasingly mandated by international and national policies, and enables improved management of invasive species. Biological invasions proceed through a series of transition probabilities (i.e., introduction, establishment, spread, and impact), and each of these presents opportunities for management. Recent research advances have improved estimates of probability and associated uncertainty. Improvements have come from species-specific trait-based risk assessments (of estimates of introduction, establishment, spread, and impact probabilities, especially from pathways of commerce in living organisms), spatially explicit dispersal models (introduction and spread, especially from transportation pathways), and species distribution models (establishment, spread, and impact). Results of these forecasting models combined with improved and cheaper surveillance technologies and practices [e.g., environmental DNA (eDNA), drones, citizen science] ena...
TL;DR: This work has designed a "bottom-up" approach for the synthesis of very narrow (ca. 0.5 nm) and soluble GNRs using a nonoxidative alkyne benzannulation strategy promoted by Brønsted acid.
Abstract: Since the discovery of graphene, there is an increasing amount of research devoted to graphene materials, namely, graphene nanoribbons (GNRs). The “top-down” production of narrow (<10 nm wide), unoxidized, and easily processable GNRs with atomically precise edges is challenging, and therefore, new methods need to be developed. We have designed a “bottom-up” approach for the synthesis of very narrow (ca. 0.5 nm) and soluble GNRs using a nonoxidative alkyne benzannulation strategy promoted by Bronsted acid. Suzuki polymerization was used to produce the GNR precursor, a poly(2,6-dialkynyl-p-phenylene) (PDAPP), with a weight-average molecular weight of 37.6 kg mol–1. Cyclization of the ethynylaryl side chains on PDAPP was efficiently achieved using Bronsted acids to ultimately produce the GNRs. Infrared and Raman spectroscopic characterization of the GNRs matches very well with calculated results. The formation of the GNRs was also supported by transmission electron microscopy (TEM) and scanning tunneling mic...
TL;DR: The results suggest that Fe redox cycling may be strongly impacted by pyrogenic carbon in soils with relatively high content of indigenous pyrogensic carbon or substantial application of biochar.
Abstract: As an important component of soil organic matter (SOM), the transformation of pyrogenic carbon plays a critical role in the biogeochemical cycles of carbon and other redox-active elements such as iron (Fe). Herein, we studied the influences of wheat straw-derived biochars on the microbial reduction of 100 mM of hematite by the dissimilatory metal reducing bacteria Shewanella oneidensis MR-1 under anoxic conditions. The long-term microbial reduction extent and initial reduction rate of hematite were accelerated by more than 2-fold in the presence of 10 mg L–1 biochar. Soluble leachate from 10 mg L–1 biochar enhanced Fe(III) reduction to a similar degree. Microbially prereduced biochar leachate abiotically reduced hematite, consistent with the apparent electron shuttling capacity of biochar leachate. Electron paramagnetic resonance (EPR) analysis suggested that biochar leachate-associated semiquinone functional groups were likely involved in the redox reactions. In addition to electron shuttling effects, bi...
TL;DR: An increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat.
Abstract: The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.