Publications by authors named "Ali Naji"

100Publications

Norovirus-Specific CD8 T Cell Responses in Human Blood and Tissues.

Cell Mol Gastroenterol Hepatol 2021 Jan 11. Epub 2021 Jan 11.

Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. Electronic address:

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January 2021

Confinement-induced alternating interactions between inclusions in an active fluid.

Phys Rev E 2020 Sep;102(3-1):032613

School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.

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September 2020

Identification of EGFR and RAS Inhibitors using Caenorhabditis elegans.

J Vis Exp 2020 10 5(164). Epub 2020 Oct 5.

Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center;

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October 2020

Effective interactions mediated between two permeable disks in an active fluid.

Sci Rep 2020 09 23;10(1):15570. Epub 2020 Sep 23.

School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.

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September 2020

Single-cell transcriptomics of human islet ontogeny defines the molecular basis of β-cell dedifferentiation in T2D.

Mol Metab 2020 Dec 30;42:101057. Epub 2020 Jul 30.

Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address:

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December 2020

Use of Dietary Supplements in Living Kidney Donors: A Critical Review.

Am J Kidney Dis 2020 12 10;76(6):851-860. Epub 2020 Jul 10.

Renal-Electrolyte & Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Penn Medicine Transplant Institute, Hospital of the University of Pennsylvania, Philadelphia, PA; Department of Pharmacy Services, Hospital of the University of Pennsylvania, Philadelphia, PA. Electronic address:

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December 2020

Active dipolar spheroids in shear flow and transverse field: Population splitting, cross-stream migration, and orientational pinning.

J Chem Phys 2020 May;152(20):204903

School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.

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May 2020

Surface alignment disorder and thermal Casimir forces in smectic-A liquid crystalline films.

J Phys Condens Matter 2020 Apr 2;32(32):325103. Epub 2020 Apr 2.

Faculty of Physics, Kharazmi University, Tehran 15815-3587, Iran.

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April 2020

Robust, 3-Dimensional Visualization of Human Colon Enteric Nervous System Without Tissue Sectioning.

Gastroenterology 2020 Jun 27;158(8):2221-2235.e5. Epub 2020 Feb 27.

Children's Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

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June 2020

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression.

Immunity 2020 02 11;52(2):257-274.e11. Epub 2020 Feb 11.

Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; The Human Pancreas Analysis Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA, https://hpap.pmacs.upenn.edu/. Electronic address:

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February 2020

Novel therapeutic opportunities afforded by plasma cell biology in transplantation.

Am J Transplant 2020 08 29;20(8):1984-1991. Epub 2020 Feb 29.

Department of Surgery, Division of Transplantation, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.

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August 2020

Reciprocal Learning Between Military and Civilian Surgeons: Past and Future Paths for Medical Innovation.

Ann Surg 2019 Oct 9. Epub 2019 Oct 9.

Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA.

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October 2019

Mapping the Lineage Relationship between CXCR5 and CXCR5 CD4 T Cells in HIV-Infected Human Lymph Nodes.

Cell Rep 2019 09;28(12):3047-3060.e7

Department of Medicine, Division of Rheumatology, Philadelphia VA Medical Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address:

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September 2019

NIH Initiative to Improve Understanding of the Pancreas, Islet, and Autoimmunity in Type 1 Diabetes: The Human Pancreas Analysis Program (HPAP).

Diabetes 2019 07 24;68(7):1394-1402. Epub 2019 May 24.

Departments of Pathology and Pediatrics, University of Florida Diabetes Institute, Gainesville, FL.

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July 2019

Studying Oxidative Stress Caused by the Mitis Group Streptococci in Caenorhabditis elegans.

J Vis Exp 2019 03 23(145). Epub 2019 Mar 23.

Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center;

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March 2019

Role of metallic core for the stability of virus-like particles in strongly coupled electrostatics.

Sci Rep 2019 03 7;9(1):3884. Epub 2019 Mar 7.

School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5531, Iran.

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March 2019

Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding.

ACS Omega 2019 Feb 8;4(2):2921-2930. Epub 2019 Feb 8.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States.

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February 2019

Noninvasive diagnosis of recurrent autoimmune type 1 diabetes after islet cell transplantation.

Am J Transplant 2019 06 18;19(6):1852-1858. Epub 2019 Mar 18.

Division of Cardiovascular Surgery, Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.

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June 2019

Multiplexed In Situ Imaging Mass Cytometry Analysis of the Human Endocrine Pancreas and Immune System in Type 1 Diabetes.

Cell Metab 2019 03 31;29(3):769-783.e4. Epub 2019 Jan 31.

Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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March 2019

Targeted demethylation at the CDKN1C/p57 locus induces human β cell replication.

J Clin Invest 2019 01 26;129(1):209-214. Epub 2018 Nov 26.

Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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January 2019

Charged nanorods at heterogeneously charged surfaces.

J Chem Phys 2018 Oct;149(13):134702

School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.

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October 2018

The activation of the oxidative stress response transcription factor SKN-1 in Caenorhabditis elegans by mitis group streptococci.

PLoS One 2018 16;13(8):e0202233. Epub 2018 Aug 16.

Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center, Houston, Texas, United States of America.

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February 2019

Active fluids at circular boundaries: swim pressure and anomalous droplet ripening.

Soft Matter 2018 Jun;14(23):4820-4834

School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.

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June 2018

Re-entrant bimodality in spheroidal chiral swimmers in shear flow.

Sci Rep 2018 May 29;8(1):8328. Epub 2018 May 29.

School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5531, Iran.

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May 2018

Donor tissue-specific exosome profiling enables noninvasive monitoring of acute rejection in mouse allogeneic heart transplantation.

J Thorac Cardiovasc Surg 2018 06 1;155(6):2479-2489. Epub 2018 Feb 1.

Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa. Electronic address:

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June 2018

Urinary Prostaglandin Metabolites: An Incomplete Reckoning and a Flush to Judgment.

Circ Res 2018 02;122(4):537-539

From the Institute for Translational Medicine and Therapeutics (T.G., G.A.F.) and Department of Surgery (A.N.), Perelman School of Medicine, University of Pennsylvania, Philadelphia.

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February 2018

Effective interactions between inclusions in an active bath.

J Chem Phys 2017 Nov;147(19):194901

School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.

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November 2017

Sphingomyelin Metabolism Is a Regulator of K-Ras Function.

Mol Cell Biol 2018 02 16;38(3). Epub 2018 Jan 16.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA.

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February 2018

Inhibition of cholinergic potentiation of insulin secretion from pancreatic islets by chronic elevation of glucose and fatty acids: Protection by casein kinase 2 inhibitor.

Mol Metab 2017 10 4;6(10):1240-1253. Epub 2017 Aug 4.

Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, School of Medicine, Philadelphia, PA 19104, USA.

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October 2017

Circulating B cells in type 1 diabetics exhibit fewer maturation-associated phenotypes.

Clin Immunol 2017 10 23;183:336-343. Epub 2017 Sep 23.

Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. Electronic address:

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October 2017

Intercellular Genetic Interaction Between Irf6 and Twist1 during Craniofacial Development.

Sci Rep 2017 08 2;7(1):7129. Epub 2017 Aug 2.

Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA.

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August 2017

Population splitting of rodlike swimmers in Couette flow.

Soft Matter 2017 Jun;13(25):4494-4506

School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.

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June 2017

Staged management of giant bilateral perinephric adipocytic neoplasms.

Clin Case Rep 2017 05 23;5(5):621-624. Epub 2017 Mar 23.

Endocrine and Oncologic Surgery Hospital of the University of Pennsylvania Philadelphia Pennsylvania USA.

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May 2017

Functional and Metabolomic Consequences of K Channel Inactivation in Human Islets.

Diabetes 2017 07 25;66(7):1901-1913. Epub 2017 Apr 25.

Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA

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July 2017

Menin and PRMT5 suppress GLP1 receptor transcript and PKA-mediated phosphorylation of FOXO1 and CREB.

Am J Physiol Endocrinol Metab 2017 08 7;313(2):E148-E166. Epub 2017 Mar 7.

Abramson Family Cancer Research Institute, Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania;

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August 2017

Skin-derived TSLP systemically expands regulatory T cells.

J Autoimmun 2017 May 23;79:39-52. Epub 2017 Jan 23.

Department of Pathology & Laboratory Medicine, University of Pennsylvania, United States. Electronic address:

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May 2017

Long-Term Improvement in Glucose Control and Counterregulation by Islet Transplantation for Type 1 Diabetes.

J Clin Endocrinol Metab 2016 11 29;101(11):4421-4430. Epub 2016 Aug 29.

Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism (M.R.R., A.J.P., C.D.-B., S.M.K., K.L.T.) and Department of Surgery, Division of Transplantation (E.M., A.N.), Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104; and the Monell Chemical Senses Center (K.L.T.), Philadelphia, Pennsylvania 19104.

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November 2016

Single-Cell Mass Cytometry Analysis of the Human Endocrine Pancreas.

Cell Metab 2016 10;24(4):616-626

Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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October 2016

TGF-β1 promotes acinar to ductal metaplasia of human pancreatic acinar cells.

Sci Rep 2016 08 3;6:30904. Epub 2016 Aug 3.

Departments of Cellular and Structural Biology, University of Texas Heath Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.

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August 2016

Activation of GPR119 Stimulates Human β-Cell Replication and Neogenesis in Humanized Mice with Functional Human Islets.

J Diabetes Res 2016 16;2016:1620821. Epub 2016 Jun 16.

The Sanford Project, Children Health Research Center, Sanford Research, Sioux Falls, SD 57104, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57104, USA; Department of Surgery, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57104, USA.

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May 2017

Single-Cell Transcriptomics of the Human Endocrine Pancreas.

Diabetes 2016 10 30;65(10):3028-38. Epub 2016 Jun 30.

Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA

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October 2016

Pseudo-Casimir stresses and elasticity of a confined elastomer film.

Soft Matter 2016 05;12(19):4384-96

Department of Theoretical Physics, J. Stefan Institute, 1000 Ljubljana, Slovenia.

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May 2016

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes.

Mol Metab 2016 Mar 11;5(3):233-244. Epub 2016 Jan 11.

Institute of Diabetes, Obesity, and Metabolism, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA; Department of Genetics, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA. Electronic address:

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March 2016

Accumulation of 3-hydroxytetradecenoic acid: Cause or corollary of glucolipotoxic impairment of pancreatic β-cell bioenergetics?

Mol Metab 2015 Dec 8;4(12):926-39. Epub 2015 Oct 8.

Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, United States; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, United States.

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December 2015

Pancreas Transplantation in the Modern Era.

Gastroenterol Clin North Am 2016 Mar 13;45(1):145-66. Epub 2016 Jan 13.

Division of Transplantation, Department of Surgery, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, Clinical Science Cntr-H4/772, Madison, WI 53792, USA.

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March 2016

Ion-mediated interactions between net-neutral slabs: Weak and strong disorder effects.

J Chem Phys 2015 Dec;143(23):234701

Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia.

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December 2015

Hydrodynamic fluctuation-induced forces in confined fluids.

Soft Matter 2016 Jan;12(2):441-59

Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia.

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January 2016

Bisphosphonate Induces Osteonecrosis of the Jaw in Diabetic Mice via NLRP3/Caspase-1-Dependent IL-1β Mechanism.

J Bone Miner Res 2015 Dec 14;30(12):2300-12. Epub 2015 Jul 14.

Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA.

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December 2015

Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities.

J Chem Phys 2015 Jun;142(21):214904

Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, SI-1000 Ljubljana, Slovenia.

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June 2015

Ultrasound-enhanced bevacizumab release from echogenic liposomes for inhibition of atheroma progression.

J Liposome Res 2016 13;26(1):47-56. Epub 2015 Apr 13.

a Department of Internal Medicine, Division of Cardiovascular Medicine , University of Texas Health Science Center at Houston , Houston , TX , USA .

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January 2017

Strong coupling electrostatics for randomly charged surfaces: antifragility and effective interactions.

Soft Matter 2015 May;11(17):3441-59

School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.

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May 2015

Restoration of Glucose Counterregulation by Islet Transplantation in Long-standing Type 1 Diabetes.

Diabetes 2015 May 18;64(5):1713-8. Epub 2014 Dec 18.

Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA Monell Chemical Senses Center, Philadelphia, PA.

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May 2015

Fluctuation-induced interactions in nematics with disordered anchoring energy.

J Phys Condens Matter 2014 Dec 31;26(50):505101. Epub 2014 Oct 31.

Faculty of Physics, Kharazmi University, Karaj 31979-37551, Iran.

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December 2014

Zinc and copper levels in low birth weight deliveries in Medani Hospital, Sudan.

BMC Res Notes 2014 Jun 24;7:386. Epub 2014 Jun 24.

Faculty of Medicine, Al-Neelain University, P,O, Box 12702, Khartoum, Sudan.

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June 2014

Metabolic memory of ß-cells controls insulin secretion and is mediated by CaMKII.

Mol Metab 2014 Jul 15;3(4):484-9. Epub 2014 Apr 15.

Department of Structural and Functional Biology, Institute of Biology, State University of Campinas (UNICAMP), P.O. Box 6109, Campinas, SP, CEP 13083-865, Brazil.

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July 2014

Insulin sensitivity index in type 1 diabetes and following human islet transplantation: comparison of the minimal model to euglycemic clamp measures.

Am J Physiol Endocrinol Metab 2014 May 1;306(10):E1217-24. Epub 2014 Apr 1.

Division of Transplantation, Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.

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May 2014

Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere.

Eur Phys J E Soft Matter 2014 Mar 31;37(3):21. Epub 2014 Mar 31.

Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, 14195, Berlin, Germany.

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March 2014

Structure-function hierarchies and von Kármán-Howarth relations for turbulence in magnetohydrodynamical equations.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Jan 14;89(1):012117. Epub 2014 Jan 14.

Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.

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January 2014

Grg3/TLE3 and Grg1/TLE1 induce monohormonal pancreatic β-cells while repressing α-cell functions.

Diabetes 2014 May 31;63(5):1804-16. Epub 2014 Jan 31.

Institute for Regenerative Medicine, Institute for Diabetes Obesity and Metabolism, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA.

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May 2014

Pseudo-Casimir interactions across nematic films with disordered anchoring axis.

J Phys Condens Matter 2014 Feb 22;26(7):075103. Epub 2014 Jan 22.

Faculty of Physics, Kharazmi University, Karaj 31979-37551, Iran.

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February 2014

Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets.

Cell Metab 2014 Jan 26;19(1):135-45. Epub 2013 Dec 26.

Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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January 2014

Elevated mouse hepatic betatrophin expression does not increase human β-cell replication in the transplant setting.

Diabetes 2014 Apr 18;63(4):1283-8. Epub 2013 Dec 18.

Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA.

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April 2014

Interleukin 5 immunotherapy depletes alloreactive plasma cells.

J Surg Res 2014 Mar 19;187(1):310-5. Epub 2013 Oct 19.

Harrison Department of Surgical Research, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.

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March 2014