tbuckley/cabot-search huggingface dataset:
PTU-024 Reliability of Rockall Score Calculation and its Impact on Gastroscopy in Patients with Acute upper Gastrointestinal Bleed (Augib)
Authors: A Taranath, S Gupta, S Mallick
Journal: Gut (2013)

<h3>Introduction</h3> Documentation of Rockall score (RS) in patients with AUGIB should be accurate to prioritise patients for gastroscopy. We noticed that Rockall scores were being incorrectly calculated on electronic gastroscopy request forms and decided to analyse this further. We correlated RS with findings on gastroscopy <h3>Methods</h3> Information was retrospectively collected on 100 patients who presented with AUGIB over a 2 month period between September and November 2012. Demographics, time to gastroscopy, Rockall score (RS) documented by requesting doctor, RS calculated by going through patient records (including A &amp; E, paramedic entries) were recorded. We analysed patients whose RS was either under scored or over scored by the requesting doctor (as compared to the actual score as calculated by us) and correlated this with the electronic endoscopic records <h3>Results</h3> 100 patients were included in the study with 60 males (60%) and 40 females (40%), age ranging from 17 to 92, (mean 65.2, median 69.5). Presenting symptoms were melaena in 57% of patients, haematemesis in 27%, coffee grounds vomiting in 12% and combined melaena and haematemesis in 4%. RS was calculated in 52% by Foundation Year 1 trainees (FY1), in 10% by FY2s, in 26% by Senior House officers (SHO), in 6% by Locum SHOs, in 5% by Registrars and in 1% by a consultant. 46 out of 100 Rockall scores were incorrectly scored. 28 patients (60.9%) were over scored, while 18(39.1%) were underscored FY1s were responsible for incorrect scores in 27(58.7%) of patients, FY2 for 2 (4.3%), SHOs for 12(26%), locum SHOs for 3(6.5%) and registrars for 2(4.3%). Mean time from electronic booking to endoscopy was days in patients Mean time to Gastroscopy was day in of under scored patients day in of over scored patients. Of the 18 patients whose RS was under scored, 6 (33.3%) required endoscopic intervention with heater probe and Adrenalin injection. Of the 28 patients whose RS was over scored, only 3(10.7%) needed endoscopic intervention, while 5 of the 54 (9.2%) of the correctly scored patients needed endoscopic therapy. <h3>Conclusion</h3> It is important to calculate the RS correctly at the time of first presentation rather than at the time when the admitting doctor sees the patient. Observations from A&amp;E and ambulance records should be scrutinised to document the accurate RS thus helping endoscopy units to correctly prioritise patients for gastroscopy. Incorrect calculation of RS can have adverse impact on patient outcomes – under scored patients may be delayed while over scored patients may use up vital endoscopy slots. <h3>Disclosure of Interest</h3> None Declared
REVIEW OF CT COLONOGRAPHY: REAL-LIFE EXPERIENCE OF ONE THOUSAND CASES IN A TERTIARY REFERRAL CENTRE
Authors: A E Smyth, C F Healy, P MacMathuna, H M Fenlon
Journal: Gut (2013)

<h3>Introduction</h3> CT Colonography is increasingly being utilised to investigate patients with lower gastrointestinal symptoms and in screening for colorectal carcinoma in the at risk population. <h3>Aims/Background</h3> This review aimed to quantify results from a real life experience of 1000 CT Colonography examinations in a tertiary referral hospital campus. <h3>Method</h3> Data on patient demographics, indications and findings were analysed retrospectively from a dedicated database. <h3>Results</h3> Over a five year period (January 2008–December 2012) 1000 CT Colonography examinations were performed. The median age was 70 years (IQR 60–79). Patients were symptomatic in 86% of cases, screening accounted for 7% and surveillance in patients with a history of polyps or colorectal cancer for 7%. In 45% of patients it was documented that the study was performed following an incomplete optical colonoscopy. CT Colonography had normal or benign colonic findings in 75% of patients. 6% had incomplete examinations performed. Neoplasia was observed in 14%: colorectal carcinoma 6%, polyps &gt;1cm in 3% and 5% were found to have &lt;3 polyps of 6–9 mm. 5% had findings of wall thickening or strictures that were suspected to be benign but required further endoscopy and biopsy. There was an extracolonic finding that required further evaluation in 19% with 6% found to have a potentially clinically significant finding. There were no significant procedure related complications. <h3>Conclusion</h3> This review describes the real life experience of CT Colonography in a largely elderly, symptomatic patient group. In this patient group, CT Colonography safely confirmed the need for no further bowel tests in 75%, identified colorectal cancer in 6% and clinically significant extracolonic findings in 6% of cases without any significant complications.
Lupus-Erythematosus-like Syndrome with a Familial Defect of Complement
Authors: Benjamin Moncada, Noorbibi K. B. Day, Robert A. Good, Dorothy B. Windhorst
Journal: New England Journal of Medicine (1972)

Two siblings had illnesses consisting of combinations of fever, skin lesions, vasculitis, arthralgia and glomerular deposits that suggested lupus erythematosus (LE) or a similar connective-tissue syndrome. One other sibling had died of similar findings at the age of 12. Neither patient had any evidence of antibodies against DNA or other nuclear material. These patients were found to have abnormally low levels of the first component of complement, even when their disease was quiescent. Other complement components, usually seen to be depressed in LE, were consistently normal. This appears to be a hereditary defect in the first component of complement, to which the pathologic process is related. The need for nonspecific assays is indicated by the fact that the defect was missed on testing with the more common but limited β1c determination.
Michigan Named Clinical Cancer Center
Authors: K. L. Smigel
Journal: JNCI Journal of the National Cancer Institute (1988)

Michigan Named Clinical Cancer Center Get access Kara L. Smigel Kara L. Smigel Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 80, Issue 17, 2 November 1988, Page 1360, https://doi.org/10.1093/jnci/80.17.1360 Published: 02 November 1988
DISECCIÓN SUBMUCOSA ENDOSCÓPICA: EFICACIA Y SEGURIDAD DURANTE FASE INICIAL
Authors: A Herreros De Tejada Echanojauregui, C Cueto Moore, JL Calleja Panero, P Matallanos, E Blazquez, JC Fernandez-Rial, A Sanchez-Movilla, V Rojo, L Abreu Garcia
Journal: Endoscopy (2013)

Introducción: La disección submucosa endoscópica (DSE) es una técnica avanzada en el abordaje de neoplasias precoces del tracto digestivo. Objetivo: Analizar la eficacia y seguridad de la DSE en el tratamiento de neoplasias esofágicas, gástricas y colorrectales. Material y Métodos: Estudio prospectivo de DSE realizadas en nuestro centro con sospecha de neoplasia precoz. Todos salvo 1 caso se realizaron en la Unidad de Endoscopia y estuvo a cargo anestesista; en los casos de DSE esofágica o gástrica se realizó intervención bajo anestesia general. Se utilizaron endoscopios modelos GIF N180J/HQ190, PCF H180, CF H180/HQ190 (Olympus, Japan). Se usó como bisturí principal Flush knife BT® (Fujifilm, Japan) en sus versiones 1.5 (esófago, colon y recto) y 2.0 (estómago), asociando ocasionalmente Hook-knife® y Dual-knife® (Olympus, Japan). Resultados: Tras 18 meses (Enero 2012-Julio 2013) se completó DSE en 20 pacientes. La edad media fue 62,6 años (DE 12,9) e idéntica proporción de mujeres y hombres. La localización de las lesiones fue: estómago 40%, colon 30%, recto 20%, esófago 10%. La tasa de resección en bloque fue del 90% y el tamaño medio del espécimen de 14,85 cm2 (eje mayor media de 4,8 cm), con una mediana de tiempo de 124 minutos (34 – 256). La tasa de resección R0 de neoplasias avanzadas (AdenoCa/DAG/Neuroendocrino) fue del 100% (7 casos). Se observaron 8 casos (40%) de complicación inmediata (perforación), de los cuales 7 fueron tratados endoscópicamente, 6 de ellos (85%) con éxito. Hubo 2 casos de complicación tardía (rotura esplénica y hemorragia digestiva baja). No hubo mortalidad asociada a DSE o alguna de sus complicaciones. Conclusiones: La DSE es una técnica eficaz en el tratamiento de lesiones neoplásicas de gran tamaño y diversa localización. El tiempo requerido y el riesgo de complicaciones graves son limitaciones significativas en el aprendizaje y desarrollo de la técnica.
S121 The Utility Of The Incremental Shuttle Walking Test In Pulmonary Hypertension: Results From The Aspire Registry
Authors: C. Billings, J. Hurdman, R. Condliffe, I. Armstrong, I. Smith, C. Elliot, D. Kiely
Journal: Thorax (2014)

<h3>Introduction</h3> The Incremental Shuttle Walk Test (ISWT) has been evaluated in a number of diseases and found to be a safe, reproducible test which correlates better with VO<sub>2 </sub>max than the Six-Minute Walk Test (6MWT). We aimed to evaluate the utility of the ISWT as a prognostic indicator in pulmonary hypertension (PH). <h3>Methods</h3> Data was retrieved for consecutive cases of PH diagnosed in our unit from 2001–2010, a cohort previously described.<sup>1</sup> ISWT was performed routinely as part of baseline assessment according to a modified protocol of Singh <i>et al</i>.<sup>2</sup> Data was analysed in 5 Groups according to the distance achieved based on ISWT level. A p-value of was deemed statistically significant. <h3>Results</h3> 1002 of 1,344 patients diagnosed with PH underwent baseline ISWT within 3 months of cardiac catheterization and prior to pulmonary vascular therapy. Complete baseline data was available for 998 patients. Kaplan-Meier analysis showed that increasing level of ISWT was associated with increased survival (Figure 1), including the PAH sub-group, with no ceiling effect. ISWT distance correlated with WHO Functional Class, right atrial pressure, pulmonary vascular resistance, cardiac index, mixed venous oxygen saturation and percent predicted carbon monoxide diffusion (DLco) (p all ≤0.01). Multivariate Cox regression survival analysis including sex, body mass index, age, haemodynamic parameters and percent predicted DLco, demonstrated that ISWT distance was an independent predictor of survival. One year follow-up data was available for 397 patients. Kaplan-Meier analysis showed that ISWT level on treatment at 1 year was predictive of survival (p &lt; 0.001). Survival was also superior in patients whose ISWT distance improved from baseline ≥30 m compared to those whose distance remained stable (-20 to +20 m) or declined by ≥30 m (p = 0.20). <h3>Conclusion</h3> Baseline ISWT distance correlates with WHO functional class and pulmonary haemodynamics with no ceiling effect. It is an independent predictor of survival and change in ISWT predicts outcome. These features make it a viable alternative to the 6MWT in the assessment of patients with pulmonary hypertension, with a number of potential advantages. <h3>References</h3> Hurdman <i>et al</i>.<i> Eur Respir J</i> 2012:39:945–955 Singh <i>et al</i><i>Thorax</i> 1992:47:1019–1024
EAGER: efficient ancient genome reconstruction
Authors: Alexander Peltzer, Günter Jäger, Alexander Herbig, Alexander Seitz, Christian Kniep, Johannes Krause, Kay Nieselt
Journal: Genome biology (2016)

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.
Kt/Vurea and Nonurea Small Solute Levels in the Hemodialysis Study
Authors: Timothy W. Meyer, Tammy L. Sirich, Kara D. Fong, Natalie S. Plummer, Tariq Shafi, Seungyoung Hwang, Tanushree Banerjee, Yunnuo Zhu, Neil R. Powe, Xin Hai, Thomas H. Hostetter
Journal: Journal of the American Society of Nephrology (2016)

The Hemodialysis (HEMO) Study showed that high-dose hemodialysis providing a single-pool Kt/Vurea of 1.71 provided no benefit over a standard treatment providing a single-pool Kt/Vurea of 1.32. Here, we assessed whether the high-dose treatment used lowered plasma levels of small uremic solutes other than urea. Measurements made ≥3 months after randomization in 1281 patients in the HEMO Study showed a range in the effect of high-dose treatment compared with that of standard treatment: from no reduction in the level of p-cresol sulfate or asymmetric dimethylarginine to significant reductions in the levels of trimethylamine oxide (-9%; 95% confidence interval [95% CI], -2% to -15%), indoxyl sulfate (-11%; 95% CI, -6% to -15%), and methylguanidine (-22%; 95% CI, -18% to -27%). Levels of three other small solutes also decreased slightly; the level of urea decreased 9%. All-cause mortality did not significantly relate to the level of any of the solutes measured. Modeling indicated that the intermittency of treatment along with the presence of nondialytic clearance and/or increased solute production accounted for the limited reduction in solute levels with the higher Kt/Vurea In conclusion, failure to achieve greater reductions in solute levels may explain the failure of high Kt/Vurea treatment to improve outcomes in the HEMO Study. Furthermore, levels of the nonurea solutes varied widely among patients in the HEMO Study, and achieved Kt/Vurea accounted for very little of this variation. These results further suggest that an index only on the basis of urea does not provide a sufficient measure of dialysis adequacy.
Abstract 3972: The role of the TGF-β type III receptor in colon carcinogenesis
Authors: Alisha Holtzhausen, Catherine E. Gatza, Kellye C. Kirkbride
Journal: Cancer Research (2010)

Abstract The loss of the TGF-β type III receptor (TβRIII), a TGF-β superfamily co-receptor, correlates with disease progression in multiple cancer types, suggesting that TβRIII plays a role in regulating tumor progression. TGF-β superfamily signaling is frequently dysregulated in colon cancer but the specific role of TβRIII in colon carcinogenesis has not been examined. In contrast to other cancer types, TβRIII mRNA expression is not altered in colon cancer and there is not a significant change in TβRIII protein expression in tumors compared to normal colon tissue. HT29 colon cancer cells overexpressing TβRIII (HT29-RIII) exhibit an increase in proliferation in response to TGF-β and BMP2 stimulation compared to HT29-Neo cells. This increase in proliferation is mediated through the down-regulation of p21. In a soft agar assay HT29-RIII cells demonstrate increased colony formation in response to ligand treatment. Additionally, HT29-RIII cells are resistant to anoikis and 5FU-induced apoptosis. Colon cancer cells expressing TβRIII also exhibit increased migration potential and this increase in migration can be abrogated by knockdown of TβRIII expression. Furthermore, cells over-expressing TβRIII show alterations in E-cadherin and actin organization. Taken together, these data suggest that TβRIII may have a pro-tumorigenic role in colon cancer tumorigenesis as it mediates ligand stimulated proliferation, resistance to apoptosis and increased migration. Further work is currently underway to more fully elucidate the role of TβRIII in colon cancer progression in vitro and in vivo. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3972.
Can evolution provide perfectly optimal solutions for a universal model of reading?
Authors: Christina Behme
Journal: Behavioral and Brain Sciences (2012)

Frost has given us good reason to question the universality of existing computational models of reading. Yet, he has not provided arguments showing that all languages share fundamental and invariant reading universals. His goal of outlining the blueprint principles for a universal model of reading is premature. Further, it is questionable whether natural evolution can provide the optimal solutions that Frost invokes.
Abstract 163: mRNA and miRNA profiling of platinum-resistant non-small cell lung cancer cell clones identifies potential targets involved in DNA metabolism and DNA replication
Authors: Hogir M. Salim, Lovisa Lundholm, Dali Zong, Petra Hååg, Birgitta Mörk, Kristina Viktorsson, Rolf Lewensohn
Journal: Cancer Research (2011)

Abstract Non small cell lung cancer (NSCLC) constitutes the majority of lung cancer diagnoses and platinum-based chemotherapy regimen is the standard treatment. Unfortunately, a large proportion do not respond or relapse on such treatment regimens for yet only partly revealed mechanisms. We profiled residual clones of NSCLC cells after treatment with cisplatin. The mRNA and miRNA pattern was compared between untreated and cisplatin-resistant NSCLC clones using Affymetrix gene and miRNA expression arrays, respectively. We found that around 1100 genes were up regulated (at least two fold) and about 1200 genes were down regulated (at least two fold) in the cisplatin-resistant clones compared with untreated NSCLCs. We then used the Gene Set Enrichment Analysis (GSEA) to find the over- and underrepresented gene sets in large datasets like, Gene Trail and Gene Ontology. We found that cisplatin-refractory NSCLCs showed increased expression of genes involved in different cellular mechanisms including DNA metabolic processes, DNA replication and DNA-dependent DNA replication initiation for example, XRCC2, FANCI, FANCD2, RRM1, MRE11A, BLM, RRM2 and TOP2A which were validated on RNA, protein and functional level for their role in cisplatin sensitivity of NSCLC. We also found a few miRNAs that were up regulated in cisplatin refractory NSCLC by a least 1.3-fold e.g. miRNA-25 star and miRNA-1290. Interestingly, only 14 miRNAs were down regulated (by at least 1.3 fold) in the surviving cisplatin refractory NSCLC cells. Among these miRNAs were (miR-29b, miR-210, miR-486-3p, miR-324-5p, miR-572, miR-30a, e, miR-424, miR-449a, b, miR-301a, miR-153, miR-150 star and miR-34c-5p). We then looked for the predicted targets of these miRNAs using Target scan and microcosm and we found a large list of genes to be potential targets of the miRNAs among them are genes involved in apoptosis, cell cycle regulation, Wnt signaling pathway and other cellular processes (ex. VDAC, SMAD2, RAN, etc.). Correlation analysis between miRNA gene targets and gene expression data is ongoing with the aim to identify and validate putative targets on RNA, protein and functional level. In conclusion, our data show that cisplatin refractory NSCLC tumors have dysregulated mRNAs and miRNAs. Among the dysregulated genes, are certain genes involved in DNA metabolism, DNA replication and DNA-dependent DNA replication initiation which may be novel targets for improved platinum-based therapy response of NSCLC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 163. doi:10.1158/1538-7445.AM2011-163
A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology
Authors: Jesús A. Ballesteros, Gustavo Hormiga
Journal: Molecular Biology and Evolution (2016)

Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO.
Abstract 165: Predicting risk of colorectal cancer depending on tumor pathology features for first-degree relatives of persons with colorectal cancer.
Authors: Aung K. Win, Daniel D. Buchanan, Christophe Rosty, Graham G. Giles, John L. Hopper, Mark A. Jenkins
Journal: Cancer Research (2013)

Abstract Background: We hypothesised that colorectal cancer (CRC) risk for relatives of persons diagnosed with CRC could be predicted by tumor molecular pathology features. Methods: We studied a cohort of 5200 first-degree relatives (2550 women) of 792 probands with an incident invasive CRC who were recruited to the Australasian Colorectal Cancer Family Registry via population cancer registries. We excluded 32 families that were known to be Lynch syndrome. For the probands, a standardised tumor morphology review had been conducted; BRAF V600E mutation testing had been performed; and the DNA mismatch repair (MMR) status was determined by microsatellite instability and/or immunohistochemistry for MMR proteins. We calculated standardized incidence ratios (SIR) by comparing the number of CRCs observed in relatives with the number expected based on Australian incidence rates specific for age and sex. We also compared CRC risks for relatives of probands depending on the presence or absence of specific tumor pathology features. Results: We observed 191 CRCs in relatives at mean age at diagnosis of 62.7 (SD 14.3) years and SIR was 2.14 (95% confidence interval, CI 1.85-2.48). Compared with the general population, an increased risk of CRC was observed for relatives of probands with MMR-proficient CRC (SIR 1.98, 95% CI 1.71-2.32), MMR-deficient CRC (SIR 3.60, 95% CI 2.20-6.23), rectal cancer (SIR 1.71, 95% CI 1.36-2.18), distal colon cancer (SIR 2.12, 95% CI 1.63-2.82) and proximal colon cancer (SIR 2.90, 95%CI 2.27-3.75). An increased risk of CRC was observed for relatives of probands with proximal colon cancer compared with rectal cancer (hazard ratio, HR 1.70, 95% CI 1.21-2.39, p=0.002) and for relatives of probands with MMR-deficient CRC compared with MMR-proficient CRC (HR 1.84, 95% CI 1.09-3.12, p=0.02). There was no evidence of increased risk of CRC for relatives of probands with other pathology features of CRC (tumor grade, margin, peritumoral lymphocytes, tumor infiltrating lymphocytes, Crohn-like reactions, venous invasion, BRAF mutation and contiguous adenoma) compared with those without these features. Conclusions: First-degree relatives of persons with MMR-deficient CRC (not caused by Lynch syndrome) have a higher risk of CRC compared with first-degree relatives of persons with MMR-proficient CRC. Citation Format: Aung K. Win, Daniel D. Buchanan, Christophe Rosty, Graham G. Giles, John L. Hopper, Mark A. Jenkins. Predicting risk of colorectal cancer depending on tumor pathology features for first-degree relatives of persons with colorectal cancer. [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 165. doi:10.1158/1538-7445.AM2013-165