tbuckley/cabot-search huggingface dataset:
Validation of an Array CGH Test for HER2 Status Using Tumor-Targeted DNA Extraction from Formalin Fixed Tissue: Comparison with Fresh Frozen Tissue Results.
Authors: S. Gunn, M. Gorre, M. Mohammed, C. McCaskill, M. Hibbard, T. Barry, I. Yeh
Journal: Cancer Research (2009)

Abstract Background: Recent clinical validation of a commercially available array CGH test (HerScan™) for determination of HER2 status in 97 cases of newly diagnosed breast cancer showed high accuracy and 97% concordance with fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) results meeting the CAP/ASCO validation requirements for HER2 testing. However, the validation study was performed using fresh frozen tissue, a requirement which precludes the clinical use of array CGH in the majority of breast cancer workups. In this study, 55 additional cases with known HER2 status by IHC and FISH were analyzed by array CGH using a tumor-targeted DNA extraction method designed to achieve optimal results from formalin fixed paraffin embedded (FFPE) tissue.Methods: Tumor tissue from 55 cases of invasive ductal, invasive lobular, and one mucinous carcinoma was visualized and marked on H&amp;E stained sections cut from the FFPE block, with targeted areas captured by slide scraping or 4mm punch. Following proteinase K digestion, DNA was extracted from known HER2 positive (n=25), HER2 negative (n=25), and HER2 equivocal (n=5) samples. Verification of high molecular weight DNA was accomplished by agarose gel electropheresis followed by analysis of the tumor genomes using the HerScan test, a 1524 clone whole genome BAC microarray including 64 probes targeting the HER2/TOP2A amplicons on chromosome 17q.Results: Concordance equivalent to fresh frozen tissue results (&amp;gt;95%) was found between HER2 status obtained by IHC/FISH and array CGH on FFPE tissue. Five cases with equivocal results by IHC/FISH were resolved by array CGH and found to have unamplified partial chromosome 17 polysomy (n=4) and normal HER2 status (n=1). In addition, chromosome 17 status, overall genomic stability, and the presence of co-amplified genes including EGFR, MYC, MDM2, CCND1, and PDGFRalpha were clearly revealed by microarray evaluation in all cases.Conclusions: Array CGH analysis of DNA extracted from FFPE tissue provides a robust and accurate alternative for the clinical determination of HER2 status in newly diagnosed breast cancer. In addition, the complete genomic evaluation of core biopsy specimens afforded by array CGH allows clinicians to deliver personalized cancer care through incorporation of prognostic markers and potential therapeutic targets into treatment planning and prediction of disease outcome. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6038.
IMPACT OF INSTITUTIONAL REVIEW OF PCI APPROPRIATENESS ON QUALITY OF CARE AND OUTCOMES: AN ANALYSIS FROM THE TOP PCI STUDY AND THE NCDR-CATH PCI REGISTRY
Authors: Nihar Desai, Craig Parzynski, Karl Minges, Henry Ting, John Messenger, Brahmajee Nallamothu, Jeptha Curtis
Journal: Journal of the American College of Cardiology (2015)
Gonococcal infections and emergence of gonococcal decreased susceptibility to cephalosporins in France, 2001 to 2012
Authors: G La Ruche, A Goubard, B Berçot, E Cambau, C Semaille, P Sednaoui
Journal: Eurosurveillance (2014)

Resistance to cephalosporins may lead to untreatable gonococcal infections. We describe the results of the sentinel surveillance of gonococcal infections and the evolution of the resistance of Neisseria gonorrhoeae to antibiotics in France from 2001 to 2012. We also analyse the factors associated with decreased susceptibility to third generation cephalosporins. In France, surveillance of gonococcal infections is conducted through a network of voluntarily participating laboratories. Strains are sent to the national reference laboratory to determine the minimum inhibitory concentration (MIC) for six antibiotics. During the study period, the number of gonococcal infections increased steadily. The susceptibility of 8,649 strains was studied for this period. The proportion of strains with decreased susceptibility to cefixime (MIC&gt;0.125 mg/L) quadrupled between 2011 (0.7%:10/1,521) and 2012 (3.0%: 33/1,093; p&lt;0.001). Between 2001 and 2012, only two of the 8,649 strains, both collected in 2010, had a MIC&gt;0.125 mg/L for ceftriaxone. Decreased susceptibility to cephalosporins increased with older age and was more common in pharyngeal strains. Decreased susceptibility to cefixime may indicate that the national recommendation to use ceftriaxone as a first line treatment for cases of urethritis and cervicitis has not been fully implemented. Enhanced surveillance of pharyngeal strains is strongly suggested.
P1121 EARLY STOPPING RULES FOR FALDAPREVIR PLUS PEGYLATED INTERFERON a-2a AND RIBAVIRIN IN TREATMENT-NAIVE PATIENTS: EXPLORATORY STUDY OF POOLED DATA FROM PHASE III TRIALS
Authors: P. Ferenci, D. Dieterich, S. Zeuzem, P. Mantry, C. Sarrazin, J. Crespo, E. Tam, J.-F. Dufour, E.M. Yoshida, S. Nishiguchi, M. Bourlière, M. Omata, A. Abergel, M. Kuboki, A. Carvalho, C.-Y. Peng, M. Romero-Gómez, D. Wright, J.O. Stern, W. Böcher, G. Kukolj, J.-P. Gallivan, J. Scherer, D.M. Jensen
Journal: Journal of Hepatology (2014)
SPLEEN EMBOLIZATION IN RENAL TRANSPLANT PATIENTS: FOLLOWUP ANALYSIS &amp; RESULTS.
Authors: M P Sandler, M Mazer, G A Sacks, J A Patton, T Ertzner, R MacDonnell, M V Kulkarni, C L Partain
Journal: Clinical Nuclear Medicine (1984)

Sandler, M P; Mazer, M; Sacks, G A; Patton, J A; Ertzner, T; MacDonnell, R; Kulkarni, M V; Partain, C L Author Information
PCSM-03PHYSICAL DISABILITY AND ANXIETY ARE INDEPENDENT PREDICTORS OF FATIGUE IN STABLE PRIMARY BRAIN TUMOUR PATIENTS
Authors: Julia Day, Britt Berntzen, Sharon Harden, Stevie Williams, Sharon Peoples, Sara Erridge, Robin Grant
Journal: Neuro-Oncology (2015)

BACKGROUND: Fatigue is the most common symptom reported by primary brain tumour patients; causes are multi-factorial. The aim of the study was to further explore fatigue in relation to co-occurring symptoms. METHODS: A single-centre cross-sectional prospective study design was used. Inclusion criteria were: histological diagnosis of a primary brain tumour, ≥ 18 years, stable disease, able to provide informed consent, and treatment-free for 3 months prior to participation. NHS ethical approval was obtained. Objective and subjective measures were used to assess fatigue (BFI), cognition (HVLT-R, COWA, Trail Making Test, IQ), sleep (Actigraphy, Epworth Sleepiness Scale), mood (HADS) and physical function (EDSS, nine hole peg test, 10m walk). RESULTS: Eighty-five patients with a primary brain tumour were recruited; 16% reported severe fatigue (Mage = 49.8, SD = 13.3), 48% reported moderate fatigue (Mage = 48.3, SD = 9.6), 33% reported mild fatigue (Mage = 46.9, SD = 12.1). Fatigue severity was significantly positively related to anxiety (p = 0.008), depression (p =< 0.0001), daily activity percentage (p = 0.035), information processing speed (p = 0.0006), physical impairment (p =< 0.0001) and the use of non-enzyme inducing anti-epileptic drugs (p = 0.011). Using multivariate logistic regression, physical function (p = 0.0003) and anxiety (p = 0.017) were found to be independent predictors of fatigue. CONCLUSIONS: Fatigue continues to be prevalent in primary brain tumour patients. As previously found, fatigue co-occurs with other symptoms. Physical disability and anxiety predict fatigue. Screening for fatigue and other symptoms may help to determine avenues for physical interventions and/or psychological interventions.
Abstract 2155: The origins and functional consequences of ETS gene fusions in prostate cancer
Authors: Ram S. Mani, Scott A. Tomlins, Chad J. Brenner, Lei Wang, Matthew Iyer, Jindan Yu, Qi Cao, Kaitlin Callahan, Aparna Ghosh, Mukesh K. Nyati, Sooryanarayana Varambally, Nallasivam Palanisamy, Arul M. Chinnaiyan
Journal: Cancer Research (2011)

Abstract The purpose of this study is to unravel the cellular mechanisms underlying the oncogenic ETS gene fusions, which are a hallmark of prostate cancer development. Recurrent gene fusions involving the 5’untranslated region of the androgen-regulated gene TMPRSS2 and the ETS family genes are observed in a majority of prostate cancers. Among the ETS family gene fusions, the TMPRSS2-ERG fusions involving the 5’untranslated region of TMPRSS2 with the ERG gene are the most common and found in approximately 50% of prostate cancers. However, the origins and functional consequences of ETS gene fusions are not clear. Using dual color fluorescence in situ hybridization (FISH), we demonstrate that stimulation with dihydrotestosterone (DHT) induces proximity between TMPRSS2 and ERG genomic loci in LNCaP cells, which are androgen sensitive and lack the TMPRSS2-ERG gene fusions. This effect was dependent on androgen receptor (AR). Importantly, androgen did not induce proximity between the TMPRSS2 and ERG loci in DU145 human prostate cancer cells, which are androgen insensitive. Further, a combination of androgen signaling and genotoxic stress that induces DNA double strand breaks results in the formation of TMPRSS2-ERG gene fusions in LNCaP cells. Interestingly, we observe that the ERG protein formed as a result of gene fusion binds to the promoter of wild type ERG and activates its transcription. The VCaP cell line that endogenously harbors the TMPRSS2-ERG gene fusion has high levels of wild type ERG. Treatment with androgens induces the expression of both the TMPRSS2-ERG and wild type ERG transcripts in VCaP cells. Lenti virus mediated stable over expression of TMPRSS2-ERG in PC3 cells results in an increase in the expression levels of wild type ERG. This auto-activation of wild type ERG is observed in about 50% of clinically localized and 25% of metastatic prostate cancers harboring the TMPRSS2-ERG gene fusions, but not in ETS negative prostate cancers. Taken together, our studies provide a mechanistic framework for the up-regulation of ERG transcription in prostate cancer. 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 2155. doi:10.1158/1538-7445.AM2011-2155
AB0472 Primary and secondary central nervous system vasculitis: clinical manifestations, laboratory findings, neuroimaging, and treatment analysis
Authors: O. Vera-Lastra, J. Sepúlveda Delgado, M. D. P. Cruz-Domínguez, G. Medina, M. Casarrubias Ramírez, L. E. Molina Carrión, L. Pineda Galindo, L. J. Jara
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Primary central nervous system vasculitis (PCNSV) is a challenging clinical problem due to itsnon- specific signs and symptoms, inaccessibility of the central nervous system (CNS) tissue for pathologic examination, lack of efficient non-invasive diagnostic tests and the relative rarity of it presentation. Secondary central nervous system vasculitis (SCNSV) occurs in association with autoimmune rheumatic diseases (ARD), infections, lymphoproliferative diseases, drug abuse, and systemic vasculitis. <h3>Objectives</h3> To compare the initial clinical, laboratory and imaging features in primary central nervous system vaculitis (PCNSV) versus secondary central nervous system vasculitis (SCNSV) and follow-up after treatment with intravenous cyclophosphamide (IV CYC) plus methylprednisolone (MP). <h3>Methods</h3> Neurological (focal and non-focal manifestations), laboratory (cerebrospinal fluid and immunological tests) and neuroimaging findings were analyzed in PCNSV and SCNSV patients. Both groups received at onset MP<i>plus IV CYC during 6 months, followed by bimonthly IV CYC plus oral glucocorticosteroids (CGS) for 12 months. All the patients were followed for 36 months.</i> <h3>Results</h3> Thirty patients were included (12 PCNSV and 18 SCNSV). Focal and non- focal manifestations were similar in both groups (p=NS); headache being the most frequent manifestation in both groups. Fatigue, myalgias, arthralgias, neuropathy low leukocytes and platelets, elevatederythrocyte sedimentation rate, positive ANA, anti ds-DNA, ANCA, low complement, and rheumatoid factor were more frequent in SCNSV (p&lt;0.05). In cerebrospinal fluid (CSF) pleocytosis and proteins were higher in PCNSV (p&lt;0.05). Periventricular and subcortical hyperintense lesions were observed in<i>cranial magnetic resonance imaging</i> in both vasculitides. Cerebral angiography and angioresonance showed narrowing of vasculature in both groups. After treatment, Kaplan-Meier survival curve showed higher relapse free survival in PCNSV (p&lt;0.05). <h3>Conclusions</h3> There are significant differences in the clinical manifestations, laboratory, and CSF findings between PCNSV and SCNSV. After treatment with IV CYC and GCS patients with PCNSV had higher relapse-free survival than SCNSV. <h3>Disclosure of Interest</h3> None Declared
Case 22-1993
Authors: Richard C. Cabot, Robert E. Scully, Eugene J. Mark, William F. McNeely, Betty U. McNeely, Thomas G. Cropley, Judith A. Ferry
Journal: New England Journal of Medicine (1993)

Presentation of CaseA 22-year-old man was admitted to the hospital because of increasing swelling of the face.The patient had been well until 20 months earlier, when a swelling developed on the inner aspect of the right upper lip, with firm, slightly tender nodules. The lesions enlarged gradually, and the patient soon detected a second, similarly affected area along the buccal mucosa beside the right lower jaw.Ten months before admission a biopsy of the lesions was performed elsewhere. Microscopical examination of the specimen was reported to show a dense inflammatory infiltrate that included lymphocytes and histiocytes, with foci . . .
Stat Bite: Increases in Screening Mammography U.S. Women 40 and Older
Authors: N. Breen, L. Kessler
Journal: JNCI Journal of the National Cancer Institute (1992)

Stat Bite : Increases in Screening Mammography U.S. Women 40 and Older Get access Nancy Breen, Ph.D., Nancy Breen, Ph.D. Search for other works by this author on: Oxford Academic PubMed Google Scholar Larry Kessler, Sc.D. Larry Kessler, Sc.D. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 84, Issue 20, 21 October 1992, Page 1549, https://doi.org/10.1093/jnci/84.20.1549 Published: 21 October 1992
Enhancing the Biomechanical Performance of Anisotropic Nanofibrous Scaffolds in Tendon Tissue Engineering: Reinforcement with Cellulose Nanocrystals
Authors: Rui M. A. Domingues, Silvia Chiera, Pavel Gershovich, Antonella Motta, Rui L. Reis, Manuela E. Gomes
Journal: Advanced Healthcare Materials (2016)

Anisotropically aligned electrospun nanofibrous scaffolds based on natural/synthetic polymer blends have been established as a reasonable compromise between biological and biomechanical performance for tendon tissue engineering (TE) strategies. However, the limited tensile properties of these biomaterials restrict their application in this field due to the load‐bearing nature of tendon/ligament tissues. Herein, the use of cellulose nanocrystals (CNCs) as reinforcing nanofillers in aligned electrospun scaffolds based on a natural/synthetic polymer blend matrix, poly‐ε‐caprolactone/chitosan (PCL/CHT) is reported. The incorporation of small amounts of CNCs (up to 3 wt%) into tendon mimetic nanofiber bundles has a remarkable biomaterial‐toughing effect (85% ± 5%, p &lt; 0.0002) and raises the scaffolds mechanical properties to tendon/ligament relevant range (σ = 39.3 ± 1.9 MPa and E = 540.5 ± 83.7 MPa, p &lt; 0.0001). Aligned PCL/CHT/CNC nanocomposite fibrous scaffolds meet not only the mechanical requirements for tendon TE applications but also provide tendon mimetic extracellular matrix (ECM) topographic cues, a key feature for maintaining tendon cell's morphology and behavior. The strategy proposed here may be extended to other anisotropic aligned nanofibrous scaffolds based on natural/synthetic polymer blends and enable the full exploitation of the advantages provided by their tendon mimetic fibrous structures in tendon TE.
SAFETY AND EFFICACY OF THE COMBINATION SIROLIMUS-ELUTING ENDOTHELIAL PROGENITOR CELL CAPTURE STENT IN PATIENTS WITH ST-SEGMENT ELEVATION ACUTE MYOCARDIAL INFARCTION: ONE YEAR FOLLOW-UP
Authors: Joshua Ping Yun Loh, Leonardo Carvalho, Edgar Tay, Chi-Hang Lee, Koo Chan, Mark Chan, Adrian Low, Poay Huan Loh, Huay-Cheem Tan
Journal: Journal of the American College of Cardiology (2016)
FRI0437 How to identify patients at high risk for rapid radiographic spinal progression early in the course of axial spondyloarthritis?
Authors: D. Poddubnyy, H. Haibel, J. Listing, J. Braun, M. Rudwaleit, J. Sieper
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Identification of patients with axial spondyloarthritis (axSpA) who are at high risk for rapid radiographic progression is of high relevance, because these patients might require an active treatment and they would be the most appropriate candidates for a continuous therapy with non-steroidal anti-inflammatory drugs (NSAIDs). <h3>Objectives</h3> To identify factors associated with rapid radiographic spinal progression in patients with early axSpA. <h3>Methods</h3> In total, 210 patients with early axial SpA (115 with ankylosing spondylitis (AS) and symptom duration ≤10 years, and 95 with non-radiographic axSpA (nr-axSpA) and symptom duration ≤5 years) from the German Spondyloarthritis Inception Cohort (GESPIC) were selected for this analysis based on the availability of spinal radiographs at baseline and after 2 years of follow-up. Spinal radiographs were scored according to the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS) independently by two trained readers. Rapid radiographic spinal progression was defined as a worsening of the mSASSS score by ≥4 units over 2 years. <h3>Results</h3> In total, 15 (7.1%) rapid progressors were identified. The mean±SD worsening of the mSASSS was 7.2±3.9 (range 4.0 to 17.0). Rapid progressors in comparison to those without such a progression had higher level of structural damage in the spine at baseline as assessed by absolute mSASSS values (18.0±15.4 vs. 3.2±6.4, p&lt;0.001) and by the proportion of patients with syndesmophytes (73.3% vs. 19.0%, p&lt;0.001), higher level of functional disability / limitation of spinal mobility as measured by BASFI (4.1±2.2 vs. 2.8±2.3, p=0.030) and BASMI (3.6±1.7 vs. 1.6±1.6, p&lt;0.001), and higher levels of acute phase reactants: C-reactive protein (CRP: 17.9±15.2 vs. 9.1±15.1 mg/l, p=0.001) and erythrocyte sedimentation rate (ESR: 31.5±13.7 vs. 15.9±15.9 mm/h, p&lt;0.001). A higher proportion of heavy smokers (&gt;10 cigarettes a day) among rapid progressors (33.3% vs. 11.8%, p=0.017) was also found. All but one patient (92.3%) in the rapid progression group had low NSAIDs intake over 2 years (ASAS NSAIDs intake score &lt;50) as compared to 72.7% in the remaining patients (p=0.19). There were no statistically significant differences in the prevalence of males, HLA-B27 positivity, and clinical disease activity as measured by BASDAI. Detailed information on the performance of single risk factors and their combinations is presented in table. <h3>Image/graph</h3> <h3>Conclusions</h3> Prediction of rapid radiographic progression can be reliably done early in the course of axial SpA using assessment of risk factors. Smoking cessation and continuous NSAIDs therapy in these patients might retard radiographic progression. <h3>Disclosure of Interest</h3> None Declared
Angiosarcoma at the anastomotic site mimicking local recurrence of rectal adenocarcinoma
Authors: S. Jahn, B. Liegl, H. Leskowschek, C. Spreizer, C. Langner
Journal: Endoscopy (2011)

A 76-year-old man was diagnosed with rectal adenocarcinoma in January 2007. The patient underwent neoadjuvant radiochemotherapy followed by low anterior resection with total mesorectal excision. Histology showed foci of residual cancer tissue within the muscularis propria, and clear resection margins.
FDG PET/CT in Early and Late Stages of SAPHO Syndrome
Authors: Aisheng Dong, Yushu Bai, Yong Cui, Jian Zhang, Changjing Zuo
Journal: Clinical Nuclear Medicine (2015)

Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is a rare disease, which may be underdiagnosed or misdiagnosed because of nonspecific clinical and imaging findings. We present 2 cases of SAPHO syndrome with MRI, bone scintigraphy, and FDG PET/CT findings. In case 1 with early-stage disease, the active osteitis showed osteolytic bone destruction with increased FDG uptake. In case 2 with late-stage disease, the inactive bone lesions presented as osteosclerosis with normal FDG uptake. Familiarity with the FDG PET/CT findings of SAPHO syndrome in different stages may be helpful for correct diagnosis.
Pertechnetate Activity in the Gastric Fundus and a Small Left Kidney Simulating an Enlarged Hydronephrotic Kidney
Authors: EUNA JUNG, BORYS KRYNYCKYI, CHUN KI KIM, JOSEF MACHAC
Journal: Clinical Nuclear Medicine (2000)

The authors report a case of renal scintigraphy in which uptake of free Tc-99m pertechnetate in the gastric fundus of a patient with a history of left renal obstruction erroneously simulated a dilated (obstructed) left kidney. In addition, left renal function could have been erroneously overestimated based on the early set of images. In reality, the left kidney was small and had decreased function.
Toward Trusting Therapeutic Relationships — In Favor of the Annual Physical
Authors: Allan H. Goroll
Journal: New England Journal of Medicine (2015)

Interview with Drs. Allan Goroll and Ateev Mehrotra on whether the annual physical should be retained, eliminated, or modified for 21st-century realities. (15:51)Download Continued enthusiasm for annual physicals may be driven by the desire or need to establish and maintain a close, trusting relationship with one's personal physician. We could preserve and enhance the annual visit's benefits by turning it into an annual health review.