tbuckley/cabot-search huggingface dataset:
Abstract 89: BamBam: Simultaneous processing of tumor and germline sequencing data
Authors: John Z. Sanborn, David Haussler
Journal: Cancer Research (2010)

Abstract With the release of multiple fully-sequenced tumor and matched normal genomes from The Cancer Genome Atlas (TCGA), there is great need for tools that can efficiently analyze these enormous datasets. To this end, we developed BamBam, a method that interfaces with the SAMtools library to simultaneously analyze a patient's tumor and germline genomes using short-read alignments stored in SAM/BAM-formatted files. BamBam enables an efficient calculation of regional copy number, loss of heterozygosity (LOH), and the discovery of both somatic and germline sequence variants and structural rearrangements. Chromosomal regions that experience single copy loss or copy neutral LOH are used to phase heterozygous sites and construct germline haplotypes. We used BamBam to analyze the short-read sequencing data of several glioblastoma multiforme and ovarian serous carcinoma tumors produced by the TCGA genome sequencing centers at the Broad Institute and Washington University in St. Louis. In each tumor, BamBam identified somatic homozygous and heterozygous small indels and single nucleotide variants, inferred regions exhibiting large-scale loss of heterozygosity, estimated relative copy number, and identified sites of structural variation. The intra- and inter-chromosomal rearrangements we infer are often found at the boundary of copy number alterations, implicating homology-driven mechanisms. We identified variants shared by more than one tumor as well as events restricted to individual tumors. Strikingly, in each tumor processed thus far, distinct regions of localized chromosomal instability were observed. The inferred haplotypes share substantial regions of identity with the germline haplotypes of the other TCGA samples and phased SNPs from samples of 11 HapMap populations, indicating they have high accuracy. BamBam is a computationally efficient method for surveying large sequencing datasets to produce a set of high-quality genomic events that occur within each tumor relative to its germline. These results provide a glimpse into the chromosomal dynamics of tumors, improving our understanding of these tumors’ final states and the events that led to them. 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 89.
1052 PERFORMANCE OF REAL-TIME STRAIN ELASTOGRAPHY, SHEAR WAVE ELASTOGRAPHY, AND TRANSIENT ELASTOGRAPHY IN ASSESSING SIGNIFICANT FIBROSIS IN CHRONIC VIRAL HEPATITIS
Authors: G. Ferraioli, C. Tinelli, B. Dal Bello, R. Lissandrin, M. Zicchetti, C. Filice
Journal: Journal of Hepatology (2012)
PWE-135 Does Afp Predict Survival In Patients With Hepatocellular Carcinoma (hcc)?
Authors: F Yousuf, W Ding, PD Richardson, D Palmer, I Patanwala, TJ Cross
Journal: Gut (2014)

<h3>Introduction</h3> AFP is a tumour marker that is elevated in some patients with HCC and has been recommended as a method of screening for HCC in at risk patients. The authors wished to assess the level of AFP at diagnosis to determine if this was related with survival. <h3>Methods</h3> A single centre, retrospective cohort analysis was performed. Patients with HCC were identified from the department's database (2008–2014). The diagnosis of HCC was made on internationally agreed criteria. Screening for HCC was based on 6-monthly liver ultrasound and serum measurement of AFP. The point of diagnosis was taken as the date when the diagnosis was confirmed radiological or histologically. The severity of patient's disease was scored using the Barcelona Liver Cancer Clinic (BCLC) classification. The serum AFP was measured at diagnosis. The end-point for the study was patient death. <h3>Results</h3> 180 patients were identified in our cohort. The median age was 68 years (58–75), the number of males was 142 (79%), and aetiology was as follows: ALD (50, 39%), NASH (17, 13.3%), HCV (22, 17.2%), HBV (10, 7.8%), haemochromatosis (10, 7.8%), others 19 (14.8%). The stage of BCLC at presentation was: 0–18 (10%), A – 43 (24%), B 30 (16.7%), C 19 (10.6%), and D 25 (13.3%). Survival at 1 and 5 years from diagnosis was 69% and 46% respectively. AFP was available in 93 cases. AFP was elevated (&gt;10) in 37 cases (40%). On univariate analysis the following variables were associated with a poor outcome at 1 year (AFP p = 0.001, tumour diameter 0.06) and 5 years (AFP p &lt; 0.0001 and tumour diameter 0.04). The median AFP in survivors at 5 years was 4(3–6), and in non-survivors was 97(24–673). An AFP &gt;100 at presentation was associated with an increased risk of death at 1 (OR 4.5(2–10) and 5 years (OR 7.2(3–17) irrespective of treatment modality employed. <h3>Conclusion</h3> AFP does have prognostic utility in patients with HCC. It is a poor screening tool as it is not elevated in the majority of patients with HCC. New biomarkers are needed to help earlier detection when the disease is at a potentially curative stage. <h3>Disclosure of Interest</h3> None Declared.
Case 7-2001
Authors: Mark S. Volk, G. Petur Nielsen
Journal: New England Journal of Medicine (2001)

Presentation of CaseA 10-week-old boy was evaluated at Massachusetts Eye and Ear Infirmary because of progressive swelling in the region of the right side of the upper lip of two weeks' duration.The boy had been born at full term and had had no perinatal problems. He was described as colicky but was eating adequately, with satisfactory growth. There was no history of trauma, fever, nasal congestion, rhinorrhea, or cough.On physical examination, the infant appeared well, and there was no craniofacial dysmorphism. There was firm, nontender swelling of the subcutaneous tissue of the right side of the upper . . .
THU0193 Comparative evaluation of cumulative damage in adult and childhood onset systemic lupus erythematosus
Authors: K.D.O. Peliçari, M. Postal, N.A. Sinicato, L.T.L. Costallat, R. Marini, S. Appenzeller
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Systemic lupus erythematosus (SLE) is a chronic, multisystemic disease affecting predominantly woman in reproductive age. Previous studies have reported childhood-onset (c)SLE to be more severe than adult-onset (a)SLE. <h3>Objectives</h3> The aim of this study was to compare the prevalence and types of cumulative damage in SLE according to age of disease onset. <h3>Methods</h3> We conducted a cross-sectional study including 247 adult and 63 cSLE SLE patients matched for disease duration and followed at Rheumatology and Pediatric Rheumatology Unit of the State University of Campinas. Damage was analyzed according to Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SDI) and data were extracted from patients charts. <h3>Results</h3> We included 247 aSLE patients (234 women; mean age 38.7 years (SD =12.4) and 63 cSLE patients (61 women; mean age 18.6 years (SD =5.6). SDI scores ≥1 were observed in 166 aSLE and 28 patients cSLE (p&lt;0.001). The mean SDI in aSLE (mean =2; SD=1.2) was similar to cSLE (mean =1.5, DP =0.7) (p&gt;0.05). In aSLE we observed the following frequency of damage: musculoskeletal 66/166 (37.3%), premature gonadal failure 55/166 (33.1%), cardiovascular in 44/166 (26.5%), ocular 29/166 (17.5%), neuropsychiatric 28/166 (16.7%), vascular 19/166 (11.4%), pulmonary 17/166 (10.2%), renal 15/166 (9%), diabetes with 14/166 (8.4%), gastrointestinal 12/166 (7.2%), skin 7/166 (4.2%) and malignancy in 1/166 (0.6%) patient. In cSLE we observed the following prevalence of damage: musculoskeletal 13/28 (46.4%), cardiovascular 7/28 (25%), ocular 6/28 (21.4%), neuropsychiatric 5/28 (18%), pulmonary 3/28 (11%), diabetes 2/28 (7.1%), renal 1/28 (36%), gastrointestinal 1/28 (3.6%), skin 1/28 (3,6%), malignancy 1/28 (3.6%). The prevalence of cardiovascular damage was high in our cSLE cohort and was due mainly to valvular stenosis and diastolic dysfunction. Although the types of damage was similar among groups, aSLE patients had significantly more premature gonadal failure and cSLE patients had more cardiovascular damage (p&lt;0.05). <h3>Conclusions</h3> aSLE have more damage than cSLE. However when present, the types of damage are similar between groups except for gonadal failure that is more frequently observed in aSLE and cardiovascular damage more frequently observed in cSLE. cSLE patients have a greater life expectancy and have therefore a greater tendency to present more damage later in life. Close follow-up for permanent damage is necessary in SLE. <h3>Disclosure of Interest</h3> K. Peliçari Grant/Research support from: FAPESP - 2010.13636-2, M. Postal Grant/Research support from: FAPESP - 2009.10744.1, N. Sinicato Grant/Research support from: FAPESP - 2010.13637.9, L. Costallat: None Declared, R. Marini: None Declared, S. Appenzeller: None Declared
Giant Papillae in Vernal Keratoconjunctivitis
Authors: Jagat Ram, Aniruddha Agarwal
Journal: New England Journal of Medicine (2014)

A 7-year-old boy presented with a 3-year history of severe itching and ropy discharge in both eyes. There was no family history of atopic disease. A pattern of seasonal variation was noted, with an increase in symptoms during the summer.
AB0375 Efficacy and safety of non-biologic immunusuppresants in the treatment of non-renal systemic lupus erythematosus: a systematic review
Authors: J. M. Pego-Reigosa, T. Cobo-Ibañez, J. Calvo-Alén, C. Mouriño-Rodriguez, E. Loza-Santamaría, M. P. Rosario-Lozano, A. Rahman, S. Muñoz-Fernández, Í. Rúa-Figueroa
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> To date, few randomised clinical trials (RCTs) have analyzed the effect of the available therapies on non-renal manifestations of SLE. Specifically, there is limited evidence on the efficacy of non-biologic immunosuppressants for the treatment of non-renal manifestations of the disease. In spite of that, several of those manifestations are frequently treated with off-label medications. <h3>Objectives</h3> To systematically review the available literature regarding the efficacy and safety of non-biologic immunosuppressive therapies in the treatment of non-renal systemic lupus erythematosus (SLE). <h3>Methods</h3> Systematic review performed by members of the Systemic Autoimmune Diseases Study Group and Research Unit of the Spanish Society of Rheumatology. We conducted a sensitive literature search in Medline, Embase, and the Cochrane Central Register of Controlled Trials up to October 2011. Selection criteria: a) population: adult patients with SLE, b) intervention: treatment with non-biologic immunosuppressant, c) comparator: placebo or active comparator, d) outcome measures assessing efficacy: non-renal manifestations, scores by activity indices, SLE flares, steroid-sparing effect, etc., and e) outcome measures assessing safety: infections, cardiovascular events, malignancies, etc. Meta-analyses, systematic reviews, clinical trials and cohort studies were included. The quality of each study was evaluated using the Jadad's scale and Oxford Levels of Evidence. <h3>Results</h3> One hundred fifty-eight articles were selected for detailed review of the 2,827 initially found. Finally, 63 articles fulfilled the predetermined criteria. Overall, they were low-quality studies with only 11 RCTs. Cyclophosphamide demonstrated efficacy for neuropsychiatric SLE preventing relapses with additional steroid-sparing effect although its use was associated with cumulative damage, development of cervical intraepithelial neoplasia and ovarian failure. Other immunosuppressants (azathioprine, methotrexate, leflunomide, mycophenolate mofetil and cyclosporine A) demonstrated efficacy in reducing non-renal activity and flares with a steroid-sparing effect, although on occasions in non placebo-controlled RCTs of small number of patients. <h3>Conclusions</h3> Several immunosuppressants have demonstrated their safety and efficacy in non-renal SLE. A specific drug for each particular manifestation cannot be recommended although cyclophosphamide may be kept to be used in more severe cases and methotrexate may be the first option in most cases of moderately active SLE. High-quality RCTs of a larger number of patients are needed <h3>Disclosure of Interest</h3> None Declared
A Not-So-Obscure Cause of Gastrointestinal Bleeding
Authors: Andrew S. Brock, Jennifer L. Cook, Nathaniel Ranney, Don C. Rockey
Journal: New England Journal of Medicine (2015)

A 66-year-old man with ischemic cardiomyopathy presented to the hospital with a 2-day history of fatigue, dizziness on standing, and bright red blood from the rectum that transitioned to black, tarry stools.
Abstract 1472: Comprehensive evaluation of PEGylated gold nanorods for two photon photoluminescence image guided radiation therapy enhancement
Authors: Rajiv Kumar, Janki Patel, Houari Korideck, Ross I. Berbeco, Mike G. Makrigiorgos, Srinivas Sridhar
Journal: Cancer Research (2012)

Abstract Nanoparticle formulations of gold have shown a tremendous potential in various biomedical applications. The use of high atomic number (Z) materials presents an attractive approach in enhancing the therapeutic efficacy of the radiation therapy. The high Z number for gold (Z=79) makes them an ideal candidate for radiosensitization enhancement. The ability of the anisotropic gold nanorods to sustain the resonating surface plasmon with minimal damping results in highly efficient two-photon induced photoluminescence imaging. Here we present the synthesis and in vitro characterization of PEGylated gold nanorods as efficient radiosensitizing agents which can be imaged using inherent two-photon photoluminescence without a conjugated fluorophore. We have synthesized gold nanorods with an aspect ratio of 2.5 and functionalized the surface with different ratios of methoxy and amine PEG for modulating the charge and imparting the functional groups. The cellular uptake behavior in prostate cancer cell line PC3 was studied and the results indicated a robust uptake of the amine functionalized nanorods. The quantitative estimation of the nanorods uptake was performed with BCA assay as amount of nanorods present in per microgram of protein. Two photon photoluminescence imaging also confirmed a robust cellular uptake of the amine functionalized nanorods. The radiation damage enhancement of the gold nanorods was confirmed using PC3 cells. The cells treated with gold nanorods were irradiated with kilovoltage X-rays. A γH2AX assay was used for quantitation of the DNA damage with and without nanorods as controls. The results indicated an increased highly efficient DNA damage in cells treated with gold nanorods. The outcome of this research will enable further application of targeted nanorods in advanced animal models as efficient radiation dose enhancement agents wherein two-photon photoluminescence imaging will provide a real time assessment of the therapeutic response and disease progression. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1472. doi:1538-7445.AM2012-1472
Abstract SY06-02: The nontraditional peptide therapeutics
Authors: Hiroaki Suga
Journal: Cancer Research (2012)

Abstract Despite the fact that some peptides had strong affinity or inhibitory activity to certain proteins, because of their poor in-vivo stability there are only a limited number of drugs based on the peptide scaffold to date. However, non-standard peptides, represented by cyclosporine A that is originally isolated as a natural product and developed as an oral available immunosuppressive agent, have remarkable in-vivo stability and membrane permeability, unlike ordinary peptides. To uncover and develop more cyclosporine A-like peptide drugs, it is critical to build a non-traditional strategy involving a system that enables us to discover non-standard peptides quickly and less expensively against a wide variety of intra- and extra-cellular targets. In this talk, I shall introduce a new technology, involving genetic code reprogramming coupled with an in-vitro display, referred to as referred to as RaPID (Random non-standard Peptide Integrated Discovery) system. By means of the RaPID system, we are able to ribosomally express natural product-like peptides containing the features of macrocyclic and N-methylated backbone, and rapidly select highly active sequences against various targets. In this seminar, I shall discuss our recent advance in the discovery of macrocyclic non-standard peptides against EpCAM, Sirt2, E6AP, and JMJD2a, as examples. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY06-02. doi:1538-7445.AM2012-SY06-02
Woman with anorexia is discharged after doctors say that she is untreatable
Authors: Clare Dyer
Journal: BMJ (2016)

A High Court judge has authorised the discharge of a 28 year old woman with anorexia nervosa into the community after 10 years of inpatient treatment failed to stop her starving herself.

The woman, referred to as W, weighed less than 30 kg and had been losing weight at the rate of 0.5 to 1 kg a week. Her history showed that she would eat only when she believed that she might be in imminent danger of death.

The judge, Peter Jackson, acknowledged that “it would at first seem counterintuitive that someone so ill should be discharged from hospital.” He added, “The conventional assumption is that hospital treatment is likely to bring benefits, but the evidence has persuaded me that in this case that is not so.”

Her latest …
Abstract 5151: Integrative genomic analysis identifies cancer-testis antigen LEMD1 as a prognostic biomarker.
Authors: Jenny Park, Beatrice Chiu, Joe Delaney, Cate Paschal, Daniel Roche, James Shima, Anita Umesh, Robert Wisotzkey, Mamatha Shekar, Ilya Kupershmidt
Journal: Cancer Research (2013)

Abstract The ability to molecularly distinguish disease states can improve prognostic resolution and therapeutic options. Cancer-testis antigens (CTA), expressed in germ cells of the testis and in a variety of cancers, are of particular interest for their potential use as targets for anti-cancer vaccines. We highlight the application of the NextBio platform, which integrates multiple datatypes such as RNA/miRNA expression, copy number variation, epigenetic changes, and next-generation sequencing with clinical attributes to identify and characterize novel disease associations in multiple myeloma. Genomic and clinical data of 2,546 multiple myeloma patients obtained from public data sources were investigated in the NextBio platform. We initially analyzed the gene expression of various clinical subgroups to the median expression of all groups to identify genes significantly correlated to patient survival. We filtered for patients with advanced disease, defined as those with beta-2 microglobulin blood levels greater than 5.5mg/L, and identified LEMD1, a CTA, as positively correlated with survival (p=2.3E-6). We then analyzed the gene expression of LEMD1 in patients of all disease stages, and found those with increased expression of LEMD1 had improved survival compared to those who did not (p=9.4E-3). Patients with increased expression of LEMD1, however, had concomitant decreased expression in 14/20 CTAs of the MAGE family (p &amp;lt; 0.05), members of which were previously described as expressed in multiple myeloma patients with reduced survival. A preliminary exploration of LEMD1 expression in other cancers found increased expression of LEMD1 to be significantly associated with improved survival in ovarian cancer (p=5.4E-3) but reduced survival in renal cancer (p=0.01). Further analysis of LEMD1 expression in normal tissues showed high expression of LEMD1 in spermatozoa and limited expression in 315 other tissue and cell types. As tissue specific antigens behind the blood-testis barrier, the expression of CTAs in cancer can potentially serve as immunogenic targets, and further investigation is warranted to explore their use in tumor immunotherapy. Citation Format: Jenny Park, Beatrice Chiu, Joe Delaney, Cate Paschal, Daniel Roche, James Shima, Anita Umesh, Robert Wisotzkey, Mamatha Shekar, Ilya Kupershmidt. Integrative genomic analysis identifies cancer-testis antigen LEMD1 as a prognostic biomarker. [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 5151. doi:10.1158/1538-7445.AM2013-5151
F-MuLV acceleration of myelomonocytic tumorigenesis in SV40 large T antigen transgenic mice is accompanied by retroviral insertion at Fli1 and a novel locus, Fim4
Authors: J Kone, J Arroyo, T Savinelli, S Lin, K Boyd, Y Wu, M Nimmakayalu, NG Copeland, NA Jenkins, M Qumsiyeh, P Hu, A Prescott, H Wu, L Yang, B Roe, AS Perkins
Journal: Leukemia (2002)
BM-04 * IMAGE GUIDED STEREOTACTIC RAPID ARC(R) TO SINGLE BRAIN METASTATIC ASSISTED BY INTRACRANIAL CALCIFICATION
Authors: R. Arauz
Journal: Neuro-Oncology (2014)

BACKGROUND: Image-guided radiation therapy (IGRT) cone-beam CT (CBCT) is delivering important improvements in the stereotactic radiotherapy. Volumetric Modulated Arc Therapy (VMAT), known as Rapid Arc® from Varian Medical Systems has the ability to deliver radiation in less time and treat several targets simultaneously. METHODS: We review a single case report of 82 yrs. old, female, with a contrast magnetic resonance diagnosis of enhanced single left occipital lobe brain metastases from a colorectal cancer. ECOG 1. The mental and neurologic physical examination is age-appropriate. Maximum diameter size of the single lesion was 3.8 cm (volume: 33.3 cm3). Previous immobilization with a thermoplastic head mask and brain CT scan for planning were done. Whole brain radiotherapy with simultaneous integrated boost (WBRT&SIB) for dual Rapid Arc® was planned after delineated planning tumor volume (PTV) and organs at risks (OAR). The prescribed dose to metastatic lesion (PTV 1) was 37,5Gy and normal brain (PTV 2) in 25Gy, both PTV in 10 fractions (2 weeks). A daily CBCT was applied with the auxiliary use of natural intracranial calcifications for improve the frameless position of the targets. Shift table displacements after setup using online CBCT in anterior-posterior (AP), right-left (RL), superior-inferior (SI) directions was annotated in centimeters +/- standard deviation (cm +/- SD). RESULTS: Mean dose for PTV 1 and PTV 2 was 38.9 Gy and 26.8 Gy respectively. PTV 1 Conformity Index (CI) was 1.06. Mean +/- SD residual setup shift table displacements were registered in AP: -0.01 +/- 0.06 cm; RL: -0.04 +/- 0.14 cm; SI: -0.14 +/- 0.14 cm. CONCLUSION: IN this only patient experience, frameless double arc VMAT WBRT&SIB was optimal delivered with the use of online CBCT and intracranial calcifications reposition.