tbuckley/cabot-search huggingface dataset:
Abstract 63: Alview (ALignment VIEWer): A software tool to visualize next generation sequencing (NGS) data
Authors: Daoud Meerzaman, Richard Finney, Qing-Rong Chen, Cu Nguyen, Chih Hao Hsu, Barbra Dunn
Journal: Cancer Research (2015)

Abstract Widespread use of NGS has led to the increasing sizes of high throughput sequencing data of various types from different platforms. Review of alignment data by experienced genomics researchers is an important quality control element in this process. Key to this activity is visual inspection of the sequencing data in order to eliminate false positives and document the likelihood of true positives. Furthermore, such manual, or visual, examination of data must occur at extremely rapid speeds. Alview (for “ALignment VIEWer”) is a compiled to native architecture software tool for visualizing the alignment of sequencing data. The inputs data are in the SAM/BAM format short read sequences that are aligned to a reference genome sequence. Outputs are images’ representing these short reads aligned to the reference genome. Alview is written in portable C with optional Graphical User Interface (GUI) code written in C,C++ or Objective C. Alview can be compiled to run in three different ways: (1) as a webserver, (2) as a command line tool, or (3) Alview is executable as a native graphical user interface. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. Our new tool saves time and addresses specific regions of interest (for example, regions containing known or novel mutations or SNPS) and peruses these regions in the manner of a “slideshow”, enabling the scanning of a large number of samples in a short time Citation Format: Daoud Meerzaman, Richard Finney, Qing-Rong Chen, Cu Nguyen, Chih Hao Hsu, Barbra Dunn. Alview (ALignment VIEWer): A software tool to visualize next generation sequencing (NGS) data. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 63. doi:10.1158/1538-7445.AM2015-63
Abstract 13340: Contemporary Use and Clinical Outcomes Following Non-Emergent Electrical Cardioversion for Atrial Fibrillation
Authors: Benjamin A Steinberg, Philip Schulte, Paul Hofmann, Mads Ersboll, John H Alexander, Kathleen Broderick-Forsgren, Kevin J Anstrom, Christopher B Granger, Jonathan P Piccini, Eric J Velazquez, Bimal R Shah
Journal: Circulation (2014)

Background: Electrical cardioversion (ECV) is recommended as one means of rhythm control for patients with atrial arrhythmias. However, the use of and outcomes following ECV in practice are not well described. Methods: We reviewed all, non-emergent ECVs for atrial arrhythmias at a tertiary care center from 2010 through 2013. Patients were stratified by use of TEE prior to ECV and demographics, history, vitals, and laboratory studies were compared. Outcomes included immediate ECV success, complications, repeat cardioversion, rehospitalization, and death at 30 days. Results: Overall 1,017 patients underwent ECV during the study period, most for atrial fibrillation (n=760, 75%) or atrial flutter (n=240, 24%); 633 underwent TEE prior to ECV and 384 did not. Those who had a TEE were more likely to be inpatients (74% vs. 44%, p<0.001), had higher mean CHADS2 scores (2.6 vs. 2.4, p=0.03), and lower INRs (mean 1.2 vs. 2.1, p<0.001). Overall, 8.8% (n=89) did not achieve sinus rhythm and there were 14 immediate com...
Rationalizing Medical Work: Decision-Support Techniques and Medical Practices, by Marc Berg
Authors: P. Taylor
Journal: BMJ (1997)

Marc Berg, MIT Press, $30, pp 256 ISBN 0 262 02417 9

Three decades of research into computer aids for medical decision making have resulted in thousands of systems and a growing number of successful clinical trials; yet only a handful of applications are in everyday use. This striking failure has led some to question the basis for this research.

Any system which corrects medical decision making must be built around an idea of “rational” practice. Marc Berg's monograph discusses changing ideas of rational or scientific medicine, and then explores how computer systems based on these different …
Mobilization of epidermal Langerhans cells - reply from the authors
Authors: I. Kimber, M. Cumberbatch, R.J. Dearman, M. Bhushan, C.E.M. Griffiths
Journal: British Journal of Dermatology (2000)

Journal Article Mobilization of epidermal Langerhans cells – reply from the authors Get access I. Kimber, I. Kimber AstraZeneca Central Toxicology Laboratory, Alderley Park, Macclesfield, Cheshire SK10 4TJ, U.K. *Dermatology Centre, University of Manchester, Hope Hospital, Salford M6 8HD, U.K.E‐mail: ian.kimber@ctl.zeneca.com Search for other works by this author on: Oxford Academic Google Scholar M. Cumberbatch, M. Cumberbatch AstraZeneca Central Toxicology Laboratory, Alderley Park, Macclesfield, Cheshire SK10 4TJ, U.K. *Dermatology Centre, University of Manchester, Hope Hospital, Salford M6 8HD, U.K.E‐mail: ian.kimber@ctl.zeneca.com Search for other works by this author on: Oxford Academic Google Scholar R.J. Dearman, R.J. Dearman AstraZeneca Central Toxicology Laboratory, Alderley Park, Macclesfield, Cheshire SK10 4TJ, U.K. *Dermatology Centre, University of Manchester, Hope Hospital, Salford M6 8HD, U.K.E‐mail: ian.kimber@ctl.zeneca.com Search for other works by this author on: Oxford Academic Google Scholar M. Bhushan, M. Bhushan AstraZeneca Central Toxicology Laboratory, Alderley Park, Macclesfield, Cheshire SK10 4TJ, U.K. *Dermatology Centre, University of Manchester, Hope Hospital, Salford M6 8HD, U.K.E‐mail: ian.kimber@ctl.zeneca.com Search for other works by this author on: Oxford Academic Google Scholar C.E.M. Griffiths C.E.M. Griffiths AstraZeneca Central Toxicology Laboratory, Alderley Park, Macclesfield, Cheshire SK10 4TJ, U.K. *Dermatology Centre, University of Manchester, Hope Hospital, Salford M6 8HD, U.K.E‐mail: ian.kimber@ctl.zeneca.com Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 143, Issue 4, 1 October 2000, Page 894, https://doi.org/10.1046/j.1365-2133.2000.03856.x Published: 01 October 2000
Education at Harvard
Authors: David Riesman
Journal: New England Journal of Medicine (1950)

cratic society in which most of the winners would have high morale because in a contest situation they gained their places by socially defined merit. But he also saw a revolt by some disenchanted winners, who included a few surly, old-fashioned Populists and romantic high-status women, who would side with the losers and lead the revolt. Meritocracy is both a procedure for distributing scarce educational and occupational resources and for determining how the work of society shall get accomplished in an intricate, still largely industrial world. It has acquired a pejorative connotation, although it is often unclear what the critic would put in its place as a mode of distributing scarce positions and opportunities in a nation of 220-million people linked to a world economy. Sometimes there is the implication that all people are in some sense equal in merit, as I believe people to be in a basically religious sense. Sometimes merit is defined too narrowly, even if one focuses on the allocation of scarce resources. But other criti-
Abstract 12873: Androgen Receptor is Essential for Cell Survival and Neovascularization After Ischemia.
Authors: Sumiko Yoshida, Ken-Ichi Aihara, Yasumasa Ikeda, Takayuki Ise, Yuka Ueda, Takashi Iwase, Masashi Akaike, Masataka Sata, Toshio Matsumoto
Journal: Circulation (2010)

Background: Androgens, male sex hormones, exert their biological effects in various target organs by genomic and non-genomic actions through the androgen receptor (AR) activation. Recently, we have...
The psychiatrist's role, responses, and responsibilities when a patient commits suicide
Authors: N S Kaye, S M Soreff
Journal: American Journal of Psychiatry (1991)

The suicide of a patient is not an infrequent event in a psychiatrist's practice, and it has a major impact on the clinician as well as on the patient's family and the hospital staff. Dealing with a patient's suicide is a neglected topic in residency training, and many psychiatrists are never taught how to cope with such a situation. The authors review the relevant literature and draw on this as well as on their own clinical experience to recommend specific interventions. They point out that the psychiatrist has a leadership role and a number of responsibilities in the aftermath of a suicide, including notifying the family, the hospital staff, hospital officials, and patients who knew the deceased patient; meeting with the family, the staff, and the patients to encourage discussion and venting of feelings; attending the funeral; and accurately documenting events in the medical record. The psychiatrist should also attend to his or her own needs by seeking support from a colleague and should ensure that a psychological autopsy is performed in order to facilitate learning, improve care of patients in the future, and help bring about closure for the psychiatrist so that the quality of his or her care of other patients is not compromised.
248. cFLIP or IKBSR Inhibition of NF-κB Activation in Mouse Myoblast Cells: Potential Application of Gene Therapy for Cancer Cachexia
Authors: Yongping Yue, Jeffrey W. Skimming, Mingju Liu, Yujiang Fang, Tammy Strawn, Dongsheng Duan
Journal: Molecular Therapy (2004)

Cardiomyopathy is a major determinant of the clinical outcome in Duchenne and Becker muscular dystrophy (DMD, BMD). Nearly every DMD and BMD patient suffers from some degree of cardiomyopathy. More then one tenth of DMD patients eventually die of heart failure. Clinical success of DMD gene therapy will depend upon functional improvement in both skeletal and cardiac muscle. Substantial progress has been made in DMD skeletal muscle disease gene therapy. However, few studies have been done in DMD cardiomyopathy gene therapy. We recently reported that micro-dystrophin was equally efficient in restoring the dystrophin-glycoprotein complex and maintaining sarcolemma integrity in the mdx heart (Yue et al Circulation 108:1626,2003). The minimal number of dystrophin expressing cells needed for cardiomyopathy therapy has not been determined however. In this study, we used female heterozygous mice (F1 from BL10 and mdx crossing) as an experimental model to evaluate whether dystrophin expression in half of the cardiomyocytes was enough to improve heart function in mdx mice. Consistent with the random X-chromosome inactivation theory, we found that 51.22% and 55.40% of the heart cells were expression dystrophin in maternal and paternal heterozygous mice respectively. The mdx mouse hearts were heavier than the BL10 hearts. Interestingly, weights of the heterozygous mice hearts were similar to those of the BL10. In contrast to previous reports of the benign histology in the mdx hearts, we detected fibrosis in 85.71% of the mdx hearts (N=42). More than half of the fibrosis was in the range of medium-to-large size. Only 43.59% of the heterozygous mice had hearts that contained fibrous regions, and the majority of the fibrosis was localized to small areas. To determine whether full-length dystrophin expression in half of the cardiomyocytes can protect the heart from mechanical-stress induced injury, we challenged the hearts with the inotrope b-isoproterenol. After administrating a vital dye, Evans blue (EBD), we found that 11.26 3.40% of the heart area was EBD positive in mdx mice. In the heterozygous mouse hearts, the EBD positive area was reduced to 2.37 0.70%. This result suggests that a significant improvement in cardiomyocyte sarcolemma integrity has been achieved in the heterozygous mouse hearts. In summary, our results suggest that a 50% correction in the mdx heart is sufficient to ameliorate cardiomyopathy in mdx mice.
852. Development of Systemic Non-Viral Gene Delivery Systems: Cationic Nanogels
Authors: Serguei V. Vinogradov, Alexander V. Kabanov
Journal: Molecular Therapy (2004)

Development of injectable non-viral gene delivery systems as an alternative of sometimes unsafe viral gene therapy is a fast-growing area of research. However, many of the existing non-viral DNA delivery systems show poor performance in vivo. Cationic Nanogel particles have been recently used in delivery of antisense oligonucleotides. They are constructed from interpenetrated chains of branched PEI with molecular weight 25KDa (PEI25) and covalently-linked polyethylene glycol forming cationic hydrogel network with particle size of 200 nm (Figure 1). These carriers have been shown to provide an excellent nuclease protection of plasmid DNA in circulation. We report here first steps toward an improvement of transfection efficacy of Nanogel/plasmid complexes in cancer cell cultures. First, Nanogel formed compact complexes with plasmid at high excess of charged PEI amino groups over phosphates of DNA, forming spherical particles with diameter of 80 nm. These complexes were stable in dispersion and formed even smaller particles in the presence of serum. Transfection of prostate carcinoma PC-3 cells with plasmid encoding the firefly luciferase gene was dose-dependent process and very low cellular toxicity of Nanogel was observed at DNA doses 2-5 μg/ml. Transfection by the Nanogel/plasmid complex did not depend on presence of serum (10% FBS) in the medium. Second, a surface modification of Nanogel with human transferrin via non-degradable linker demonstrated 30-40-fold increase of transfection efficacy of corresponding hTf-Nanogel/plasmid complexes. hTf-Nanogel having 5-7% of attached protein by weight was found the most active and did not loose useful properties. hTf-Nanogel and plasmid formed complex of 100 nm in diameter, which was stable in the presence of serum. This binding of hTf-Nanogel was receptor-mediated and suppressed by the presence of free transferrin in the medium. Third, preformulation of DNA with protamine (PA) in quantity of 10% of total DNA phosphates, before formation of complex with Nanogel additionally enhanced the efficacy of transfection approximately 2-fold. We hypothesize that PA is left bound to the plasmid following its release from Nanogel into cytosol and provides protective function and effective nuclear translocation of the intact DNA. It results in high level of transfection even in presence of serum compared to the known efficient transfection agent, branched PEI25 (Figure 2). Authors believe that Nanogel can be a convenient platform for development of plasmid DNA carriers with properties of artificial virus.
Abstract 20042: Comparison Between Alcohol Septal Ablation and Myomectomy for Hypertrophic Obstructive Cardiomyopahty: A Meta-Analysis
Authors: Daniel Garcia, Mohammad Mehdi Ansari, Rhanderson Nascimento, Carlos Alfonso, Alan Heldman
Journal: Circulation (2014)

Introduction: Both myomectomy and alcohol septal ablation (ASA) are used to treat patients with symptomatic hypertrophic obstructive cardiolmyopathy (HOCM). There is limited evidence to guide decision making between the two. Our aim was to compare the clinical and procedural outcomes among septal ablation and surgical myomectomy in patients with HOCM. Methods: We systematically searched PubMed, EMBASE, and Cochrane for studies comparing septal ablation to surgical myomectomy between January 1966 and June 2014. Primary end-point was 30 day mortality. Secondary end-points were long-term mortality (&gt;12 months), and peak LVOT gradient reduction. We used RevMan 5.1.7 software. Heterogeneity was defined as I2 values &gt; 25%. Results: A total of 11 observational and case-control studies were included and provided a total of 1155 patients. Myomectomy group was younger than septal ablation (9.37± 4 years; p&lt;0.01).There was no difference in 30 day mortality between septal ablation and surgical myomectomy 1.7% vs. 1.4% (95% CI: 0.39-2.57;p=0.99) (Figure A). There was no difference on long term mortality among groups (5.9% vs. 5.3%; 95% CI: 0.47-1.98; p=0.92) (Figure B). There was a significant 64.43% reduction of LVOT gradient in SA group and 71.03% in the surgical groups (p&lt;0.01) respectively (Figures C,D). Conclusion: Patients undergoing myomectomy are significantly younger than those having ASA. Short and long term mortality were similar. Clinical and anatomical features favoring one or the other strategy were not captured by our analysis. Further studies are required to resolve clinical equipoise.
Pancreatic Cancer Combination Therapy Using a BH3 Mimetic and a Synthetic Tetracycline
Authors: Bridget A. Quinn, Rupesh Dash, Siddik Sarkar, Belal Azab, Praveen Bhoopathi, Swadesh K. Das, Luni Emdad, Jun Wei, Maurizio Pellecchia, Devanand Sarkar, Paul B. Fisher
Journal: Cancer Research (2015)

Abstract Improved treatments for pancreatic cancer remain a clinical imperative. Sabutoclax, a small-molecule BH3 mimetic, inhibits the function of antiapoptotic Bcl-2 proteins. Minocycline, a synthetic tetracycline, displays antitumor activity. Here, we offer evidence of the combinatorial antitumor potency of these agents in several preclinical models of pancreatic cancer. Sabutoclax induced growth arrest and apoptosis in pancreatic cancer cells and synergized with minocycline to yield a robust mitochondria-mediated caspase-dependent cytotoxicity. This combinatorial property relied upon loss of phosphorylated Stat3 insofar as reintroduction of activated Stat3-rescued cells from toxicity. Tumor growth was inhibited potently in both immune-deficient and immune-competent models with evidence of extended survival. Overall, our results showed that the combination of sabutoclax and minocycline was highly cytotoxic to pancreatic cancer cells and safely efficacious in vivo. Cancer Res; 75(11); 2305–15. ©2015 AACR.
Undervaccination of Children
Authors: Tracy Hampton
Journal: JAMA (2004)

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Prenatal and perinatal risk factors for schizophrenia, affective psychosis, and reactive psychosis of early onset: case-control study Prenatal and perinatal risk factors for early onset schizophrenia, affective psychosis, and reactive psychosis
Authors: C. M Hultman, P. Sparen, N. Takei, R. M Murray, S. Cnattingius, J. Geddes
Journal: BMJ (1999)

# Prenatal and perinatal risk factors for schizophrenia, affective psychosis, and reactive psychosis of early onset: case-control study {#article-title-2} Objective: To examine prenatal and perinatal risk factors for subsequent development of schizophrenia and affective and reactive psychosis. Design: Three population based, case-control studies conducted within a Sweden-wide cohort of all children born during 1973-9.This was done by linking individual data from the Swedish birth register, which represents 99% of all births in Sweden, to the Swedish inpatient register. Subjects: Patients listed in inpatient register as having been first admitted to hospital aged 15-21years with a main diagnosis of schizophrenia (n=167), affective psychosis (n=198), or reactive psychosis (n=292). For each case, five controls were selected. Main outcome measures: Risks of schizophrenia and affective and reactive psychosis in relation to pregnancy and perinatal characteristics. Results: Schizophrenia was positively associated with multiparity (odds ratio 2.0), maternal bleeding during pregnancy (odds ratio 3.5), and birth in late winter (odds ratio 1.4). Affective psychosis was associated with uterine atony (odds ratio 2.2) and late winter birth (odds ratio 1.5). Reactive psychosis was related to multiparity (odds ratio 2.1). An increased risk for schizophrenia was found in boys who were small for their gestational age at birth (odds ratio 3.2), who were number four or more in birth order (odds ratio 3.6), and whose mothers had had bleeding during late pregnancy (odds ratio 4.0). Conclusions: A few specific pregnancy and perinatal factors were associated with the subsequent development of psychotic disorder, particularly schizophrenia, in early adult life. The association of small size for gestational age and bleeding during pregnancy with increased risk of early onset schizophrenia among males could reflect placental insufficiency. # Prenatal and perinatal risk factors for early onset schizophrenia, affective psychosis, and reactive psychosis {#article-title-34}
Donor Age and Corneal Endothelial Cell Loss 5 Years after Successful Corneal Transplantation
Authors: Lass Jh, Gal Rl, Dontchev M, Beck Rw, Kollman C, Dunn Sp, Heck E, Holland Ej, Mannis Mj, Montoya Mm, Schultze Rl, Stulting Rd, Sugar A, Sugar J, Tennant B, Verdier Dd
Journal: Ophthalmology (2008)
Bacterial profile, antibiotic sensitivity and resistance of lower respiratory tract infections in upper Egypt
Authors: Sherif Mohamed, Gamal Agmy, Yaser Gad, Esam Farghally, Hamdy Mohammedin, Hebba Rashed
Journal: European Respiratory Journal (2011)

Purpose:  To identify causative bacteria,antibiotic sensitivity/resistance of lower respiratory tract infections (LRTIs) in Upper Egypt.   Methods:  A multicentre prospective study was performed. Sampling was done for all patients including,sputum and/or BAL for Gram stain and culture. Samples were cultured on 3 media (Nutrient,Chocolate and MaConkey9s agars).Indirect Fluorescent Antibody was used to detect atypical pathogens.   Results:  Predominant isolates in patients with CAP were  S.pneumoniae  (36%),  C.pneumoniae (18%),  M. pneumoniae (12%) and  K. pneumoniae  (10%). A higher sensitivity was recorded for moxifloxacin, levofloxacin, macrolides, and cefepime. A higher rate of resistance was recorded for tetracyclines, cephalosporins, lincomycin, and β-lactam-β-lactamase inhibitor. Predominant isolates in patients with HAP were, MRSA (23%),  K.pneumoniae  (14%), E.coli (11%),  P.aeruginosa  (9%). A higher sensitivity was recorded for vancomycin,amikacin,and respiratory quinolones.An absolute resistance was recorded for β-lactam-β-lactamase inhibitor,high rates were recorded for cephalosporins.Predominant isolates in patients with AECOPD were  H.influnzae  (30%),  S.pneumoniae  (25%),  M.catarrhalis  (18%),  K.pneumoniae  (12%) and  C. pneumoniae  (5%). A higher sensitivity was recorded for quinolones,macrolides and cefepime. High resistance was recorded for amikacin,clindamycin, and cephalosporins.   Conclusion:  The most predominant bacteria for CAP in Upper Egypt are  S.pneumoniae  and atypical organisms,while that for HAP are MRSA and Gram negative bacteria. For AECOPD, H.influnzae  is the commonest. Respiratory quinolones,linezolides,and cefepime are the most efficient antibiotics in treatment of LRTIs in our locality.