426 Works

Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Eric J. B. Von Wettberg, Peter L Chang, Fatma Başdemir, Noelia Carrasquila-Garcia, Lijalem Korbu, Susan M. Moenga, Gashaw Bedada, Alex Greenlon, Ken S. Moriuchi, Vasantika Suryawanshi, Matilde A Cordeiro, Nina V. Noujdina, Kassaye Negash Dinegde, Syed Gul Abbas Shah Sani, Tsegaye Getahun, Lisa Vance, Emily Bergmann, Donna Lindsay, Bullo Erena Mamo, Emily J. Warschefsky, Emmanuel Dacosta-Calheiros, Edward Marques, Mustafa Abdullah Yilmaz, Ahmet Murat Cakmak, Janna Rose … & Douglas R. Cook
Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related...

Data from: Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies

Mashaal Sohail, Robert M. Maier, Andrea Ganna, Alex Bloemendal, Alicia R. Martin, Michael C. Turchin, Charleston W. K. Chang, Joel Hirschhorn, Mark J. Daly, Nick Patterson, Benjamin Neale, Iain Mathieson, David Reich & Shamil R. Sunyaev
Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Louis V. Plough
Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which substantial mortality occurs in both field and laboratory settings. Previous pair-crossing experiments with the Pacific oyster Crassostrea gigas have revealed significant selective or genotype-dependent mortality around the metamorphic transition, but the fine-scale nature and timing of this mortality is not known, particularly whether it occurs before, during or after metamorphosis. In this laboratory study, microsatellite marker segregation ratios were...

Data from: Too constrained to converse: the effect of financial constraints on word-of-mouth

Anna Paley, Stephanie M. Tully & Eesha Sharma
Existing research demonstrates that financial constraints are widespread and influence consumer attention, preference, choice, and consumption in a variety of ways. Despite the growing knowledge of how financial constraints affect the consumer decision making process, less is known about its impact on post-purchase behavior. This work examines whether financial constraints impact an important post-purchase behavior—word-of-mouth—and in what direction. Seven studies show that financial constraints reduce purchase-related word-of-mouth. This effect emerges across consumers’ reported frequencies of...

Southern San Andreas Fault Zone

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The San Andreas Fault (SAF) in California is a mature plate boundary fault capable of great (magnitude 8 or greater) earthquakes. The southern section of the SAF has not produced a major event in historic times (over the last 300 years), and is currently believed to pose the largest seismic risk in California (Weldon et al., 2005; Field et al., 2014). While much progress was made toward understanding seismic potential of the Southern San Andreas...

Data from: Landscape of tumor mutation load, mismatch repair deficiency, and PD-L1 expression in a large patient cohort of gastrointestinal cancers

Mohamed E. Salem, Alberto Puccini, Axel Grothey, Derek Raghavan, Richard M. Goldberg, Joanne Xiu, W. Michael Korn, Benjamin A. Weinberg, Jimmy J. Hwang, Anthony F. Shields, John L. Marshall, Philip A. Philip & Heinz-Josef Lenz
Purpose: The efficacy of immunotherapy varies widely among different gastrointestinal cancers. Response to immune checkpoint inhibitors is shown to correlate with tumor mutation load (TML), mismatch repair deficiency status (dMMR), and programmed cell death-ligand 1 (PD-L1) expression. Herein, we attempt to quantify TML, dMMR, and PD-L1 expression and determine their interrelationship in gastrointestinal cancers. Experimental Design: A total of 4125 tumors from 14 different gastrointestinal cancer sites were studied. Next-generation sequencing was performed on genomic...

Fine particulate matter and neuroanatomic risk for Alzheimer’s disease in older women

Diana Younan, Xinhui Wang, Ramon Casanova, Ryan Barnard, Sarah Gaussoin, Santiago Saldana, Andrew Petkus, Daniel Beavers, Susan Resnick, JoAnn Manson, Marc Serre, William Vizuete, Victor Henderson, Bonnie Sachs, Joel Salinas, Margaret Gatz, Mark Espeland, Helena Chui, Sally Shumaker, Stephen Rapp & Jiu-Chiuan Chen
Objective: To examine whether late-life exposure to PM2.5 (particulate matter with aerodynamic diameters <2.5-µm) contributes to progressive brain atrophy predictive of Alzheimer’s disease (AD) using a community-dwelling cohort of women (aged 71-89) with up to two brain MRI scans (MRI-1: 2005-6; MRI-2: 2010-11). Methods: AD pattern similarity (AD-PS) scores, developed by supervised machine learning and validated with MRI data from the AD Neuroimaging Initiative, was used to capture high-dimensional gray matter atrophy in brain areas...

Data from: GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126

, Xin Geng, YenChun Ho, Boksik Cha, Yuenhee Kim, Jing Ma, Lijuan Chen, Greggory Myers, Sally Camper, Debbie Mustacich, Marlys Witte, Dongwon Choi, Young-Kwon Hong, Hong Chen, Gaurav Varshney, James D Engel, Shusheng Wang, Tae-Hoon Kim, Kim-Chew Lim & Sathish Srinivasan
Mutations in the transcription factor GATA2 cause lymphedema. GATA2 is necessary for the development of lymphatic valves (LVs) and lymphovenous valves (LVVs), and for the patterning of lymphatic vessels. Here, we report that GATA2 is not necessary for valvular endothelial cell (VEC) differentiation. Instead, GATA2 is required for VEC maintenance and morphogenesis. GATA2 is also necessary for the expression of cell junction molecules VE-Cadherin and Claudin5 in lymphatic vessels. We identified miR-126 as a target...

Ligand-dependent effects of methionine-8 oxidation in parathyroid hormone peptide analogs

Thomas Gardella, Vsevolod Katritch, Saheem Zaidi, Eileen Daley, Ashok Khatri & Jean-Pierre Vilardaga
LA-PTH is a long-acting parathyroid hormone (PTH) peptide analog in pre-clinical development for hypoparathyroidism (HP). Like native PTH, LA-PTH contains a methionine at position 8 that is predicted to be critical for function. We assessed the impact of methionine oxidation on the functional properties of LA-PTH and control PTH ligands. Oxidation of PTH(1-34) resulted in marked (~20-fold) reductions in binding affinity on the PTH receptor-1 (PTHR1) in cell membranes, similarly diminished potency for cAMP signaling...

Examining the Impact of Early Maternal Psychopathology on Children’s Frontal Alpha Asymmetry and Psychopathology

Alexis Hernandez & Santiago Morales
Internalizing and externalizing disorders impact the child’s social, emotional, and cognitive development, including difficulties in school, increased risk for physical health problems, substance misuse, higher risk taking behaviors, and suicide (Coleman et al., 2007; Jesulola et al., 2015). One main influence on children’s internalizing and externalizing disorders are maternal characteristics such as mothers’ perinatal psychopathology (Monk et al., 2019). Perinatal maternal psychopathology like depression and anxiety have been found to be associated with higher risk...

Geographic and temporal morphological stasis in the latest Cretaceous ammonoid Discoscaphites iris from the U.S. Gulf and Atlantic Coastal Plains

James Witts, Corinne Myers, Matthew Garb, Kayla Irizarry, Ekaterina Larina, Anastasia Rashkova & Neil Landman
We examine temporal and spatial variation in morphology of the ammonoid cephalopod Discoscaphites iris using a large dataset from multiple localities in the Late Cretaceous (Maastrichtian) of the United States Gulf and Atlantic Coastal Plains, spanning a distance of 2000 km along the paleoshoreline. Our results suggest that the fossil record of D. iris is consistent with no within species net accumulation of phyletic evolutionary change across morphological traits or the lifetime of this species....

Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids

Deming Yang, Asli Pisano, Joan Kolasa, Tea Jashashvili, Job Kibii, Ana Gomez Cano, Laurent Viriot, Frederick Grine & Antoine Souron
Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the...

Young children's understanding of belief formation

Qianhui Ni & Henrike Moll
This is the pre-registration of the first study on 3-year-olds' understanding of belief formation.

sj-docx-1-jdr-10.1177_00220345221126928 – Supplemental material for Accelerated Fatigue Model for Predicting Composite Restoration Failure

B. Yang, W. Aregawi, R. Chen, L. Zhang, Y. Wang & A.S.L. Fok
Supplemental material, sj-docx-1-jdr-10.1177_00220345221126928 for Accelerated Fatigue Model for Predicting Composite Restoration Failure by B. Yang, W. Aregawi, R. Chen, L. Zhang, Y. Wang and A.S.L. Fok in Journal of Dental Research

Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort

Caitlin G. Howe, Helen B. Foley, Shohreh F. Farzan, Thomas A. Chavez, Mark Johnson, John D. Meeker, Theresa M. Bastain, Carmen J. Marsit & Carrie V. Breton
Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated...

Additional file 1 of Increased cognitive load in immersive virtual reality during visuomotor adaptation is associated with decreased long-term retention and context transfer

Julia M. Juliano, Nicolas Schweighofer & Sook-Lei Liew
Additional file 1. Statistical analysis and Cognitive load is greater acrossvisuomotor adaptation in HMD-VR compared to CS.

Microstructure evolution and mechanical properties of CNT/Al composite joints via friction stir welding

Xiaopeng Li, Zeyu Zhang, Yong Wang, Yong Peng, Dejun Yan, Zhanqiu Tan, Qi Zhou & Kehong Wang
The traditional fusion welding of carbon nanotubes (CNTs) reinforcement aluminium matrix composites has serious welding defects due to the violent interfacial reaction and the brittle secondary phase. In this paper, friction stir welding (FSW), a solid-phase welding technique, was applied to join the CNT/Al matrix composites. The result shows that the tensile strength of the FSW joint fabricated at 800 rev min–1 and 100 mm min–1 is 511 MPa, reaching 92.1% of the CNT/Al composites....

Additional file 1 of Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

Qing Kay Li, Yingwei Hu, Lijun Chen, Michael Schnaubelt, Daniel Cui Zhou, Yize Li, Rita Jui-Hsien Lu, Mathangi Thiagarajan, Galen Hostetter, Chelsea J. Newton, Scott D. Jewell, Gil Omenn, Ana I. Robles, Mehdi Mesri, Oliver F. Bathe, Bing Zhang, Li Ding, Ralph H. Hruban, Daniel W. Chan & Hui Zhang
Additional file 1: Table S1. Clinical information of study cases. Table S2. Expression of proteins from the PDAC tumors and NATs

sj-docx-1-jdr-10.1177_00220345221128202 – Supplemental material for Oral Pathobionts Promote MS-like Symptoms in Mice

L.-J. Zhou, W.-Z. Lin, T. Liu, B.-Y. Chen, X.-Q. Meng, Y.-L. Li, L.-J. Du, Y. Liu, Y.-C. Qian, Y.-Q. Zhu & S.-Z. Duan
Supplemental material, sj-docx-1-jdr-10.1177_00220345221128202 for Oral Pathobionts Promote MS-like Symptoms in Mice by L.-J. Zhou, W.-Z. Lin, T. Liu, B.-Y. Chen, X.-Q. Meng, Y.-L. Li, L.-J. Du, Y. Liu, Y.-C. Qian, Y.-Q. Zhu and S.-Z. Duan in Journal of Dental Research

Additional file 2 of Gene Identification, expression analysis and molecular docking of ATP sulfurylase in the selenization pathway of Cardamine hupingshanensis

Zhijing Xiao, Yanke Lu, Yi Zou, Chi Zhang, Li Ding, Kai Luo, Qiaoyu Tang & Yifeng Zhou
Supplementary Material 2

Additional file 2 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 2. Figure S1, related to Figure 3 — measuring NRAS and KRT8 expression over time after gene silencing.

Additional file 4 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 4: Table S3. NRAS overexpression induces basal-like features in a human luminal DCIS model SUM225 cells.

Additional file 1 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 1: Table S1. Pathological, Biomarker and Demographic Characteristics of the patients in the TMAs.

A practical Alzheimer’s disease classifier via brain imaging-based deep learning on 85,721 samples

Bin Lu, Hui-Xian Li, Zhi-Kai Chang, Le Li, Ning-Xuan Chen, Zhi-Chen Zhu, Hui-Xia Zhou, Xue-Ying Li, Yu-Wei Wang, Shi-Xian Cui, Zhao-Yu Deng, Zhen Fan, Hong Yang, Xiao Chen, Paul M. Thompson, Francisco Xavier Castellanos & Chao-Gan Yan
Abstract Beyond detecting brain lesions or tumors, comparatively little success has been attained in identifying brain disorders such as Alzheimer’s disease (AD), based on magnetic resonance imaging (MRI). Many machine learning algorithms to detect AD have been trained using limited training data, meaning they often generalize poorly when applied to scans from previously unseen scanners/populations. Therefore, we built a practical brain MRI-based AD diagnostic classifier using deep learning/transfer learning on a dataset of unprecedented size...

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