tbuckley/cabot-search huggingface dataset:
The SWPER index for women's empowerment in Africa: development and validation of an index based on survey data
Authors: Fernanda Ewerling, John W Lynch, Cesar G Victora, Anouka van Eerdewijk, Marcelo Tyszler, Aluisio J D Barros
Journal: The Lancet Global Health (2017)

BackgroundThe Sustainable Development Goals strongly focus on equity. Goal 5 explicitly aims to empower all women and girls, reinforcing the need to have a reliable indicator to track progress. Our objective was to develop a novel women's empowerment indicator from widely available data sources, broadening opportunities for monitoring and research on women's empowerment.MethodsWe used Demographic and Health Survey data from 34 African countries, targeting currently partnered women. We identified items related to women's empowerment present in most surveys, and used principal component analysis to extract the components. We carried out a convergent validation process using coverage of three health interventions as outcomes; and an external validation process by analysing correlations with the Gender Development Index.Findings15 items related to women's empowerment were selected. We retained three components (50% of total variation) which, after rotation, were identified as three dimensions of empowerment: attitude to violence, social independence, and decision making. All dimensions had moderate to high correlation with the Gender Development Index. Social independence was associated with higher coverage of maternal and child interventions; attitude to violence and decision making were more consistently associated with the use of modern contraception.InterpretationThe index, named Survey-based Women's emPowERment index (SWPER), has potential to widen the research on women's empowerment and to give a better estimate of its effect on health interventions and outcomes. It allows within-country and between-country comparison, as well as time trend analysis, which no other survey-based index provides.FundingBill & Melinda Gates Foundation.
Just five words… ‘How physically active are you?’
Authors: Abigail Guerrier Sadler
Journal: British Journal of Sports Medicine (2017)

I have read with interest articles published by British Journal of Sports Medicine in recent years highlighting the need for greater emphasis on physical activity (PA) in medical student curricula.1 2 Physical inactivity debilitates the nation and puts pressure on the UK National Health Service (NHS).3 PA reduces type 2 diabetes risk, cardiovascular disease and obesity, as well as improves mental well-being.4 5 Despite the importance of regular PA, it is not routinely included in health conversations with patients. I agree with Osborne et al 1 that medical school should provide students with the skills to discuss and advise patients on PA, but this should extend to …
Abstract P326: An Innovative Peptide Spectral Library Search Engine for Cardiovascular Proteomics
Authors: Haomin Li, Ning Deng, Nobel Zong, Anna Zolyan, Melissa Chan, Jenny Kim, Rolf Apweiler, Huilong Duan, Peipei Ping
Journal: Circulation Research (2011)

We developed a peptide spectral library search engine for the cardiovascular community. Over 50,000,000 spectra obtained with LTQ-Orbitrap instrument on cardiac mitochondria and proteasome were analyzed, and 108,268 representative spectra were included in this organelle-based library. An improved dot product algorithm, slide dot product, was coded to query user spectra against spectra in the library. This procedure provides a solution to optimally balance the speed and sensitivity in peptide identification. In addition, an innovative noise decoy protocol was engineered to distinguish spectra correlation attributed to noise signals of the analytical instruments. The immediate advantages include an effective improvement of both specificity and accuracy in protein identification, overcoming a long-lasting concern in experimental spectra library, the possibility of propagating spectra with inaccuracy and error. With an independent test dataset collected by LTQ-Orbitrap (∼10,000 spectra), this novel search engine identified 20% more spectra matches within 10% analytical time compared to other existing theoretical database search route. Furthermore, the broad utility of this search engine was also demonstrated in characterizing spectra collected by LCQ and Q-TOF instrumentation. This peptide spectral library search engine has been incorporated into the Cardiac Organellar Peptide Atals Library (COPa Library) of NHLBI Proteomics Center at UCLA and will be made accessible at www.HeartProteome.org .
Liver disease predicts mortality in patients with X-linked immunodeficiency with hyper-IgM but can be prevented by early hematopoietic stem cell transplantation
Authors: Vian Azzu, Lucinda Kennard, Beatriz Morillo-Gutierrez, Mary Slatter, J. David M. Edgar, Dinakantha S. Kumararatne, William J.H. Griffiths
Journal: Journal of Allergy and Clinical Immunology (2017)
TPF plus cetuximab (E) induction chemotherapy (ICT) followed by biochemoradiation (BCRT) with weekly E plus weekly cisplatin (P) or carboplatin (C) in stage III/IV squamous cell carcinoma of the head and neck (HNSCC): A randomized phase II EORTC trial.
Authors: Pol M. Specenier, Eva Remenar, J. Buter, Dirk L. Schrijvers, Lisa F. Licitra, Ahmad Awada, Paul M. Clement, Catherine Fortpied, Ravi Karra Gurunath, Jan Baptist Vermorken
Journal: Journal of Clinical Oncology (2016)

6076Background: To test the safety of BCRT with P and C after TPF-E. Methods: Stage III/IV unresectable, HNSCC pts received up to 4 cycles (cy) of TPF-E (P and docetaxel [D] 75 mg/m² d 1, 5-FU 750 mg/m²/d d1-5, cetuximab [E, 400/250 mg/m²/wk]), with prophylactic antibiotics, no G-CSF. Pts with no PD after 4 cy were randomly assigned to BCRT (70 Gy/7 weeks/2 Gy fractions), weekly E, with either P 40 mg/m²/wk or C AUC 1.5/wk. Primary endpoint: feasibility of BCRT ( > 80% dose intensity (DI) of RT, P or C, and E). Results: 46 patients started TPF-E, 30 started BCRT. Median age: 57 (48-72), 41 male. WHO 0/1: 29/17. Stage III/IV: 4/42. 4 oral cavity, 24 oropharynx, 12 hypopharynx, 4 larynx, 2 unknown. 34, 4, 6, 2 pts received 4,3,2, and 1 TPF-E cy. Median DI (mg/m²/wk): D: 24.4, P: 24.4, 5-FU: 1220.9, E: 255.4. ICT was discontinued in 12 pts (6 toxicity [1 grade 5], 1 protocol violation, 2 medical decision, 1 pt refusal, 1 death [cause unknown], 1 cerebrovascular accident). 3 were not randomized: 1 PD under IC...
Proteogenomic Landscape of Squamous Cell Lung Cancer
Authors: P.A. Stewart, R.J.C. Slebos, E.A. Welsh, L. Cen, Y. Zhang, Z. Chen, C.-H. Cheng, F. Pettersson, A. Berglund, G. Zhang, B. Fang, V. Izumi, S. Yoder, K. Fellows, Y.A. Chen, J.K. Teer, S.A. Eschrich, J.M. Koomen, E.B. Haura
Journal: Journal of Thoracic Oncology (2017)
Diagnostic Accuracy of Coronary CT Angiography for the Evaluation of Bioresorbable Vascular Scaffolds
Authors: Carlos Collet, Bernard Chevalier, Angel Cequier, Jean Fajadet, Marcello Dominici, Steffen Helqvist, Ad J. Van Boven, Dariusz Dudek, Dougal McClean, Manuel Almeida, Jan J. Piek, Erhan Tenekecioglu, Antonio Bartorelli, Stephan Windecker, Patrick W. Serruys, Yoshinobu Onuma
Journal: JACC. Cardiovascular imaging (2017)
Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R. Elphick, Paola Oliveri
Journal: Genome biology (2018)

Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm-the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ .
AB0363 Results of screening for viral hepatitis in ra patients treated with biologics: hur-bio real life results
Authors: A Sari, B Armagan, A Erden, L Kilic, A Akdogan, S Apras Bilgen, I Ertenli, U Kalyoncu, S Kiraz
Journal: Annals of the Rheumatic Diseases (2017)

<h3>Background</h3> Turkish Society of Rheumatology (TSR) proposed a guideline of recommendations for viral hepatitis screening before biological therapy in 2015.<sup>1</sup> <h3>Objectives</h3> The aim of this study was to assess results of viral hepatitis serological tests performed before biologics in RA patients. <h3>Methods</h3> HUR-BIO (Hacettepe University Rheumatology Biologic Registry) is a prospective,single center database of biological treatments including 1229 RA patients by August 2016. Results of serological tests for HBV of 468 RA patients were evaluated. The guideline includes 5 groups according to hepatitis B virus (HBV) serology; group 1 –HBV seronegative [HbsAg (-),anti HbS (-), anti-Hbc total (-)], group 2-vaccinated [HBsAg (-), anti-HBs (+), anti-HBc total (-)], group 3-previous HBV infection [HBsAg (-), anti-HBs (-), anti-HBc total (+)], group 4- Chronic HBV infection [HBsAg (+), anti-HBs (-), anti-HBc total (+)], group 5- secondary immunity [HBsAg (-), anti-HBs (+), anti-HBc total (+)]. Patients were also classified according to risk for HBV reactivation as very high risk (Group 4 patients receiving rituximab), high risk (group 3 patients receiving rituximab) and medium risk (Group3 or Group 4 patients receiving TNFi or T-cell blockers,IL12/23 pathway inhibitor). Screening results for hepatitis C virus (HCV) were also evaluated. <h3>Results</h3> Among 1229 patients (79.7% female), mean age was 54.9±11.7 and mean disease duration was 12.3±8.2 years. In total, 104 (22.2%) of patients had received rituximab. Serology for HbsAg, anti-Hbs and anti-HbC were avaliable in 468 patients. There were 273 (58.3%) patients in group 1, 81 (17.3%) in group 2, 19 (4.1%) in group 3, 9 (1.9%) in group 4 and 86 (18.3%) in group 5. Table 1 represents distribution of patients according to HBV reactivation risk. Anti-HCV was positive in 21 (2.5%) of patients. <h3>Conclusions</h3> Among patients registered in HUR-BIO, 1.9% had chronic HBV infection and 2.5% anti-HCV positivity. 5.0% of them were under high and/or very high risk for HBV reactivation. Medium risk group which includes 17.0% of patients, seems to deserve most of the attention. Screening for viral hepatitis must be performed before biologics and TSR guideline may be useful in this matter. <h3>References</h3> Karadag O, Kasifoglu T et al. Guideline of the viral hepatitis screening before biologic agents use in patients with rheumatic diseases. RAED Journal;7:28–32. <h3>Disclosure of Interest</h3> None declared
Pharmaceutical companies’ policies on access to trial data, results, and methods: audit study
Authors: Ben Goldacre, Síle Lane, Kamal R Mahtani, Carl Heneghan, Igho Onakpoya, Ian Bushfield, Liam Smeeth
Journal: BMJ (2017)

Objectives To identify the policies of major pharmaceutical companies on transparency of trials, to extract structured data detailing each companies' commitments, and to assess concordance with ethical and professional guidance.Design Structured audit.Setting Pharmaceutical companies, worldwide.Participants 42 pharmaceutical companies.Main outcome measures Companies' commitments on sharing summary results, clinical study reports (CSRs), individual patient data (IPD), and trial registration, for prospective and retrospective trials.Results Policies were highly variable. Of 23 companies eligible from the top 25 companies by revenue, 21 (91%) committed to register all trials and 22 (96%) committed to share summary results; however, policies commonly lacked timelines for disclosure, and trials on unlicensed medicines and off-label uses were only included in six (26%). 17 companies (74%) committed to share the summary results of past trials. The median start date for this commitment was 2005. 22 companies (96%) had a policy on sharing CSRs, mostly on request: two committed to share only synopses and only two policies included unlicensed treatments. 22 companies (96%) had a policy to share IPD; 14 included phase IV trials (one included trials on unlicensed medicines and off-label uses). Policies in the exploratory group of smaller companies made fewer transparency commitments. Two companies fell short of industry body commitments on registration, three on summary results. Examples of contradictory and ambiguous language were documented and summarised by theme. 23/42 companies (55%) responded to feedback; 7/1806 scored policy elements were revised in light of feedback from companies (0.4%). Several companies committed to changing policy; some made changes immediately.Conclusions The commitments made by companies to transparency of trials were highly variable. Other than journal submission for all trials within 12 months, all elements of best practice were met by at least one company, showing that these commitments are realistic targets.
The Saliva Exposome for Monitoring of Individuals’ Health Trajectories
Authors: Vincent Bessonneau, Janusz Pawliszyn, Stephen M. Rappaport
Journal: Environmental Health Perspectives (2017)

Background: There is increasing evidence that environmental, rather than genetic, factors are the major causes of most chronic diseases. By measuring entire classes of chemicals in archived biospecimens, exposome-wide association studies (EWAS) are being conducted to investigate associations between a myriad of exposures received during life and chronic diseases. Objectives: Because the intraindividual variability in biomarker levels, arising from changes in environmental exposures from conception onwards, leads to attenuation of exposure–disease associations, we posit that saliva can be collected repeatedly in longitudinal studies to reduce exposure–measurement errors in EWAS. Methods: From the literature and an open-source saliva–metabolome database, we obtained concentrations of 1,233 chemicals that had been detected in saliva. We connected salivary metabolites with human metabolic pathways and PubMed Medical Subject Heading (MeSH) terms, and performed pathway enrichment and pathway topology analyses. Results: One hundred ninety-six salivary metabolites were mapped into 49 metabolic pathways and connected with human metabolic diseases, central nervous system diseases, and neoplasms. We found that the saliva exposome represents at least 14 metabolic pathways, including amino acid metabolism, TCA cycle, gluconeogenesis, glutathione metabolism, pantothenate and CoA biosynthesis, and butanoate metabolism. Conclusions: Saliva contains molecular information worthy of interrogation via EWAS. The simplicity of specimen collection suggests that saliva offers a practical alternative to blood for measurements that can be used to characterize individual exposomes. https://doi.org/10.1289/EHP1011
FFA4/GPR120: Pharmacology and Therapeutic Opportunities
Authors: Graeme Milligan, Elisa Alvarez-Curto, Brian D. Hudson, Rudi Prihandoko, Andrew B. Tobin
Journal: Trends in Pharmacological Sciences (2017)

Free Fatty Acid receptor 4 (FFA4), also known as GPR120, is a G-protein-coupled receptor (GPCR) responsive to long-chain fatty acids that is attracting considerable attention as a potential novel therapeutic target for the treatment of type 2 diabetes mellitus (T2DM). Although no clinical studies have yet been initiated to assess efficacy in this indication, a significant number of primary publications and patents have highlighted the ability of agonists with potency at FFA4 to improve glucose disposition and enhance insulin sensitivity in animal models. However, the distribution pattern of the receptor suggests that targeting FFA4 may also be useful in other conditions, ranging from cancer to lung function. Here, we discuss and contextualise the basis for these ideas and the results to support these conclusions.
Evaluation of an innovative retinoid, Ro 41-5253, as a chemopreventive agent
Authors: Sandro Grilli, Maria Grazia Mascolo, Paola Silingardi, Wolfango Horn, Daniela Chiozzotto, Cinzia Severini, Laura Zanghi, Monica Vaccari, Annamaria Colacci
Journal: Cancer Research (2005)

6078  Retinoids have been used as chemopreventive agents in the treatment of different tumors including breast cancer. The synthetic retinoid Ro 41-5253 (Ro) is a selective RARalfa antagonist, exerting antiproliferative activity without inducing the known toxic side effects of retinoids. A pattern of in vitro tests was performed in order to verify the potential chemopreventive activity of Ro. The ability of Ro to inhibit the 3-MCA induced cell transformation was assessed by a modified BALB/c 3T3 cell transformation assay. The plating efficiency and the proliferation rate of BALB/c 3T3 clone A31 cells were significantly reduced when the cells were exposed to 10 μM Ro. In the anti-transformation assay, carcinogen-treated BALB/c-3T3 cells were chronically exposed to several concentrations (0.1-10 μM) of Ro throughout the duration of the experiment. A dose-related reduction of the transformation frequency (TF) induced by Ro was observed . A significant inhibition of foci occurrence was detected after the chronic administration of 1 e 10 μM Ro. The potential anti-cancer effects of Ro were also analyzed on human breast and colon carcinoma cell models, differing for the estrogen receptor expression (MCF-7 and Caco-2, ER+; HuMi-TTu2 and HT29, ER-). The GI50 values showed a different degree of susceptibility of the assayed cell lines (HT29 > Caco-2 > HuMi-TTu2 = MCF-7). These toxicological profiles, which were evaluated in both cytotoxicity and viability assays, were suggestive of apoptosis induction. The enhancement of apoptotic cell death 4 and 6 days after the exposure to 0.01-10 μM Ro was dose- and time-dependent. The growth of breast and colon cell lines in soft agar was strongly reduced by Ro treatment; the number of colonies in the semisolid medium was lowered nearly by 50% at 0.1 μM Ro. The experimental results showed that Ro was able to modulate either the programmed cell death and the anchorage independent growth, which are key steps in the neoplastic process. Ten μM Ro was the most effective dose in the antitransformation assay since it almost completely inhibited the clonogenicity. Ro 41-5253 seemed to be effective in inhibiting both chemical transformation and proliferation of malignant cells. Results gave also evidence for a high responsiveness of the target cells to this potential antitumor agent, therefore Ro could be regarded as a promising candidate for cancer therapy. This work was cofinanced by the National Research Program, Ministry of Education, University and Research (MIUR, Rome), and by Bologna University, Italy.
Prospective, Multicenter Clinical Trial of Everolimus As Primary Therapy in Waldenstrom Macroglobulinemia (WMCTG 09-214)
Authors: Steven P Treon, Kirsten Meid, Christina K. Tripsas, Leonard T. Heffner, Herbert Eradat, Ashraf Z Badros, Lian Xu, Zachary Hunter, Guang Yang, Christopher J Patterson, Joshua Gustine, Jorge J. Castillo, Jeffrey V. Matous, Irene M. Ghobrial
Journal: Blood (2016)
D-mannose induces regulatory T cells and suppresses immunopathology
Authors: Dunfang Zhang, Cheryl Chia, Xue Jiao, Wenwen Jin, Shimpei Kasagi, Ruiqing Wu, Joanne E Konkel, Hiroko Nakatsukasa, Peter Zanvit, Nathan Goldberg, Qianming Chen, Lingyun Sun, Zi-Jiang Chen, WanJun Chen
Journal: Nature Medicine (2017)
E-cigarette use and associated changes in population smoking cessation: evidence from US current population surveys
Authors: Shu-Hong Zhu, Yue-Lin Zhuang, Shiushing Wong, Sharon E Cummins, Gary J Tedeschi
Journal: BMJ (2017)

<b>Objective</b>&nbsp;To examine whether the increase in use of electronic cigarettes in the USA, which became noticeable around 2010 and increased dramatically by 2014, was associated with a change in overall smoking cessation rate at the population level. <b>Design</b>&nbsp;Population surveys with nationally representative samples. <b>Setting</b>&nbsp;Five of the US Current Population Survey-Tobacco Use Supplement (CPS-TUS) in 2001-02, 2003, 2006-07, 2010-11, and 2014-15. <b>Participants</b>&nbsp;Data on e-cigarette use were obtained from the total sample of the 2014-15 CPS-TUS (n=161 054). Smoking cessation rates were obtained from those who reported smoking cigarettes 12 months before the survey (n=23 270). Rates from 2014-15 CPS-TUS were then compared with those from 2010-11 CPS-TUS (n=27 280) and those from three other previous surveys. <b>Main outcome measures</b>&nbsp;Rate of attempt to quit cigarette smoking and the rate of successfully quitting smoking, defined as having quit smoking for at least three months. <b>Results</b>&nbsp;Of 161 054 respondents to the 2014-15 survey, 22 548 were current smokers and 2136 recent quitters. Among them, 38.2% of current smokers and 49.3% of recent quitters had tried e-cigarettes, and 11.5% and 19.0% used them currently (every day or some days). E-cigarette users were more likely than non-users to attempt to quit smoking, 65.1% <i>v</i> 40.1% (change=25.0%, 95% confidence interval 23.2% to 26.9%), and more likely to succeed in quitting, 8.2% <i>v</i> 4.8% (3.5%, 2.5% to 4.5%). The overall population cessation rate for 2014-15 was significantly higher than that for 2010-11, 5.6% <i>v</i> 4.5% (1.1%, 0.6% to 1.5%), and higher than those for all other survey years (range 4.3-4.5%). <b>Conclusion</b>&nbsp;The substantial increase in e-cigarette use among US adult smokers was associated with a statistically significant increase in the smoking cessation rate at the population level. These findings need to be weighed carefully in regulatory policy making regarding e-cigarettes and in planning tobacco control interventions.
Clinical significance of monitoring <i>KRAS</i> in the blood of pancreatic cancer patients.
Authors: Fumiaki Watanabe, Koichi Suzuki, Kosuke Ichida, Yuji Takayama, Taro Fukui, Nao Kakizawa, Yuhei Endo, Yuji Kaneda, Hiroshi Noda, Toshiki Rikiyama
Journal: Journal of Clinical Oncology (2017)

e23042 Background: KRAS monitoring provides valuable information for early diagnosis and prediction of treatment outcome in colorectal cancer. KRAS mutation is observed in only half of colon cancer patients, whereas it is detected in 90% of pancreatic cancer patients. Therefore, investigating tumor DNA in blood by KRAS monitoring may be even more valuable in pancreatic cancer patients. In this study, we elucidated the clinical significance of KRAS monitoring in pancreatic cancer patients during treatment. Methods: KRAS in tumor tissues was analyzed for mutations by Scorpion ARMS or RASKET in 38 patients with pancreatic tumors. KRAS in blood was analyzed for mutations (G12D, G12V, G12C, G12A, G12S, G12R, G13D, Q61L, and Q61H) using droplet digital polymerase chain reaction in 23 patients who underwent chemotherapy and who had KRAS mutation in their tissues. Results: KRAS mutation in tumor tissues was detected in 27 of 38 patients (71.1%). These 27 patients showed significantly poorer prognosis (24.4 months median overall survival time [MST]) than the six patients without mutation (p = 0.04), who were all alive. Patients with mutation of 12D in tumor tissues showed better prognosis than patients with other types of mutation; thus, mutation of 12D may have a different biological effect to other mutations. Monitoring of KRAS in blood revealed KRAS mutation in 14 of 23 patients (60.9%). These 14 patients exhibited significantly poorer treatment outcomes than patients without mutation. The MST of patients with KRAS mutation in their blood was significantly shorter than that of patients without KRAS mutation (17.7 months vs. 44.3 months, p = 0.03). Conclusions: KRAS mutation in blood could be a valuable predictive and prognostic biomarker in pancreatic cancer patients who undergo chemotherapy. Additionally, assessment of KRAS in tumor tissues may provide information about individual tumor biology.