tbuckley/cabot-search huggingface dataset:
Abstract LB-231: Decoding complex patterns of structural variations in hepatocellular carcinoma.
Authors: Julio Fernandez-Banet, Nikki P. Lee, Kin Tak Chan, Huan Gao, Xiao Liu, Wing Kin Sun, Winnie Tan, Sheung Tat Fan, Ronnie T. Poon, Shiyong Li, Keith Ching, Paul Rejto, Mao Mao, Zhengyan Kan
Journal: Cancer Research (2013)

Abstract Elucidating the molecular basis of Hepatocellular Carcinoma (HCC) is crucial to developing targeted diagnostics and therapies for this deadly disease. Somatically acquired structural variations (SVs) can lead to oncogenic gene fusions and gene expression deregulation in tumors. Although recent studies have delineated HCC genomic alterations including copy number variations, somatic mutations and HBV integrations, the landscape of SVs remains poorly characterized in HCC. We have predicted 4,314 SVs including large-scale insertions, deletions, inversions and translocations based on the whole-genome sequencing data for 88 primary HCC tumor/non-tumor tissues. We identified chromothripsis in 5 HCC genomes (5.7%) recurrently affecting chromosomal arms 1q and 8q. TP53 and RB1 alterations appear to cause increased levels of genomic arrangement and chromosomal instability. Albumin (ALB) was found to be the most significantly affected by SVs and harbor genomic alterations including deactivating mutations and deletions in 10.2% of cohort. Integrative analysis revealed a causal link between genomic rearrangements and copy number variations, such as focal amplifications of the CCND1/FGF19 loci, and distinctive patterns of copy number variation flanking SV breakpoints. Furthermore, we predicted 260 gene fusions which frequently result in aberrant over-expression of the 3′ genes in tumors. Citation Format: Julio Fernandez-Banet, Nikki P. Lee, Kin Tak Chan, Huan Gao, Xiao Liu, Wing Kin Sun, Winnie Tan, Sheung Tat Fan, Ronnie T. Poon, Shiyong Li, Keith Ching, Paul Rejto, Mao Mao, Zhengyan Kan. Decoding complex patterns of structural variations in hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-231. doi:10.1158/1538-7445.AM2013-LB-231
Associations of kidney disease measures with mortality and end-stage renal disease in individuals with and without diabetes: a meta-analysis
Authors: Caroline S Fox, Kunihiro Matsushita, Mark Woodward, Henk JG Bilo, John Chalmers, Hiddo J Lambers Heerspink, Brian J Lee, Robert M Perkins, Peter Rossing, Toshimi Sairenchi, Marcello Tonelli, Joseph A Vassalotti, Kazumasa Yamagishi, Josef Coresh, Paul E de Jong, Chi-Pang Wen, Robert G Nelson
Journal: The Lancet (2012)
The Effect of Treatment Expectation on Drug Efficacy: Imaging the Analgesic Benefit of the Opioid Remifentanil
Authors: Ulrike Bingel, Vishvarani Wanigasekera, Katja Wiech, Roisin Ni Mhuircheartaigh, Michael C. Lee, Markus Ploner, Irene Tracey
Journal: Science Translational Medicine (2011)

An individual’s expectation that a pain treatment will or will not work can alter both its subjective effectiveness and the pain-related activity in the brain.
Corticosteroid injections for osteoarthritis of the knee: meta-analysis
Authors: Bruce Arroll, Felicity Goodyear-Smith
Journal: BMJ (2004)

Objectives To determine the efficacy of intra-articular corticosteroid injections for osteoarthritis of the knee and to identify numbers needed to treat. Data sources Cochrane controlled trials register, Medline (1966 to 2003), Embase (1980 to 2003), hand searches, and contact with authors. Inclusion criteria Randomised controlled trial in which the efficacy of intra-articular corticosteroid injections for osteoarthritis of the knee could be ascertained. Results In high quality studies, the pooled relative risk for improvement in symptoms of osteoarthritis of the knee at 16-24 weeks after intra-articular corticosteroid injections was 2.09 (95% confidence interval 1.2 to 3.7) and the number needed to treat was 4.4. The pooled relative risk for improvement up to two weeks after injections was 1.66 (1.37 to 2.0). The numbers needed to treat to get one improvement in the statistically significant studies was 1.3 to 3.5 patients. Conclusion Evidence supports short term (up to two weeks) improvement in symptoms of osteoarthritis of the knee after intra-articular corticosteroid injection. Significant improvement was also shown in the only methodologically sound studies addressing longer term response (16-24 weeks). A dose equivalent to 50 mg of prednisone may be needed to show benefit at 16-24 weeks.
Cabergoline plus Lanreotide for Ectopic Cushing's Syndrome
Authors: Rosario Pivonello, Diego Ferone, Steven W J Lamberts, Annamaria Colao
Journal: New England Journal of Medicine (2005)

myocardial dysfunction developed in our patient after the administration of doxorubicin in a single dose well below that typically associated with cardiotoxic effects.The rapid improvement in left ventricular function observed in this patient within four weeks suggests that substantial myocardial stunning was present.Although it is very rare, acute reversible left ventricular failure should be considered in patients in whom respiratory failure or shock develops after the administration of even a single dose of doxorubicin.
Clinical Value of Routine Serum Squamous Cell Carcinoma Antigen in Follow-Up of Patients With Early-Stage Cervical Cancer
Authors: Martha D. Esajas, Jitze M. Duk, Henk W.A. de Bruijn, Jan G. Aalders, Pax H.B. Willemse, Wim Sluiter, Betty Pras, Klaske ten Hoor, Harry Hollema, Ate G.J. van der Zee
Journal: Journal of Clinical Oncology (2001)

To investigate the contribution to recurrence detection and survival of serum squamous cell carcinoma antigen (SCC-ag) analysis in the follow-up of early-stage cervical cancer patients.Follow-up data were evaluated in patients with early-stage squamous cell cervical cancer treated by radical hysterectomy and pelvic lymphadenectomy with or without radiotherapy. Routine serum SCC-ag determination was performed at each follow-up visit.Recurrent disease occurred in 35 (16%) of 225 patients and was preceded or accompanied by serum SCC-ag elevation 26 times (sensitivity, 74%). In five (14%) of these 35 patients, elevated serum SCC-ag was the first measured clinical indicator. Desite salvage therapy, all five patients died of disease. In the other 31 patients (21 with serum SCC-ag elevation), either symptoms and/or positive signs led to recurrence detection. Median survival time after recurrence was worse (9 months; range, 2 to 112+) for patients with an elevated serum SCC-ag value at recurrence in comparison with patients with normal serum SCC-ag values (20 months; range, 4 to 96; P <.01). In 23 of the 190 patients without recurrences, serum SCC-ag values became falsely elevated. In 16 of these 23 patients, the repeat sample after 6 weeks showed a normal SCC-ag, and in seven patients benign (especially skin) disorders were found.Serum SCC-ag analysis results in earlier recurrence detection in a small proportion (14%) of patients but did not contribute to better survival. As long as treatment possibilities for recurrent cervical cancer patients are not improved, serum SCC-ag analysis should not be carried out in routine follow-up.
Outbreak of Salmonella Montevideo associated with a dietary food supplement flagged in the Rapid Alert System for Food and Feed (RASFF) in Germany, 2010
Authors: P Stöcker, B Rosner, D Werber, M Kirchner, A Reinecke, H Wichmann-Schauer, R Prager, W Rabsch, C Frank
Journal: Eurosurveillance (2011)

Binary file ES_Abstracts_Final_ECDC.txt matches
Apoptosis and Caspase-3 in Experimental Anti-Glomerular Basement Membrane Nephritis
Authors: BIN YANG, TIMOTHY S. JOHNSON, GRAHAM L. THOMAS, PHILIP F. WATSON, BART WAGNER, A. MEGUID EL NAHAS
Journal: Journal of the American Society of Nephrology (2001)

Abstract. The caspase family is central to the proteolytic events of apoptosis. In particular, caspase-3 plays a key role in the execution of apoptosis. However, the importance of caspase-3 in renal cell apoptosis during kidney scarring has not been established. Here, nephrotoxic nephritis (NTN) was induced in Wistar Kyoto rats by a single intravenous injection of rabbit anti-rat glomerular basement membrane serum, with analysis at days 7, 15, 30, and 45 after injection. Cell apoptosis ( in situ end labeling of DNA, light and electron microscopy), proliferation (proliferating cell nuclear antigen-positive cells), and inflammation (ED1-positive cells) all increased in NTN kidneys, peaking early (day 7) in the glomeruli and later (days 30 to 45) in the tubules and interstititum. The expression of caspase-3 mRNA (Northern blotting) was increased in NTN kidneys on days 7, 30, and 45 (173.3%, 228%, and 241.7%, respectively; P &lt; 0.05). Western blotting showed that a 24-kD protein band (caspase-3 active subunit) increased with time in NTN kidneys ( P &lt; 0.01) and reached a maximum on day 45 (6.08-fold increase). A 32 kD band (caspase-3 precursor) was also increased on day 45 (3.92-fold; P &lt; 0.01). Elevated caspase-3 activity (two- to threefold) was observed in NTN kidneys at all time points ( P &lt; 0.01). Upregulated expression of caspase-3 at all levels positively correlated with apoptosis, whereas both correlated closely with inflammation, proliferation, and subsequent fibrosis in glomeruli, tubules, and interstitium ( P &lt; 0.05). Inhibition of caspase-3 during the course of experimental nephritis may offer a new therapeutic approach for the prevention of renal apoptosis and the associated renal tubular atrophy and fibrosis.
Energy expenditure during a single-handed transatlantic yacht race
Authors: S D Myers, S M Leamon, V R Nevola, M G L Llewellyn
Journal: British Journal of Sports Medicine (2007)

Background: The popularity of sports that expose people to consecutive days of high-intensity physical activity continues to increase. The ability to adequately nourish the human body to sustain the required level of competitive performance may be a key contributor to success in such events. Methods: The energy expenditure of a male competitor in a single-handed, transatlantic race (Transat 2004) was assessed using the doubly-labelled water technique. Results: Mean total daily energy expenditure (TDEE) during the race (13 days) was 14.5 MJ/day with a peak expenditure of 18.6 MJ during the most physically demanding 24-hour period. Discussion: This mean TDEE was approximately 25% lower than that reported in a previous study (14.5 vs. 19.3 MJ/day) for a 13-day leg of a fully crewed offshore race. The difference in results was probably due to the fact that in the previous study, the crew operated in “watches” (work shifts), affording each crew member greater opportunity to eat, rest and sleep. Effective planning and efficient management of resources is essential to the success of the solo sailor. However, the extent to which maintenance of energy balance underpins competitive success remains to be established. To maintain energy balance during the race, a mean daily energy intake of 14.5 MJ/day was necessary for the subject in this study. However, this mean value for energy intake would have been inadequate to match the peak energy expended during the most physically demanding 24 hours of the race.
Influence of noninvasive positive pressure ventilation on inspiratory muscle activity in obese subjects
Authors: W Pankow, N Hijjeh, F Schuttler, T Penzel, HF Becker, JH Peter, P von Wichert
Journal: European Respiratory Journal (1997)

Noninvasive positive pressure ventilation (NPPV) can improve ventilation in obese subjects during the postoperative period after abdominal surgery. Compared to nasal continuous positive airway pressure (nCPAP), NPPV was superior in correcting blood gas abnormalities both during the night-time and during the daytime in a subgroup of patients with the obesity hypoventilation syndrome (OHS). However, as it is unknown, if and to what extent NPPV can unload the respiratory muscles in the face of the increased impedance of the respiratory system in obesity, this is what was investigated. Eighteen obese subjects with a body mass index &gt; or = 40 kg x m(-2) were investigated during the daytime, which included five healthy controls (simple obesity (SO)), seven patients with obstructive sleep apnoea (OSA) and six patients with the obesity hypoventilation syndrome (OHS). Assisted PPV was performed with bi-level positive airway pressure (BiPAP), applied via a face mask. Inspiratory positive airway pressure (IPAP) was set to 1.2 or 1.6 kPa and expiratory positive airway pressure (EPAP) was set to 0.5 kPa. Inspiratory muscle activity was measured as diaphragmatic pressure time product (PTPdi). Comparison of spontaneous breathing with BiPAP ventilation showed no significant difference in breathing pattern, although there was a tendency towards an increase in tidal volume (VT) in all three groups and a decrease in respiratory frequency (fR) in patients with OSA and OHS. End-tidal carbon dioxide (PET,CO2) with BiPAP was unchanged in SO and OSA, but was decreased in OHS. In contrast, inspiratory muscle activity was reduced by at least 40% in each group. This was indicated by a decrease in PTPdi with BiPAP 1.2/0.5 kPa from mean+/-SD 39+/-5 to 20+/-9 kPa x s (p&lt;0.05) in SO, from 42+/-7 to 21+/-8 kPa x s (p&lt;0.05) in OSA, and from 64+/-20 to 38+/-17 kPa x s (p&lt;0.05) in OHS. With BiPAP 1.6/0.5 kPa, PTPdi was further reduced to 17+/-6 kPa x s in SO, and to 17+/-6 kPa x s in OSA, but not in OHS (40+/-22 kPa x s). We conclude that noninvasive assisted ventilation unloads the inspiratory muscles in patients with gross obesity.
Intensive Dose-Dense Compared With Conventionally Scheduled Preoperative Chemotherapy for High-Risk Primary Breast Cancer
Authors: Michael Untch, Volker Möbus, Walther Kuhn, Bernd Rudolph Muck, Christoph Thomssen, Ingo Bauerfeind, Nadia Harbeck, Christoph Werner, Annette Lebeau, Andreas Schneeweiss, Stephen Kahlert, Franz von Koch, Karl Ulrich Petry, Diethelm Wallwiener, Rolf Kreienberg, Ute-Susann Albert, Hans-Joachim Lück, Axel Hinke, Fritz Jänicke, Gottfried E. Konecny
Journal: Journal of Clinical Oncology (2009)

Purpose To compare preoperative intense dose-dense (IDD) chemotherapy with conventionally scheduled preoperative chemotherapy in high-risk primary breast cancer (BC). Patients and Methods In this randomized phase III trial a total of 668 eligible primary BC patients stratified for tumors ≥ 3 cm (n = 567) or inflammatory BC (n = 101) were randomly assigned to receive concurrent preoperative epirubicin/paclitaxel every 3 weeks or dose-dense and dose-escalated sequential epirubicin followed by paclitaxel every 2 weeks. All patients received three cycles of cyclophosphamide, methotrexate, and fluorouracil chemotherapy after surgery. Results IDD treatment significantly improved pathologic complete response rate (18% v 10%; odds ratio [OR] 1.89; P = .008), disease-free survival (DFS; hazard ratio [HR], 0.71; P = .011), and overall survival (OS; HR, 0.83; P = .041) compared to epirubicin/paclitaxel. Patients with inflammatory BC had a particularly poor prognosis and did not appear to benefit from IDD therapy in this trial (DFS HR, 1.10; P = .739; OS HR, 1.25; P = .544). In contrast, patients with noninflammatory BC significantly benefited from IDD treatment (DFS HR, 0.65, P = .005; OS HR, 0.77, P = .013). Treatment effects in multivariate analysis were significant for noninflammatory BC (DFS HR, 0.65, P = .015; OS HR, 0.79, P = .034), but not for all patients (DFS HR, 0.76; P = .088; OS HR, 0.82; P = .059). IDD therapy was associated with significantly more nonhematologic toxicities, anemia, and thrombocytopenia, but with similar neutropenia and infection rates. Conclusion Our results support the efficacy and short-term safety of IDD as preoperative chemotherapy. IDD was less well tolerated compared to standard treatment, but improved clinical outcomes in patients with noninflammatory high-risk primary BC.
Primary leiomyosarcoma of the lung
Authors: T. Ramanathan
Journal: Thorax (1974)

<b>Ramanathan, T. (1974).</b><i>Thorax</i>, 482-489. <b>Primary leiomyosarcoma of the lung.</b> Three new cases of primary leiomyosarcoma of the lung are presented. The relevant literature has been reviewed. The similarity in the clinical features between bronchogenic carcinoma and leiomyosarcoma is emphasized. The only distinctive feature of leiomyosarcoma is the absence of lymph node involvement.
Value of Coronary Artery Calcium Scanning by Computed Tomography for Predicting Coronary Heart Disease in Diabetic Subjects
Authors: Wenchun Qu, Thuy T. Le, Stanley P. Azen, Min Xiang, Nathan D. Wong, Terence M. Doherty, Robert C. Detrano
Journal: Diabetes Care (2003)

OBJECTIVE—The South Bay Heart Watch is a cohort study designed to determine the significance of coronary calcium in high-risk asymptomatic patients. This is a report of the relative risk (RR) for outcomes of coronary artery calcium in diabetic and nondiabetic subjects. RESEARCH DESIGN AND METHODS—A total of 1,312 diabetic and nondiabetic subjects underwent risk factor screening and computed tomography testing for coronary calcium at baseline and were followed clinically for 6.3 ± 1.4 years. End points were either 1) hard events of nonfatal myocardial infarction (MI) or coronary death or 2) any cardiovascular event (nonfatal MI, coronary death, coronary revascularization, or stroke). RESULTS—The incidence rates of a hard event and any cardiovascular event for diabetic and nondiabetic subjects were 14.5 and 6.1% and 23.8 and 12.2%, respectively (P &amp;lt; 0.001). Cox regression analyses of the combined risk relationship of diabetes status and calcium score demonstrated that relative to nondiabetic subjects with low calcium scores (&amp;lt;2.8), diabetic subjects with calcium scores ≥2.8 exhibited at least a fourfold increase in the risk of either a hard or any cardiovascular event (P &amp;lt; 0.001). Cox regression analyses conducted separately for nondiabetic and diabetic subjects revealed that coronary calcium score risk groups were significantly associated with events in nondiabetic subjects (RR ≥ 2.6, P ≤ 0.01), but not in diabetic subjects (RR ≤ 1.7, P &amp;gt; 0.05). CONCLUSIONS—The risk of coronary heart disease increases with increasing calcium scores and diabetes status. Calcium scores have less prognostic value in diabetic subjects.
Switching tumour necrosis factor antagonists in patients with ankylosing spondylitis and psoriatic arthritis: an observational study over a 5-year period
Authors: F. Conti, F. Ceccarelli, E. Marocchi, L. Magrini, F. R. Spinelli, A. Spadaro, R. Scrivo, G. Valesini
Journal: Annals of the Rheumatic Diseases (2007)

<h3>Objective:</h3> To evaluate the clinical response after switching from one tumour necrosis factor (TNF)α antagonist to another in patients with ankylosing spondylitis (AS) and psoriatic arthritis (PsA). <h3>Methods:</h3> In this ongoing, longitudinal, observational study, data were prospectively collected on efficacy and safety since 2000 for patients starting biological treatments. The present analysis was restricted to patients with a diagnosis of spondyloarthropathy (SpA) who switched from one TNFα antagonist to another because of inadequate efficacy or adverse events. <h3>Results:</h3> In total, 589 anti-TNFα-naive patients were registered, of whom 165 had a diagnosis of SpA; 7 patients with AS and 15 with PsA received &gt;1 TNFα antagonist. Two patients with PsA were treated with all the drugs. In all, 16 subjects switched from infliximab to etanercept, 7 from etanercept to adalimumab and 1 from etanercept to infliximab. Overall, a clinical response was seen in 75% of patients who changed from infliximab to etanercept, and in 57.1% who switched from etanercept to adalimumab. <h3>Conclusions:</h3> The findings of this study on a selected population of patients with SpA indicate that the failure of an initial TNFα antagonist does not preclude the response to another one. Further trials are needed to confirm this preliminary observation.
Patients get four choices for NHS treatments
Authors: Rebecca Coombes
Journal: BMJ (2006)

GPs making referrals for elective treatment now have to offer patients a choice of four providers, under changes that started on 2 January. New information leaflets have been prepared by the Department of Health, setting out which local treatment centres offer the services required by a patient. The leaflets include tables about performance, such as waiting times, rates of methicillin resistant Staphylococcus aureus infection, and cancelled operations.

Not all areas will offer the choice of an independent sector provider. Instead the selection will depend on which centres the local primary care trust chooses to commission. In Eastern Leicester, for example, …
Scalds of the elderly in residential care.
Authors: L. C. Bainbridge, M. J. Black
Journal: BMJ (1988)

2) Such consensus statements should be distributed to the medical profession, be made available upon request to all interested bodies, and be re- evaluated and updated on a regular basis.The demand on resources ofdifferent treatments should be included in these reviews.(3) Action should be taken to establish consensus panels without delay.This will require the active support of both physicians and those agencies con- cerned with the delivery ofcare to patients with cancer.(4) Savings achieved by rationalisation of cancer management should remain available for reallocation to other areas of cancer care.
Effects of obesity on lung function and SaO2 in children with habitual snoring
Authors: Valeria Lollobrigida, Anna Maria Zicari, Azzurra Cesoni Marcelli, Paola Pansa, Giovanni Ragusa, Lucia Leonardi, Giancarlo Tancredi, Marzia Duse
Journal: European Respiratory Journal (2012)

BACKGROUND: Habitual Snoring (HS) is a common pediatric condition with a prevalence ranged between 7 and 10 %. It has a multifactorial etiology and it is often associated with several comorbilities. Many studies showed low spirometric values in overweight and obese children, but the association with HS is still unclear.

AIM: The purpose of this Study is to evaluate the relationship between obesity, lung function and nocturnal minimum oxygen saturation (SaO2) in a pediatric population with HS.

METHODS: We enrolled 53 children (mean age 9,5, 34 male) in the Pediatric Department of Immunology and Allergology of Policlinico Umberto I in Rome. All patients were positive to a validated questionnaire for sleep disordered breathing, performed a spirometry and a nocturnal pulse oximetry. Percentile Body Mass Index (BMI) was calculated for each patient.

The selected patients were divided into 4 percentile BMI groups (Group I: percentile 0-25, group II: percentile 26-50, group III: percentile 51-75, group IV: percentile 76-100).

RESULTS: We found that group IV (BMI>75th percentile) had significantly lower values of SaO2 and forced expiratory volume in one second (FEV1) when compared with the other groups (respectively p<0,02 and p<0, 05).

CONCLUSIONS:Lung function (reduced FEV1) and minimum SaO2 areinfluenced by the progressive increase in percentile BMI with changes in FEV1 better demonstrated when BMI >75th percentile. Our findings suggest that in children with HS, the presence of obesity can cause a sistemic inflammatory pattern that negatively influence lung function and blood SaO.
New consultant contract marks huge step forward
Authors: P. Hawker
Journal: BMJ (2002)

EDITOR—You report that your 22 respondents were unanimous in their condemnation of the proposed new consultant contract.1 As the regional roadshows roll out and the detail is explained, views are changing.

We have succeeded in securing a contract that gives consultants a substantial pay rise, a time limited contract, recognition of emergency work, payment for being on- call, extra payments for working beyond 40 hours per week, protected time for teaching, research, audit and continuing professional development, and a major boost to their pensionable salary. There is a lot at stake here. I make no apologies for trying to persuade my colleagues that they should accept it.

Respondents complain of excessive management control. Consultants asked us to deliver a …