VI. Genome Structure and Cognitive Map of Williams Syndrome

2000 ◽  
Vol 12 (supplement 1) ◽  
pp. 89-107 ◽  
Author(s):  
Julie R. Korenberg ◽  
Xiao-Ning Chen ◽  
Hamao Hirota ◽  
Zona Lai ◽  
Ursula Bellugi ◽  
...  
Keyword(s):  
Williams Syndrome ◽  
Large Scale ◽  
Hot Spot ◽  
Genome Structure ◽  
Single Copy ◽  
Human Cognition ◽  
Chromosome Band ◽  
Gene Marker ◽  
Artificial Chromosomes ◽  
Visual Spatial

Williams syndrome (WMS) is a most compelling model of human cognition, of human genome organization, and of evolution. Due to a deletion in chromosome band 7q11.23, subjects have cardiovascular, connective tissue, and neurode-velopmental deficits. Given the striking peaks and valleys in neurocognition including deficits in visual-spatial and global processing, preserved language and face processing, hypersociability, and heightened affect, the goal of this work has been to identify the genes that are responsible, the cause of the deletion, and its origin in primate evolution. To do this, we have generated an integrated physical, genetic, and transcriptional map of the WMS and flanking regions using multicolor metaphase and interphase fluorescence in situ hybridization (FISH) of bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs), BAC end sequencing, PCR gene marker and microsatellite, large-scale sequencing, cDNA library, and database analyses. The results indicate the genomic organization of the WMS region as two nested duplicated regions flanking a largely single-copy region. There are at least two common deletion breakpoints, one in the centromeric and at least two in the telomeric repeated regions. Clones anchoring the unique to the repeated regions are defined along with three new pseudogene families. Primate studies indicate an evolutionary hot spot for chromosomal inversion in the WMS region. A cognitive phenotypic map of WMS is presented, which combines previous data with five further WMS subjects and three atypical WMS subjects with deletions; two larger (deleted for D7S489L) and one smaller, deleted for genes telomeric to FZD9, through LIMK1, but not WSCR1 or telomeric. The results establish regions and consequent gene candidates for WMS features including mental retardation, hypersociability, and facial features. The approach provides the basis for defining pathways linking genetic underpinnings with the neuroanatomical, functional, and behavioral consequences that result in human cognition.

scholarly journals Development and Evaluation of Geostatistical Methods for Estimating Weather Related Collisions: A Large-Scale Case Study

2021 ◽  
pp. 036119812110200
Author(s):  
Andy H. Wong ◽  
Tae J. Kwon
Keyword(s):  
Large Scale ◽  
Mean Squared Error ◽  
Hot Spot ◽  
High Ratio ◽  
Contributing Factors ◽  
Geostatistical Methods ◽  
Road Users ◽  
Statistical Measures ◽  
Weather Events

Winter driving conditions pose a real hazard to road users with increased chance of collisions during inclement weather events. As such, road authorities strive to service the hazardous roads or collision hot spots by increasing road safety, mobility, and accessibility. One measure of a hot spot would be winter collision statistics. Using the ratio of winter collisions (WC) to all collisions, roads that show a high ratio of WC should be given a high priority for further diagnosis and countermeasure selection. This study presents a unique methodological framework that is built on one of the least explored yet most powerful geostatistical techniques, namely, regression kriging (RK). Unlike other variants of kriging, RK uses auxiliary variables to gain a deeper understanding of contributing factors while also utilizing the spatial autocorrelation structure for predicting WC ratios. The applicability and validity of RK for a large-scale hot spot analysis is evaluated using the northeast quarter of the State of Iowa, spanning five winter seasons from 2013/14 to 2017/18. The findings of the case study assessed via three different statistical measures (mean squared error, root mean square error, and root mean squared standardized error) suggest that RK is very effective for modeling WC ratios, thereby further supporting its robustness and feasibility for a statewide implementation.

scholarly journals Cross-Species RNAi Rescue Platform in Drosophila melanogaster

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1165-1173 ◽  
Author(s):  
Shu Kondo ◽  
Matthew Booker ◽  
Norbert Perrimon
Keyword(s):  
Cell Culture ◽  
Drosophila Melanogaster ◽  
Large Scale ◽  
Transgenic Animals ◽  
Selection Marker ◽  
Bacterial Artificial Chromosomes ◽  
Loss Of Function ◽  
Artificial Chromosomes ◽  
Target Effects

RNAi-mediated gene knockdown in Drosophila melanogaster is a powerful method to analyze loss-of-function phenotypes both in cell culture and in vivo. However, it has also become clear that false positives caused by off-target effects are prevalent, requiring careful validation of RNAi-induced phenotypes. The most rigorous proof that an RNAi-induced phenotype is due to loss of its intended target is to rescue the phenotype by a transgene impervious to RNAi. For large-scale validations in the mouse and Caenorhabditis elegans, this has been accomplished by using bacterial artificial chromosomes (BACs) of related species. However, in Drosophila, this approach is not feasible because transformation of large BACs is inefficient. We have therefore developed a general RNAi rescue approach for Drosophila that employs Cre/loxP-mediated recombination to rapidly retrofit existing fosmid clones into rescue constructs. Retrofitted fosmid clones carry a selection marker and a phiC31 attB site, which facilitates the production of transgenic animals. Here, we describe our approach and demonstrate proof-of-principle experiments showing that D. pseudoobscura fosmids can successfully rescue RNAi-induced phenotypes in D. melanogaster, both in cell culture and in vivo. Altogether, the tools and method that we have developed provide a gold standard for validation of Drosophila RNAi experiments.

High-Resolution Pachytene Chromosome Mapping of Bacterial Artificial Chromosomes Anchored by Genetic Markers Reveals the Centromere Location and the Distribution of Genetic Recombination Along Chromosome 10 of Rice

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1749-1757 ◽  
Author(s):  
Zhukuan Cheng ◽  
Gernot G Presting ◽  
C Robin Buell ◽  
Rod A Wing ◽  
Jiming Jiang
Keyword(s):  
Large Scale ◽  
Genetic Recombination ◽  
Physical Map ◽  
Rice Chromosome ◽  
Resolving Power ◽  
Pachytene Chromosome ◽  
Chromosome 10 ◽  
Bac Clone ◽  
Fish Mapping ◽  
Artificial Chromosomes

AbstractLarge-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.

scholarly journals Remote sensing of <i>Trichodesmium</i> spp. mats in the western tropical South Pacific

2018 ◽  
Vol 15 (16) ◽  
pp. 5203-5219 ◽  
Author(s):  
Guillaume Rousset ◽  
Florian De Boissieu ◽  
Christophe E. Menkes ◽  
Jérôme Lefèvre ◽  
Robert Frouin ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Large Scale ◽  
New Caledonia ◽  
Hot Spot ◽  
Regional Scale ◽  
Atmospheric Correction ◽  
South Pacific ◽  
Aggregation Processes ◽  
Modis Imagery ◽  
Generate Surface

Abstract. Trichodesmium is the major nitrogen-fixing species in the western tropical South Pacific (WTSP) region, a hot spot of diazotrophy. Due to the paucity of in situ observations, remote-sensing methods for detecting Trichodesmium presence on a large scale have been investigated to assess the regional-to-global impact of this organism on primary production and carbon cycling. A number of algorithms have been developed to identify Trichodesmium surface blooms from space, but determining with confidence their accuracy has been difficult, chiefly because of the scarcity of sea-truth information at the time of satellite overpass. Here, we use a series of new cruises as well as airborne surveys over the WTSP to evaluate their ability to detect Trichodesmium surface blooms in the satellite imagery. The evaluation, performed on MODIS data at 250 m and 1 km resolution acquired over the region, shows limitations due to spatial resolution, clouds, and atmospheric correction. A new satellite-based algorithm is designed to alleviate some of these limitations, by exploiting optimally spectral features in the atmospherically corrected reflectance at 531, 645, 678, 748, and 869 nm. This algorithm outperforms former ones near clouds, limiting false positive detection and allowing regional-scale automation. Compared with observations, 80 % of the detected mats are within a 2 km range, demonstrating the good statistical skill of the new algorithm. Application to MODIS imagery acquired during the February-March 2015 OUTPACE campaign reveals the presence of surface blooms northwest and east of New Caledonia and near 20∘ S–172∘ W in qualitative agreement with measured nitrogen fixation rates. Improving Trichodesmium detection requires measuring ocean color at higher spectral and spatial (<250 m) resolution than MODIS, taking into account environment properties (e.g., wind, sea surface temperature), fluorescence, and spatial structure of filaments, and a better understanding of Trichodesmium dynamics, including aggregation processes to generate surface mats. Such sub-mesoscale aggregation processes for Trichodesmium are yet to be understood.

scholarly journals Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition

2016 ◽  
Author(s):  
Timothy N. Rubin ◽  
Oluwasanmi Koyejo ◽  
Krzysztof J. Gorgolewski ◽  
Michael N. Jones ◽  
Russell A. Poldrack ◽  
...  
Keyword(s):  
Large Scale ◽  
Latent Dirichlet Allocation ◽  
Topic Model ◽  
Brain Activity ◽  
Human Cognition ◽  
Brain Images ◽  
Whole Brain ◽  
Context Sensitive ◽  
Cognitive States ◽  
Small Set

AbstractA central goal of cognitive neuroscience is to decode human brain activity--i.e., to infer mental processes from observed patterns of whole-brain activation. Previous decoding efforts have focused on classifying brain activity into a small set of discrete cognitive states. To attain maximal utility, a decoding framework must be open-ended, systematic, and context-sensitive--i.e., capable of interpreting numerous brain states, presented in arbitrary combinations, in light of prior information. Here we take steps towards this objective by introducing a Bayesian decoding framework based on a novel topic model---Generalized Correspondence Latent Dirichlet Allocation---that learns latent topics from a database of over 11,000 published fMRI studies. The model produces highly interpretable, spatially-circumscribed topics that enable flexible decoding of whole-brain images. Importantly, the Bayesian nature of the model allows one to “seed” decoder priors with arbitrary images and text--enabling researchers, for the first time, to generative quantitative, context-sensitive interpretations of whole-brain patterns of brain activity.

scholarly journals Applied science facilitates the large-scale expansion of protected areas in an Amazonian hot spot

2021 ◽  
Vol 7 (31) ◽  
pp. eabe2998
Author(s):  
Nigel C.A. Pitman ◽  
Corine F. Vriesendorp ◽  
Diana Alvira Reyes ◽  
Debra K. Moskovits ◽  
Nicholas Kotlinski ◽  
...  
Keyword(s):  
Land Use ◽  
Protected Areas ◽  
Large Scale ◽  
Amazon Basin ◽  
Hot Spot ◽  
Terrestrial Ecosystems ◽  
Local Communities ◽  
Decision Makers ◽  
Social Scientists ◽  
International Commitments

Meeting international commitments to protect 17% of terrestrial ecosystems worldwide will require >3 million square kilometers of new protected areas and strategies to create those areas in a way that respects local communities and land use. In 2000–2016, biological and social scientists worked to increase the protected proportion of Peru’s largest department via 14 interdisciplinary inventories covering >9 million hectares of this megadiverse corner of the Amazon basin. In each landscape, the strategy was the same: convene diverse partners, identify biological and sociocultural assets, document residents’ use of natural resources, and tailor the findings to the needs of decision-makers. Nine of the 14 landscapes have since been protected (5.7 million hectares of new protected areas), contributing to a quadrupling of conservation coverage in Loreto (from 6 to 23%). We outline the methods and enabling conditions most crucial for successfully applying similar campaigns elsewhere on Earth.

scholarly journals From Text to Thought: How Analyzing Language Can Advance Psychological Science

2020 ◽  
Author(s):  
Joshua Conrad Jackson ◽  
Joseph Watts ◽  
Johann-Mattis List ◽  
Ryan Drabble ◽  
Kristen Lindquist
Keyword(s):  
Natural Language ◽  
Language Processing ◽  
Statistical Power ◽  
Culturally Diverse ◽  
Large Scale ◽  
Human Cognition ◽  
Comparative Linguistics ◽  
Psychological Science ◽  
Language Analysis ◽  
The Mind

Humans have been using language for thousands of years, but psychologists seldom consider what natural language can tell us about the mind. Here we propose that language offers a unique window into human cognition. After briefly summarizing the legacy of language analyses in psychological science, we show how methodological advances have made these analyses more feasible and insightful than ever before. In particular, we describe how two forms of language analysis—comparative linguistics and natural language processing—are already contributing to how we understand emotion, creativity, and religion, and overcoming methodological obstacles related to statistical power and culturally diverse samples. We summarize resources for learning both of these methods, and highlight the best way to combine language analysis techniques with behavioral paradigms. Applying language analysis to large-scale and cross-cultural datasets promises to provide major breakthroughs in psychological science.

scholarly journals Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

2021 ◽  
Author(s):  
Romain Feron ◽  
Robert Michael Waterhouse
Keyword(s):  
Large Scale ◽  
Automated Analysis ◽  
Single Copy ◽  
The United States ◽  
Community Resource ◽  
Assembly Quality ◽  
Sequencing Technologies ◽  
Analysis Workflow ◽  
Genome Assemblies

Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

scholarly journals Collecting public RGB-D datasets for human daily activity recognition

2017 ◽  
Vol 14 (4) ◽  
pp. 172988141770907 ◽  
Author(s):  
Hanbo Wu ◽  
Xin Ma ◽  
Zhimeng Zhang ◽  
Haibo Wang ◽  
Yibin Li
Keyword(s):  
Activity Recognition ◽  
Daily Activity ◽  
Visual Cues ◽  
Large Scale ◽  
Hot Spot ◽  
Feature Representation ◽  
Data Sets ◽  
Activity Data ◽  
Data Set ◽  
Depth Motion Maps

Human daily activity recognition has been a hot spot in the field of computer vision for many decades. Despite best efforts, activity recognition in naturally uncontrolled settings remains a challenging problem. Recently, by being able to perceive depth and visual cues simultaneously, RGB-D cameras greatly boost the performance of activity recognition. However, due to some practical difficulties, the publicly available RGB-D data sets are not sufficiently large for benchmarking when considering the diversity of their activities, subjects, and background. This severely affects the applicability of complicated learning-based recognition approaches. To address the issue, this article provides a large-scale RGB-D activity data set by merging five public RGB-D data sets that differ from each other on many aspects such as length of actions, nationality of subjects, or camera angles. This data set comprises 4528 samples depicting 7 action categories (up to 46 subcategories) performed by 74 subjects. To verify the challengeness of the data set, three feature representation methods are evaluated, which are depth motion maps, spatiotemporal depth cuboid similarity feature, and curvature space scale. Results show that the merged large-scale data set is more realistic and challenging and therefore more suitable for benchmarking.

Large-scale drivers of the Mediterranean climate change hot-spot

2021 ◽  
Author(s):  
Roman Brogli ◽  
Silje Lund Sørland ◽  
Nico Kröner ◽  
Christoph Schär
Keyword(s):  
Climate Change ◽  
Large Scale ◽  
Hot Spot ◽  
Regional Climate ◽  
Lapse Rate ◽  
Summer Climate ◽  
Climate Simulations ◽  
Summer Warming ◽  
The Mediterranean ◽  
Circulation Changes

&lt;div&gt; &lt;p&gt;&lt;span&gt;It has long been recognized that the Mediterranean is a &amp;#8216;hot-spot&amp;#8217; of climate change. The model-projected year-round precipitation decline and amplified summer warming are among the leading causes of the vulnerability of the Mediterranean to greenhouse gas-driven warming. We investigate large-scale drivers influencing both the Mediterranean drying and summer warming in regional climate simulations. To isolate the influence of multiple large-scale drivers, we sequentially add the respective drivers from global models to regional climate model simulations. Additionally, we confirm the robustness of our results across multiple ensembles of global and regional climate simulations.&lt;/span&gt;&lt;/p&gt; &lt;/div&gt;&lt;div&gt; &lt;p&gt;&lt;span&gt;We will present in detail how changes in the atmospheric stratification are key in causing the amplified Mediterranean summer warming. Together with the land-ocean warming contrast, stratification changes also drive the summer precipitation decline. Summer circulation changes generally have a surprisingly small influence on the changing Mediterranean summer climate. In contrast, changes in the circulation are the primary driver for the projected winter precipitation decline. Since land-ocean contrast and stratification changes are more robust in global climate simulations than circulation changes, we argue that the uncertainty associated with the projected climate change patterns should be considered smaller in summer than in winter.&lt;/span&gt;&lt;/p&gt; &lt;/div&gt;&lt;div&gt; &lt;p&gt;&lt;span&gt;References:&lt;/span&gt;&lt;/p&gt; &lt;/div&gt;&lt;div&gt; &lt;p&gt;&lt;span&gt;Brogli, R., S. L. S&amp;#248;rland, N. Kr&amp;#246;ner, and C. Sch&amp;#228;r, 2019: Causes of future Mediterranean precipitation decline depend on the season. Environmental Research Letters, 14, 114017, doi:10.1088/1748-9326/ab4438.&lt;/span&gt;&lt;/p&gt; &lt;/div&gt;&lt;div&gt; &lt;p&gt;&lt;span&gt;Brogli, R., N. Kr&amp;#246;ner, S. L. S&amp;#248;rland, D. L&amp;#252;thi and C. Sch&amp;#228;r, 2019: The Role of Hadley Circulation and Lapse-Rate Changes for the Future European Summer Climate. Journal of Climate, 32, 385-404, doi:10.1175/JCLI-D-18-0431.1&lt;/span&gt;&lt;/p&gt; &lt;/div&gt;

Sign in / Sign up

Export Citation Format

Share Document