20 Works

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

Elliot Gardner, Matthew Johnson, Joan Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Sahromi Sahromi, Norman Wickett & Nyree Zerega
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the...

Neurological deterioration in patients with acute ischemic stroke or transient ischemic attack

Tai Hwan Park, Jeong-Kon Lee, Moo-Seok Park, Sang-Soon Park, Keun-Sik Hong, Wi-Sun Ryu, Dong-Eog Kim, Man Seok Park, Kang-Ho Choi, Joon-Tae Kim, Jihoon Kang, Beom Joon Kim, Moon-Ku Han, Jun Lee, Jae-Kwan Cha, Dae-Hyun Kim, Jae Guk Kim, Soo Joo Lee, Yong-Jin Cho, Jee-Hyun Kwon, Dong-Ick Shin, Min-Ju Yeo, Sung Il Sohn, Jeong-Ho Hong, Ji Sung Lee … & Hee-Joon Bae
Objective: To improve epidemiological knowledge of neurological deterioration (ND) in patients with acute ischemic stroke (AIS). Methods: In this prospective observational study, we captured ND prospectively in 29,446 AIS patients admitted to 15 hospitals in Korea within 7 days of stroke onset. ND was defined as an increase in National Institutes of Health Stroke Scale (NIHSS) score ≥2 (total), or ≥1 (motor or consciousness), or any new neurological symptoms. Change of incidence rate after stroke...

Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein

Sarah Lapidus, Feimei Liu, Arnau Casanovas-Massana, Yile Dai, John D. Huck, Carolina Lucas, Jon Klein, Renata B. Filler, Madison S. Strine, Mouhamad Sy, Awa B. Deme, Aida S. Badiane, Baba Dieye, Ibrahima Mbaye Ndiaye, Younous Diedhiou, Amadou Moctar Mbaye, Cheikh Tidiane Diagne, Inés Vigan-Womas, Alassane Mbengue, Bacary D. Sadio, Moussa M. Diagne, Adam J. Moore, Khadidiatou Mangou, Fatoumata Diallo, Seynabou D. Sene … & Amy K. Bei
Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody test results can produce false positive results, limiting their efficacy as a sero-surveillance tool to estimate population-level SARS-CoV-2 exposure. False positive SARS-CoV-2 antibody results have been associated with malaria exposure, and understanding this association is essential to interpret sero-surveillance results from malaria-endemic countries. Here, pre-pandemic samples from eight malaria endemic and non-endemic countries and four continents were tested by ELISA to measure SARS-CoV-2...

Understanding degraded speech leads to perceptual gating of a brainstem reflex in human listeners

Heivet Hernandez Perez, Jason Mikiel-Hunter, David McAlpine, Sumitrajit Dhar, Sriram Boothalingam, Jessica J.M. Monaghan & Catherine M. McMahon
The ability to navigate “cocktail-party” situations by focussing on sounds of interest over irrelevant, background sounds is often considered in terms of cortical mechanisms. However, subcortical circuits such as the pathway underlying the medial olivocochlear (MOC) reflex modulate the activity of the inner ear itself, supporting the extraction of salient features from auditory scene prior to any cortical processing. To understand the contribution of auditory subcortical nuclei and the cochlea in complex listening tasks, we...

Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy

Miriam Sarah Weber, Matthias Eibauer, Suganya Sivagurunathan, Thomas Magin, Robert Goldman & Ohad Medalia
Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell periphery, which provides resistance to mechanical stresses. Mutations in keratin genes are related to a variety of epithelial tissue diseases. Despite their importance, the molecular structure of keratin filaments remains largely unknown. In this study, we analyzed the structure of keratin 5/keratin 14 filaments within...

The synaptic marker neurogranin as a disease state biomarker in Alzheimer’s disease: a systematic review and meta-analysis

Zhibin Wang, Jianwei Yang, Wei Zhu, Yi Tang & Jianping Jia
Objective: Synaptic degeneration is the pathologic foundation of cognitive decline in the Alzheimer’s disease (AD) continuum. We aimed to determine whether cerebrospinal fluid (CSF) synaptic marker neurogranin (Ng) is a disease state or a disease stage biomarker in the AD continuum. Methods: Studies comparing CSF Ng levels among AD, mild cognitive impairment (MCI) and healthy participants were included. Studies were eligible if the correlation between CSF Ng levels and Mini-Mental Status Examination (MMSE) scores was...

Protective effect of Qingre Huoxue decoction against myocardial infarction via PI3K/Akt autophagy pathway based on UPLC-MS, network pharmacology, and in vivo evidence

Zheng Jin, Wenbo Zhang, Yuan Luo, Xiushen Li, Lijin Qing, Qiang Zuo, Junfeng Fang & Wei Wu
Qingre Huoxue (QRHX) decoction, a traditional Chinese medicine, has been widely used to prevent and treat myocardial infarction (MI). This study elucidates the possible mechanisms of QRHX in preventing or treating MI in a rat model. The chemical constituents of QRHX were identified by UPLC-MS. Sprague-Dawley rats were randomly divided into the Sham (normal saline), Model (normal saline), QRHX-L, QRHX-M and QRHX-H group (n = 10 per group). QRHX decoction was administered by gavage to...

Social Interaction and Pain Threshold in Virtual Reality

Andrea Stevenson Won, Swati Pandita & Kaylee Payne Kruzan
This experiment examined the effects of social presence and perceived location of a virtual environment on participants’ pain thresholds in a pre-registered, within-subjects experiment. First, we examined the effects of social interaction vs being alone in a virtual environment. Second, we compared a virtual environment representing a remote location to a replication of the lab environment. While the "location" of the virtual environment did affect social presence, such that participants reported greater social presence with...

Circulating microRNA profile unveils mechanisms of action of acitretin for psoriasis vulgaris

Lin Chen, Jie Li, Ying Yao, Shanlong Wang, Shuangjin Zheng, Xinggang Ju & Bin Zhang
Psoriasis vulgaris is a common chronic and recurrent inflammatory skin disease. In clinical practice, acitretin is the first-line treatment drug for psoriasis vulgaris. MicroRNAs (miRNAs) play a vital role in the initiation and development of psoriasis vulgaris. However few studies focused on the mechanisms of acitretin in the treatment of psoriasis vulgaris from the perspective of miRNAs. Here, the expression profiles of circulating miRNAs in the plasma of 12 patients with psoriasis vulgaris before and...

Circulating microRNA profile unveils mechanisms of action of acitretin for psoriasis vulgaris

Lin Chen, Jie Li, Ying Yao, Shanlong Wang, Shuangjin Zheng, Xinggang Ju & Bin Zhang
Psoriasis vulgaris is a common chronic and recurrent inflammatory skin disease. In clinical practice, acitretin is the first-line treatment drug for psoriasis vulgaris. MicroRNAs (miRNAs) play a vital role in the initiation and development of psoriasis vulgaris. However few studies focused on the mechanisms of acitretin in the treatment of psoriasis vulgaris from the perspective of miRNAs. Here, the expression profiles of circulating miRNAs in the plasma of 12 patients with psoriasis vulgaris before and...

The synaptic marker neurogranin as a disease state biomarker in Alzheimer’s disease: a systematic review and meta-analysis

Zhibin Wang, Jianwei Yang, Wei Zhu, Yi Tang & Jianping Jia
Objective: Synaptic degeneration is the pathologic foundation of cognitive decline in the Alzheimer’s disease (AD) continuum. We aimed to determine whether cerebrospinal fluid (CSF) synaptic marker neurogranin (Ng) is a disease state or a disease stage biomarker in the AD continuum. Methods: Studies comparing CSF Ng levels among AD, mild cognitive impairment (MCI) and healthy participants were included. Studies were eligible if the correlation between CSF Ng levels and Mini-Mental Status Examination (MMSE) scores was...

ExBox: A Polycyclic Aromatic Hydrocarbon Scavenger

Jonathan C. Barnes, Michal Juríček, Nathan L. Strutt, Marco Frasconi, Srinivasan Sampath, Marc A. Giesener, Psaras L. McGrier, Carson J. Bruns, Charlotte L. Stern, Amy A. Sarjeant & J. Fraser Stoddart
A template-directed protocol, which capitalizes on donor–acceptor interactions, is employed to synthesize a semi-rigid cyclophane (ExBox4+) that adopts a box-like geometry and is comprised of π-electron-poor 1,4-phenylene-bridged (“extended”) bipyridinium units (ExBIPY2+). ExBox4+ functions as a high-affinity scavenger of an array of different polycyclic aromatic hydrocarbons (PAHs), ranging from two to seven fused rings, as a result of its large, accommodating cavity (approximately 3.5 Å in width and 11.2 Å in length when considering the van...

Development and application of a hybrid implementation research framework to understand success in reducing under-5 mortality in Rwanda

Lisa Hirschhorn, Miriam Frisch, Jovial Thomas Ntawukuriryayo, Amelia VanderZanden, Kateri Donahoe, Kedest Mathewos, Felix Sayinzoga & Agnes Binagwaho
Exemplars U5M Interview Guide: This is an example of the semi-structured interview guide used for key informant interviews described in the article, "Development and application of a hybrid implementation research framework to understand success in reducing under-5 mortality in Rwanda." Extended data (supplemental) tables and figures: These are the supplemental tables and figures to accompany the article, "Development and application of a hybrid implementation research framework to understand success in reducing under-5 mortality in Rwanda."...

The invasion paradox dissolves when using phylogenetic and temporal perspectives

Adrienne Ernst, Rebecca Barak, Andrew Hipp, Andrea Kramer, Hannah Marx & Daniel Larkin
1. Elton’s prediction that higher biodiversity leads to denser niche-packing and thus higher community resistance to invasion has long been studied, with species richness as the predominant measure of diversity. However, few studies have explored how phylogenetic and functional diversity, which should represent niche space more faithfully than taxonomic diversity, influence community invasibility, especially across longer time frames and over larger spatial extents. 2. We used a 15-year, 150-site grassland dataset to assess relationships between...

Genetic and fitness measurements of Brighamia accessions for APPS

Jeremie Fant, Seana Walsh & Jeremy Foster
Premise of the study: Living collections maintained for generations are at risk of diversity loss, inbreeding, and adaptation to cultivation. To address these concerns the zoo community uses pedigrees to track individuals and implement crosses that maximize founder contributions and minimize inbreeding. Using a pedigree management approach in an exceptional plant, we demonstrate how conducting such strategic crosses can minimize genetic issues that have arisen under current practices. Methods: We performed crosses between these collections...

Protective effect of Qingre Huoxue decoction against myocardial infarction via PI3K/Akt autophagy pathway based on UPLC-MS, network pharmacology, and in vivo evidence

Zheng Jin, Wenbo Zhang, Yuan Luo, Xiushen Li, Lijin Qing, Qiang Zuo, Junfeng Fang & Wei Wu
Qingre Huoxue (QRHX) decoction, a traditional Chinese medicine, has been widely used to prevent and treat myocardial infarction (MI). This study elucidates the possible mechanisms of QRHX in preventing or treating MI in a rat model. The chemical constituents of QRHX were identified by UPLC-MS. Sprague-Dawley rats were randomly divided into the Sham (normal saline), Model (normal saline), QRHX-L, QRHX-M and QRHX-H group (n = 10 per group). QRHX decoction was administered by gavage to...

Caltech Mouse Social Interactions (CalMS21) Dataset

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Multi-agent behavior modeling aims to understand the interactions that occur between agents. We present a multi-agent dataset from behavioral neuroscience, the Caltech Mouse Social Interactions (CalMS21) Dataset. Our dataset consists of trajectory data of social interactions, recorded from videos of freely behaving mice in a standard resident-intruder assay. To help accelerate behavioral studies, the CalMS21 dataset provides benchmarks to evaluate the performance of automated behavior classification methods in three settings: (1) for training on large...

Prenatal medication use in a prospective pregnancy cohort by pre-pregnancy obesity status

Yassaman Vafai, Edwina H. Yeung, Rajeshwari Sundaram, Melissa M. Smarr, Nicole Gerlanc, William A. Grobman, Daniel Skupski, Edward K. Chien, Stefanie N. Hinkle, Roger B. Newman, Deborah A. Wing, Angela C. Ranzini, Anthony Sciscione, Jagteshwar Grewal, Cuilin Zhang & Katherine L. Grantz
The association between obesity (body mass index (BMI) ≥ 30 kg/m2) and pattern of medication use during pregnancy in the United States is not well-studied. Higher pre-pregnancy BMI may be associated with increases or decreases in medication use across pregnancy as symptoms (e.g. reflux) or comorbidities (e.g. gestational diabetes) requiring treatment that may be associated with higher BMI could also change with advancing gestation. To determine whether prenatal medication use, by the number and types...

Prenatal medication use in a prospective pregnancy cohort by pre-pregnancy obesity status

Yassaman Vafai, Edwina H. Yeung, Rajeshwari Sundaram, Melissa M. Smarr, Nicole Gerlanc, William A. Grobman, Daniel Skupski, Edward K. Chien, Stefanie N. Hinkle, Roger B. Newman, Deborah A. Wing, Angela C. Ranzini, Anthony Sciscione, Jagteshwar Grewal, Cuilin Zhang & Katherine L. Grantz
The association between obesity (body mass index (BMI) ≥ 30 kg/m2) and pattern of medication use during pregnancy in the United States is not well-studied. Higher pre-pregnancy BMI may be associated with increases or decreases in medication use across pregnancy as symptoms (e.g. reflux) or comorbidities (e.g. gestational diabetes) requiring treatment that may be associated with higher BMI could also change with advancing gestation. To determine whether prenatal medication use, by the number and types...

Registration Year

  • 2021
    20

Resource Types

  • Dataset
    20

Affiliations

  • Northwestern University
    20
  • Sun Yat-sen University
    6
  • Zhejiang University
    6
  • Central South University
    6
  • Huazhong University of Science and Technology
    4
  • Guangzhou Medical University
    4
  • Sichuan University
    4
  • Capital Medical University
    4
  • Peking University People's Hospital
    3
  • Shanghai Sixth People's Hospital
    3