tbuckley/cabot-search huggingface dataset:
Correlation, Comparison, and Combined Analysis of KI-67 and Histological Grade for Early Luminal Breast Cancer
Authors: Y. Naito, S. Fujii, K. Itoh, M. Nezu, N. Matsubara, M. Sasaki, N. Wada, K. Yoneyama, H. Mukai
Journal: Annals of Oncology (2012)
Disentangling Population History and Character Evolution among Hybridizing Lineages
Authors: Sean P Mullen, Nicholas W VanKuren, Wei Zhang, Sumitha Nallu, Evan B Kristiansen, Qiqige Wuyun, Kevin Liu, Ryan I Hill, Adriana D Briscoe, Marcus R Kronforst
Journal: Molecular Biology and Evolution (2020)

Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.
The Predictive Role of MTHFR and ABCG2 Single Nucleotide Polymorphisms on the Outcome of Advanced Colorectal Cancer Treated with First-Line Chemotherapy
Authors: J. Zhao, W. Zhang, W. Li, J. Li, W. Guo, S. Cai, M. Sun, Z. Zhang, D. Zhu, Q. Yu
Journal: Annals of Oncology (2012)
shinyChromosome: An R/Shiny Application for Interactive Creation of Non-Circular Plots of Whole Genomes
Authors: Yiming Yu, Wen Yao, Yuping Wang, Fangfang Huang
Journal: Genomics Proteomics & Bioinformatics (2019)

Abstract Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes. Currently, there is no specialized graphical user interface (GUI) designed to produce non-circular whole genome diagrams, and the use of existing tools requires considerable coding effort from users. Moreover, such tools also require improvement, including the addition of new functionalities. To address these issues, we developed a new R/Shiny application, named shinyChromosome, as a GUI for the interactive creation of non-circular whole genome diagrams. shinyChromosome can be easily installed on personal computers for own use as well as on local or public servers for community use. Publication-quality images can be readily generated and annotated from user input using diverse widgets. shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinyChromosome.ncpgr.cn, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome.
Cardiovascular risk associated with serum potassium in the context of mineralocorticoid receptor antagonist use in patients with heart failure and left ventricular dysfunction
Authors: Patrick Rossignol, Kevin Duarte, Nicolas Girerd, Moez Karoui, John J.V. McMurray, Karl Swedberg, Dirk J. van Veldhuisen, Stuart Pocock, Kenneth Dickstein, Faiez Zannad, Bertram Pitt
Journal: European Journal of Heart Failure (2020)
Ivermectin as a novel complementary malaria control tool to reduce incidence and prevalence: a modelling study
Authors: Hannah C Slater, Brian D Foy, Kevin Kobylinski, Carlos Chaccour, Oliver J Watson, Joel Hellewell, Ghaith Aljayyoussi, Teun Bousema, Jeremy Burrows, Umberto D'Alessandro, Haoues Alout, Feiko O Ter Kuile, Patrick G T Walker, Azra C Ghani, Menno R Smit
Journal: The Lancet Infectious Diseases (2020)
An unsupervised learning approach to identify novel signatures of health and disease from multimodal data
Authors: Ilan Shomorony, Elizabeth T. Cirulli, Lei Huang, Lori A. Napier, Robyn R. Heister, Michael Hicks, Isaac V. Cohen, Hung-Chun Yu, Christine Leon Swisher, Natalie M. Schenker-Ahmed, Weizhong Li, Karen E. Nelson, Pamila Brar, Andrew M. Kahn, Timothy D. Spector, C. Thomas Caskey, J. Craig Venter, David S. Karow, Ewen F. Kirkness, Naisha Shah
Journal: Genome Medicine (2020)

Abstract Background Modern medicine is rapidly moving towards a data-driven paradigm based on comprehensive multimodal health assessments. Integrated analysis of data from different modalities has the potential of uncovering novel biomarkers and disease signatures. Methods We collected 1385 data features from diverse modalities, including metabolome, microbiome, genetics, and advanced imaging, from 1253 individuals and from a longitudinal validation cohort of 1083 individuals. We utilized a combination of unsupervised machine learning methods to identify multimodal biomarker signatures of health and disease risk. Results Our method identified a set of cardiometabolic biomarkers that goes beyond standard clinical biomarkers. Stratification of individuals based on the signatures of these biomarkers identified distinct subsets of individuals with similar health statuses. Subset membership was a better predictor for diabetes than established clinical biomarkers such as glucose, insulin resistance, and body mass index. The novel biomarkers in the diabetes signature included 1-stearoyl-2-dihomo-linolenoyl-GPC and 1-(1-enyl-palmitoyl)-2-oleoyl-GPC. Another metabolite, cinnamoylglycine, was identified as a potential biomarker for both gut microbiome health and lean mass percentage. We identified potential early signatures for hypertension and a poor metabolic health outcome. Additionally, we found novel associations between a uremic toxin, p- cresol sulfate, and the abundance of the microbiome genera Intestinimonas and an unclassified genus in the Erysipelotrichaceae family. Conclusions Our methodology and results demonstrate the potential of multimodal data integration, from the identification of novel biomarker signatures to a data-driven stratification of individuals into disease subtypes and stages—an essential step towards personalized, preventative health risk assessment.
Denosumab Versus Placebo as Adjuvant Treatment for Women With Early-Stage Breast Cancer at High Risk of Disease Recurrence (D-CARE): An in Progress, Phase 3 Clinical Trial
Authors: R.E. Coleman, C. Barrios, R. Bell, D.M. Finkelstein, H. Iwata, M. Martin, A. Braun, C. Ke, T. Maniar, P.E. Goss
Journal: Annals of Oncology (2012)
Proposal for a credentials-based clinical trials system.
Authors: Lillian P. Burke
Journal: Journal of Clinical Oncology (2012)

e13012 Background: Molecular subtyping has identified drugable targets in many cancers; yet, often only a small proportion of cancers are affected by any specific alteration. This results in small patient subgroups, even for common cancers such as lung cancer. Agents such as imatinib and crizotinib have shown dramatic clinical efficacy but others with promise, e.g., PARP inhibitors, have difficulty in obtaining trial resources despite scientific rationale and support from both patients and physicians. Rare malignancies are not studied. The current clinical trials system makes it expensive to open a trial for rare cancers as reimbursement occurs only when patients are entered, leading to high costs per patient. Methods: Critical requirements for clinical trials in patient subgroups were identified and a system proposed to address these needs. Results: Requirements are: patient safety, oversight, data and biospecimen management, accurate imaging and dosing of drugs and radiation, pharmacy accountability, and efficiency. Regulations emphasize errors of commission while ignoring ethical issues related to failure to study rare cancers (i.e., errors of omission). A trials system that can address these concerns is proposed and is based on the well-established privileging system at hospitals. Physicians and others (e.g., nurses, data managers, pathology and radiology departments) would be credentialed to participate in trials depending on the skills required, e.g., PIs might be credentialed by study type/procedure (e.g., first in Man; phase I; phase I/II trials, or only phase IV; pharmacokinetic studies; Whipple procedures; sentinel node biopsies, biospecimen collection). Protocols could access this network only after rigorous review by a panel of experts. When a patient with a rare cancer/subtype is diagnosed, the PI would download the protocol from the internet and put the patient on study if the PI/institution met required credentials. Local IRBs would sign off on privileges, investigate complaints and monitor adherence to guidelines. Conclusions: A credential-based system might allow safe trials for rare patient groups although substantial regulatory issues would need to be addressed.
標的B細胞上Fcガンマ受容体がリツキシマブの内在化を促進および臨床的有効性を減少 | 文献情報 | J-GLOBAL 科学技術総合リンクセンター
Authors: H Lim Sean, T Vaughan Andrew, Ashton-Key Margaret, L Williams Emily, V Dixon Sandra, Chan H. T. Claude, A Beers Stephen, R French Ruth, L Cox Kerry, J Davies Andrew, N Potter Kathleen, Mockridge C. Ian, G Oscier David, W M Johnson Peter, S Cragg Mark, J Glennie Martin
Journal: Blood (2011)
mRECIST for HCC: Performance and novel refinements
Authors: Josep M. Llovet, Riccardo Lencioni
Journal: Journal of Hepatology (2020)

In 2010, modified RECIST (mRECIST) criteria were proposed as a way of adapting the RECIST criteria to the particularities of hepatocellular carcinoma (HCC). We intended to overcome some limitations of RECIST in measuring tumour shrinkage with local and systemic therapies, and also to refine the assessment of progression that could be misinterpreted with conventional RECIST 1.1, due to clinical events related to the natural progression of chronic liver disease (development of ascites, enlargement of lymph nodes, etc.). mRECIST has served its purpose since being adopted or included in clinical practice guidelines (European, American and Asian) for the management of HCC; it has also been instrumental for assessing response and time-to-event endpoints in several phase II and III investigations. Nowadays, mRECIST has become the standard tool for measurement of radiological endpoints at early/intermediate stages of HCC. At advanced stages, guidelines recommend both methods. mRECIST has been proven to capture higher objective response rates in tumours treated with molecular therapies and those responses have shown to be independently associated with better survival. With the advent of novel treatment approaches (i.e. immunotherapy) and combination therapies there is a need to further refine and clarify some concepts around the performance of mRECIST. Similarly, changes in the landscape of standard of care at advanced stages of the disease are pointing towards progression-free survival as a potential primary endpoint in some phase III investigations, as effective therapies applied beyond progression might mask overall survival results. Strict recommendations for adopting this endpoint have been reported. Overall, we review the performance of mRECIST during the last decade, incorporating novel clarifications and refinements in light of emerging challenges in the study and management of HCC.
EORTCの食道癌クオリティオブライフモジュール(QLQ-OES18)のペルシャ語翻訳及びパイロット試験 | 文献情報 | J-GLOBAL 科学技術総合リンクセンター
Authors: Haddad P, Kalaghchi B, Amouzegar-Hashemi F
Journal: Annals of Oncology (2009)
Evaluation of Safety, Tolerability and Efficacy of Temsirolimus in Patients with Relapsed or Refractory Mantle Cell Lymphoma (REL/REFR MCL) in the Usual Health Care Setting
Authors: G. Krekeler, C. Herzberg, M.H. Dreyling, G. Hess, D. Kalanovic
Journal: Annals of Oncology (2012)
Trastuzumab-Based Chemotherapy (CT) for HER2-Positive Metastatic Breast Cancer (MBC): Which Optimal Partner Beyond the First Line? A Single-Centre Retrospective Study
Authors: R. Palumbo, A. Bernardo, A. Riccardi, F. Sottotetti, M. Azzarà, B. Tagliaferri, E. Pozzi, C.M. Teragni, G. Bernardo
Journal: Annals of Oncology (2012)
Prognositc Inpact of Tumor-Infiltrating FOXP3+ Regulatory T Cells in Dlbcl Treated with R-CHOP
Authors: R. Mauchi, N. Goto, H. Tsurumi, T. Hara, N. Nakamura, H. Nakamura, J. Nagano, J. Kitagawa, N. Kanemura, T. Takami, H. Moriwaki
Journal: Annals of Oncology (2012)
N‐terminal peptide deletion influences immunological and structural features of Blo t 5
Authors: Eduardo Santos da Silva, Sara Huber, Neuza Maria Alcantara‐Neves, Claudia Asam, Elisânia Fontes Silveira, Emília Maria Medeiros de Andrade Belitardo, Lorenz Aglas, Michael Wallner, Gabriele Gadermaier, Peter Briza, Ingrid Karner, Rogério Tanan Torres, Juan Ricardo Urrego Alvarez, Sabina Wuenschmann, Martin Chapman, Fatima Ferreira, Carina Silva Pinheiro
Journal: Allergy (2020)

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O-0003 Phase I/II Study of 90Y-Clivatuzumab Tetraxetan (90Y-hPAM4) Combined with Gemcitabine (GEM) in Advanced Pancreatic Cancer (APC)
Authors: Edith Mitchell, Allyson Ocean, Michael Guarino, Kenneth Pennington, Gregory Springett, David Gold, Bekaii-saab Tanio, William Wegener, David Goldenberg, Heather Horne, Alberto Montero, John Kauh, Max Sung
Journal: Annals of Oncology (2012)
A revised nomenclature for allergy: An EAACI position statement from the EAACI nomenclature task force
Authors: S. G. O. Johansson, J.O'B Hourihane, J. Bousquet, C. Bruijnzeel‐Koomen, S. Dreborg, T. Haahtela, M. L. Kowalski, N. Mygind, J. Ring, P. Van Cauwenberge, M. Van Hage‐Hamsten, B. Wüthrich
Journal: Allergy (2001)

This report has been prepared by an EAACI task force representing the five EAACI Sections and the EAACI Executive Committee composed of specialists that reflect the broad opinion on allergy expressed by various clinical and basic specialties dealing with allergy. The aim of this report is to propose a revised nomenclature for allergic and related reactions that can be used independently of target organ or patient age group. The nomenclature is based on the present knowledge of the mechanisms which initiate and mediate allergic reactions. However, the intention has not been to revise the nomenclature of nonallergic hypersensitivity.
Number of general practices in breach of contract is rising, figures show
Authors: Gareth Iacobucci
Journal: BMJ (2020)

The number of general practices in England that have been subject to contractual sanctions rose by 56% last year, an analysis by The BMJ has found. GP leaders said the increasing number of practices being found in breach of their contracts was due to funding, workforce, and premises pressures and called for struggling practices to be supported rather than penalised. Clinical commissioning groups or NHS England issue notices of breach of contract if they believe that a practice has failed to deliver on a specific aspect of its contract or is at risk of doing so (box 1). Box 1 ### What are contractual breach notices? Commissioners can issue contract breach notices to a general practice if they deem that it has failed to deliver on any national or local aspect of its contract or is at risk of doing so because of specific behaviours. Practices are entitled to appeal within 28 days of a notice being issued. Notices fall into … RETURN TO TEXT
Molecular Profiling of Peripheral Blood Is Associated with Circulating Tumor Cells (CTCS) Content and Survival in Metastatic Castration-Resistant Prostate Cancer (MCRPC)
Authors: L. Gaba Garcia, M. Marín-Aguilera, J.J. Lozano, A. Tagliapietra, V. Ortega, P. Gascón, B. Mellado
Journal: Annals of Oncology (2012)
Wertheim Surgery for Locally Advanced Cervical Cancer Following Chemoradiation with Intensity Modulated Arc Therapy. Prospective Analysis
Authors: A.P. Makar, K. Vandecasteele, P. Tummers, P. Ost, L. Delrue, B. Speelers, S. Van Belle, R. Van den Broecke, V. Fonteyne, G. De Meerleer
Journal: Annals of Oncology (2012)
Anthracycline-Induced Cardiotoxicity in Mice is Prevented by Late INa Inhibition with Ranolazine, With Improvement in Heart Function, Fibrosis and Apoptosis
Authors: N. Maurea, C. Coppola, C. Quintavalle, D. Rea, A. Barbieri, G. Piscopo, R.V. Iaffaioli, G. Condorelli, C. Arra, C.G. Tocchetti
Journal: Annals of Oncology (2012)
Will ‘Fit’ Older Cancer Patients as Assessed by Frailty Screening Tools Tolerate the First Cycle of (Radio) Chemotherapy Without Serious Adverse Events?
Authors: A. Baitar, F. van Fraeyenhove, A. Vandebroek, E. De Droogh, D. Galdermans, J. Mebis, D. Schrijvers
Journal: Annals of Oncology (2012)
Phase I Study of Ombrabulin in Combination with Cisplatin (CDDP) Administered Every 3 Weeks to Japanese Patients with Advanced Solid Tumors
Authors: S. Takahashi, T. Ura, K. Nakano, K. Chin, M. Yokoyama, K. Hatake, T. Yokota, K. Shitara, K. Muro, T. Aoyama
Journal: Annals of Oncology (2012)
Pertuzumab in Combination with Trastuzumab and a Taxane for the First-Line Treatment of Patients with HER2-Positive Advanced Breast Cancer: A Single Arm Phase IIIB Study (Peruse)
Authors: D. Miles, T. Peretz-Yablonski, E. Ciruelos, F. Puglisi, A. Schneeweiss, L. Mitchell, A. Dünne, T. Bachelot
Journal: Annals of Oncology (2012)
薬物溶出ステント留置術後のステント内ネオアテローム性動脈硬化症のin vivo評価-光干渉断層法研究 | 文献情報 | J-GLOBAL 科学技術総合リンクセンター
Authors: Miwa Kenji, Matsubara Takao, Yasuda Toshihiko, Inoue Masaru, Ukawa Nobuo, Okada Hirofumi, Yakuta Yohei, Matsui Takao, Kawashiri Masaaki, Yamagishi Masakazu, Kanaya Honin
Journal: Circulation (2013)
Dacarbazine Mono-Therapy for Unresectable Neuroendocrine Tumor: A Retrospective Analysis
Authors: Y. Imamura, Y. Fujiwara, M. Toyoda, N. Chyayahara, M. Nishimura, Y. Funakoshi, H. Tomioka, T. Shimada, K. Yakushijin, A. Okamura, N. Kiyota, T. Mukohara, H. Matsuoka, H. Minami
Journal: Annals of Oncology (2012)
The Role of Mutations of EGFR, K-RAS, EML4-ALK, and B-RAF Genes in Resected Pathological Stage I Lung Adenocarcinoma
Authors: G. Toyokawa, T. Ohba, K. Sugio, Y. Morodomi, T. Takenaka, M. Yamaguchi, F. Hirai, K. Taguchi, T. Seto, Y. Ichinose
Journal: Annals of Oncology (2012)
A systematic review and meta-analysis of the 2007 WCRF/AICR score in relation to cancer-related health outcomes
Authors: M. Solans, D.S.M. Chan, P. Mitrou, T. Norat, D. Romaguera
Journal: Annals of Oncology (2020)

We conducted a systematic literature review and meta-analysis of observational studies investigating adherence to the 2007 World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) lifestyle recommendations for cancer prevention and health outcomes.We searched PubMed and the in-house database of the WCRF Continuous Update Project for publications up to June 2019. Cross-sectional studies were only narratively reviewed given their heterogeneity while findings of cohort/case-control studies were synthesized in umbrella reviews and meta-analyses. Summary relative risks (RRs) and 95% confidence intervals (CI) were estimated using a random-effects model when at least two studies reported results on a specific outcome.Thirty-eight articles (17 prospective, 8 case-control, and 13 cross-sectional studies) were included. The summary RR per each point increment in the 2007 WCRF/AICR score was 0.90 (95% CI: 0.87-0.93, n = 11) for breast cancer, regardless of hormone receptor and menopausal status, 0.86 (95% CI: 0.82-0.89, n = 10) for colorectal cancer, and 0.93 (95% CI: 0.89-0.96, n = 2) for lung cancer risk. No statistically significant associations were reported for prostate (n = 6) and pancreatic cancers (n = 2). Adherence to the recommendations was associated with lower overall mortality (RR = 0.90, 95% CI 0.84-0.96, n = 3) and cancer-specific mortality (RR = 0.91, 95% CI 0.89-0.92; n = 3) in healthy populations, as well as with higher survival in cancer patients (n = 2). In cross-sectional studies, a healthier plasma marker profile and lower cancer risk factors in the general population and a better health status and quality of life in cancer patients/survivors were reported.Adhering to the 2007 WCRF/AICR recommendations is associated with lower risks of cancer incidence, namely breast and colorectal cancers, and mortality. Primary prevention of cancer should emphasize modification of multiple lifestyle factors. Upcoming studies examining the recently updated 2018 guidelines will further clarify such associations.
Cenicriviroc Treatment for Adults With Nonalcoholic Steatohepatitis and Fibrosis: Final Analysis of the Phase 2b CENTAUR Study
Authors: Vlad Ratziu, Arun Sanyal, Stephen A. Harrison, Vincent Wai‐Sun Wong, Sven Francque, Zachary Goodman, Guruprasad P. Aithal, Kris V. Kowdley, Star Seyedkazemi, Laurent Fischer, Rohit Loomba, Manal F. Abdelmalek, Frank Tacke
Journal: Hepatology (2020)

Cenicriviroc (CVC) is a C-C chemokine receptors type 2 and 5 dual antagonist under evaluation for treating liver fibrosis in adults with nonalcoholic steatohepatitis (NASH). Year 1 primary analysis of the 2-year CENTAUR study showed that CVC had an antifibrotic effect without impacting steatohepatitis. Herein, we report the final data from year 2 exploratory analyses.This was a randomized, controlled study of adults with NASH, nonalcoholic fatty liver disease activity score ≥4, and NASH Clinical Research Network stage 1-3 fibrosis. Participants in arms A and C received CVC 150 mg or placebo, respectively, for 2 years; arm B received placebo in year 1 and switched to CVC in year 2. Liver biopsy was performed at baseline, year 1, and year 2. Of 289 randomized participants, 242 entered year 2. At year 2, 24% of patients who switched to CVC and 17% who remained on placebo achieved ≥1-stage fibrosis improvement and no worsening of NASH (P = 0.37). Twice the proportion on CVC who achieved fibrosis response at year 1 maintained benefit at year 2 (60% arm A versus 30% arm C), including 86% on CVC who had stage 3 fibrosis at baseline. Over 2 years, a similar proportion on CVC or placebo achieved ≥1-stage fibrosis improvement and no worsening of NASH (15% arm A versus 17% arm C). In patients with fibrosis responses, we observed consistent reductions in levels of N-terminal type 3 collagen propeptide and enhanced liver fibrosis scores, while increases in aspartate aminotransferase-to-platelet ratio index and Fibrosis-4 scores were consistently observed in nonresponders. Safety profile was comparable across groups.CVC was well tolerated, and year 2 data corroborate antifibrotic findings from year 1. The majority on CVC who achieved fibrosis response at year 1 maintained it at year 2, with greater effect in advanced fibrosis. ClinicalTrials.gov number, NCT02217475 (CENTAUR).
P-0088 Sorafenib as First Line Treatment for Advanced Liver Cancer-Are Expiries
Authors: Jelena Rozic, Gojkovic Zdenka, Sasa Jungic, Ivanka Rakita, Zivko Vranjes, Radmila Raseta, Gordana Maric, Vjestica Milka, Stanka Mijatovic, Predrag Dasic, Marina Vizin
Journal: Annals of Oncology (2012)
A Phase II Trial of Bevacizumab Combined with Chemotherapy in Patients with Metastatic Well-Differentiated Duodeno-Pancreatic Endocrine Tumors (Better Study)
Authors: J. Seitz, D. Smith, D. O'Toole, C. Lepère, C. Dromain, A. Gorana, E. Mitry, M.P. Ducreux
Journal: Annals of Oncology (2012)