tbuckley/cabot-search huggingface dataset:
Establishment of the European meningococcal strain collection genome library (EMSC-GL) for the 2011 to 2012 epidemiological year
Authors: Holly B Bratcher, Carina Brehony, Sigrid Heuberger, Despo Pieridou-Bagatzouni, Pavla Křížová, Steen Hoffmann, Maija Toropainen, Muhamed-Kheir Taha, Heike Claus, Georgina Tzanakaki, Tímea Erdôsi, Jelena Galajeva, Arie van der Ende, Anna Skoczyńska, Marina Pana, Alena Vaculíková, Metka Paragi, Martin CJ Maiden, Dominique A Caugant
Journal: Eurosurveillance (2018)

Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011–June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance. Most genomes contained genes encoding B (n = 525; 65.7%) or C (n = 163; 20.4%) capsules; isolates were genetically highly diverse, with &gt;20 genomic lineages, five of which comprising 60.7% (n = 485) of isolates. There were &gt;350 antigenic fine-types: 307 were present once, the most frequent (P1.7-2,4:F5-1) comprised 8% (n = 64) of isolates. Each genome was characterised for Bexsero Antigen Sequence Typing (BAST): 25.5% (n = 204) of isolates contained alleles encoding the fHbp and/or the PorA VR1 vaccine component, but most genomes (n = 513; 64.2%) did not contain the NadA component. EMSC-GL will support an integrated surveillance of disease-associated genotypes in Europe, enabling the monitoring of hyperinvasive lineages, outbreak identification, and supporting vaccine programme implementation.
Smoking and Death From Prostate Cancer
Authors: Stephen J. Freedland
Journal: JAMA Oncology (2018)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Abstract B38: In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis
Authors: Jatin Roper, Tuomas Tammela, Naniye Malli Cetinbas, Adam Akkad, Ali Roghanian, Steffen Rickelt, Mohammad Almeqdadi, Katherine Wu, Matthias Oberli, Francisco Sánchez-Rivera, Yoona Park, Xu Liang, George Eng, Martin S. Taylor, Roxana Azimi, Dmitriy Kedrin, Rachit Neupane, Semir Beyaz, Ewa T. Sicinska, Yvelisse Suarez, James Yoo, Lillian Chen, Lawrence Zukerberg, Pekka Katajisto, Vikram Deshpande, Adam Bass, Philip N. Tsichlis, Jacqueline Lees, Robert Langer, Richard O. Hynes, Jianzhu Chen, Arjun J. Bhutkar, Tyler Jacks, Ömer H. Yilmaz
Journal: Cancer Research (2018)

Abstract In vivo interrogation of the function of genes implicated in tumorigenesis is limited by the need to generate and cross germline mutant mice. Here we describe approaches to model colorectal cancer (CRC) and metastasis that rely on in situ gene editing and orthotopic organoid transplantation in mice without cancer-predisposing mutations. Autochthonous tumor formation is induced by CRISPR/Cas9-based editing of the Apc and Trp53 tumor suppressor genes in colon epithelial cells and by orthotopic transplantation of Apc-edited colon organoids. ApcΔ/Δ;KrasG12D/+;Trp53Δ/Δ (AKP) mouse colon organoids and human CRC organoids engraft in the distal colon and metastasize to the liver. Finally, we apply the orthotopic transplantation model to characterize the clonal dynamics of Lgr5+ stem cells and demonstrate sequential activation of an oncogene in established colon adenomas. These experimental systems enable rapid in vivo characterization of cancer-associated genes and reproduce the entire spectrum of tumor progression and metastasis. Citation Format: Jatin Roper, Tuomas Tammela, Naniye Malli Cetinbas, Adam Akkad, Ali Roghanian, Steffen Rickelt, Mohammad Almeqdadi, Katherine Wu, Matthias Oberli, Francisco Sánchez-Rivera, Yoona Park, Xu Liang, George Eng, Martin S. Taylor, Roxana Azimi, Dmitriy Kedrin, Rachit Neupane, Semir Beyaz, Ewa T. Sicinska, Yvelisse Suarez, James Yoo, Lillian Chen, Lawrence Zukerberg, Pekka Katajisto, Vikram Deshpande, Adam Bass, Philip N. Tsichlis, Jacqueline Lees, Robert Langer, Richard O. Hynes, Jianzhu Chen, Arjun J. Bhutkar, Tyler Jacks, Ömer H. Yilmaz. In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr B38.
Histopathologic response and growth patterns of colorectal cancer liver metastases (CRCLM) in patients treated with triplets plus bevacizumab (bev) or anti-EGFRs.
Authors: Federica Marmorino, Chiara Cremolini, Filippo Pietrantonio, Alessio Pellegrinelli, Gemma Zucchelli, Fotios Loupakis, Sara Lonardi, Giuseppe Aprile, Federica Morano, Michele Prisciandaro, Gianluca Masi, Alessia Mennitto, Francesca Bergamo, Giovanni Gerardo Cardellino, Matteo Fassan, Mariaelena Casagrande, Massimo Milione, Gabriella Fontanini, Filippo de Braud, Alfredo Falcone
Journal: Journal of Clinical Oncology (2018)

636 Background: The histopathological response to pre-operative chemotherapy is associated with clinical outcome in patients (pts) undergoing secondary resection of CRCLM. Three different histopathological growth patterns (HGPs) of CRCLM have been described: desmoplastic (i.e. with a capsule of stroma separating tumor and normal cells), pushing (i.e. with limited infiltration of normal hepatic plates by tumor cells) and replacement (i.e. with abundant infiltration of normal hepatic plates by tumor cells and vessel cooption). Methods: Histopathological parameters of response were evaluated in specimens from 159 pts who underwent secondary resection of CRCLM, after receiving triplet (FOLFOXIRI or COI) plus bev (N = 103) or anti-EGFR (N = 56) in 5 first-line clinical studies (TRIBE, MOMA, MACBETH, COI-B and COI-E). The aims of this analysis were to evaluate the prognostic role of histopathologic response and to investigate the prognostic role of HGPs and their potential different sensitivity to targeted agents. Results: When compared with partial (TRG 3) and no (TRG 4-5) pathologic response (N = 118), major response (TRG 1-2, N = 41) was associated with longer RFS (mRFS: 28.0 versus 11.0 mos, HR = 0.57, 95%CI = 0.39–0.86; p = 0.007) and OS (mOS: unreached versus 42.1 mos, HR = 0.54, 95%CI = 0.31-0.93; p = 0.027). No association of baseline clinical characteristics and RAS and BRAF status with major response was found. Major response was more frequent among pts treated with bev than with anti-EGFRs (OR = 2.83, 95%CI = 1.20–6.65; p = 0.015) and was associated with deepness of response as a continuous variable (HR = 1.02, 95% CI = 1.00–1.04; p = 0.011). In the desmoplastic HGP (N = 28) a higher percentage of major response was reported (57% vs 17% in pushing and 22% in replacement HGP, p &lt; 0.001) and a numerical advantage from anti-EGFR vs bev was evident in terms of both major response and RFS. Conversely, in the pushing HGP (N = 66) a significant benefit from bev vs anti-EGFR in major response and RFS was observed. No difference was described in the replacement HGP (N = 65). Conclusions: The assessment of HGPs may be useful to predict benefit from available targeted agents.
A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease
Authors: Sara Mostafavi, Chris Gaiteri, Sarah E. Sullivan, Charles C. White, Shinya Tasaki, Jishu Xu, Mariko Taga, Hans-Ulrich Klein, Ellis Patrick, Vitalina Komashko, Cristin McCabe, Robert Smith, Elizabeth M. Bradshaw, David E. Root, Aviv Regev, Lei Yu, Lori B. Chibnik, Julie A. Schneider, Tracy L. Young-Pearse, David A. Bennett, Philip L. De Jager
Journal: Nature Neuroscience (2018)
Abstract P245: Is Self-efficacy Associated with Patterns of Self-weighing Behavior?
Authors: Yaguang Zheng, Susan M Sereika, Linda J Ewing, Cynthia A Danford, Martha A Terry, Christopher Imes, Rachel W Goode, Dara D Mendez, Meghan K Mattos, Lu Hu, Ran Sun, Lora E Burke
Journal: Circulation (2016)

Introduction: Our recent work demonstrated that obese/overweight individuals exhibit different patterns of self-weighing behavior over time. To identify possible contributors to varying patterns, we examined the differences in changes in self-efficacy (SE) by self-weighing pattern groups. Hypothesis: Higher self-weighing group would have greater increases in SE levels. Methods: This was an analysis of data from a 12-mo behavioral weight-loss intervention study. Each participant was given a Wi-Fi-enabled scale to transmit weight data to a server. Three self-weighing patterns were determined by group-based trajectory modeling: high/consistent (&gt;6 days/week); moderate/declined (declined from 4-5 to 2 days/week); minimal/declined (5-6 to 0 days/week). SE was assessed semiannually by the Weight Efficacy Lifestyle (WEL) Scale, yielding ratings of one’s confidence to avoid eating under varied conditions (e.g., home, social settings) and moods (e.g., depressed, stressed). Higher scores indicate greater levels of SE. Linear mixed modeling was used for data analysis. Results: The sample (N=148) was 90.5% female, 81.1% White, with mean (SD) age of 51.3 (10.1) years and BMI of 34.1 (4.6) kg/m 2 . There were no significant differences in self-weighing groups for WEL total and subscale scores at baseline. There was significant group effect for changes in subscale score of Negative Emotions, group by time effect for Social Pressure and time effect for Positive Activities. The high/consistent self-weighing group showed significant increases in each subscale score and total score from 0 mos to 6 or 12 mos, with the subscale score of Social Pressure having a marginally significant increase at 12 mos, while the other two groups had no changes over time (see table). Conclusions: Participants in the high/consistent self-weighing group reported increased SE over time for eating in different contexts. Future work needs to explore strategies to improve eating self-efficacy and self-weighing for those unable to establish this habit.
Frank Arthur Fairweather
Authors: Dorothy Fairweather
Journal: BMJ (2018)

Frank Fairweather started his long and distinguished career at the Ipswich group of hospitals before returning to the Middlesex Hospital as a pathologist in 1956. He became chief medical adviser and consultant pathologist at the Benger Laboratories in 1962 while also sharing his growing expertise with the Royal College of Surgeons as honorary senior lecturer. His work further expanded with a series …
Abstract 12147: P2y12 Antagonism Enhances the Release of Anti-apoptotic Exosomes From Human Cardiac Progenitor Cells in vitro
Authors: Valentina Casieri, Marco Matteucci, Lucio Barile, Emilio M Pasanisi, Regina Fritsche-Danielson, Vincenzo Lionetti
Journal: Circulation (2017)

Introduction: Recent experimental evidences suggest that long-term antagonism of P2Y12, a G protein-coupled (GPCR) purinergic receptor, protect the heart against ischemic injury. However, the mecha...
Association of Depressive Symptoms and Heart Rate Variability in Vietnam War–Era Twins
Authors: Minxuan Huang, Amit Shah, Shaoyong Su, Jack Goldberg, Rachel J. Lampert, Oleksiy M. Levantsevych, Lucy Shallenberger, Pratik Pimple, J. Douglas Bremner, Viola Vaccarino
Journal: JAMA Psychiatry (2018)

Depressive symptoms are associated with lower heart rate variability (HRV), an index of autonomic dysregulation, but the direction of the association remains unclear.To investigate the temporal association between depression and HRV.A longitudinal, cross-lagged twin difference study, with baseline assessments from March 2002 to March 2006 (visit 1) and a 7-year follow-up (visit 2) at an academic research center with participants recruited from a national twin registry. Twins (n = 166) from the Vietnam Era Twin Registry, who served in the US military during the Vietnam War, and were discordant for depression at baseline were recruited.At both visits, depressive symptoms were measured using the Beck Depression Inventory-II (BDI-II), and HRV was measured through 24-hour electrocardiogram monitoring. To assess the direction of the association, within-pair differences in multivariable mixed-effects regression models were examined, and standardized β coefficients for both pathways were calculated. The associations were evaluated separately in monozygotic and dizygotic twins.In the final analytic sample (N = 146), all participants were men, 138 (95%) were white, and the mean (SD) age was 54 (3) years at baseline. Results showed consistent associations between visit 1 HRV and visit 2 BDI score across all HRV domains and models (β coefficients ranging from -0.14 to -0.29), which were not explained by antidepressants or other participant characteristics. The magnitude of the association was similar in the opposite pathway linking visit 1 BDI score to visit 2 HRV, with β coefficients ranging from 0.05 to -0.30, but it was largely explained by antidepressant use. In stratified analysis by zygosity, significant associations were observed in monozygotic and dizygotic twins for the path linking visit 1 HRV to visit 2 BDI score, although the associations were slightly stronger in dizygotic twins.The association between depression and autonomic dysregulation, indexed by HRV, is bidirectional, with stronger evidence suggesting that autonomic function affects depression risk rather than vice versa. The opposite causal pathway from depression to lower HRV is mostly driven by antidepressant use. These findings highlight an important role of autonomic nervous system in the risk of depression and contribute new understanding of the mechanisms underlying the comorbidity of depression and cardiovascular disease.
Adult rat myelin enhances axonal outgrowth from neural stem cells
Authors: Gunnar H. D. Poplawski, Richard Lie, Matt Hunt, Hiromi Kumamaru, Riki Kawaguchi, Paul Lu, Michael K. E. Schäfer, Grace Woodruff, Jacob Robinson, Philip Canete, Jennifer N. Dulin, Cedric G. Geoffroy, Lutz Menzel, Binhai Zheng, Giovanni Coppola, Mark H. Tuszynski
Journal: Science Translational Medicine (2018)

Axons emerging from rat neural stem cell implants in the injured spinal cord of rat recipients are stimulated to grow by myelin.
Do the folk need a meta-ethics?
Authors: Shivam Patel, Edouard Machery
Journal: Behavioral and Brain Sciences (2018)

Abstract Stanford argues that cooperators achieve and maintain correlated interaction through the objectification of moral norms. We first challenge the moral/non-moral distinction that frames Stanford's discussion. We then argue that to the extent that norms are objectified (and we hold that they are at most objectified in a very thin sense), it is not for the sake of achieving correlated interaction.
Primary Congenital Lymphedema
Authors: Lubomir Mrhac, Kamil Bukovansky, Jana Kafkova, Otakar Kraft
Journal: Clinical Nuclear Medicine (2018)

We present the case of a 26-year-old man with congenital primary lymphedema. A lymphedema of the right upper limb appeared at the age of 2 years, followed by edemas of the right lower limb and of the right part of the head and neck. A lymphedema of the left lower limb began 5 years ago, and finally an edema of the external genitalia began 2 years ago. Lymphoscintigraphy of the lower limbs and pelvic/abdominal region (including SPECT/ldCT) revealed interesting abnormalities.
Abstract IA13: Imaging stem cell signals in cancer heterogeneity and therapy resistance
Authors: Tannishtha Reya
Journal: Cancer Research (2018)

Abstract Our research focuses on the signals that control stem cell self-renewal and how these signals are hijacked in cancer. Using a series of genetic models, we have studied how classic developmental signaling pathways such as Wnt, Hedgehog, and Notch play key roles in hematopoietic stem cell growth and regeneration and are dysregulated during leukemia development. In addition, using real-time imaging strategies we have found that hematopoietic stem cells have the capacity to undergo both symmetric and asymmetric division, and that shifts in the balance between these modes of division are subverted by oncogenes. Further, regulators of this process, including the cell fate determinant Musashi, are critical players in driving progression of solid and liquid cancers and could serve as targets for diagnostics and therapy. Ongoing work is focused on understanding the mechanisms that drive therapy resistance after drug delivery, as well as developing high-resolution in vivo imaging approaches to map normal stem cell behavior and interactions within living animals, and to define how these change during cancer formation. Citation Format: Tannishtha Reya. Imaging stem cell signals in cancer heterogeneity and therapy resistance [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr IA13.
Characteristics of Radiotherapy Trials Compared With Other Oncological Clinical Trials in the Past 10 Years
Authors: Xu Liu, Yuan Zhang, Ling-Long Tang, Quynh Thu Le, Melvin L. K. Chua, Joseph T. S. Wee, Nancy Y. Lee, Brian O’Sullivan, Anne W. M. Lee, Ying Sun, Jun Ma
Journal: JAMA Oncology (2018)

Modern precision radiotherapy is an innovative and effective treatment of cancer, yet it is unclear how radiotherapy trials are affected by expanding targeted and immune therapies and declining National Institutes of Health funding.To analyze and compare the characteristics of radiotherapy trials with other oncological trials registered on ClinicalTrials.gov.This is a cross-sectional analysis of trials registered on ClinicalTrials.gov between June 1, 2007, and May 8, 2017. Records of all 243 758 clinical studies registered by May 8, 2017, were downloaded, but only 25 907 interventional oncological trials registered between June 1, 2007, and May 8, 2017, and whose primary purpose was "treatment" were included in the final analysis. Trials were categorized according to cancer type and other registration information.Characteristics of radiotherapy trials were compared with characteristics of other oncological trials. Chronological shifts in radiotherapy trials were also analyzed.Of the 25 907 trials selected, 1378 (5.3%) were radiotherapy trials and 24 529 (94.7%) were other oncological studies. The number of radiotherapy trials increased gradually from 94 (June 1, 2007, through May 31, 2008) to 192 (June 1, 2015, through May 31, 2016). Radiotherapy trials were less likely than other oncological studies to be registered before participant enrollment (763 of 1370 [55.7%] vs 16 105 of 24 434 [65.9%]; P < .001), to be blinded (45 of 1378 [3.3%] vs 2784 of 24 529 [11.3%]; P < .001), or to involve multiple geographic regions (2.4% vs 9.5%; P < .001), but they were more likely to be phase 2 to 3 (773 of 1124 [68.8%] vs 12 910 of 22 300 [57.9%]; P < .001) and to have a data-monitoring committee (839 of 1264 [66.4%] vs 11 728 of 21 060 [55.7%]; P < .001). Only a minority of radiotherapy trials were industry sponsored, which was significantly lower than for other oncological trials (80 of 1378 [5.8%] vs 10 651 of 24 529 [43.4%]; P < .001; adjusted odds ratio, 0.08; 95% CI, 0.06-0.10). The number of National Institutes of Health-sponsored radiotherapy trials decreased from 80 of 544 trials (14.7%) from 2007 to 2012 to 72 of 834 trials (8.6%) from 2012 to 2017 (P < .001). Radiotherapy trials with a sample size of more than 100 patients decreased from 155 of 543 trials (28.5%) from 2007 to 2012 to 157 of 833 trials (18.8%) from 2012 to 2017 (P < .001).The limited number of and the scarcity of funding for radiotherapy trials is concerning given the integral role of radiotherapy in the clinical management of patients with cancer worldwide. A multidisciplinary collaboration to promote and fund more radiotherapy research is warranted.
Prolonged and large outbreak of invasive group A Streptococcus disease within a nursing home: repeated intrafacility transmission of a single strain
Authors: S.A. Nanduri, B.J. Metcalf, M.A. Arwady, C. Edens, M.A. Lavin, J. Morgan, W. Clegg, A. Beron, J.P. Albertson, R. Link-Gelles, A. Ogundimu, J. Gold, D. Jackson, S. Chochua, N. Stone, C. Van Beneden, K. Fleming-Dutra, B. Beall
Journal: Clinical Microbiology and Infection (2018)
Hepatitis A: an epidemiological survey in blood donors, France 2015 to 2017
Authors: Pierre Gallian, Valérie Barlet, Lina Mouna, Sylvie Gross, Sophie Lecam, Céline Ricard, Françoise Wind, Elodie Pouchol, Cécile Fabra, Benoit Flan, Catherine Visse, Rachid Djoudi, Elisabeth Couturier, Henriette de Valk, Pierre Tiberghien, Anne-Marie Roque-Afonso
Journal: Eurosurveillance (2018)

Since mid-2016, hepatitis A virus (HAV) outbreaks, involving predominantly men who have sex with men (MSM), have affected countries in Europe and overseas. In France, HAV screening of blood donations in 2017 revealed a HAV-RNA prevalence ca fivefold higher than during 2015-16 (4.42/106 vs 0.86/106; p = 0.0005). In 2017, despite a higher male-to-female ratio (5.5 vs 0.7) and the identification of MSM-associated outbreak strains, only one of 11 infected male donors self-reported being a MSM.