tbuckley/cabot-search huggingface dataset:
Changes in gut microbial metagenomic pathways associated with clinical outcomes after the elimination of malabsorbed sugars in an IBS cohort
Authors: A. Mack, J.S. Bobardt, A. Haß, K.B. Nichols, R.M. Schmid, C.K. Stein-Thoeringer
Journal: Gut Microbes (2019)

Specific diets to manage sugar malabsorption are reported to reduce clinical symptoms of irritable bowel syndrome (IBS). However, the effects of diets for malabsorbed sugars on gut microbiota signatures have not been studied, and associations with clinical outcomes in IBS have not been characterized. 22 IBS patients positively tested for either lactose-, fructose-, sorbitol- or combined malabsorptions were subjected to 2-weeks sugar elimination and subsequent 4-weeks re-introduction. 7 IBS patients tested negative for sugar malabsorption were used as controls. Nutrition and clinical symptoms were recorded throughout the study. Fecal samples were serially collected for 16S rRNA amplicon and shotgun-metagenome sequencing.Dietary intervention supervised by nutrition counseling reduced IBS symptoms during the elimination and tolerance phases. Varying clinical response rates were observed between subjects, and used to dichotomize our cohort into visual analogue scale (VAS) responders and non-responders. Alpha -and beta-diversity analyzes revealed only minor differences regarding 16S rRNA-based fecal microbiota compositions between responder and non-responder patients during baseline or tolerance phase. In shotgun-metagenome analyzes, however, we analyzed microbial metabolic pathways and found significant differences in pathways encoding starch degradation and complex amino acid biosynthesis at baseline between IBS controls and malabsorbers, and notably, between diet responder and non-responders. Faecalibacterium prausnitzii, Ruminococcus spp. and Bifidobacterium longum largely informed these metabolic pathways.Our study demonstrates that diet interventions for specific, malabsorbed carbohydrates reshaped the metagenomic composition of the gut microbiota, with a small community of bacterial taxa contributing to these changes rather than a single species.
Protein Kinase CK2 Is Associated with Poor Clinical Outcome and Regulates the Expression of Anti-Apoptotic Proteins and PTEN Phosphorylation in Acute Myeloid Leukemia.
Authors: June-Won Cheong, Ju In Eom, Jin Koo Lee, Sun Young Park, Yuri Kim, In Hae Park, Jin Seok Kim, Yoo-Hong Min
Journal: Blood (2005)
Features of Chromosomal Karyotype in 351 Chinese Adult Patients with Primary Myelodysplastic Syndromes: A Retrospective Analysis from a Single Institution
Authors: Lin Li, Xuping Liu, Ling Nie, Shihe Liu, Minghua Yu, Yue Zhang, Tiejun Qin, Jianxiang Wang, Zhijian Xiao
Journal: Blood (2008)
Multi-Institutional Validation of Deep Learning for Pretreatment Identification of Extranodal Extension in Head and Neck Squamous Cell Carcinoma
Authors: Benjamin H. Kann, Daniel F. Hicks, Sam Payabvash, Amit Mahajan, Justin Du, Vishal Gupta, Henry S. Park, James B. Yu, Wendell G. Yarbrough, Barbara A. Burtness, Zain A. Husain, Sanjay Aneja
Journal: Journal of Clinical Oncology (2019)

Extranodal extension (ENE) is a well-established poor prognosticator and an indication for adjuvant treatment escalation in patients with head and neck squamous cell carcinoma (HNSCC). Identification of ENE on pretreatment imaging represents a diagnostic challenge that limits its clinical utility. We previously developed a deep learning algorithm that identifies ENE on pretreatment computed tomography (CT) imaging in patients with HNSCC. We sought to validate our algorithm performance for patients from a diverse set of institutions and compare its diagnostic ability to that of expert diagnosticians.We obtained preoperative, contrast-enhanced CT scans and corresponding pathology results from two external data sets of patients with HNSCC: an external institution and The Cancer Genome Atlas (TCGA) HNSCC imaging data. Lymph nodes were segmented and annotated as ENE-positive or ENE-negative on the basis of pathologic confirmation. Deep learning algorithm performance was evaluated and compared directly to two board-certified neuroradiologists.A total of 200 lymph nodes were examined in the external validation data sets. For lymph nodes from the external institution, the algorithm achieved an area under the receiver operating characteristic curve (AUC) of 0.84 (83.1% accuracy), outperforming radiologists' AUCs of 0.70 and 0.71 (P = .02 and P = .01). Similarly, for lymph nodes from the TCGA, the algorithm achieved an AUC of 0.90 (88.6% accuracy), outperforming radiologist AUCs of 0.60 and 0.82 (P < .0001 and P = .16). Radiologist diagnostic accuracy improved when receiving deep learning assistance.Deep learning successfully identified ENE on pretreatment imaging across multiple institutions, exceeding the diagnostic ability of radiologists with specialized head and neck experience. Our findings suggest that deep learning has utility in the identification of ENE in patients with HNSCC and has the potential to be integrated into clinical decision making.
Less invasive ventricular reconstruction for ischaemic heart failure
Authors: Patrick Klein, Stefan D. Anker, Andrew Wechsler, Ivo Skalsky, Petr Neuzil, Lon S. Annest, Mauro Bifi, Theresa McDonagh, Christian Frerker, Tobias Schmidt, Horst Sievert, Anthony N. Demaria, Sebastian Kelle
Journal: European Journal of Heart Failure (2019)

ABSTRACT Aims Surgical ventricular reconstruction to remodel, reshape, and reduce ventricular volume is an effective therapy in selected patients with chronic heart failure (HF) of ischaemic aetiology. The BioVentrix Revivent TC System offers efficacy comparable to conventional surgical ventricular reconstruction and is less invasive utilizing micro‐anchor pairs to exclude scarred myocardium on the beating heart. Here, we present 12‐months follow‐up data of an international multicenter study. Methods and results Patients were considered eligible for the procedure when they presented with symptomatic HF [New York Heart Association (NYHA) class ≥II], left ventricular (LV) dilatation and dysfunction caused by myocardial infarction, and akinetic and/or dyskinetic transmural scarred myocardium located in the anteroseptal, anterolateral, and/or apical regions. A total of 89 patients were enrolled and 86 patients were successfully treated (97%). At 12 months, a significant improvement in LV ejection fraction (29 ± 8% vs. 34 ± 9%, P &lt; 0.005) and a reduction of LV volumes was observed (LV end‐systolic and end‐diastolic volume index both decreased: 74 ± 28 mL/m 2 vs. 54 ± 23 mL/m 2 , P &lt; 0.001; and 106 ± 33 mL/m 2 vs. 80 ± 26 mL/m 2 , respectively, P &lt; 0.0001). Four patients (4.5%) died in hospital and survival at 12 months was 90.6%. At baseline, 59% of HF patients were in NYHA class III compared with 22% at 12‐month follow‐up. Improvements in quality of life measures (Minnesota Living with Heart Failure Questionnaire 39 vs. 26 points, P &lt; 0.001) and 6‐min walking test distance (363 m vs. 416 m, P = &lt;0.001) were also significant. Conclusions Treatment with the Revivent TC System in patients with symptomatic HF results in significant and sustained reduction of LV volumes and improvement of LV function, symptoms, and quality of life.
Stage-specific prognostic value of molecular markers in colon cancer: Results of the translational study on the PETACC 3-EORTC 40993-SAKK 60–00 trial
Authors: A. D. Roth, S. Tejpar, P. Yan, R. Fiocca, D. Dietrich, M. Delorenzi, R. Labianca, D. Cunningham, E. Van Cutsem, F. Bosman
Journal: Journal of Clinical Oncology (2009)

4002 Background: We compared the incidence of molecular markers in stage II (SII) and III (SIII) colon cancer and tested their prognostic value per stage, using PETACC 3, an adjuvant trial with 3,278 patients. We included expression of P53, SMAD4, thymidylate synthetase (TS) and hTERT, mutations of KRAS and BRAF, microsatellite instability (MSI) and 18qLOH. Methods: 1,564 formalin fixed paraffin embedded tissue blocks were prospectively collected and DNA from normal and tumor tissue was extracted after macrodissection. High P53, TS and hTERT expression and SMAD4 loss were assessed by immunohistochemistry. MSI was studied with 10 markers. KRAS exon 2 and BRAF exon 15 mutations were analyzed by allele specific real time PCR. 18qLOH was studied by pyrosequencing 7 SNPs. Prognostic value of the markers was analysed per stage by Cox regression for Relapse Free Survival (RFS). Results: marker frequencies and stage specific p-values in prognostic models in 420 SII and 984 SIII patients are listed in the table . Significant differences in frequency per stage were found for all markers except KRAS and BRAF. An interaction test for differences between marker prognostic value for SII and SIII was significant for MSI (p=0.04) and 18qLOH (p=0.04) in SII. Multivariate analysis including markers, T stage, N stage (for SIII), Tu grade, age &lt;60, sex, treatment arm, and Tu site found T stage (p=0.0001) and MSI (p=0.02) as independently significant clinical predictors in SII; N stage (p&lt;0.0001), T stage (p&lt;0.0001), SMAD4 (p&lt;0.0001) and P53 (p=0.01) in SIII. Conclusions: Molecular markers in colon cancer have a stage specific prognostic value. The possibility that the stages represent different diseases, rather than sequential steps in the evolution of a single disease, needs to be considered. [Table: see text] [Table: see text]
Abstract 12693: A 10-RR-Interval-Based Rhythm Classifier Using a Deep Neural Network
Authors: Takehiro Kimura, Seiji Takatsuki, Hiromasa Yamashita, Hiroshi Miyama, Taishi Fujisawa, Kazuaki Nakajima, Yoshinori Katsumata, Takahiko Nishiyama, Yoshiyasu Aizawa, Keiichi Fukuda
Journal: Circulation (2018)

Introduction: Detecting undiagnosed arrhythmias is important but difficult. An instant screening method utilizing a heart rate record obtained from a commercially available pulse meter or sphygmoma...
Febrile Reactions Occurring with Second Cycle of High Dose Melphalan and Stem Cell Transplantation in Patients with AL Amyloidosis: A “Melphalan Recall” Reaction.
Authors: Michael Rosenzweig, David C. Seldin, Daniel G Remick, Martha Skinner, Karen Quillen, Betul Oran, Kathleen T. Finn, Vaishali Sanchorawala
Journal: Blood (2008)
Specific targeting of PDGFRβ in the stroma inhibits growth and angiogenesis in tumors with high PDGF-BB expression
Authors: Maria Tsioumpekou, Sara I. Cunha, Haisha Ma, Aive Åhgren, Jessica Cedervall, Anna-Karin Olsson, Carl-Henrik Heldin, Johan Lennartsson
Journal: Theranostics (2019)

PDGF-BB/PDGFRβ signaling plays an important role during vascularization by mediating pericyte recruitment to the vasculature, promoting the integrity and function of vessels. Until now it has not been possible to assess the specific role of PDGFRβ signaling in tumor progression and angiogenesis due to lack of appropriate animal models and molecular tools. Methods: In the present study, we used a transgenic knock-in mouse strain carrying a silent mutation in the PDGFRβ ATP binding site that allows specific targeting of PDGFRβ using the compound 1-NaPP1. To evaluate the impact of selective PDGFRβ inhibition of stromal cells on tumor growth we investigated four tumor cell lines with no or low PDGFRβ expression, i.e. Lewis lung carcinoma (LLC), EO771 breast carcinoma, B16 melanoma and a version of B16 that had been engineered to overexpress PDGF-BB (B16/PDGF-BB). Results: We found that specific impairment of PDGFRβ kinase activity by 1-NaPP1 treatment efficiently suppressed growth in tumors with high expression of PDGF-BB, i.e. LLC and B16/PDGF-BB, while the clinically used PDGFRβ kinase inhibitor imatinib did not suppress tumor growth. Notably, tumors with low levels of PDGF-BB, i.e. EO771 and B16, neither responded to 1-NaPP1 nor to imatinib treatment. Inhibition of PDGFRβ by either drug impaired tumor vascularization and also affected pericyte coverage; however, specific targeting of PDGFRβ by 1-NaPP1 resulted in a more pronounced decrease in vessel function with increased vessel apoptosis in high PDGF-BB expressing tumors, compared to treatment with imatinib. In vitro analysis of PDGFRβ ASKA mouse embryo fibroblasts and the mesenchymal progenitor cell line 10T1/2 revealed that PDGF-BB induced NG2 expression, consistent with the in vivo data. Conclusion: Specific targeting of PDGFRβ signaling significantly inhibits tumor progression and angiogenesis depending on PDGF-BB expression. Our data suggest that targeting PDGFRβ in the tumor stroma could have therapeutic value in patients with high tumor PDGF-BB expression.
Inclusion of All Patients Admitted for Trauma in Trauma Registries
Authors: Quirine M. J. van der Vliet, Falco Hietbrink, Luke P. H. Leenen
Journal: JAMA Surgery (2019)

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Hemolysis in the spleen drives erythrocyte turnover
Authors: Thomas robert leon Klei, Jill Jasmine Dalimot, Benjamin Nota, Martijn Veldthuis, Erik Mul, Timo Rademakers, Mark Hoogenboezem, Sietse Quirijn Nagelkerke, Wilfred F.J. van IJcken, Edwin Oole, Pia Svendsen, Soren k Moestrup, Floris van Alphen, Alexander B Meijer, Taco W. Kuijpers, Rob van Zwieten, Robin van Bruggen
Journal: Blood (2020)
A Randomized Phase II Study of Xcellerated T Cells™ with or without Prior Fludarabine Therapy in Patients with Relapsed or Refractory Multiple Myeloma.
Authors: James R. Berenson, Ivan M. Borrello, Ravi Vij, Asad Bashey, Thomas Martin, Ralph V. Boccia, Ann Mohrbacher, Aleksandra Simic, Gary Spitzer, Jayne Meyer, Ron J. Berenson11, Mark W. Frohlich12
Journal: Blood (2004)
Imatinib 800 mg: Preliminary Results of a Phase II Trial of the GIMEMA CML Working Party in Intermediate Sokal Risk Patients and Status-of-the-Art of an Ongoing Multinational, Prospective Randomized Trial of Imatinib Standard Dose (400 mg Daily) vs High Dose (800 mg Daily) in High Sokal Risk Patients.
Authors: Gianantonio Rosti, Giovanni Martinelli, Fausto Castagnetti, Nicoletta Testoni, Giorgina Specchia, Renato Bassan, Fabio Stagno, Massimo Breccia, Elisabetta Abruzzese, Giuseppe Saglio, Fabrizio Pane, Bengt Simonsson, Johan L. Nielsen, Henrik Hjorth-Hansen, Kimmo PorkKa, Ibrahim Haznedaroglu, Arnon Nagler, Marco Vignetti, Domenico Russo, Marilina Amabile, Michele Baccarani
Journal: Blood (2005)
Prognosis Value of [18f] FDG-PET Prior Versus after Autologous Stem Cells Transplantation in High Grade Non-Hodgkin’s Lymphoma.
Authors: Virginie Roland, Caroline Bodet Milin, Anne Moreau, Thomas Gastinne, Beatrice Mahe, Viviane Dubruille, Hervé Maisonneuve, Nadine Morineau, Philippe Moreau, Henri Jardel, Lucie Planche, Philippe Moreau, Jean- Luc Harousseau, Françoise Kraeber bodere, Steven Le Gouill
Journal: Blood (2008)
Detection of Activated STAT5 in Neoplastic Mast Cells in Patients with Systemic Mastocytosis: Role of c-kit D816V.
Authors: Karoline Sonneck, Matthias Mayerhofer, Karoline V. Gleixner, Marc Kerenyi, Maria-Theresa Krauth, Richard Fritz, Christian Sillaber, Richard Moriggl, Peter Valent
Journal: Blood (2005)
Aberrant Overexpression Of CD14 In Granulocytes Sensitizes Innate Immune Response In mDia1 Heterozygous Myelodysplastic Syndromes
Authors: Ganesan Keerthivasan, Baobing Zhao, Chad E Harris, Ling Zhang, Juehua Gao, James McElherne, Jing Yang, Ashley A Basiorka, Matthew Schipma, Jacqueline Boultwood, Amit Verma, Alan List, David A. Williams, Peng Ji
Journal: Blood (2013)
Second Allogeneic Stem Cell Transplantation in Acute Myeloid Leukemia and Myelodysplastic Syndrome
Authors: Maite Hartwig, Sunday Ocheni, Nikolaus Kröger, Tatjana Zabelina, Evgeny Klyuchnikov, Svetlana Asenova, Hartmut Kabisch, Rudolf Erttmann, Axel R. Zander, Ulrike Bacher
Journal: Blood (2008)
Metabolic state of perifocal zone and resection line of skin melanoma.
Authors: Elena Frantziyantz, Farkhad Dzhabarov, Liudmila Rosenko, Victoria Pozdnyakova, Ekaterina Komarova
Journal: Journal of Clinical Oncology (2012)

e19049 Background: The state of metabolism in perifocal zone and morphologically intact skin along resection line is of importance for the processes of neoplasm metastasizing and relapse, including skin melanoma. Normalization of the state of free-radical processes, first of all along resection line, and then in neoplasm perifocal zone, should be a characteristic of pathogenically substantiated neoadjuvant influence. Methods: to study activity of free-radical processes in tissue of skin melanoma relapse, its perifocal zone (PZ) (1 cm from tumour edge) and in skin along resection line (3-5 cm from tumour edge) we investigated concentration of vitamins E and A, activity of superoxide dismutase (SOD), catalase, summary peroxidase activity (SPA), and malonic dialdehyde level (MDA) in patients with skin melanoma (pT 2-3 N 1-2 M 0 ). The study group included 54 samples after treatment (chemotherapy and radiation). Control groups: 45 samples before treatment (CG1) and 27 samples of intact skin after plastic operations (CG2). Results: After treatment MDA concentration in tumour tissue increased by 33.4% in comparison with the CG1, but remained 17.7% lower than in CG2. Average increase in concentration of vitamins E and A was equal to 1.8 times, catalase activity decreased by 30.3% in comparison with parameters before treatment (p&lt;0.05). SOD/catalase coefficient was 1.3 times higher than in the CG1, but 3.4 times lower than CG2.More manifested changes in activity of free-radical processes were observed in PZ: MDA concentration level after treatment increased by 30% in comparison with the CG1, and differed from the one in CG2 only by 10% (p&lt;0.05). Catalase activity decreased by 1.5 times and didn’t significantly differ from the corresponding parameter in tumour tissue after treatment. Normalization of concentration level of vitamins A and E without change of their ratio was observed. There was 1.6-fold increase of SOD/SPA coefficient in comparison with the CG1, however it was 2.4 times lower than CG2 (p&lt;0.05). All parameters under study along resection line after treatment didn’t significantly differ from parameters in CG2. Conclusions: The performed treatment completely restores broken metabolism in skin along resection line, partially–in tumour perifocal zone.
Circulating B-cell chronic lymphocytic leukemia cells display impaired migration to lymph nodes due to reduced LFA-1 expression
Authors: Tanja Nicole Hartmann, Valentin Grabovsky, Wei Wang, Petra Desch, Stefan Wollner, Inbal Binsky, Alexandra Vallon-Eberhard, Anita Sapoznikow, Michal Haran, Idit Shachar, Meike Burger, Marek Honczarenko, Richard Greil, Ronen Alon
Journal: Blood (2008)
More Evidence That the Phenomenon of “Plasticity” of Hematopoietic Stem Cells (HSC) and Potential Involvement of BM-Derived Cells in Organ Regeneration Could Be Explained by the Presence of a Heterogenous Population of Tissue Committed Stem Cells (TCSC) Residing/Hiding out in Bone Marrow.
Authors: Magda Kucia, Marcin Wysoczynski, Ryan Reca, Marcin Majka, Janina Ratajczak, Mariusz Z. Ratajczak
Journal: Blood (2004)
Morphomolecular motifs of pulmonary neoangiogenesis in interstitial lung diseases
Authors: Maximilian Ackermann, Helge Stark, Lavinia Neubert, Stephanie Schubert, Paul Borchert, Friedemann Linz, Willi L. Wagner, Wolfram Stiller, Mark Wielpütz, Anne Hoefer, Axel Haverich, Steven J. Mentzer, Harshit R. Shah, Tobias Welte, Mark Kuehnel, Danny Jonigk
Journal: European Respiratory Journal (2019)

The pathogenetic role of angiogenesis in interstitial lung diseases (ILDs) is controversial. This study represents the first investigation of the spatial complexity and molecular motifs of microvascular architecture in important subsets of human ILD. The aim of our study was to identify specific variants of neoangiogenesis in three common pulmonary injury patterns in human ILD. We performed comprehensive and compartment-specific analysis of 24 human lung explants with usual intersitial pneumonia (UIP), nonspecific interstitial pneumonia (NSIP) and alveolar fibroelastosis (AFE) using histopathology, microvascular corrosion casting, micro-comupted tomography based volumetry and gene expression analysis using Nanostring as well as immunohistochemistry to assess remodelling-associated angiogenesis. Morphometrical assessment of vessel diameters and intervascular distances showed significant differences in neoangiogenesis in characteristically remodelled areas of UIP, NSIP and AFE lungs. Likewise, gene expression analysis revealed distinct and specific angiogenic profiles in UIP, NSIP and AFE lungs. Whereas UIP lungs showed a higher density of upstream vascularity and lower density in perifocal blood vessels, NSIP and AFE lungs revealed densely packed alveolar septal blood vessels. Vascular remodelling in NSIP and AFE is characterised by a prominent intussusceptive neoangiogenesis, in contrast to UIP, in which sprouting of new vessels into the fibrotic areas is characteristic. The molecular analyses of the gene expression provide a foundation for understanding these fundamental differences between AFE and UIP and give insight into the cellular functions involved.
Identification of Intronic RNA Expression in CD34+ Cells of Patients with Myelodysplatic Syndrome by RNA Microarray Analysis.
Authors: Mariana O. Baratti, Yuri B. Moreira, Fabiola Traina, Luciene Borges, Fernando F. Costa, Sergio Verjovski-Almeida, Sara T.O. Saad
Journal: Blood (2007)
Breast Milk Transmission of Maternal Alloantibodies Activates a Postnatal Immune Response That Limits Allogeneic Engraftment after in Utero Hematopoietic Stem Cell Transplantation in the Murine Model
Authors: Demetri J. Merianos, Eleonor Tiblad, Pablo Laje, Masayuki Endo, Philip W. Zoltick, Alan W. Flake
Journal: Blood (2008)
Mitochondrial DNA stress signalling protects the nuclear genome
Authors: Zheng Wu, Sebastian Oeck, A. Phillip West, Kailash C. Mangalhara, Alva G. Sainz, Laura E. Newman, Xiao-Ou Zhang, Lizhen Wu, Qin Yan, Marcus Bosenberg, Yanfeng Liu, Parker L. Sulkowski, Victoria Tripple, Susan M. Kaech, Peter M. Glazer, Gerald S. Shadel
Journal: Nature Metabolism (2019)