171 Works

Multifaceted characteristics of aridity changes and causal mechanisms in Chinese drylands

Ying Hu, Fangli Wei, Bojie Fu, Shuai Wang, Lanhui Wang & Yongzhe Chen
The water cycle is accelerating in the context of global warming. However, how the multifaceted characteristics of aridity, particularly atmospheric, hydrological, and ecological drying, change and interact with each other are largely unknown. A gap we bridged was discovering the causal relationships underlying the atmosphere-hydrosphere-biosphere nexus from the nonlinear dynamic system perspective based on convergent cross mapping (CCM). Dryland area in China has expanded since 1982, while the vegetation greenness indicated by leaf area index...

Multifaceted characteristics of aridity changes and causal mechanisms in Chinese drylands

Ying Hu, Fangli Wei, Bojie Fu, Shuai Wang, Lanhui Wang & Yongzhe Chen
The water cycle is accelerating in the context of global warming. However, how the multifaceted characteristics of aridity, particularly atmospheric, hydrological, and ecological drying, change and interact with each other are largely unknown. A gap we bridged was discovering the causal relationships underlying the atmosphere-hydrosphere-biosphere nexus from the nonlinear dynamic system perspective based on convergent cross mapping (CCM). Dryland area in China has expanded since 1982, while the vegetation greenness indicated by leaf area index...

Discrepancies in Work Relative Value Unit Assignment Based on Operative Time in Hand Surgery

Joshua B. Cadwell, Joseph S. Weisberger, Cyril S. Gary, Shreya Patel, Rose S. Maisner & Ashley Ignatiuk
Background:Work relative value units (wRVUs) are an intricate component of physician reimbursement determination in the United States. This paper assesses whether wRVUs appropriately consider operative time in hand surgery.Methods:The 50 most common single Current Procedural Terminology code hand surgery cases were queried from the 2013 to 2018 National Surgical Quality Improvement Program database. The average assigned wRVUs and median operative times were calculated for each CPT. Linear regressions were calculated between operative time, wRVUs, and...

Metabolomic profile of prostate cancer-specific survival among 1812 Finnish men

Jiaqi Huang, Bin Zhao, Stephanie J. Weinstein, Demetrius Albanes & Alison M. Mondul
Abstract Background Abnormal metabolism and perturbations in metabolic pathways play significant roles in the development and progression of prostate cancer; however, comprehensive metabolomic analyses of human data are lacking and needed to elucidate the interrelationships. Methods We examined the serum metabolome in relation to prostate cancer survival in a cohort of 1812 cases in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. Using an ultrahigh-performance LC-MS/MS platform, we identified 961 known metabolites in prospectively collected serum....

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
Abstract Background The identification of differentially expressed tumor-associated proteins and genomic alterations driving neoplasia is critical in the development of clinical assays to detect cancers and forms the foundation for understanding cancer biology. One of the challenges in the analysis of pancreatic ductal adenocarcinoma (PDAC) is the low neoplastic cellularity and heterogeneous composition of bulk tumors. To enrich neoplastic cells from bulk tumor tissue, coring, and laser microdissection (LMD) sampling techniques have been employed. In...

Additional file 4 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 4: Figure S4. Percentage of integration events at each genomic features based on gender and transduction efficiency. Related to Figure 6.

Additional file 9 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 9: Table S4. Differential integration sites at gene locus based on clinical outcomes.

Additional file 2 of Collection of peripheral blood mononucleated cells for chronic graft-versus-host disease immunology research: safety and effectiveness of leukapheresis in 132 patients

Alain Mina, Lauren Curtis, Kamille West, Yu Ying Yau, Edward W. Cowen, Frances Hakim & Steven Z. Pavletic
Supplementary Material 2

Additional file 1 of CC16 polymorphisms in asthma, asthma subtypes, and asthma control in adults from the Agricultural Lung Health Study

KC Gribben, AB Wyss, JA Poole, PA Farazi, C Wichman, M Richards-Barber, LE Beane Freeman, PK Henneberger, DM Umbach, SJ London, TD LeVan & Kelli C. Gribben
Supplementary Material 1

Additional file 1 of PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~ 200,000 patients

Daniele Giardiello, Maartje J. Hooning, Michael Hauptmann, Renske Keeman, B. A. M. Heemskerk-Gerritsen, Heiko Becher, Carl Blomqvist, Stig E. Bojesen, Manjeet K. Bolla, Nicola J. Camp, Kamila Czene, Peter Devilee, Diana M. Eccles, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García-Closas, Christopher A. Haiman, Ute Hamann, John L. Hopper, Anna Jakubowska, Floor E. Leeuwen, Annika Lindblom, Jan Lubiński, Sara Margolin … & Marjanka K. Schmidt
Additional file 1. Supplementary methods also including the following tables and figures Table S2. List of BCAC studies (including ABCS source) with the corresponding country and geographic area. Table S4: Clinical utility of the 5-year contralateral breast cancer risk prediction models (PredictCBC-1A with PredictCBC-2.0A and PredictCBC-1B with PredictCBC-2.0B). Figure S1. Visual assessment of calibration through calibration plots in the internal–external cross-validation at 5 years for the PredictCBC-2.0A model. Figure S2. Visual assessment of calibration through...

Additional file 2 of PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~ 200,000 patients

Daniele Giardiello, Maartje J. Hooning, Michael Hauptmann, Renske Keeman, B. A. M. Heemskerk-Gerritsen, Heiko Becher, Carl Blomqvist, Stig E. Bojesen, Manjeet K. Bolla, Nicola J. Camp, Kamila Czene, Peter Devilee, Diana M. Eccles, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García-Closas, Christopher A. Haiman, Ute Hamann, John L. Hopper, Anna Jakubowska, Floor E. Leeuwen, Annika Lindblom, Jan Lubiński, Sara Margolin … & Marjanka K. Schmidt
Additional file 2: Table S1. Description of the studies included in the analyses.

Additional file 2 of Parental coping with uncertainties along the severe combined immunodeficiency journey

Oksana Kutsa, Sara M. Andrews, Erin Mallonee, Angela Gwaltney, Alissa Creamer, Paul K. J. Han, Melissa Raspa & Barbara B. Biesecker
Additional file 2. Coping Codebook.

Additional file 2 of Parental coping with uncertainties along the severe combined immunodeficiency journey

Oksana Kutsa, Sara M. Andrews, Erin Mallonee, Angela Gwaltney, Alissa Creamer, Paul K. J. Han, Melissa Raspa & Barbara B. Biesecker
Additional file 2. Coping Codebook.

Additional file 5 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 5. Fig. S4. B1/P/Rbf tumors show amplification of Erbb2 gene (Her2). FISH for murine Erbb2 (green signal) detects an additional copy on chromosome 14 (labelled in orange) besides the 2 endogenous copies on chromosomes 11 (unlabeled).

Additional file 14 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 14. Table S5. List of significantly enriched canonical pathways obtained from GSEA for tumors of all three genotypes when compared to control mammary glands. Listed pathways were used in single-sample GSEA (ssGSEA) on all samples.

Additional file 10 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 10. Table S3. Gene Set Enrichment Analysis (GSEA) results for all models. GSEA against a ranked set of genes (MSigDB v6.2 Human/Mouse/Macaque) was performed for each contrast using C2 curated gene sets. Only significantly enriched gene sets are listed (p adj <0.05). Gene sets for which heat maps are shown in figures are highlighted in yellow.

Additional file 15 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 15. Table S6. Differential expression of genes (DEG) analysis among tumor models. DEG was performed by applying Limma Voom package at p value threshold set to 0.05. Data are ordered by contrast and logFC values.

Additional file 6 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 6. Fig. S5. Orthotopic allograft tumors recapitulate marker expression in GEM tumors. IHC analysis of molecular markers in mammary allograft tumors of B1/P/Rbf (A) and B1/P (B) genotypes. ER=estrogen receptor, PR=progesterone receptor, Her2= human epidermal growth factor receptor 2, CK14=cytokeratin 14, CK18=cytokeratin 18, VIM=vimentin, Ki67= marker of cell proliferation Ki-67. Brown (DAB) or red stain (Nova red) indicate positive staining. Scale bar 200µm

Additional file 1 of Epidemiologic patterns of biliary tract cancer in the United States: 2001–2015

Jill Koshiol, Binbing Yu, Shaum M. Kabadi, Katherine Baria & Rachna T. Shroff
Additional file 1: Supplementary Methods. Supplementary Table 1. Codes used for cancer classifications. Supplementary Table 2. BTC incidence rate by race/ethnicity: 2001–2015. Supplementary Table 3. Annual percent change in BTC rates: 2001–2015. Supplementary Table 4. The 10-year prevalence of BTC overall and by anatomic site across different races/ethnicities in 2015. Supplementary Table 5. Five-year relative survival for patients with BTC overall and by anatomic site across different races/ethnicities. Supplementary Table 6. Percentage lost to follow-up...

Additional file 2 of Epidemiologic patterns of biliary tract cancer in the United States: 2001–2015

Jill Koshiol, Binbing Yu, Shaum M. Kabadi, Katherine Baria & Rachna T. Shroff
Additional file 2. Original survival data for the Asian/Pacific Islander population with distant BTC and the SEER*Stat Survival Session.

Additional file 2 of Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma

Amelia L. Parker, Elise Bowman, Adriana Zingone, Brid M. Ryan, Wendy A. Cooper, Maija Kohonen-Corish, Curtis C. Harris & Thomas R. Cox
Additional file 2: Table S1. Differentially Expressed Hallmark Pathways in ECM-High vs ECM-Low Tumors. Table S2. Differentially Expressed MSigDb C2 Pathways in ECM-High vs ECM-Low Tumors. Table S3. Ligand-Receptor Interactions in ECM-High vs ECM-Low Tumors.

Effect of exposure to ionizing radiation on competitive proliferation and differentiation of hESC

Irina V. Panyutin, Paul G. Wakim, Roberto Maass-Moreno, William F. Pritchard, Ronald D. Neumann & Igor G. Panyutin
We studied the effects of computed tomography (CT) scan irradiation on proliferation and differentiation of human embryonic stem cells (hESCs). It was reported that hESC is extremely radiosensitive; exposure of hESC in cultures to 1 Gy of ionizing radiation (IR) results in massive apoptosis of the damaged cells and, thus, they are eliminated from the cultures. However, after recovery the surviving cells proliferate and differentiate normally. We hypothesized that IR-exposed hESC may still have growth...

Effect of exposure to ionizing radiation on competitive proliferation and differentiation of hESC

Irina V. Panyutin, Paul G. Wakim, Roberto Maass-Moreno, William F. Pritchard, Ronald D. Neumann & Igor G. Panyutin
We studied the effects of computed tomography (CT) scan irradiation on proliferation and differentiation of human embryonic stem cells (hESCs). It was reported that hESC is extremely radiosensitive; exposure of hESC in cultures to 1 Gy of ionizing radiation (IR) results in massive apoptosis of the damaged cells and, thus, they are eliminated from the cultures. However, after recovery the surviving cells proliferate and differentiate normally. We hypothesized that IR-exposed hESC may still have growth...

Additional file 13 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 13. Fig. S9. Several examples of pathways enriched in GSEA comparing B1/P/Rbf and P/Rbff models. Relative enrichment was observed in cell cycle A, DNA replication B and nucleotide excision repair C gene sets. Differences in expression of Mcm gene family D were common for several of these pathways (orange rectangles in A and B). E Expression of genes in the Mcm family in all three tumor models and control mammary glands. Highest expression...

Additional file 10 of Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins

Ludmila Szabova, Melanie B. Gordon, Lucy Lu, Nathan Pate, Laura Bassel, Anthony J. Iacovelli, Baktiar Karim, Philip J. Homan, Deborah B. Householder, Theresa M. Guerin, Sandra Burkett, Amanda M. Day, Wendi Custer & Zoe Weaver Ohler
Additional file 10. Table S3. Gene Set Enrichment Analysis (GSEA) results for all models. GSEA against a ranked set of genes (MSigDB v6.2 Human/Mouse/Macaque) was performed for each contrast using C2 curated gene sets. Only significantly enriched gene sets are listed (p adj <0.05). Gene sets for which heat maps are shown in figures are highlighted in yellow.

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