The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

Authors: Yaniv, Ziv, Anidi, Ifeanyichukwu U., Arakkal, Leanne, Arroyo-Mejías, Armando J., Beuschel, Rebecca T., Börner, Katy, Chu, Colin J., Clark, Beatrice, Clatworthy, Menna R., Colautti, Jake, Coscia, Fabian, Croteau, Joshua, Denha, Saven, Dever, Rose, Dutra, Walderez O., Fritzsche, Sonja, Fullam, Spencer, Gerner, Michael Y., Gola, Anita, Gollob, Kenneth J., Hernandez, Jonathan M., Hor, Jyh Liang, Ichise, Hiroshi, Jing, Zhixin, Jonigk, Danny, Kandov, Evelyn, Kastenmüller, Wolfgang, Koenig, Joshua F. E., Kothurkar, Aanandita, Kortekaas, Rosa K., Kreins, Alexandra Y., Lamborn, Ian T., Lin, Yuri, Morais, Katia Luciano Pereira, Lunich, Aleksandra, Luz, Jean C. S., MacDonald, Ryan B., Makranz, Chen, Maltez, Vivien I., McDonough, John E., Moriarty, Ryan V., Ocampo-Godinez, Juan M., Olyntho, Vitoria M., Oxenius, Annette, Padhan, Kartika, Remmert, Kirsten, Richoz, Nathan, Schrom, Edward C., Shang, Wanjing, Shi, Lihong, Shih, Rochelle M., Speranza, Emily, Stierli, Salome, Teichmann, Sarah A., Veres, Tibor Z., Vierhout, Megan, Wachter, Brianna T., Williams, Margaret, Zangger, Nathan, Germain, Ronald N., Radtke, Andrea J.

Subject Terms: Quantitative Biology - Tissues and Organs, Electrical Engineering and Systems Science - Image and Video Processing

Access URL: http://arxiv.org/abs/2412.12965

The IBEX Knowledge-Base: Achieving more together with open science

Authors: Radtke, Andrea J., Anidi, Ifeanyichukwu, Arakkal, Leanne, Arroyo-Mejias, Armando, Beuschel, Rebecca T., Borner, Katy, Chu, Colin J., Clark, Beatrice, Clatworthy, Menna R., Colautti, Jake, Croteau, Joshua, Denha, Saven, Dever, Rose, Dutra, Walderez O., Fritzsche, Sonja, Fullam, Spencer, Gerner, Michael Y., Gola, Anita, Gollob, Kenneth J., Hernandez, Jonathan M., Hor, Jyh Liang, Ichise, Hiroshi, Jing, Zhixin, Jonigk, Danny, Kandov, Evelyn, Kastenmueller, Wolfgang, Koenig, Joshua F. E., Kothurkar, Aanandita, Kreins, Alexandra Y., Lamborn, Ian, Lin, Yuri, Morais, Katia Luciano Pereira, Lunich, Aleksandra, Luz, Jean C. S., MacDonald, Ryan B., Makranz, Chen, Maltez, Vivien I., Moriaty, Ryan V., Ocampo-Godinez, Juan M., Olyntho, Vitoria M., Padhan, Kartika, Remmert, Kirsten, Richoz, Nathan, Schrom, Edward C., Shang, Wanjing, Shi, Lihong, Shih, Rochelle M., Speranza, Emily, Stierli, Salome, Teichmann, Sarah A., Veres, Tibor Z., Vierhout, Megan, Wachter, Brianna T., Wade-Vallance, Adam K., Williams, Margaret, Zangger, Nathan, Germain, Ronald N., Yaniv, Ziv

Subject Terms: Quantitative Biology - Tissues and Organs

Access URL: http://arxiv.org/abs/2407.19059

Ex vivo T-lymphopoiesis assays assisting corrective treatment choice for genetically undefined T-lymphocytopenia

Authors: Golwala, Zainab M. ^{a, b, 1}, Spiridou Goncalves, Helena ^{a, 1}, Moirangthem, Ranjita Devi ^{c, d}, Evans, Grace ^a, Lizot, Sabrina ^c, de Koning, Coco ^e, Garrigue, Alexandrine ^c, Corredera, Marta Martin ^{c, d}, Ocampo-Godinez, Juan Moises ^a, Howley, Evey ^b, Kricke, Susanne ^f, Awuah, Arnold ^b, Obiri-Yeboa, Irene ^b, Rai, Rajeev ^a, Sebire, Neil ^g, Bernard, Fanette ^h, Bordon Cueto De Braem, Victoria ⁱ, Boztug, Kaan ^{j, k, l, m}, Cole, Theresa ⁿ, Gennery, Andrew R. ^{o, p}, Hackett, Scott ^q, Hambleton, Sophie ^{o, p}, Holm, Mette ^r, Kusters, Maaike A. ^b, Klocperk, Adam ^s, Marzollo, Antonio ^t, Marcus, Nufar ^{u, v}, Nademi, Zohreh ^{o, p}, Pachlopnik Schmid, Jana ^{w, x}, Pichler, Herbert ^{j, m}, Sellmer, Anna ^r, Soler-Palacin, Pere ^{y, z, aa}, Soomann, Maarja ^w, Torpiano, Paul ^b, van Montfrans, Joris ^ab, Nierkens, Stefan ^{e, ac}, Adams, Stuart ^f, Buckland, Matthew ^b, Gilmour, Kimberly ^b, Worth, Austen ^b, Thrasher, Adrian J. ^a, Davies, E. Graham ^{a, b}, André, Isabelle ^c, Kreins, Alexandra Y. ^{a, b, ⁎}

Source: In Clinical Immunology May 2025 274

European Society for Immunodeficiencies guidelines for the management of patients with congenital athymia

Authors: Burns, Siobhan O., Carrabba, Maria, Gardulf, Ann, Haerynck, Filomeen, Hauck, Fabian, Jandus, Peter, Meyts, Isabelle, Klocperk, Adam, Neven, Bénédicte, Pac, Malgorzata, Pergent, Martine, Sediva, Anna, Soler-Palacín, Pere, Velcheva, Margarita, Warnatz, Klaus, Kreins, Alexandra Y., Dhalla, Fatima, Flinn, Aisling M., Howley, Evey, Ekwall, Olov, Villa, Anna, Staal, Frank J.T., Anderson, Graham, Gennery, Andrew R., Holländer, Georg A., Davies, E. Graham

Source: In The Journal of Allergy and Clinical Immunology December 2024 154(6):1391-1408

Favipiravir induces HuNoV viral mutagenesis and infectivity loss with clinical improvement in immunocompromised patients

Authors: Kreins, Alexandra Y., Roux, Emma, Pang, Juanita, Cheng, Iek, Charles, Oscar, Roy, Sunando, Mohammed, Reem, Owens, Stephen, Lowe, David M., Brugha, Rossa, Williams, Rachel, Howley, Evey, Best, Timothy, Davies, E. Graham, Worth, Austen, Solas, Caroline, Standing, Joseph F., Goldstein, Richard A., Rocha-Pereira, Joana, Breuer, Judith

Source: In Clinical Immunology February 2024 259

Impact of newborn screening for SCID on the management of congenital athymia

Authors: Howley, Evey, Golwala, Zainab, Buckland, Matthew, Barzaghi, Federica, Ghosh, Sujal, Hackett, Scott, Hague, Rosie, Hauck, Fabian, Holzer, Ursula, Klocperk, Adam, Koskenvuo, Minna, Marcus, Nufar, Marzollo, Antonio, Pac, Malgorzata, Sinclair, Jan, Speckmann, Carsten, Soomann, Maarja, Speirs, Lynne, Suresh, Sneha, Taque, Sophie, van Montfrans, Joris, von Bernuth, Horst, Wainstein, Brynn K., Worth, Austen, Davies, E. Graham, Kreins, Alexandra Y.

Source: In The Journal of Allergy and Clinical Immunology January 2024 153(1):330-334

Expanding the clinical and immunological phenotypes of PAX1-deficient SCID and CID patients

Authors: Yakici, Nalan, Kreins, Alexandra Y., Catak, Mehmet Cihangir, Babayeva, Royala, Erman, Baran, Kenney, Heather, Gungor, Hatice Eke, Cea, Pablo A., Kawai, Tomoki, Bosticardo, Marita, Delmonte, Ottavia Maria, Adams, Stuart, Fan, Yu-Tong, Pala, Francesca, Turkyilmaz, Ayberk, Howley, Evey, Worth, Austen, Kot, Hakan, Sefer, Asena Pinar, Kara, Altan, Bulutoglu, Alper, Bilgic-Eltan, Sevgi, Altunbas, Melek Yorgun, Bayram Catak, Feyza, Karakus, Ibrahim Serhat, Karatay, Emrah, Tekeoglu, Sidem Didar, Eser, Metin, Albayrak, Davut, Citli, Senol, Kiykim, Ayca, Karakoc-Aydiner, Elif, Ozen, Ahmet, Ghosh, Sujal, Gohlke, Holger, Orhan, Fazil, Notarangelo, Luigi D., Davies, E. Graham, Baris, Safa

Source: In Clinical Immunology October 2023 255

European Society for Immunodeficiencies guidelines for the management of patients with congenital athymia.

Authors: Kreins, Alexandra Y., Dhalla, Fatima, Flinn, Aisling M., Howley, Evey, Ekwall, Olov, Villa, Anna, Staal, Frank J.T., Anderson, Graham, Gennery, Andrew R., Holländer, Georg A., Davies, E. Graham

Source: Journal of Allergy & Clinical Immunology; Dec2024, Vol. 154 Issue 6, p1391-1408, 18p

A spatial human thymus cell atlas mapped to a continuous tissue axis.

Authors: Yayon, Nadav, Kedlian, Veronika R., Boehme, Lena, Suo, Chenqu, Wachter, Brianna T., Beuschel, Rebecca T., Amsalem, Oren, Polanski, Krzysztof, Koplev, Simon, Tuck, Elizabeth, Dann, Emma, Van Hulle, Jolien, Perera, Shani, Putteman, Tom, Predeus, Alexander V., Dabrowska, Monika, Richardson, Laura, Tudor, Catherine, Kreins, Alexandra Y., Engelbert, Justin

Source: Nature; Nov2024, Vol. 635 Issue 8039, p708-718, 11p

Combination therapy of favipiravir and nitazoxanide to treat respiratory viral infections in severe T-cell deficient children: A single centre experience

Authors: Arlabosse, Tiphaine, Kreins, Alexandra Y., Ancliff, Philip, Brugha, Rossa, Cheng, Iek Leng, Chiesa, Robert, Indrakumar, Bairavi, Ip, Winnie, Jacobs, Amy I., Lucchini, Giovanna, Marks, Stephen D, Rivers, Elizabeth, Spencer, Helen, Worth, Austen, Kadambari, Seilesh, Breuer, Judith

Source: In Journal of Infection December 2024 89(6)

Novel antivirals for severe enterovirus infection in immunocompromised hosts; A case series

Authors: Meinhardt, Andrea, Reilly, Liam, Kaliakatsos, Marios, Abdel-Aziz, Khaled, Alsharidah, Sondus, Bodi, Istvan, Booth, Claire, Chetty, Kritika, Evans, Jennifer, Ferreras-Antolín, Laura, Froude, Susannah, Galtrey, Clare M., Guruprasad, Suba, Hadden, Robert D., Hassell, Jane, Hyöty, Heikki, Kreins, Alexandra Y., Laiho, Jutta E., Lowe, David M., Lunn, Michael P., Mankad, Kshitij, Struik, Siske, Whittaker, Elizabeth, Worth, Austen, Yong, Patrick, Zhang, Liqun, Breuer, Judith, Kadambari, Seilesh

Source: In Journal of Infection May 2024 88(5)

Parental Engagement in Identifying Information Needs After Newborn Screening for Families of Infants with Suspected Athymia.

Authors: Howley, Evey, Soomann, Maarja, Kreins, Alexandra Y.

Source: Journal of Clinical Immunology; Mar2024, Vol. 44 Issue 3, p1-10, 10p

Corrigendum to “Expanding the clinical and immunological phenotypes of PAX1-deficient SCID and CID patients” [Clinical Immunology 255 (2023) 109757]

Authors: Yakici, Nalan, Kreins, Alexandra Y., Catak, Mehmet Cihangir, Babayeva, Royala, Erman, Baran, Kenney, Heather, Eke-Gungor, Hatice, Cea, Pablo A., Kawai, Tomoki, Bosticardo, Marita, Delmonte, Ottavia Maria, Adams, Stuart, Fan, Yu-Tong, Pala, Francesca, Turkyilmaz, Ayberk, Howley, Evey, Worth, Austen, Kot, Hakan, Sefer, Asena Pinar, Kara, Altan, Bulutoglu, Alper, Bilgic-Eltan, Sevgi, Yorgun Altunbas, Melek, Bayram Catak, Feyza, Karakus, Ibrahim Serhat, Karatay, Emrah, Tekeoglu, Sidem Didar, Eser, Metin, Albayrak, Davut, Citli, Senol, Kiykim, Ayca, Karakoc-Aydiner, Elif, Ozen, Ahmet, Ghosh, Sujal, Gohlke, Holger, Orhan, Fazil, Notarangelo, Luigi D., Davies, E. Graham, Baris, Safa

Source: In Clinical Immunology November 2023 256

Inborn errors of thymic stromal cell development and function.

Authors: Kreins, Alexandra Y.^1,2 (AUTHOR), Maio, Stefano³ (AUTHOR), Dhalla, Fatima^3,4 (AUTHOR) fatima.dhalla@paediatrics.ox.ac.uk

Source: Seminars in Immunopathology. Feb2021, Vol. 43 Issue 1, p85-100. 16p.

Subject Terms: *STROMAL cells, *CELL physiology, *EPITHELIAL cells, *T cells, *EMBRYOLOGY

Partial IFN-γR2 deficiency is due to protein misfolding and can be rescued by inhibitors of glycosylation

Authors: Moncada-Vélez, Marcela, Martinez-Barricarte, Rubén, Bogunovic, Dusan, Kong, Xiao-Fei, Blancas-Galicia, Lizbeth, Tirpan, Cengiz, Aksu, Guzide, Vincent, Quentin B., Boisson, Bertrand, Itan, Yuval, Ramírez-Alejo, Noé, Okada, Satoshi, Kreins, Alexandra Y., Bryant, Vanessa L., Franco, Jose Luis, Migaud, Mélanie, Espinosa-Padilla, Sara, Yamazaki-Nakashimada, Marco, Espinosa-Rosales, Francisco, Kutukculer, Necil, Abel, Laurent, Bustamante, Jacinta, Vogt, Guillaume, Casanova, Jean-Laurent ^*, Boisson-Dupuis, Stéphanie ^*

Source: In Blood 3 October 2013 122(14):2390-2401

Simultaneous quantitation of favipiravir and its hydroxide metabolite in human plasma and hamster matrices using a UPLC–MS/MS method.

Authors: Bekegnran, Cesar P., Driouich, Jean‐Selim, Breuer, Judith, Barthelemy, Karine, Giocanti, Madeleine, de Lamballerie, Xavier, Kreins, Alexandra Y., Nougairede, Antoine, Solas, Caroline

Source: Biomedical Chromatography; Sep2023, Vol. 37 Issue 9, p1-10, 10p

First Use of Thymus Transplantation in PAX1 Deficiency.

Authors: Kreins, Alexandra Y.^1,2 (AUTHOR) a.kreins@ucl.ac.uk, Worth, Austen² (AUTHOR), Ghosh, Sujal³ (AUTHOR), Mohammed, Reem W.⁴ (AUTHOR), Davies, E. Graham^1,2 (AUTHOR)

Source: Journal of Clinical Immunology. Aug2023, Vol. 43 Issue 6, p1127-1130. 4p.

Subject Terms: *SEVERE combined immunodeficiency, *THYMUS tumors, *STEM cell transplantation, *HOMOGRAFTS, *THYMUS, *INDUCED pluripotent stem cells

A Patient with Tyrosine Kinase 2 Deficiency without Hyper-IgE Syndrome

Authors: Kilic, Sara S., Hacimustafaoglu, Mustafa, Boisson-Dupuis, Stéphanie, Kreins, Alexandra Y., Grant, Audrey V., Abel, Laurent, Casanova, Jean-Laurent

Source: In The Journal of Pediatrics June 2012 160(6):1055-1057

Functional STAT3 deficiency compromises the generation of human T follicular helper cells

Authors: Ma, Cindy S., Avery, Danielle T., Chan, Anna, Batten, Marcel, Bustamante, Jacinta, Boisson-Dupuis, Stephanie, Arkwright, Peter D., Kreins, Alexandra Y., Averbuch, Diana, Engelhard, Dan, Magdorf, Klaus, Kilic, Sara S., Minegishi, Yoshiyuki, Nonoyama, Shigeaki, French, Martyn A., Choo, Sharon, Smart, Joanne M., Peake, Jane, Wong, Melanie, Gray, Paul, Cook, Matthew C., Fulcher, David A., Casanova, Jean-Laurent, Deenick, Elissa K., Tangye, Stuart G.

Source: In Blood 26 April 2012 119(17):3997-4008

Congenital Athymia: Unmet Needs and Practical Guidance.

Authors: Howley, Evey, Davies, E Graham, Kreins, Alexandra Y

Source: Therapeutics & Clinical Risk Management; Mar2023, Vol. 19, p239-254, 16p

Subject Terms: SEVERE combined immunodeficiency, MEDICAL care, DELAYED diagnosis, ACADEMIC medical centers, PATIENTS, MEDICAL research

Company/Entity: DUKE University Hospital