// +author:s arman +author:arman 
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{userid:"melslater", "articletype":"article","pages":"497-503","author":"M Usoh, E Catena, S Arman, M Slater","year":"2000","title":"Using presence questionnaires in reality","month":"","journal":"Presence-Teleoperators And Virtual Environments","publisher":"","volume":"9","number":"5","note":"Using presence questionnaires in reality xD;TY  - JOUR Y2  - Oct ISI:000165086200007 ISI Document Delivery No.: 369UW xD;http:\/\/www.cs.ucl.ac.uk\/staff\/m.slater\/Papers\/questionnaire-paper.pdf","tags":"","booktitle":"","editor":"","abstract":"","address":"","school":"","issn":"","doi":"","isi":"","pubmed":"","key":"ref61","howpublished":"","urllink":"","refid":50}
,

{userid:"iaeme", "articletype":"article","pages":"","author":"Swapnil C Parmar, Ankesh G Rokad, Arman G Rokad, Dr Vishal S Makadia","year":"2013","title":"Studies on Effectiveness of Various Ion Leaching Techniques on Geological Samples","month":"","journal":"International Journal of Advanced Research in Engineering and Technology (IJARET)","publisher":"","volume":"4","number":"7","note":"","tags":"","booktitle":"","editor":"","abstract":"","address":"","school":"","issn":"","doi":"","isi":"","pubmed":"","key":"parmar2013studies","howpublished":"","urllink":"","refid":1817,"weight":1817}
,

{userid:"nicolas.karakatsanis", "refid":29,"repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Monte-Carlo Based Characterization of the Counting Rate (NECR) Response for Personalized Optimization of the Administered Activity in Clinical PET Imaging","year":"2014","author":"Nicolas A. Karakatsanis, George Loudos, Arman Rahmim, Konstantina S. Nikita","journal":"Frontiers in Biomedical Tecnologies","volume":"1","number":"1","pages":"14-34","month":"January","doi":"","pubmed":"","pdflink":"http:\/\/nkarakatsanis.files.wordpress.com\/2014\/02\/karakatsanis_fbt14_necrbasedoptimization.pdf","urllink":"http:\/\/fbt.tums.ac.ir\/index.php\/fbt\/article\/view\/68","abstract":"Purpose: The statistical quality of a PET scan can be significantly affected by the associated patient and scanner characteristics. Standard protocols could be optimized by regulating the administered activity Aadm such that the statistical quality is maximized for each individual patient for a given scan time. The objective is to model the direct relationship between the noise equivalent count rate NECR and Aadm for a wide range of scanner and patient parameters employed in clinical scans.\r\n\r\nMethods: A series of extensive and validated Monte Carlo simulations is utilized to systematically investigate, under realistic and controlled conditions, the effect of a wide set of (i) phantom sizes modeling children, slim and obese patients, (ii) bed positions, (iii) energy windows, (iv) coincidence time windows, (v) and combination of dead times and detector responses on the NECR for a range of Aadm.\r\n\r\nResults: A wide plateau is observed in NECR(Aadm) curves particularly for large patients, suggesting that 90-95% of peak NECR can still be obtained with considerably less Aadm. Moreover, for default scanner configurations and cardiac beds, an optimal Aadm range of 55-65 MBq for HR+ and 300-450 MBq for Biograph scanners, with the maximum NECR being considerably higher for the latter.\r\n\r\nConclusions: The generalized NECR(Aadm) model can be utilized to predict for each individual Optimization, patient scan an optimal range of Aadm for which NECR is maximized, thus potentially allowing (a) for efficient utilization of the available activity in PET centers and (b) for minimization of cumulative radiation exposure.","note":"","tags":"NECR, Dose, Optimization, PET, Protocol","weight":29}
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{userid:"isabel.little", "refid":"2","repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Trauma, Critical Care, and Emergency Care Anesthesiology: A New Paradigm for the \"Acute Care\" Anesthesiologist?","year":"2015","author":"Maureen McCunn, Richard P Dutton, Arman Dagal, Albert J Varon, Olga Kaslow, Corry Jeb Kucik, Carin A Hagberg, Joseph H McIsaac, Jean-Francois Pittet, Peter J Dunbar, Thomas Grissom, Monica S Vavilala","journal":"Anesthesia and analgesia","volume":"121","number":"6","pages":"1668-1673","month":"Dec","doi":"10.1213\/ANE.0000000000000782","pubmed":"26579665","pdflink":"","urllink":"","abstract":"","note":"","tags":"Anesthesiology,Clinical Competence,Critical Care,Emergency Medical Services,Humans,Internship and Residency,Physicians","weight":2,"publisher":"","booktitle":"","editor":"","address":"","school":"","issn":"1526-7598","isi":"","key":"McCunn2015","howpublished":""}
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{userid:"stefan.michiels", "refid":"302","repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer.","year":"2023","author":"David B Page, Glenn Broeckx, Chowdhury Arif Jahangir, Sara Verbandt, Rajarsi R Gupta, Jeppe Thagaard, Reena Khiroya, Zuzana Kos, Khalid Abduljabbar, Gabriela Acosta Haab, Balazs Acs, Guray Akturk, Jonas S Almeida, Isabel Alvarado-Cabrero, Farid Azmoudeh-Ardalan, Sunil Badve, Nurkhairul Bariyah Baharun, Enrique R Bellolio, Vydehi Bheemaraju, Kim Rm Blenman, Luciana Botinelly Mendon\u00e7a Fujimoto, Najat Bouchmaa, Octavio Burgues, Maggie Chon U Cheang, Francesco Ciompi, Lee Ad Cooper, An Coosemans, Germ\u00e1n Corredor, Flavio Luis Dantas Portela, Frederik Deman, Sandra Demaria, Sarah N Dudgeon, Mahmoud Elghazawy, Scott Ely, Claudio Fernandez-Mart\u00edn, Susan Fineberg, Stephen B Fox, William M Gallagher, Jennifer M Giltnane, Sacha Gnjatic, Paula I Gonzalez-Ericsson, Anita Grigoriadis, Niels Halama, Matthew G Hanna, Aparna Harbhajanka, Alexandros Hardas, Steven N Hart, Johan Hartman, Stephen Hewitt, Akira I Hida, Hugo M Horlings, Zaheed Husain, Evangelos Hytopoulos, Sheeba Irshad, Emiel Am Janssen, Mohamed Kahila, Tatsuki R Kataoka, Kosuke Kawaguchi, Durga Kharidehal, Andrey I Khramtsov, Umay Kiraz, Pawan Kirtani, Liudmila L Kodach, Konstanty Korski, Anik\u00f3 Kov\u00e1cs, Anne-Vibeke Laenkholm, Corinna Lang-Schwarz, Denis Larsimont, Jochen K Lennerz, Marvin Lerousseau, Xiaoxian Li, Amy Ly, Anant Madabhushi, Sai K Maley, Vidya Manur Narasimhamurthy, Douglas K Marks, Elizabeth S McDonald, Ravi Mehrotra, Stefan Michiels, Fayyaz Ul Amir Afsar Minhas, Shachi Mittal, David A Moore, Shamim Mushtaq, Hussain Nighat, Thomas Papathomas, Frederique Penault-Llorca, Rashindrie D Perera, Christopher J Pinard, Juan Carlos Pinto-Cardenas, Giancarlo Pruneri, Lajos Pusztai, Arman Rahman, Nasir Mahmood Rajpoot, Bernardo Leon Rapoport, Tilman T Rau, Jorge S Reis-Filho, Joana M Ribeiro, David Rimm, Anne Vincent-Salomon, Manuel Salto-Tellez, Joel Saltz, Shahin Sayed, Kalliopi P Siziopikou, Christos Sotiriou, Albrecht Stenzinger, Maher A Sughayer, Daniel Sur, Fraser Symmans, Sunao Tanaka, Timothy Taxter, Sabine Tejpar, Jonas Teuwen, E Aubrey Thompson, Trine Tramm, William T Tran, Jeroen van der Laak, Paul J van Diest, Gregory E Verghese, Giuseppe Viale, Michael Vieth, Noorul Wahab, Thomas Walter, Yannick Waumans, Hannah Y Wen, Wentao Yang, Yinyin Yuan, Sylvia Adams, John Mark Seaverns Bartlett, Sibylle Loibl, Carsten Denkert, Peter Savas, Sherene Loi, Roberto Salgado, Elisabeth Specht Stovgaard","journal":"The Journal of pathology","volume":"260","number":"5","pages":"514-532","month":"Aug","doi":"10.1002\/path.6165","pubmed":"37608771","pdflink":"","urllink":"","abstract":"Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for describing or analyzing spatial immune cell data, and most reported spatial analyses are rudimentary. In this review, we provide an overview of two approaches for reporting and analyzing spatial data (raster versus vector-based). We then provide a compendium of spatial immune cell metrics that have been reported in the literature, summarizing prognostic associations in the context of a variety of cancers. We conclude by discussing two well-described clinical biomarkers, the breast cancer stromal tumor infiltrating lymphocytes score and the colon cancer Immunoscore, and describe investigative opportunities to improve clinical utility of these spatial biomarkers. \u00a9 2023 The Pathological Society of Great Britain and Ireland.","note":"","tags":"Humans,Colonic Neoplasms,Biomarkers,Benchmarking,Lymphocytes, Tumor-Infiltrating,Spatial Analysis,Tumor Microenvironment","weight":302,"publisher":"","booktitle":"","editor":"","address":"","school":"","issn":"1096-9896","isi":"","key":"Page2023","howpublished":""}
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{userid:"stefan.michiels", "refid":"301","repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: a report of the international immuno-oncology biomarker working group.","year":"2023","author":"Jeppe Thagaard, Glenn Broeckx, David B Page, Chowdhury Arif Jahangir, Sara Verbandt, Zuzana Kos, Rajarsi Gupta, Reena Khiroya, Khalid Abduljabbar, Gabriela Acosta Haab, Balazs Acs, Guray Akturk, Jonas S Almeida, Isabel Alvarado-Cabrero, Mohamed Amgad, Farid Azmoudeh-Ardalan, Sunil Badve, Nurkhairul Bariyah Baharun, Eva Balslev, Enrique R Bellolio, Vydehi Bheemaraju, Kim Rm Blenman, Luciana Botinelly Mendon\u00e7a Fujimoto, Najat Bouchmaa, Octavio Burgues, Alexandros Chardas, Maggie Chon U Cheang, Francesco Ciompi, Lee Ad Cooper, An Coosemans, Germ\u00e1n Corredor, Anders B Dahl, Flavio Luis Dantas Portela, Frederik Deman, Sandra Demaria, Johan Dor\u00e9 Hansen, Sarah N Dudgeon, Thomas Ebstrup, Mahmoud Elghazawy, Claudio Fernandez-Mart\u00edn, Stephen B Fox, William M Gallagher, Jennifer M Giltnane, Sacha Gnjatic, Paula I Gonzalez-Ericsson, Anita Grigoriadis, Niels Halama, Matthew G Hanna, Aparna Harbhajanka, Steven N Hart, Johan Hartman, S\u00f8ren Hauberg, Stephen Hewitt, Akira I Hida, Hugo M Horlings, Zaheed Husain, Evangelos Hytopoulos, Sheeba Irshad, Emiel Am Janssen, Mohamed Kahila, Tatsuki R Kataoka, Kosuke Kawaguchi, Durga Kharidehal, Andrey I Khramtsov, Umay Kiraz, Pawan Kirtani, Liudmila L Kodach, Konstanty Korski, Anik\u00f3 Kov\u00e1cs, Anne-Vibeke Laenkholm, Corinna Lang-Schwarz, Denis Larsimont, Jochen K Lennerz, Marvin Lerousseau, Xiaoxian Li, Amy Ly, Anant Madabhushi, Sai K Maley, Vidya Manur Narasimhamurthy, Douglas K Marks, Elizabeth S McDonald, Ravi Mehrotra, Stefan Michiels, Fayyaz Ul Amir Afsar Minhas, Shachi Mittal, David A Moore, Shamim Mushtaq, Hussain Nighat, Thomas Papathomas, Frederique Penault-Llorca, Rashindrie D Perera, Christopher J Pinard, Juan Carlos Pinto-Cardenas, Giancarlo Pruneri, Lajos Pusztai, Arman Rahman, Nasir Mahmood Rajpoot, Bernardo Leon Rapoport, Tilman T Rau, Jorge S Reis-Filho, Joana M Ribeiro, David Rimm, Anne Roslind, Anne Vincent-Salomon, Manuel Salto-Tellez, Joel Saltz, Shahin Sayed, Ely Scott, Kalliopi P Siziopikou, Christos Sotiriou, Albrecht Stenzinger, Maher A Sughayer, Daniel Sur, Susan Fineberg, Fraser Symmans, Sunao Tanaka, Timothy Taxter, Sabine Tejpar, Jonas Teuwen, E Aubrey Thompson, Trine Tramm, William T Tran, Jeroen van der Laak, Paul J van Diest, Gregory E Verghese, Giuseppe Viale, Michael Vieth, Noorul Wahab, Thomas Walter, Yannick Waumans, Hannah Y Wen, Wentao Yang, Yinyin Yuan, Reena Md Zin, Sylvia Adams, John Bartlett, Sibylle Loibl, Carsten Denkert, Peter Savas, Sherene Loi, Roberto Salgado, Elisabeth Specht Stovgaard","journal":"The Journal of pathology","volume":"260","number":"5","pages":"498-513","month":"Aug","doi":"10.1002\/path.6155","pubmed":"37608772","pdflink":"","urllink":"","abstract":"The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer. \u00a9 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.","note":"","tags":"Humans,Animals,Lymphocytes, Tumor-Infiltrating,Triple Negative Breast Neoplasms,Mammary Neoplasms, Animal,Biomarkers,Machine Learning","weight":301,"publisher":"","booktitle":"","editor":"","address":"","school":"","issn":"1096-9896","isi":"","key":"Thagaard2023","howpublished":""}
,

{userid:"stefan.michiels", "refid":"306","repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer.","year":"2024","author":"Chowdhury Arif Jahangir, David B Page, Glenn Broeckx, Claudia A Gonzalez, Caoimbhe Burke, Clodagh Murphy, Jorge S Reis-Filho, Amy Ly, Paul W Harms, Rajarsi R Gupta, Michael Vieth, Akira I Hida, Mohamed Kahila, Zuzana Kos, Paul J van Diest, Sara Verbandt, Jeppe Thagaard, Reena Khiroya, Khalid Abduljabbar, Gabriela Acosta Haab, Balazs Acs, Sylvia Adams, Jonas S Almeida, Isabel Alvarado-Cabrero, Farid Azmoudeh-Ardalan, Sunil Badve, Nurkhairul Bariyah Baharun, Enrique R Bellolio, Vydehi Bheemaraju, Kim Rm Blenman, Luciana Botinelly Mendon\u00e7a Fujimoto, Octavio Burgues, Alexandros Chardas, Maggie Chon U Cheang, Francesco Ciompi, Lee Ad Cooper, An Coosemans, Germ\u00e1n Corredor, Flavio Luis Dantas Portela, Frederik Deman, Sandra Demaria, Sarah N Dudgeon, Mahmoud Elghazawy, Claudio Fernandez-Mart\u00edn, Susan Fineberg, Stephen B Fox, Jennifer M Giltnane, Sacha Gnjatic, Paula I Gonzalez-Ericsson, Anita Grigoriadis, Niels Halama, Matthew G Hanna, Aparna Harbhajanka, Steven N Hart, Johan Hartman, Stephen Hewitt, Hugo M Horlings, Zaheed Husain, Sheeba Irshad, Emiel Am Janssen, Tatsuki R Kataoka, Kosuke Kawaguchi, Andrey I Khramtsov, Umay Kiraz, Pawan Kirtani, Liudmila L Kodach, Konstanty Korski, Guray Akturk, Ely Scott, Anik\u00f3 Kov\u00e1cs, Anne-Vibeke Laenkholm, Corinna Lang-Schwarz, Denis Larsimont, Jochen K Lennerz, Marvin Lerousseau, Xiaoxian Li, Anant Madabhushi, Sai K Maley, Vidya Manur Narasimhamurthy, Douglas K Marks, Elizabeth S McDonald, Ravi Mehrotra, Stefan Michiels, Durga Kharidehal, Fayyaz Ul Amir Afsar Minhas, Shachi Mittal, David A Moore, Shamim Mushtaq, Hussain Nighat, Thomas Papathomas, Frederique Penault-Llorca, Rashindrie D Perera, Christopher J Pinard, Juan Carlos Pinto-Cardenas, Giancarlo Pruneri, Lajos Pusztai, Nasir Mahmood Rajpoot, Bernardo Leon Rapoport, Tilman T Rau, Joana M Ribeiro, David Rimm, Anne Vincent-Salomon, Joel Saltz, Shahin Sayed, Evangelos Hytopoulos, Sarah Mahon, Kalliopi P Siziopikou, Christos Sotiriou, Albrecht Stenzinger, Maher A Sughayer, Daniel Sur, Fraser Symmans, Sunao Tanaka, Timothy Taxter, Sabine Tejpar, Jonas Teuwen, E Aubrey Thompson, Trine Tramm, William T Tran, Jeroen van der Laak, Gregory E Verghese, Giuseppe Viale, Noorul Wahab, Thomas Walter, Yannick Waumans, Hannah Y Wen, Wentao Yang, Yinyin Yuan, John Bartlett, Sibylle Loibl, Carsten Denkert, Peter Savas, Sherene Loi, Elisabeth Specht Stovgaard, Roberto Salgado, William M Gallagher, Arman Rahman","journal":"The Journal of pathology","volume":"262","number":"3","pages":"271-288","month":"Mar","doi":"10.1002\/path.6238","pubmed":"38230434","pdflink":"","urllink":"","abstract":"Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. \u00a9 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.","note":"","tags":"Humans,Female,Breast Neoplasms,Biomarkers, Tumor,Prognosis,Phenotype,United Kingdom,Tumor Microenvironment","weight":306,"publisher":"","booktitle":"","editor":"","address":"","school":"","issn":"1096-9896","isi":"","key":"Jahangir2024","howpublished":""}
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