scholarly journals The Diversity of Primates: From Biomedicine to Conservation Genomics

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Joseph D. Orkin ◽  
Lukas F.K. Kuderna ◽  
Tomas Marques-Bonet
Keyword(s):  
Population Level ◽  
Primate Species ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Conservation Genomics ◽  
Technological Advances ◽  
Primate Diversity ◽  
The Cost ◽  
Genome Scale

Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Electronic, Ionic, and Mixed Conduction in Polymeric Systems

2021 ◽  
Vol 51 (1) ◽  
Author(s):  
Elayne M. Thomas ◽  
Phong H. Nguyen ◽  
Seamus D. Jones ◽  
Michael L. Chabinyc ◽  
Rachel A. Segalman
Keyword(s):  
Materials Science ◽  
Transport Coefficients ◽  
Polymeric Materials ◽  
Annual Review ◽  
Publication Date ◽  
Energy Storage Devices ◽  
Polymeric Systems ◽  
Storage Devices ◽  
Technological Advances ◽  
Performance Benchmark

Polymers that simultaneously transport electrons and ions are paramount to drive the technological advances necessary for next-generation electrochemical devices, including energy storage devices and bioelectronics. However, efforts to describe the motion of ions or electrons separately within polymeric systems become inaccurate when both species are present. Herein, we highlight the basic transport equations necessary to rationalize mixed transport and the multiscale materials properties that influence their transport coefficients. Potential figures of merit that enable a suitable performance benchmark in mixed conducting systems independent of end application are discussed. Practical design and implementation of mixed conducting polymers require an understanding of the evolving nature of structure and transport with ionic and electronic carrier density to capture the dynamic disorder inherent in polymeric materials. Expected final online publication date for the Annual Review of Materials Science, Volume 51 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Biotic and Abiotic Controls on the Phanerozoic History of Marine Animal Biodiversity

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Andrew M. Bush ◽  
Jonathan L. Payne
Keyword(s):  
Biotic Interactions ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Marine Animal ◽  
Marine Animals ◽  
Marine Habitat ◽  
Positive Feedbacks ◽  
Abiotic Controls ◽  
Time Changes

During the past 541 million years, marine animals underwent three intervals of diversification (early Cambrian, Ordovician, Cretaceous–Cenozoic) separated by nondirectional fluctuation, suggesting diversity-dependent dynamics with the equilibrium diversity shifting through time. Changes in factors such as shallow-marine habitat area and climate appear to have modulated the nondirectional fluctuations. Directional increases in diversity are best explained by evolutionary innovations in marine animals and primary producers coupled with stepwise increases in the availability of food and oxygen. Increasing intensity of biotic interactions such as predation and disturbance may have led to positive feedbacks on diversification as ecosystems became more complex. Important areas for further research include improving the geographic coverage and temporal resolution of paleontological data sets, as well as deepening our understanding of Earth system evolution and the physiological and ecological traits that modulated organismal responses to environmental change. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Smartphones and the Neuroscience of Mental Health

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
Claire M. Gillan ◽  
Robb B. Rutledge
Keyword(s):  
Mental Health ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Daily Lives ◽  
Neuroscience Research ◽  
Health And Illness ◽  
Passive Data ◽  
Smartphone Sensors ◽  
Rich Data

Improvements in understanding the neurobiological basis of mental illness have unfortunately not translated into major advances in treatment. At this point, it is clear that psychiatric disorders are exceedingly complex and that, in order to account for and leverage this complexity, we need to collect longitudinal datasets from much larger and more diverse samples than is practical using traditional methods. We discuss how smartphone-based research methods have the potential to dramatically advance our understanding of the neuroscience of mental health. This, we expect, will take the form of complementing lab-based hard neuroscience research with dense sampling of cognitive tests, clinical questionnaires, passive data from smartphone sensors, and experience-sampling data as people go about their daily lives. Theory- and data-driven approaches can help make sense of these rich data sets, and the combination of computational tools and the big data that smartphones make possible has great potential value for researchers wishing to understand how aspects of brain function give rise to, or emerge from, states of mental health and illness. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nikhil Mishra ◽  
Carl-Philipp Heisenberg
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Annual Review ◽  
Publication Date ◽  
Technological Advances ◽  
Complex Shapes ◽  
Gene Regulatory ◽  
And Mathematics ◽  
Multicellular Organisms ◽  
Shape Changes

Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Synthetic Data

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Trivellore E. Raghunathan
Keyword(s):  
Synthetic Data ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Sensitive Information ◽  
Inferential Justification ◽  
Widespread Access ◽  
Access To Data ◽  
Privacy And Confidentiality

Demand for access to data, especially data collected using public funds, is ever growing. At the same time, concerns about the disclosure of the identities of and sensitive information about the respondents providing the data are making the data collectors limit the access to data. Synthetic data sets, generated to emulate certain key information found in the actual data and provide the ability to draw valid statistical inferences, are an attractive framework to afford widespread access to data for analysis while mitigating privacy and confidentiality concerns. The goal of this article is to provide a review of various approaches for generating and analyzing synthetic data sets, inferential justification, limitations of the approaches, and directions for future research. Expected final online publication date for the Annual Review of Statistics, Volume 8 is March 8, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Deciphering Temperature Seasonality in Earth's Ancient Oceans

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Linda C. Ivany ◽  
Emily J. Judd
Keyword(s):  
Climate Model ◽  
Temperature Data ◽  
Temperature Cycle ◽  
Annual Review ◽  
Publication Date ◽  
Mean Annual Temperature ◽  
Data Sets ◽  
Proxy Data ◽  
Seamless Integration ◽  
Seasonal Data

Ongoing global warming due to anthropogenic climate change has long been recognized, yet uncertainties regarding how seasonal extremes will change in the future persist. Paleoseasonal proxy data from intervals when global climate differed from today can help constrain how and why the annual temperature cycle has varied through space and time. Records of past seasonal variation in marine temperatures are available in the oxygen isotope values of serially sampled accretionary organisms. The most useful data sets come from carefully designed and computationally robust studies that enable characterization of paleoseasonal parameters and seamless integration with mean annual temperature data sets and climate models. Seasonal data sharpen interpretations of—and quantify overlooked or unconstrained seasonal biases in—the more voluminous mean temperature data and aid in the evaluation of climate model performance. Methodologies to rigorously analyze seasonal data are now available, and the promise of paleoseasonal proxy data for the next generation of paleoclimate research is significant. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 50 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The tracrRNA in CRISPR Biology and Technologies

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Chunyu Liao ◽  
Chase L. Beisel
Keyword(s):  
Genetic Material ◽  
Immune Defense ◽  
Annual Review ◽  
Publication Date ◽  
Traditional Role ◽  
Guide Rnas ◽  
Technological Advances ◽  
Guide Sequence ◽  
The Individual ◽  
New Applications

CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a trans-activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The Society of Algorithms

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Jenna Burrell ◽  
Marion Fourcade
Keyword(s):  
Social Reproduction ◽  
Mathematical Optimization ◽  
Computer Code ◽  
Social Institution ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Occupational Class ◽  
Tight Coupling ◽  
Technical Control

The pairing of massive data sets with processes—or algorithms—written in computer code to sort through, organize, extract, or mine them has made inroads in almost every major social institution. This article proposes a reading of the scholarly literature concerned with the social implications of this transformation. First, we discuss the rise of a new occupational class, which we call the coding elite. This group has consolidated power through their technical control over the digital means of production and by extracting labor from a newly marginalized or unpaid workforce, the cybertariat. Second, we show that the implementation of techniques of mathematical optimization across domains as varied as education, medicine, credit and finance, and criminal justice has intensified the dominance of actuarial logics of decision-making, potentially transforming pathways to social reproduction and mobility but also generating a pushback by those so governed. Third, we explore how the same pervasive algorithmic intermediation in digital communication is transforming the way people interact, associate, and think. We conclude by cautioning against the wildest promises of artificial intelligence but acknowledging the increasingly tight coupling between algorithmic processes, social structures, and subjectivities. Expected final online publication date for the Annual Review of Sociology, Volume 47 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Neurocomputational Models of Language Processing

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
John T. Hale ◽  
Luca Campanelli ◽  
Jixing Li ◽  
Shohini Bhattasali ◽  
Christophe Pallier ◽  
...  
Keyword(s):  
Language Processing ◽  
Computational Models ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Linguistic Features ◽  
Neural Signals ◽  
Data Set ◽  
Interpretable Models ◽  
Compare And Contrast

Efforts to understand the brain bases of language face the Mapping Problem: At what level do linguistic computations and representations connect to human neurobiology? We review one approach to this problem that relies on rigorously defined computational models to specify the links between linguistic features and neural signals. Such tools can be used to estimate linguistic predictions, model linguistic features, and specify a sequence of processing steps that may be quantitatively fit to neural signals collected while participants use language. Progress has been helped by advances in machine learning, attention to linguistically interpretable models, and openly shared data sets that allow researchers to compare and contrast a variety of models. We describe one such data set in detail in the Supplementary Appendix. Expected final online publication date for the Annual Review of Linguistics, Volume 8 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Toward an Integrative Geological and Geophysical View of Cascadia Subduction Zone Earthquakes

2021 ◽  
Vol 49 (1) ◽  
Author(s):  
Maureen A.L. Walton ◽  
Lydia M. Staisch ◽  
Tina Dura ◽  
Jessie K. Pearl ◽  
Brian Sherrod ◽  
...  
Keyword(s):  
Subduction Zone ◽  
Pacific Northwest ◽  
Current Knowledge ◽  
Cascadia Subduction Zone ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Megathrust Earthquake ◽  
Megathrust Earthquakes ◽  
National Boundaries

The Cascadia subduction zone (CSZ) is an exceptional geologic environment for recording evidence of land-level changes, tsunamis, and ground motion that reveals at least 19 great megathrust earthquakes over the past 10 kyr. Such earthquakes are among the most impactful natural hazards on Earth, transcend national boundaries, and can have global impact. Reducing the societal impacts of future events in the US Pacific Northwest and coastal British Columbia, Canada, requires improved scientific understanding of megathrust earthquake rupture, recurrence, and corresponding hazards. Despite substantial knowledge gained from decades of research, large uncertainties remain about the characteristics and frequencies of past CSZ earthquakes. In this review, we summarize geological, geophysical, and instrumental evidence relevant to understanding megathrust earthquakes along the CSZ and associated uncertainties. We discuss how the evidence constrains various models of great megathrust earthquake recurrence in Cascadia and identify potential paths forward for the earthquake science community. ▪ Despite outstanding geologic records of past megathrust events, large uncertainty of the magnitude and frequency of CSZ earthquakes remains. ▪ This review outlines current knowledge and promising future directions to address outstanding questions on CSZ rupture characteristics and recurrence. ▪ Integration of diverse data sets with attention to the geologic processes that create different records has potential to lead to major progress. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 49 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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