60 Works

Data from: Feedback between tissue packing and neurogenesis in the zebrafish neural tube

Tom W. Hiscock, Joel B. Miesfeld, Kishore R. Mosaliganti, Brian A. Link & Sean G. Megason
Balancing the rate of differentiation and proliferation in developing tissues is essential to produce organs of robust size and composition. Although many molecular regulators have been established, how these connect to physical and geometrical aspects of tissue architecture is poorly understood. Here, using high-resolution timelapse imaging, we find that changes to cell geometry associated with dense tissue packing play a significant role in regulating differentiation rate in the zebrafish neural tube. Specifically, progenitors that are...

Population genomics of emerging Elizabethkingia anophelis pathogens reveals potential outbreak and rapid global dissemination

Shaohua Hu, Hao Xu, Xiaohua Meng, Xiangxiang Bai, Junli Xu, Jinru Ji, Chaoqun Ying, Yunbo Chen, Ping Shen, Yunxiao Zhou, Beiwen Zheng & Yonghong Xiao
Elizabethkingia anophelis is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the E. anophelis geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of E. anophelis pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed...

Precursor prioritization for p-cymene production through synergistic integration of biology and chemistry

Hsi-Hsin Lin, Daniel Mendez‐Perez, Jimin Park, Xi Wang, Yan Cheng, Jiajie Huo, Aindrila Mukhopadhyay, Taek Soon Lee & Brent H. Shanks
Abstract The strategy of synergistic application of biological and chemical catalysis is an important approach for efficiently converting renewable biomass into chemicals and fuels. In particular, the method of determining the appropriate intermediate between the two catalytic methods is critical. In this work, we demonstrate p-cymene production through the integration of biosynthesis and heterogenous catalysis and show how a preferred biologically derived precursor could be determined. On the biological side, we performed the limonene and...

CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements

Jesús-José Ferre-Fernández, Sanaa Muheisen, Samuel Thompson & Elena V. Semina
Abstract FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish–human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or...

CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements

Jesús-José Ferre-Fernández, Sanaa Muheisen, Samuel Thompson & Elena V. Semina
Abstract FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish–human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or...

Accurate Measurement of Virtual Image Distance for Near-Eye Displays Based on Auto-Focusing

Hao Xu, Satoshi Tabata, Haowen Liang, Lihui Wang & Masatoshi Ishikawa
Virtual Reality (VR) and augmented reality (AR) are able to project virtual images to human eyes at a certain depth distance. This virtual image distance can be adjusted by controlling the diopter of the near-eye display. However, it is difficult to be measured accurately and continuously since this virtual image distance spans a large range. In this work, we propose a method to accurately determine the virtual image distance of commercial VR/AR equipment. The measurement...

Data from: Developmental expression of drug metabolizing enzymes: impact on disposition in neonates and young children

D. Gail McCarver, Pippa M. Simpson, Thomas A. Kocarek, Margaret O. James, Melissa Runge-Morris, Jeffery C. Stevens, Miyoung Yoon & R.N. Hines
Profound changes in drug metabolizing enzyme expression occurs during development that impacts drug efficacy and the risk of adverse events in the neonate and young child. A review of our current knowledge suggests individual hepatic drug metabolizing enzymes can be categorized into one of three classes based on developmental trajectories. The time frame for the perinatal changes observed for both Class 1 and Class 3 enzymes varies considerably between different enzymes. However, for a given...

Longitudinal white-matter abnormalities in sports-related concussion: a diffusion MRI study of the NCAA-DoD CARE Consortium

Yu-Chien Wu, Jaroslaw Harezlak, Nahla Elsaid, Zikai Lin, Qiuting Wen, Sourajit Mustafi, Larry Riggen, Kevin Koch, Andrew Nencka, Timothy Meier, Andrew Mayer, Yang Wang, Christopher Giza, John DiFiori, Kevin Guskiewicz, Jason Mihalik, Stephen LaConte, Stefan Duma, Steven Broglio, Andrew Saykin, Michael McCrea & Thomas McAllister
Objective To study longitudinal recovery trajectories of white-matter after sports-related concussion (SRC), we performed diffusion tensor imaging (DTI) on collegiate athletes who sustained SRC. Methods Collegiate athletes (n=219, 82 concussed athletes, 68 contact-sport controls, and 69 non-contact-sport controls) were included from the Concussion Assessment, Research and Education (CARE) Consortium. The participants completed clinical assessments and DTI at four time points: 24-48-hours post-injury, asymptomatic state, seven days following return-to-play, and six-months post-injury. Tract-based spatial statistics were...

Luteolin decreases the pathogenicity of Aeromonas hydrophila via inhibiting the activity of aerolysin

Jing Dong, Lushan Zhang, Yongtao Liu, Ning Xu, Shun Zhou, Yibin Yang, Qiuhong Yang & Xiaohui Ai
Aeromonas hydrophila (A. hydrophila) can cause a number of diseases in both human and animals. A. hydrophila-related infections in aquaculture cause severe economic losses every year throughout the world. The emergence of antibiotic resistance that is due to the abuse of antibiotics has limited the application of antibiotics. Thus, novel approaches are needed to combat with treatment failure of antibiotics caused by resistant bacterial strains. Aerolysin plays a critical role in the pathogenesis of A....

Luteolin decreases the pathogenicity of Aeromonas hydrophila via inhibiting the activity of aerolysin

Jing Dong, Lushan Zhang, Yongtao Liu, Ning Xu, Shun Zhou, Yibin Yang, Qiuhong Yang & Xiaohui Ai
Aeromonas hydrophila (A. hydrophila) can cause a number of diseases in both human and animals. A. hydrophila-related infections in aquaculture cause severe economic losses every year throughout the world. The emergence of antibiotic resistance that is due to the abuse of antibiotics has limited the application of antibiotics. Thus, novel approaches are needed to combat with treatment failure of antibiotics caused by resistant bacterial strains. Aerolysin plays a critical role in the pathogenesis of A....

Identification of Rad51 as a prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma

Hao Xu, Chen Xiong, Yuan Chen, Chi Zhang & Dousheng Bai
Rad51, a DNA-repair-related gene, has been reported to be involved in multiple cancers. However, its link with immune infiltration in liver cancer still unknown. Therefore, more research into the roles and activities of Rad51 in hepatocellular carcinoma (HCC) is required. The International Cancer Genome Consortium (ICGC) was used to identify the DNA repair gene Rad51, and has been proved to be overexpressed in HCC patients. We plotted the Kapan-Meier curve, demonstrating that patients with high...

Identification of Rad51 as a prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma

Hao Xu, Chen Xiong, Yuan Chen, Chi Zhang & Dousheng Bai
Rad51, a DNA-repair-related gene, has been reported to be involved in multiple cancers. However, its link with immune infiltration in liver cancer still unknown. Therefore, more research into the roles and activities of Rad51 in hepatocellular carcinoma (HCC) is required. The International Cancer Genome Consortium (ICGC) was used to identify the DNA repair gene Rad51, and has been proved to be overexpressed in HCC patients. We plotted the Kapan-Meier curve, demonstrating that patients with high...

Additional file 1 of CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements

Jesús-José Ferre-Fernández, Sanaa Muheisen, Samuel Thompson & Elena V. Semina
Additional file 1. Supplemental material including Supplemental Figures S1 to S8 and their legends, Supplemental Tables S1 to S4 and Supplemental Videos legends.

Additional file 3 of Gastric cancer-derived exosomal miR-519a-3p promotes liver metastasis by inducing intrahepatic M2-like macrophage-mediated angiogenesis

Shengkui Qiu, Li Xie, Chen Lu, Chao Gu, Yiwen Xia, Jialun Lv, Zhe Xuan, Lang Fang, Jing Yang, Lu Zhang, Zheng Li, Weizhi Wang, Hao Xu, Bowen Li & Zekuan Xu
Additional file 3.

Is there variation in utilization of preoperative tests among patients undergoing total hip and knee replacement in the US, and does it affect outcomes? A population-based analysis

Mohamed Mosaad Hasan, Raymond Kang, Jungwha Lee, Matthew D. Beal, Abdalrahman G. Ahmed, Yao Tian & Hassan M. K. Ghomrawi
Abstract Study objective To describe recent practice patterns of preoperative tests and to examine their association with 90-day all-cause readmissions and length of stay. Design Retrospective cohort study using the New York Statewide Planning and Research Cooperative System (SPARCS). Setting SPARCS from March 1, 2016, to July 1, 2017. Participants Adults undergoing Total Hip Replacement (THR) or Total Knee Replacement (TKR) had a preoperative screening outpatient visit within two months before their surgery. Interventions Electrocardiogram...

Additional file 1 of Precursor prioritization for p-cymene production through synergistic integration of biology and chemistry

Hsi-Hsin Lin, Daniel Mendez‐Perez, Jimin Park, Xi Wang, Yan Cheng, Jiajie Huo, Aindrila Mukhopadhyay, Taek Soon Lee & Brent H. Shanks
Additional file 1: Figure S1. Nitrogen physisorption isotherms of Pd/SiAl. Figure S2. Nitrogen physisorption isotherms of Pd/SiO2. Figure S3. Nitrogen physisorption isotherms of Pd/Al2O3. Figure S4. Nitrogen physisorption isotherms of Al2O3. Figure S5. Nitrogen physisorption isotherms of Ni/Al2O3. Figure S6. Nitrogen physisorption isotherms of Cu/Al2O3. Figure S7. Nitrogen physisorption isotherms of Pt/Al2O3. Figure S8. Mass spectrum of limonene. Figure S9. Mass spectrum of 1,8-cineole. Figure S10. Mass spectrum of p-cymene. Figure S11. GC–MS spectrum of...

Data from: Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

Isaac M. Chiu, Lee B. Barrett, Erika Williams, David E. Strochlic, Seungkyu Lee, Andy D. Weyer, Shan Lou, Gregory Bryman, David P. Roberson, Nader Ghasemlou, Cara Piccoli, Ezgi Ahat, Victor Wang, Enrique J. Cobos, Cheryl L. Stucky, Qiufu Ma, Stephen D. Liberles, Clifford J. Woolf & Gregory S Bryman
The somatosensory nervous system is critical for the organism’s ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1)IB4+SNS-Cre/TdTomato+, 2)IB4-SNS-Cre/TdTomato+, and 3)Parv-Cre/TdTomato+ cells, encompassing the...

Data from: Toward translating near-infrared spectroscopy oxygen saturation data for the non-invasive prediction of spatial and temporal hemodynamics during exercise

Laura Ellwein, Margaret M. Samyn, Michael Danduran, Sheila Schindler-Ivens, Stacy Liebham, & John F. LaDisa
Image-based computational fluid dynamics (CFD) studies conducted at rest have shown that atherosclerotic plaque in the thoracic aorta (TA) correlates with adverse wall shear stress (WSS), but there is a paucity of such data under elevated flow conditions. We developed a pedaling exercise protocol to obtain phase contrast magnetic resonance imaging (PC-MRI) blood flow measurements in the TA and brachiocephalic arteries during three-tiered supine pedaling at 130, 150, and 170 % of resting heart rate...

Data from: An integrated iterative annotation technique for easing neural network training in medical image analysis

Brendon Lutnick, Brandon Ginley, Darshana Govind, Sean D. McGarry, Peter S. LaViolette, Rabi Yacoub, Sanjay Jain, John E. Tomaszewski, Kuang-Yu Jen & Pinaki Sarder
Neural networks promise to bring robust, quantitative analysis to medical fields. However, their adoption is limited by the technicalities of training these networks and the required volume and quality of human-generated annotations. To address this gap in the field of pathology, we have created an intuitive interface for data annotation and the display of neural network predictions within a commonly used digital pathology whole-slide viewer. This strategy used a ‘human-in-the-loop’ to reduce the annotation burden....

Stay on the beat with tensor-valued encoding [Dataset and Code]

Samo Lasic, Nadira Yusupovna Yuldasheva, Filip Szczepankiewicz, Markus Nilsson, MATTHEW BUDDE, Erica Dall'Armellina, Jurgen E. Schneider, Irvin Teh & Henrik Lundell
Data and Matlab code used for the publication Lasič et al. 'Stay on the beat with tensor-valued encoding: time-dependent diffusion and cell size estimation in ex vivo heart'.

Additional file 1 of Gastric cancer-derived exosomal miR-519a-3p promotes liver metastasis by inducing intrahepatic M2-like macrophage-mediated angiogenesis

Shengkui Qiu, Li Xie, Chen Lu, Chao Gu, Yiwen Xia, Jialun Lv, Zhe Xuan, Lang Fang, Jing Yang, Lu Zhang, Zheng Li, Weizhi Wang, Hao Xu, Bowen Li & Zekuan Xu
Additional file 1.

Additional file 1 of Gastric cancer-derived exosomal miR-519a-3p promotes liver metastasis by inducing intrahepatic M2-like macrophage-mediated angiogenesis

Shengkui Qiu, Li Xie, Chen Lu, Chao Gu, Yiwen Xia, Jialun Lv, Zhe Xuan, Lang Fang, Jing Yang, Lu Zhang, Zheng Li, Weizhi Wang, Hao Xu, Bowen Li & Zekuan Xu
Additional file 1.

Additional file 2 of Gastric cancer-derived exosomal miR-519a-3p promotes liver metastasis by inducing intrahepatic M2-like macrophage-mediated angiogenesis

Shengkui Qiu, Li Xie, Chen Lu, Chao Gu, Yiwen Xia, Jialun Lv, Zhe Xuan, Lang Fang, Jing Yang, Lu Zhang, Zheng Li, Weizhi Wang, Hao Xu, Bowen Li & Zekuan Xu
Additional file 2.

Gastric cancer-derived exosomal miR-519a-3p promotes liver metastasis by inducing intrahepatic M2-like macrophage-mediated angiogenesis

Shengkui Qiu, Li Xie, Chen Lu, Chao Gu, Yiwen Xia, Jialun Lv, Zhe Xuan, Lang Fang, Jing Yang, Lu Zhang, Zheng Li, Weizhi Wang, Hao Xu, Bowen Li & Zekuan Xu
Abstract Background Liver metastasis (LM) is a major obstacle to the prognosis of gastric cancer (GC) patients, but the molecular mechanism underlying gastric cancer liver metastasis (GC-LM) remains unknown. Exosomes have been identified as an important mediator of communication between tumor cells and the microenvironment. Therefore, we sought to investigate the effects of primary GC cells on the liver microenvironment and the role of exosomal microRNAs (exo-miRNA) in GC-LM. Methods Sequential differential centrifugation, transmission electron...

Is there variation in utilization of preoperative tests among patients undergoing total hip and knee replacement in the US, and does it affect outcomes? A population-based analysis

Mohamed Mosaad Hasan, Raymond Kang, Jungwha Lee, Matthew D. Beal, Abdalrahman G. Ahmed, Yao Tian & Hassan M. K. Ghomrawi
Abstract Study objective To describe recent practice patterns of preoperative tests and to examine their association with 90-day all-cause readmissions and length of stay. Design Retrospective cohort study using the New York Statewide Planning and Research Cooperative System (SPARCS). Setting SPARCS from March 1, 2016, to July 1, 2017. Participants Adults undergoing Total Hip Replacement (THR) or Total Knee Replacement (TKR) had a preoperative screening outpatient visit within two months before their surgery. Interventions Electrocardiogram...

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  • Agricultural University of Hebei
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  • Zhejiang University
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  • Affiliated Hospital of Qingdao University
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  • Jiangsu Province Hospital
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  • Nanjing Medical University
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  • Hangzhou Medical College
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