42 Works

Geographic allele frequency variation in the 1000 Genomes hg38 NYGC dataset

Arjun Biddanda, Daniel Rice & John Novembre
A key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing rela tionships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic...

Reconstructing Ecological Niche Evolution via Ancestral State Reconstruction with Uncertainty Incorporated

Hannah Owens, Vivian Ribiero, Erin Saupe, Marlon E. Cobos, Peter Hosner, Jacob Cooper, Abdallah Samy, Vijay Barve, Narayani Barve, Carlos Muñoz & A. Townsend Peterson
Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods can infer the history of ecological niche evolution inaccurately because (1) species’ niches are often poorly characterized; and (2) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species’ environmental tolerances. Here we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty...

Life history predicts flight muscle phenotype and function in birds

Shane DuBay, Yongjie Wu, Graham Scott, Yanhua Qu, Qiao Liu, Joel Smith, Chao Xin, Andrew Hart Reeve, Chen Juncheng, Dylan Meyer, Jing Wang, Jacob Johnson, Zachary Cheviron, Fumin Lei & John Bates
1. Functional traits are the essential phenotypes that underlie an organism’s life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals’ ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. 2. We asked how age- and sex-dependent demands on...

An updated incidence trends of soft-tissue sarcoma and cancer-specific survival of patients with primary soft-tissue sarcoma of liver: a population-based study

Yaodong Zhang, Zhengshan Wu, Jiang Chang, Wangjie Jiang, Yirui Wang, Hongwei Wang, Jinyang Li, Changxian Li & Xiangcheng Li
Objectives: This study aimed to evaluate and update incidence trends of soft-tissue sarcoma (STS) and to develop a nomogram to predict cancer-specific survival (CSS) in patients diagnosed with primary STS of the liver. Methods: Patients with hepatic STS were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Joinpoint regression analyses were performed to assess the incidence trends of STS. A nomogram was developed based on the independent risk factors chosen by Cox regression...

An updated incidence trends of soft-tissue sarcoma and cancer-specific survival of patients with primary soft-tissue sarcoma of liver: a population-based study

Yaodong Zhang, Zhengshan Wu, Jiang Chang, Wangjie Jiang, Yirui Wang, Hongwei Wang, Jinyang Li, Changxian Li & Xiangcheng Li
Objectives: This study aimed to evaluate and update incidence trends of soft-tissue sarcoma (STS) and to develop a nomogram to predict cancer-specific survival (CSS) in patients diagnosed with primary STS of the liver. Methods: Patients with hepatic STS were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Joinpoint regression analyses were performed to assess the incidence trends of STS. A nomogram was developed based on the independent risk factors chosen by Cox regression...

Ligand-receptor promiscuity enables cellular addressing

Christina Su, Arvind Murugan, James Linton, Akshay Yeluri, Justin Bois, Heidi Klumpe, Matthew Langley, Yaron Antebi & Michael Elowitz
In multicellular organisms, secreted ligands selectively activate, or "address," specific target cell populations to control cell fate decision-making and other processes. Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors, provoking the question of how addressing specificity can emerge from molecular promiscuity. To investigate this issue, we developed a general mathematical modeling framework based on the bone morphogenetic protein (BMP) pathway architecture. We find that promiscuously interacting ligand-receptor systems allow a small number...

sj-docx-1-apy-10.1177_1039856220960373 – Supplemental material for What impact does illness severity have on the sexual health of young people affected by mental health disorders? A comparison of inpatients and outpatients

Nancy Pehlivan, Ellie Brown, Asiel Yair Adan Sanchez, Felix McMillan, Danielle Moore, Amit Bhaduri, Katherine Monson, Paul Badcock, Katherine Thompson, Eoin Killackey, Andrew Chanen & Brian O’Donoghue
Supplemental material, sj-docx-1-apy-10.1177_1039856220960373 for What impact does illness severity have on the sexual health of young people affected by mental health disorders? A comparison of inpatients and outpatients by Nancy Pehlivan, Ellie Brown, Asiel Yair Adan Sanchez, Felix McMillan, Danielle Moore, Amit Bhaduri, Katherine Monson, Paul Badcock, Katherine Thompson, Eoin Killackey, Andrew Chanen and Brian O�Donoghue in Australasian Psychiatry

What impact does illness severity have on the sexual health of young people affected by mental health disorders? A comparison of inpatients and outpatients

Nancy Pehlivan, Ellie Brown, Asiel Yair Adan Sanchez, Felix McMillan, Danielle Moore, Amit Bhaduri, Katherine Monson, Paul Badcock, Katherine Thompson, Eoin Killackey, Andrew Chanen & Brian O’Donoghue
Objective:Young people affected by mental health disorders have greater sexual health needs compared to their peers. Less is known about this need across illness severity.Method:A cross-sectional survey of the sexual health of those attending outpatients or inpatients within a youth mental health service was conducted. Statistical differences between groups were explored.Results:One hundred and seven young people (18–25 years) participated and of these, 37.7% were inpatients who had more severe psychiatric symptoms than outpatients. While inpatients...

Topological structure and dynamics of three-dimensional active nematics

Guillaume Duclos, Thomas Powers, Aparna Baskaran, Zvonimir Dogic, Vincenzo Vitelli, Federico Toschi, Raymond Adkins, Debarghya Banerjee, Matthew Peterson, Minu Varghese, Itamar Kolvin, Robert Pelcovits, Sebastian Streichan, Daniel Beller, Arvind Baskaran, Michael Hagan, Matthew S. E. Peterson, Robert A. Pelcovits, Thomas R. Powers, Michael F. Hagan & Sebastian J. Streichan
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination...

Spine and dine: A key defensive trait promotes ecological success in spiny ants

Benjamin Blanchard, Akihiro Nakamura, Min Cao, Stephanie Chen & Corrie Moreau
A key focus of ecologists is explaining the origin and maintenance of morphological diversity and its association with ecological success. We investigate potential benefits and costs of a common and varied morphological trait, cuticular spines, for foraging behavior, interspecific competition, and predator-prey interactions in naturally co-occurring spiny ants (Hymenoptera: Formicidae: Polyrhachis) in an experimental setting. We expect that a defensive trait like spines might be associated with more conspicuous foraging, a greater number of workers...

Mamlūk Studies Review Volume 22 (full volume)

Data from: Sensing the structural characteristics of surfaces: Texture encoding by a bottom-dwelling fish

Adam Hardy & Melina Hale
The texture of contacted surfaces influences our perception of the physical environment and modulates behavior. Texture perception and its neural encoding mechanisms have traditionally been studied in the primate hand, yet animals of all types live in richly textured environments and regularly interact with textured surfaces. Here we explore texture sensation in a different type of vertebrate limb by investigating touch and potential texture encoding mechanisms in the pectoral fins of fishes, the forelimb homologs....

SARS-COV-2 Coarse Grained Viron Model

Alvin Yu & Gregory Voth
A coarse-grained (CG) model for the SARS-CoV-2 virion developed under an NSF RAPID award 2029092 to Gregory A Voth in response to the COVID-19 pandemic.

The dynamics and stoichiometry of dissolved organic carbon release by kelp: Carbon fixation, DOC release and nutrient uptake data

Brooke Weigel & Catherine Pfister
Canopy-forming kelps are foundational species in coastal ecosystems, fixing tremendous amounts of carbon, yet we know little about the ecological and physiological determinants of dissolved organic carbon (DOC) release by kelps. We examined DOC release by the bull kelp, Nereocystis luetkeana, in relation to carbon fixation, nutrient uptake, tissue nitrogen content, and light availability. DOC release was approximately 3.5 times greater during the day than at night. During the day, N. luetkeana blades released an...

Comment on “Ancient origins of allosteric activation in a Ser-Thr kinase”

Jaeda Patton, Yeonwoo Park, Georg Hochberg & Joseph Thornton
Hadzipasic et al. used ancestral sequence reconstruction to identify historical sequence substitutions that putatively caused Aurora kinases to evolve allosteric regulation. We show that their results arise from an implausible phylogeny and sparse sequence sampling. Addressing either problem reverses their inferences: allostery and the amino acids that confer it were not gained during the diversification of eukaryotes but were lost in a subgroup of Fungi.

Data from: Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi)

Jacob C. Cooper, J. Dylan Maddox, Kellie McKague & John M. Bates
Africa’s montane ecosystems are noteworthy not only for their isolation, but for their morphologically similar bird populations that inhabit geographically disparate localities. Many species possess range disjunctions in excess of 2,000 km and appear to represent populations that have been isolated since at least the last Ice Age, including the Northern Double-collared Sunbird (Cinnyris reichenowi). Recent work on other Afromontane birds has demonstrated substantial phylogeographic structure can exist in phenotypically similar populations, with cryptic species...

Data for \"Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics\"

Zhaoyi Shen, Kyle Pressel, Zhihong Tan & Tapio Schneider
This dataset provides time-averaged GCM and LES data required to produce results in the paper "Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics". It also includes an example script that can be used to generate Figure 8.

Registration Year

  • 2020
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Affiliations

  • University of Chicago
    42
  • Field Museum of Natural History
    3
  • University of Kansas
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  • Stanford University
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  • Shanghai Veterinary Research Institute
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  • Shandong Agricultural University
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  • University of Copenhagen
    2
  • Shanghai Sixth People's Hospital
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  • Xinjiang University
    2
  • California Institute of Technology
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