tbuckley/cabot-search huggingface dataset:
Reply to Kadayifci and Yildirim
Authors: Alberto Mariani, Giuseppe Pantaleo
Journal: Endoscopy (2016)

We thank Drs. Kadayifci and Yildirim for their interest in our study [1] and for the opportunity to respond to their observations and insightful comments. In their Letters to the editor, Kadayifci and Yildirim questioned the role of “late” precut in increasing the risk of post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (PEP), while at the same time acknowledging the protective effect of early precut on PEP shown in our study, an effect already instantiating the main goal of the study.
PD-L1 expression in non-clear cell renal cell carcinoma and benign kidney tumors.
Authors: Andre Poisl Fay, Marcella Callea, Kathryn P. Gray, Thai Huu Ho, Jiaxi Song, Ingrid Carvo, Megan E. Lampron, Laurence Albiges, Melissa L. Stanton, David F. McDermott, Michael B. Atkins, Gordon James Freeman, Michelle S. Hirsch, Sabina Signoretti, Toni K. Choueiri
Journal: Journal of Clinical Oncology (2014)

4526 Background: Programmed death-1 (PD-1) receptor negatively regulates T cell-mediated responses.PD-1 ligand (PD-L1) is aberrantly expressed in clear cell renal cell carcinoma (ccRCC) and is associated with worse prognosis. PD-L1 expression and its association with clinicopathological features/clinical outcome are unknown in non-ccRCC and benign kidney tumors (BKT). Methods: Formalin-fixed paraffin embedded (FFPE) specimens were obtained from 124 patients (pts) with chromophobe RCC (CHR), papillary RCC (PAP), translocation Xp11.2 RCC (TrL), collecting duct carcinoma (CDC), oncocytoma (ONC), and angiomyolipoma (AML). PD-L1 expression was evaluated by immunohistochemistry using a mouse monoclonal anti-PD-L1 antibody (405.9A11). The assay was validated using FFPE cell line controls known to be positive or negative for PD-L1 expression by flow cytometry. PD-L1 positivity (PD-L1+) was defined as ≥5% tumor cell membrane staining. For immune cells, a combined score based on the extent of infiltrate and percentage of positive cells was used. Baseline characteristics including stage/grade and outcome data [time to recurrence (TTR) and survival (OS)] were also collected. Results: Among 124 pts, 17 (13.7%) were considered PD-L1+ in tumor cells: 2/36 (5%) of CHR, 5/50 (10%) of PAP, 4/11 (36%) of TrL, 1/5 (20%) of CDC, 5/15 (33%) of ONC and 0/7 (0%) of AML. In non-ccRCC, PD-L1+ in tumor cells was significantly associated with higher stage (p=0.025) and grade (p=0.03), as well as lower OS on univariate analysis (p<0.001). On the other hand, PD-L1+ by immune cells was observed in 73 (58.8%) pts: 13/36 (36%) of CHR, 30/50 (60%) of PAP, 10/11 (91%) of TrL, 5/5 (100%) of CDC, 8/15 (53%) of ONC and 7/7 (100%) of AML. PD-L1+ in immune cells did not correlate with stage (p=0.3) or grade (p=0.1). In non-ccRCC, a trend for lower OS was observed in pts with PD-L1+ in immune cells (p=0.08). PD-L1+ in tumor cell membrane and immune cells were associated with lower TTR (p=0.009 and p=0.019, respectively) Conclusions: PD-L1 expression is variable in non-ccRCC and BKT and depends on histology. PD-L1+ on tumors cells, but not immune cells was associated with aggressive features. In non-ccRCC, PD-L1+ pts (by either tumor or immune cells) appear to present worse TTR and OS.
Endothelium-derived hyperpolarizing factor signaling is critically regulated by caveolin-1 in endothelial cells
Authors: Julie Saliez, Caroline Bouzin, Philippe Ghisdal, Fanny Desjardins, Rita Rezzani, Luigi F Rodella, Joris Vriens, Bernd Nilius, Olivier Feron, Jean-Luc Balligand, Chantal Dessy
Journal: Circulation (2007)
P0323 : LDH serum levels as prognostic and predictive factor in advanced biliary tract cancer patients treated with first line chemotherapy
Authors: L. Faloppi, M. Del Prete, M. Bianconi, D. Santini, N. Silvestris, A. Casadei Gardini, O. Brunetti, R. Giampieri, M. Scartozzi, S. Cascinu
Journal: Journal of Hepatology (2015)
Novel Role of Plasmin in Mobilization and of uPAR in Retention of Hematopoietic Stem/Progenitor Cells in the Bone Marrow Niche: Therapeutic Implications.
Authors: Marc Tjwa, Nicolai Sidenius, Koen Theunissen, Rute Moura, Lieve Moons, Stefan Janssens, Francesco Blasi, Desire Collen, Peter Carmeliet
Journal: Blood (2004)
Microsatellite Instability (MSI) In High Risk Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukaemia (AML) Cells Promotes Frameshift Mutations In DNA Repair Genes: Indications for PARP Inhibitor Therapy.
Authors: Terry J Gaymes, Azim Mohamedali, Austin G Kulasekararaj, Sydney Shall, Ghulam J. Mufti
Journal: Blood (2010)
Modifiable Risk Factors for Stroke in High-Risk Patients following Acute Myocardial Infarction: Insights from the VALIANT Study
Authors: UK Sampson, S Kenchaiah, K Swedberg, HD White, Y Lokhnygina, Mareev, S Barvik, GS Francis, JA Marin-Neto, Frans Van de Werf, JL Rouleau, MA Pfeffer
Journal: Circulation (2004)
Incidence of liver events in patients with hepatitis B and C treated with rituximab
Authors: J. Vega, M. Khalife, A. Hanbali, N. Janakiraman
Journal: Journal of Clinical Oncology (2008)

8558 Background: Rituximab has been found to be effective in the treatment of patients with B-cell non-Hodgkin lymphomas. However, viral infections such as hepatitis B and C reactivation related to rituximab have been reported. Data on the effects of rituximab on patients with hepatitis B and C infection are limited. Methods: To investigate this topic, the records of 635 patients treated with rituximab in our institution between 1998 and 2006 were reviewed. A total of 49 patients with positive hepatitis serology was identified. Twenty seven patients had hepatitis B, 16 patients had hepatitis C and 6 patients had hepatitis B and C co-infection. Mild liver events were defined as an elevation of transaminases greater that twice the upper limit of normal. Severe liver events were defined as CT scan of the liver showing new or worsening signs of cirrhosis, liver biopsy showing evidence of necrosis, and death secondary to liver failure. Results: Twenty one (43%) patients developed one or more liver events. Median follow-up was 769 days. Elevation of transaminases occurred in 7 (26%), 8 (50%), and 4 (67%) patients with hepatitis B, C, and co-infection respectively. Three (11%) of patient with hepatitis B experienced viral reactivation. CT of the liver showing new or worsening cirrhosis occurred in 2 (7%), none, and 2 (33%) patients with hepatitis B, C, and co- infection respectively. Liver biopsy showing evidence of necrosis was present in 1 (4%) patient with hepatitis B. Death secondary to liver failure occurred in 3 (11%), none, and 1 (17%) patients with hepatitis B, C, and co-infection respectively. The overall number of severe liver events was 4 (15%), none, and 3 (50%) for patients with hepatitis B, C, and co-infection respectively (p=0.01). Baseline total bilirubin and albumin levels were observed to be significant predictors of severe adverse events. Conclusions: Treatment of patients with hepatitis B with rituximab requires careful monitoring for severe hepatic complications, especially if there is hepatitis C co-infection or evidence of baseline liver dysfunction. Rituximab appears to be safe in patients with hepatitis C. No significant financial relationships to disclose.
Acute heart failure in bone marrow transplantation: Impact of intravenous immune globulin as adjuvant therapy
Authors: P. Salcedo, E. Shpall, W. Yusuf, S. Roberson, M. Woods, D. Lenihan, J. Durand
Journal: Journal of Clinical Oncology (2006)

16512 Background: Little is known regarding management or treatment of cardiac failure after bone marrow transplantation. We investigated the management, treatment and outcome of new onset acute decompensated heart failure (ADHF) after bone marrow transplantation (BMT) with beta blockers, ace-inhibitors and adjuvant intravenous immune globulin (IVIG) therapy. Methods: We retrospectively examined 25 patients with ADHF. Eleven of these patients developed congestive heart failure within 100 days of BMT. Baseline echocardiograms were normal prior to admission and all patients were hospitalized and evaluated for left ventricular ejection fraction (LVEF), and New York Heart Association (NYHA) class. Patients with acute heart failure were treated with standard heart failure medications and patients post-BMT were treated with standard heart failure therapy plus adjuvant (IVIG) (500mg/Kg/day) for 48 hours. Baseline LVEF and NYHA class of 11 patients pre- and post-BMT were compared with LVEF and NYHA class of 14 patients with ADHF that did not receive a BMT. Results: The baseline diagnosis for all patients in the BMT group was NYHA class 4 and post-therapy improved to class 1.2. The baseline diagnosis for all patients in the non-BMT group were NYHA class 3.7 and improved to class 1.2 with medical therapy. The mean LVEF in the BMT group at diagnosis of ADHF was 27.5% and the mean post-therapy with IVIG was 57.6%. The mean baseline LVEF in the group not undergoing BMT and at diagnosis of ADHF was 28.2% and improved post-therapy to 45.2%. Conclusions: Acute decompensated heart failure in the cancer patient is highly treatable with aggressive medical management. Patients with ADHF after BMT and treated with IVIG may have potential clinical benefits with IVIG and standard medical therapy. Significant improvement in LVEF and NYHA were present in the BMT group versus the non-BMT group. These data suggest that BMT outcomes may be improved with routine heart failure management. Further randomized studies should be conducted. [Table: see text] No significant financial relationships to disclose.
Trait Impulsivity and the Externalizing Spectrum
Authors: Theodore P. Beauchaine, Aimee R. Zisner, Colin L. Sauder
Journal: Annual Review of Clinical Psychology (2017)

This article reviews evidence that trait impulsivity-expressed early in life as the hyperactive-impulsive and combined presentations of attention-deficit/hyperactivity disorder (ADHD)-is a bottom-up, subcortically mediated vulnerability to all externalizing disorders. This vulnerability arises from deficient mesolimbic dopamine responding, which imbues psychological states (irritability, discontentment) that motivate excessive approach behavior (hyperactivity, impulsivity). Through complex interactions with (a) aversive motivational states that arise from largely independent subcortical systems, (b) emotion regulatory mechanisms that arise from top-down, cortical modulation of subcortical neural function, and (c) environmental risk factors that shape and maintain emotion dysregulation, trait impulsivity confers vulnerability to increasingly severe externalizing behaviors across development. This perspective highlights the importance of identifying transdiagnostic neural vulnerabilities to psychopathology; dovetails with the hierarchical, latent structure of psychopathology; and suggests that progression along the externalizing spectrum is an ontogenic process whereby a common, multifactorially inherited trait interacts with endogenous and exogenous influences to yield increasingly intractable externalizing behaviors across development.
Nonprogressing HIV-infected children share fundamental immunological features of nonpathogenic SIV infection
Authors: Maximilian Muenchhoff, Emily Adland, Owen Karimanzira, Carol Crowther, Matthew Pace, Anna Csala, Ellen Leitman, Angeline Moonsamy, Callum McGregor, Jacob Hurst, Andreas Groll, Masahiko Mori, Smruti Sinmyee, Christina Thobakgale, Gareth Tudor-Williams, Andrew J. Prendergast, Henrik Kloverpris, Julia Roider, Alasdair Leslie, Delane Shingadia, Thea Brits, Samantha Daniels, John Frater, Christian B. Willberg, Bruce D. Walker, Thumbi Ndung’u, Pieter Jooste, Penny L. Moore, Lynn Morris, Philip Goulder
Journal: Science Translational Medicine (2016)

Pediatric HIV patients who do not rapidly develop AIDS are shown to have immunological features similar to nonhuman primates that experience nonpathogenic SIV infection.
The IASLC Mesothelioma Staging Project: Proposals for the M Descriptors and for Revision of the TNM Stage Groupings in the Forthcoming (Eighth) Edition of the TNM Classification for Mesothelioma
Authors: Valerie W. Rusch, Kari Chansky, Hedy L. Kindler, Anna K. Nowak, Harvey I. Pass, David C. Rice, Lynn Shemanski, Françoise Galateau-Sallé, Brian C. McCaughan, Takashi Nakano, Enrico Ruffini, Jan P. van Meerbeeck, Masahiro Yoshimura, Peter Goldstraw, Ramón Rami-Porta, Hisao Asamura, David Ball, David Beer, Ricardo Beyruti, Vanessa Bolejack, Kari Chansky, John Crowley, Frank C. Detterbeck, Wilfried Ernst Erich Eberhardt, John Edwards, Françoise Galateau-Sallé, Dorothy Giroux, Fergus Gleeson, Patti Groome, James Huang, Catherine Kennedy, Jhingook Kim, Young Tae Kim, Laura Kingsbury, Haruhiko Kondo, Mark Krasnik, Kaoru Kubota, Toni Lerut, Gustavo Lyons, Mirella Marino, Edith M. Marom, Jan P. van Meerbeeck, Alan Mitchell, Takashi Nakano, Andrew G. Nicholson, Anna Nowak, Michael Peake, Thomas W. Rice, Kenneth Rosenzweig, Enrico Ruffini, Valerie W. Rusch, Nagahiro Saijo, Paul Van Schil, Jean-Paul Sculier, Lynn Shemanski, Kelly Stratton, Kenji Suzuki, Yuji Tachimori, Charles F. Thomas, William D. Travis, Ming S. Tsao, Andrew Turrisi, Johan Vansteenkiste, Hirokazu Watanabe, Yi-Long Wu, Paul Baas, Jeremy Erasmus, Seiki Hasegawa, Kouki Inai, Kemp Kernstine, Hedy Kindler, Lee Krug, Kristiaan Nackaerts, Harvey Pass, David Rice, Conrad Falkson, Pier Luigi Filosso, Giuseppe Giaccone, Kazuya Kondo, Marco Lucchi, Meinoshin Okumura, Eugene Blackstone, H. Asamura, H. Batirel, A. Bille, U. Pastorino, S. Call, A. Cangir, S. Cedres, J. Friedberg, F. Galateau-Sallé, S. Hasagawa, K. Kernstine, H. Kindler, B. McCaughan, T. Nakano, A. Nowak, C. Atinkaya Ozturk, H. Pass, M. de Perrot, F. Rea, D. Rice, R. Rintoul, E. Ruffini, V. Rusch, L. Spaggiari, D. Galetta, K. Syrigos, C. Thomas, J.P. van Meerbeeck, P. Nafteux, J. Vansteenkiste, W. Weder, I. Optiz, M. Yoshimura
Journal: Journal of Thoracic Oncology (2016)
Hyperelastic “bone”: A highly versatile, growth factor–free, osteoregenerative, scalable, and surgically friendly biomaterial
Authors: Adam E. Jakus, Alexandra L. Rutz, Sumanas W. Jordan, Abhishek Kannan, Sean M. Mitchell, Chawon Yun, Katie D. Koube, Sung C. Yoo, Herbert E. Whiteley, Claus-Peter Richter, Robert D. Galiano, Wellington K. Hsu, Stuart R. Stock, Erin L. Hsu, Ramille N. Shah
Journal: Science Translational Medicine (2016)

Despite substantial attention given to the development of osteoregenerative biomaterials, severe deficiencies remain in current products. These limitations include an inability to adequately, rapidly, and reproducibly regenerate new bone; high costs and limited manufacturing capacity; and lack of surgical ease of handling. To address these shortcomings, we generated a new, synthetic osteoregenerative biomaterial, hyperelastic "bone" (HB). HB, which is composed of 90 weight % (wt %) hydroxyapatite and 10 wt % polycaprolactone or poly(lactic-co-glycolic acid), could be rapidly three-dimensionally (3D) printed (up to 275 cm(3)/hour) from room temperature extruded liquid inks. The resulting 3D-printed HB exhibited elastic mechanical properties (~32 to 67% strain to failure, ~4 to 11 MPa elastic modulus), was highly absorbent (50% material porosity), supported cell viability and proliferation, and induced osteogenic differentiation of bone marrow-derived human mesenchymal stem cells cultured in vitro over 4 weeks without any osteo-inducing factors in the medium. We evaluated HB in vivo in a mouse subcutaneous implant model for material biocompatibility (7 and 35 days), in a rat posterolateral spinal fusion model for new bone formation (8 weeks), and in a large, non-human primate calvarial defect case study (4 weeks). HB did not elicit a negative immune response, became vascularized, quickly integrated with surrounding tissues, and rapidly ossified and supported new bone growth without the need for added biological factors.
P2.43: Pembrolizumab vs Platinum-Based Chemotherapy for PD-L1+ NSCLC: Phase 3, Randomized, Open-Label KEYNOTE-042 (NCT02220894)
Authors: Gilberto De Lima Lopes, Yi-Long Wu, Sara Sadowski, Jin Zhang, Reshma Rangwala, Debra Kush, Tony Mok
Journal: Journal of Thoracic Oncology (2016)
CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types
Authors: Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer
Journal: Genome biology (2016)

We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.
Consenting factors in clinical cancer research: Observations from a cancer center tissue repository.
Authors: D. E. Gerber, D. W. Rasco, C. S. Skinner, J. Dowell, J. Yan, J. R. Sayne, Y. Xie
Journal: Journal of Clinical Oncology (2010)

6062 Background: Low rates of participation in cancer clinical trials have been attributed to patient, institutional, and study characteristics. However, few studies have examined factors related to the research consent process. We therefore examined the association between these variables and subject interest in clinical research. Methods: We performed a retrospective analysis of subjects enrolled in a cancer center tissue repository. During enrollment, subjects were asked if they were willing to be contacted in the future to (1) provide medical follow-up information and (2) participate in other clinical research. The order in which a subject was enrolled in the tissue repository by an individual consenter was employed as a marker of consenter experience. We analyzed the association between subject responses, subject and disease characteristics, and factors related to the consent process using univariate analysis and multivariate logistic regression. Results: Of 922 subjects evaluated, 83 percent agreed to be contacted to participate in other research studies. In univariate analysis, this rate was significantly associated with consenter experience (p = 0.01). Among subjects who were the first to be enrolled in the tissue repository by an individual consenter, 76% agreed, compared to 84% of subjects who were the second or third enrolled (p = 0.06), and 88% of subjects who were the tenth or later (p < 0.001). Timing between diagnosis and enrollment in the tissue repository displayed a trend toward association with willingness to be contacted for participation in other research studies (p = 0.08), with the highest rate (88%) among subjects enrolled 1-30 days after diagnosis. Subject responses were not associated with subject gender (p = 0.31), race (p = 0.40), or diagnosis (p = 0.30). In multivariate analysis, subject responses remained associated with consenter experience (p = 0.02). Conclusions: Factors related to the consent process, including consenter experience and the timing of consent in relation to diagnosis, are associated with markers of subject interest and willingness to participate in clinical research. These understudied and potentially modifiable variables warrant further evaluation. No significant financial relationships to disclose.
Abstract 032: Associations between Middle-age Risk Factors and Future Risk of Abdominal Aortic Aneurysm: The Atherosclerosis Risk in Communities (ARIC) Study
Authors: Weihong Tang, Alvaro Alonso, Pamela L Lutsey, Frank A Lederle, Lu Yao, Aaron R Folsom
Journal: Circulation (2013)

Introduction: Abdominal aortic aneurysm (AAA) is an important manifestation of vascular disease in older age and rupture of an AAA is a life threatening condition. Traditional atherosclerotic disease risk factors, particularly male sex, smoking and hypertension, are known to contribute to the etiology of AAA. However, epidemiologic studies of AAA have often been cross-sectional, and few have employed a prospective cohort design, especially with long follow-up. The objective of this study was to prospectively assess the association between atherosclerotic disease risk factors and hospitalized AAA in 15,722 participants (68% whites) of the ARIC study, a large, community-based cohort. Methods: Risk factors were measured at baseline at 45-64 year of age. Clinical AAAs were ascertained through hospital discharge diagnoses or death certificates. Over 15 years of follow-up, a total of 265 AAAs (85.3% whites) were identified, including repair procedures, AAA rupture or dissection, and incidental detection. Multivariable Cox proportional hazard models were used to estimate the association of risk factors with the risk of future AAA. Results: Consistent with the literature from prospective studies, we identified age, male gender, white race, smoking, height, total and HDL cholesterols, triglycerides, white blood cell count, and hypertension as risk factors for AAA (Table). In addition, LDL-C, fibrinogen, and peripheral artery disease that were previously reported only in cross-sectional case-control studies were also strongly associated with AAA (Table). Body mass index, diabetes, and alcohol consumption were not associated with AAA occurrence. Conclusions: Several lifestyle and clinical variables measured in middle-age were strong risk factors for future AAA during a long follow-up.
Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome
Authors: María X. Maldonado-Gómez, Inés Martínez, Francesca Bottacini, Amy O’Callaghan, Marco Ventura, Douwe van Sinderen, Benjamin Hillmann, Pajau Vangay, Dan Knights, Robert W. Hutkins, Jens Walter
Journal: Cell Host & Microbe (2016)
Widow wins right to use frozen embryos that were due to be destroyed
Authors: Clare Dyer
Journal: BMJ (2016)

The widow of a Falklands war veteran has won a High Court battle to use the frozen embryos she created with her husband, who died suddenly in 2014 from a brain haemorrhage.

Samantha and Clive Jefferies signed consent forms in July 2013 agreeing to have their embryos stored for 10 years. But someone at the Sussex Downs Fertility Centre, the clinic treating them, changed the maximum storage time to two years, the …