tbuckley/cabot-search huggingface dataset:
dStripe: Slice artefact correction in diffusion MRI via constrained neural network
Authors: Maximilian Pietsch, Daan Christiaens, Joseph V Hajnal, J-Donald Tournier
Journal: Medical Image Analysis (2021)

MRI scanner and sequence imperfections and advances in reconstruction and imaging techniques to increase motion robustness can lead to inter-slice intensity variations in Echo Planar Imaging. Leveraging deep convolutional neural networks as universal image filters, we present a data-driven method for the correction of acquisition artefacts that manifest as inter-slice inconsistencies, regardless of their origin. This technique can be applied to motion- and dropout-artefacted data by embedding it in a reconstruction pipeline. The network is trained in the absence of ground-truth data on, and finally applied to, the reconstructed multi-shell high angular resolution diffusion imaging signal to produce a corrective slice intensity modulation field. This correction can be performed in either motion-corrected or scattered source-space. We focus on gaining control over the learned filter and the image data consistency via built-in spatial frequency and intensity constraints. The end product is a corrected image reconstructed from the original raw data, modulated by a multiplicative field that can be inspected and verified to match the expected features of the artefact. In-plane, the correction approximately preserves the contrast of the diffusion signal and throughout the image series, it reduces inter-slice inconsistencies within and across subjects without biasing the data. We apply our pipeline to enhance the super-resolution reconstruction of neonatal multi-shell high angular resolution data as acquired in the developing Human Connectome Project.
52P Assessment of futibatinib exposure–response (E–R) relationships in patients with advanced solid tumors, including cholangiocarcinoma (CCA)
Authors: A. Hollebecque, J.A. Bridgewater, F. Meric-Bernstam, L. Goyal, H-T. Arkenau, I. Yamamiya, F. Yamashita, K. Li, V. Wacheck, T. Doi
Journal: Annals of Oncology (2021)
369P Characterization of the inflammatory tumor microenvironment composition in brain metastases after failure of immune checkpoint inhibitor therapy
Authors: A.M. Starzer, M. Kleinberger, K. Feldmann, J. Kreminger, S. Traint, A. Steindl, G. Widhalm, B. Gatterbauer, K. Dieckmann, M. Preusser, A.S. Berghoff
Journal: Annals of Oncology (2021)
1323P Immunotherapy for PDL1-high (TPS≥50%) metastatic NSCLC: Results in real-world oncology practice
Authors: D. Srdic, L. Bitar, F. Seiwerth, N. Nikolac Gabaj, A. Marusic, L. Batelja Vuletic, S. Badovinac, S. Plestina, M. Samarzija, M. Jakopovic
Journal: Annals of Oncology (2021)
679P Final results on efficacy and patient reported outcomes (PRO) of a randomized phase II trial investigating nivolumab switch-maintenance after TKI induction in metastatic clear cell renal cell carcinoma (mRCC) patients (NIVOSWITCH)
Authors: C. Darr, S. Zschäbitz, P. Ivanyi, M. Wirth, P. Staib, M. Schostak, L. Müller, M. Metz, L. Bergmann, T. Steiner, A. Lorch, P. Schütt, M-R. Rafiyan, E. Hellmis, A. Hinke, M. Mänz, J. Meiler, T. Kretz, A. Flörcken, V. Grünwald
Journal: Annals of Oncology (2021)
Bioinspired Artificial Liver System with hiPSC‐Derived Hepatocytes for Acute Liver Failure Treatment
Authors: Jinglin Wang, Haozhen Ren, Yuxiao Liu, Lingyu Sun, Zhuohao Zhang, Yuanjin Zhao, Xiaolei Shi
Journal: Advanced Healthcare Materials (2021)

Abstract Bioartificial liver (BAL) system has become a promising alternative to traditional liver transplantation in rescuing acute liver failure (ALF) patients. Herein, inspired by natural microstructure of hepatic lobules, a novel biomimetic bioartificial liver system (BBALS) is developed by integrating human induced pluripotent stem cell‐derived hepatocytes (hiPSC‐Heps) ‐laden microparticles and semipermeable microtubes into a microfluidic platform. As the working units are hepatic lobules‐like semipermeable microtubes surrounding with serum‐free suspension differentiated hiPSC‐Heps microcarriers, the BBALS is endowed with functional cell aggregates and effective circulation system. Thus, the BBALS possesses high cell viability, favorable function regeneration, and effective substances exchange. Based on these features, a 3D liver chip with multiple parallel BBALS units is created for filtering the plasma of ALF rabbits, which validates the research significance and application potential of the proposed BBALS. Moreover, the novel integrated BBALS is applied to treat ALF rabbits and shows great advantages in increasing survival, generating serum proteins, and decreasing inflammation. These properties point to the broad prospects of BBALS in treating related diseases and improving traditional clinical methods.
1499P Health-related quality of life in stage III melanoma patients treated with neoadjuvant ipilimumab and nivolumab: Week 60 update of the PRADO trial
Authors: N.M.J. Van Den Heuvel, I.L.M. Reijers, J.M. Versluis, E.A. Rozeman, R.P.M. Saw, K.H. Blommers, K. Józwiak, K. Suijkerbuijk, E. Kapiteijn, A.A.M. Van der Veldt, G.A. Hospers, A.J. Spillane, T.E. Pennington, M.W.J.M. Wouters, A.M. Menzies, A.C.J. van Akkooi, L.V. Van De Poll-Franse, G.V. Long, C.U. Blank, A.H. Boekhout
Journal: Annals of Oncology (2021)
The TGFβ/Notch axis facilitates Müller cell-to-epithelial transition to ultimately form a chronic glial scar
Authors: Federica Maria Conedera, Ana Maria Quintela Pousa, Nadia Mercader, Markus Tschopp, Volker Enzmann
Journal: Molecular Neurodegeneration (2021)

Contrasting with zebrafish, retinal regeneration from Müller cells (MCs) is largely limited in mammals, where they undergo reactive gliosis that consist of a hypertrophic response and ultimately results in vision loss. Transforming growth factor β (TGFβ) is essential for wound healing, including both scar formation and regeneration. However, targeting TGFβ may affect other physiological mechanisms, owing its pleiotropic nature. The regulation of various cellular activities by TGFβ relies on its interaction with other pathways including Notch. Here, we explore the interplay of TGFβ with Notch and how this regulates MC response to injury in zebrafish and mice. Furthermore, we aimed to characterize potential similarities between murine and human MCs during chronic reactive gliosis.Focal damage to photoreceptors was induced with a 532 nm diode laser in TgBAC (gfap:gfap-GFP) zebrafish (ZF) and B6-Tg (Rlbp1-GFP) mice. Transcriptomics, immunofluorescence, and flow cytometry were employed for a comparative analysis of MC response to laser-induced injury between ZF and mouse. The laser-induced injury was paired with pharmacological treatments to inhibit either Notch (DAPT) or TGFβ (Pirfenidone) or TGFβ/Notch interplay (SIS3). To determine if the murine laser-induced injury model translates to the human system, we compared the ensuing MC response to human donors with early retinal degeneration.Investigations into injury-induced changes in murine MCs revealed TGFβ/Notch interplay during reactive gliosis. We found that TGFβ1/2 and Notch1/2 interact via Smad3 to reprogram murine MCs towards an epithelial lineage and ultimately to form a glial scar. Similar to what we observed in mice, we confirmed the epithelial phenotype of human Müller cells during gliotic response.The study indicates a pivotal role for TGFβ/Notch interplay in tuning MC stemness during injury response and provides novel insights into the remodeling mechanism during retinal degenerative diseases.
1348P Long-term survival and health-related quality of life with nivolumab for previously-treated advanced non-small cell lung cancer (NSCLC): A wide prospective French real-world study (EVIDENS)
Authors: F. Barlesi, A. Dixmier, D. Debieuvre, C. Raspaud, J.B. Auliac, B. Nicolas, P. Bombaron, D. Moro-Sibilot, C. Audigier-Valette, B. Asselain, J. Dumanoir, F-E. Cotté, V. Allan, C. Calvet, D. Reynaud, M. Pérol
Journal: Annals of Oncology (2021)
LBA58 Results of the randomized, placebo (PL)-controlled phase II study evaluating the efficacy and safety of regorafenib (REGO) in patients (pts) with relapsed advanced or metastatic chordoma, on behalf of the French Sarcoma Group (FSG) and Unicancer
Authors: F. Duffaud, S. Chabaud, C.M. Chevreau, A. Italiano, C. Perrin, N. Isambert, S. Piperno-Neumann, E. Saada-Bouzid, F. Bertucci, D. Cupissol, E. Kalbacher, B. Narciso, C. Schiffler, N. de Sousa Carvalho, L. Monard, C. Bouvier, V. Vidal, J-Y. Blay, O. Mir
Journal: Annals of Oncology (2021)
Inhibition of phosphodiesterase type 9 reduces obesity and cardiometabolic syndrome in mice
Authors: Sumita Mishra, Nandhini Sadagopan, Brittany Dunkerly-Eyring, Susana Rodriguez, Dylan C. Sarver, Ryan P. Ceddia, Sean A. Murphy, Hildur Knutsdottir, Vivek P. Jani, Deepthi Ashok, Christian U. Oeing, Brian O’Rourke, Jon A. Gangoiti, Dorothy D. Sears, G. William Wong, Sheila Collins, David A. Kass
Journal: Journal of Clinical Investigation (2021)

Central obesity with cardiometabolic syndrome (CMS) is a major global contributor to human disease, and effective therapies are needed. Here, we show that cyclic GMP-selective phosphodiesterase 9A inhibition (PDE9-I) in both male and ovariectomized female mice suppresses preestablished severe diet-induced obesity/CMS with or without superimposed mild cardiac pressure load. PDE9-I reduces total body, inguinal, hepatic, and myocardial fat; stimulates mitochondrial activity in brown and white fat; and improves CMS, without significantly altering activity or food intake. PDE9 localized at mitochondria, and its inhibition in vitro stimulated lipolysis in a PPARα-dependent manner and increased mitochondrial respiration in both adipocytes and myocytes. PPARα upregulation was required to achieve the lipolytic, antiobesity, and metabolic effects of PDE9-I. All these PDE9-I-induced changes were not observed in obese/CMS nonovariectomized females, indicating a strong sexual dimorphism. We found that PPARα chromatin binding was reoriented away from fat metabolism-regulating genes when stimulated in the presence of coactivated estrogen receptor-α, and this may underlie the dimorphism. These findings have translational relevance given that PDE9-I is already being studied in humans for indications including heart failure, and efficacy against obesity/CMS would enhance its therapeutic utility.
Acute Peritoneal Dialysis with Percutaneous Catheter Insertion for COVID-19-Associated AKI in Intensive Care: Experience from a UK Tertiary Centre
Authors: Dandisonba B. Braide-Azikiwe, Elaine Bowes, Kate Bramham, Caroline Tulley, Eirini Lioudaki, Hugh Cairns, Claire C. Sharpe
Journal: Journal of the American Society of Nephrology (2020)

Braide-Azikiwe, Dandisonba B.; Bowes, Elaine; Bramham, Kate; Tulley, Caroline; Lioudaki, Eirini; Cairns, Hugh; Sharpe, Claire C. Author Information
1166P Determinants of clinical and pathological stage discordance in resected NSCLC patients: A retrospective observational cohort study
Authors: E. Samuel, C. Thomas, C. Thompson, E. Paul, S.A. Scholz, L. Zhang, J.K. Grewal, J.D. Cox, C. Yu, G. Adabi, J. Taverner, J.R. Zalcberg, R.G. Stirling
Journal: Annals of Oncology (2021)
The expansion of human T-bet <sup>high</sup> CD21 <sup>low</sup> B cells is T cell dependent
Authors: Baerbel Keller, Valentina Strohmeier, Ina Harder, Susanne Unger, Kathryn J. Payne, Geoffroy Andrieux, Melanie Boerries, Peter Tobias Felixberger, Jonathan J. M. Landry, Alexandra Nieters, Anne Rensing-Ehl, Ulrich Salzer, Natalie Frede, Susanne Usadel, Roland Elling, Carsten Speckmann, Ina Hainmann, Elizabeth Ralph, Kimberly Gilmour, Marjolein W. J. Wentink, Mirjam van der Burg, Hye Sun Kuehn, Sergio D. Rosenzweig, Uwe Kölsch, Horst von Bernuth, Petra Kaiser-Labusch, Florian Gothe, Sophie Hambleton, Alexandru Daniel Vlagea, Ana Garcia Garcia, Laia Alsina, Gašper Markelj, Tadej Avcin, Julia Vasconcelos, Margarida Guedes, Jing-Ya Ding, Cheng-Lung Ku, Bella Shadur, Danielle T. Avery, Nils Venhoff, Jens Thiel, Heiko Becker, Lucía Erazo-Borrás, Claudia Milena Trujillo-Vargas, José Luis Franco, Claire Fieschi, Satoshi Okada, Paul E. Gray, Gulbu Uzel, Jean-Laurent Casanova, Manfred Fliegauf, Bodo Grimbacher, Hermann Eibel, Stephan Ehl, Reinhard E. Voll, Marta Rizzi, Polina Stepensky, Vladimir Benes, Cindy S. Ma, Claudia Bossen, Stuart G. Tangye, Klaus Warnatz
Journal: Science Immunology (2021)

T cell–derived IFNγ and CD40L/IL-21R signals are crucial for the differentiation of human T-bet high CD21 low B cells.
LBA37 IMMUTACE: A biomarker-orientated, multi center phase II AIO study of transarterial chemoembolization (TACE) in combination with nivolumab performed for intermediate stage hepatocellular carcinoma (HCC)
Authors: A. Vogel, A. Saborowski, J. Hinrichs, T.J. Ettrich, U. Ehmer, U.M. Martens, A. Mekolli, E. De Toni, T. Berg, M. Geißler, M. Maenz, M. Kirstein, D. Waldschmidt
Journal: Annals of Oncology (2021)
469P Potential emergent role of liquid biopsy in clinical practice in metastatic colorectal cancer (mCRC) treatment
Authors: V. Zurlo, D. Lucchetti, F. Colella, C. Ricciardi Tenore, M. Di Salvatore, R. De Maria, M. Basso, A. Cassano, F. Giuliante, M. Vellone, G. Tortora, A. Sgambato
Journal: Annals of Oncology (2021)
1630P The impact of the COVID-19 outbreak on surgical site infections in elective colorectal cancer surgery: One potential benefit of the pandemic?
Authors: F. Mulita, E. Liolis, L. Tchabashvili, M. Vailas, K. Akinosoglou, S. Assimakopoulos, I. Maroulis, G. Panos
Journal: Annals of Oncology (2021)
Spred1 deficit promotes treatment resistance and transformation of chronic phase CML
Authors: Junjing Qiao, Chen Liang, Dandan Zhao, Le Xuan Truong Nguyen, Fang Chen, Shanshan Suo, Dinh Hoa Hoang, Francesca Pellicano, Ivan Rodriguez Rodriguez, Yasmin Elhajmoussa, Lucy Ghoda, Akihiko Yoshimura, Anthony S. Stein, Haris Ali, Paul Koller, Danilo Perrotti, Mhairi Copland, Anjia Han, Bin Zhang, Guido Marcucci
Journal: Leukemia (2021)
Brief homogeneous TCR signals instruct common iNKT progenitors whose effector diversification is characterized by subsequent cytokine signaling
Authors: Sabrina Bortoluzzi, Nyambayar Dashtsoodol, Thomas Engleitner, Christoph Drees, Sabine Helmrath, Jonas Mir, Albulena Toska, Michael Flossdorf, Rupert Öllinger, Maria Solovey, Maria Colomé-Tatché, Bahire Kalfaoglu, Masahiro Ono, Thorsten Buch, Tim Ammon, Roland Rad, Marc Schmidt-Supprian
Journal: Immunity (2021)
Initial Formation of the Skin Layer of PLGA Microparticles
Authors: Farrokh Sharifi, Andrew Otte, Kinam Park
Journal: Advanced Healthcare Materials (2021)

Poly(lactide-co-glycolide) (PLGA) has been extensively used in making long-acting injectable formulations. The critical factors affecting the PLGA formulation properties have been adjusted to control the drug release kinetics and obtain desirable properties of PLGA-based drug delivery systems. The PLGA microparticle formation begins as soon as the drug/PLGA-dissolved in the organic solvent phase (oil phase) is exposed to the water phase. The initial skin (or shell) formation on the oil droplets occurs very quickly, sometimes in the matter of milliseconds, and studying the process has been difficult. The skin formation on the PLGA emulsion droplet surface that can affect the subsequent hardening steps is examined. PLGA droplets with different compositions are prepared. Using collimated light and a high-speed camera made it possible to detect the diffusion of acetonitrile from the oil phase into the water phase during the oil droplet formation. Although the skin formation is not visible on the surface of the oil phase droplet with the current setup, the droplet shapes, solid strand formation, and the difference in the spreading time suggest that the initial contact time between the oil and water phases in the range of a few seconds is critical to the properties of the skin.
433P Durvalumab and tremelimumab in combination with FOLFOX in patients with previously untreated RAS-mutated metastatic colorectal cancer: First results of efficacy at one year for phase II MEDITREME trial
Authors: J-D. Fumet, B. Chibaudel, J. Bennouna, C. Borg, J. Martin-Babau, R. Cohen, M. Fonck, J. Taieb, M. Thibaudin, E. Limagne, J. Blanc, A. Bertaut, F. Ghiringhelli
Journal: Annals of Oncology (2021)
Nivolumab in Combination with Stereotactic Body Radiotherapy in Pretreated Patients with Metastatic Renal Cell Carcinoma. Results of the Phase II NIVES Study
Authors: Cristina Masini, Cinzia Iotti, Ugo De Giorgi, Roberto Salvatore Bellia, Sebastiano Buti, Francesco Salaroli, Ilaria Zampiva, Renzo Mazzarotto, Claudia Mucciarini, Maria Giuseppa Vitale, Alessio Bruni, Frank Lohr, Giuseppe Procopio, Orazio Caffo, Franco Nole, Franco Morelli, Susanne Baier, Consuelo Buttigliero, Patrizia Ciammella, Giorgia Timon, Emanuela Fantinel, Gabriele Carlinfante, Annalisa Berselli, Carmine Pinto
Journal: European Urology (2021)
1291P A phase II study of nivolumab rechallenge therapy in advanced NSCLC patients who responded to prior anti-PD-1/L1 inhibitors: West Japan Oncology Group 9616L
Authors: S. Teraoka, H. Akamatsu, S. Takamori, H. Hayashi, S. Miura, A. Hata, Y. Toi, Y. Shiraishi, N. Mamesaya, Y. Sato, N. Furuya, Y. Koh, T. Yamanaka, N. Yamamoto, K. Nakagawa
Journal: Annals of Oncology (2021)
COVID-19 and metabolic disease: mechanisms and clinical management
Authors: Charlotte Steenblock, Peter E H Schwarz, Barbara Ludwig, Andreas Linkermann, Paul Zimmet, Konstantin Kulebyakin, Vsevolod A Tkachuk, Alexander G Markov, Hendrik Lehnert, Martin Hrabě de Angelis, Hannes Rietzsch, Roman N Rodionov, Kamlesh Khunti, David Hopkins, Andreas L Birkenfeld, Bernhard Boehm, Richard I G Holt, Jay S Skyler, J Hans DeVries, Eric Renard, Robert H Eckel, K George M M Alberti, Bruno Geloneze, Juliana C Chan, Jean Claude Mbanya, Henry C Onyegbutulem, Ambady Ramachandran, Abdul Basit, Mohamed Hassanein, Gavin Bewick, Giatgen A Spinas, Felix Beuschlein, Rüdiger Landgraf, Francesco Rubino, Geltrude Mingrone, Stefan R Bornstein
Journal: The Lancet Diabetes & Endocrinology (2021)
Tonsil-derived mesenchymal stem cells incorporated in reactive oxygen species-releasing hydrogel promote bone formation by increasing the translocation of cell surface GRP78
Authors: Da Hyeon Choi, Kyeong Eun Lee, Se-Young Oh, Si Min Lee, Beom Soo Jo, Jue-Yeon Lee, Jong-Chul Park, Yoon Jeong Park, Ki Dong Park, Inho Jo, Yoon Shin Park
Journal: Biomaterials (2021)

Controlling the senescence of mesenchymal stem cells (MSCs) is essential for improving the efficacy of MSC-based therapies. Here, a model of MSC senescence was established by replicative subculture in tonsil-derived MSCs (TMSCs) using senescence-associated β-galactosidase, telomere-length related genes, stemness, and mitochondrial metabolism. Using transcriptomic and proteomic analyses, we identified glucose-regulated protein 78 (GRP78) as a unique MSC senescence marker. With increasing cell passage number, GRP78 gradually translocated from the cell surface and cytosol to the (peri)nuclear region of TMSCs. A gelatin-based hydrogel releasing a sustained, low level of reactive oxygen species (ROS-hydrogel) was used to improve TMSC quiescence and self-renewal. TMSCs expressing cell surface-specific GRP78 (csGRP78+), collected by magnetic sorting, showed better stem cell function and higher mitochondrial metabolism than unsorted cells. Implantation of csGRP78+ cells embedded in ROS-hydrogel in rats with calvarial defects resulted in increased bone regeneration. Thus, csGRP78 is a promising biomarker of senescent TMSCs, and the combined use of csGRP78+ cells and ROS-hydrogel improved the regenerative capacity of TMSCs by regulating GRP78 translocation.
A Prevascularized Polyurethane‐Reinforced Fibrin Patch Improves Regenerative Remodeling in a Rat Right Ventricle Replacement Model
Authors: Ze‐Wei Tao, Dillon K. Jarrell, Andrew Robinson, Elizabeth M. Cosgriff‐Hernandez, Jeffrey G. Jacot
Journal: Advanced Healthcare Materials (2021)

Abstract Congenital heart defects (CHDs) affect 1 in 120 newborns in the United States. Surgical repair of structural heart defects often leads to arrhythmia and increased risk of heart failure. The laboratory has previously developed an acellular fibrin patch reinforced with a biodegradable poly(ether ester urethane) urea mesh that result in improved heart function when tested in a rat right ventricle wall replacement model compared to fixed pericardium. However, this patch does not drive significant neotissue formation. The patch materials are modified here and this patch is prevascularized with human umbilical vein endothelial cells and c‐Kit + human amniotic fluid stem cells. Rudimentary capillary‐like networks form in the fibrin after culture of cell‐encapsulated patches for 3 d in vitro. Prevascularized patches and noncell loaded patch controls are implanted onto full‐thickness heart wall defects created in the right ventricle of athymic nude rats. Two months after surgery, defect repair with prevascularized patches results in improved heart function and the patched heart area exhibited greater vascularization and muscularization, less fibrosis, and increased M2 macrophage infiltration compared to acellular patches.
952P Prognostic implication of serum alpha-fetoprotein in patients with unresectable hepatocellular carcinoma treated with regorafenib
Authors: D-H. Lim, A. Casadei-Gardini, M.A. Lee, S. Lonardi, J.W. Kim, G. Masi, H.J. Chon, M. Rimini, I. Kim, J. Cheon, J-E. Hwang, J.H. Kang, H.Y. Lim, C. Yoo
Journal: Annals of Oncology (2021)
550P Initial results of a phase Ia/Ib study of NGM120, a first-in-class anti-GDNF family receptor alpha like (GFRAL) antibody in patients (pts) with advanced solid tumors
Authors: R. Jain, E.J. Kim, H-J. Lenz, W.A. Messersmith, V.J. Picozzi, M.S. Beg, B.A. Weinberg, D. Mahalingam, C. Tran-Muchowski, N. Yuan, J. Lichtman, C. Chen, L. McDonald, A. DePaoli, J. Zha, A.E. Hendifar
Journal: Annals of Oncology (2021)