tbuckley/cabot-search huggingface dataset:
Gene Discovery Using the Serial Analysis of Gene Expression Technique: Implications for Cancer Research
Authors: Kornelia Polyak, Gregory J. Riggins
Journal: Journal of Clinical Oncology (2001)

ABSTRACT: Cancer is a genetic disease. As such, our understanding of the pathobiology of tumors derives from analyses of the genes whose mutations are responsible for those tumors. The cancer phenotype, however, likely reflects the changes in the expression patterns of hundreds or even thousands of genes that occur as a consequence of the primary mutation of an oncogene or a tumor suppressor gene. Recently developed functional genomic approaches, such as DNA microarrays and serial analysis of gene expression (SAGE), have enabled researchers to determine the expression level of every gene in a given cell population, which represents that cell population’s entire transcriptome. The most attractive feature of SAGE is its ability to evaluate the expression pattern of thousands of genes in a quantitative manner without prior sequence information. This feature has been exploited in three extremely powerful applications of the technology: the definition of transcriptomes, the analysis of differences between the gene expression patterns of cancer cells and their normal counterparts, and the identification of downstream targets of oncogenes and tumor suppressor genes. Comprehensive analyses of gene expression not only will further understanding of growth regulatory pathways and the processes of tumorigenesis but also may identify new diagnostic and prognostic markers as well as potential targets for therapeutic intervention.
Teniposide and etoposide in previously untreated small-cell lung cancer: a randomized study.
Authors: E Bork, J Ersbøll, P Dombernowsky, B Bergman, M Hansen, H H Hansen
Journal: Journal of Clinical Oncology (1991)

A randomized study comparing teniposide (VM-26) and etoposide (VP-16) was performed to investigate whether there are any differences in the activity and toxicity of these two analogs in small-cell lung cancer (SCLC). Only previously untreated patients with SCLC were included; 46 and 48 patients receiving VP-16 and VM-26, respectively, are assessable for response. There were no differences between the two groups with respect to extent of disease, median age, and performance status (PS). The initial doses were for both compounds 70 mg/m2 intravenously (IV) daily for 5 days every 3 weeks. After inclusion of 25 patients in the study, the doses were increased to 80 mg/m2 for VM-26 and 90 mg/m2 for VP-16 because of differences in toxicity. VM-26 caused more hematologic toxicity than VP-16 throughout the study. The overall responses (complete response [CR] plus partial response [PR]) were 65% for VP-16 and 71% for VM-26, with CR occurring in 24% and 23%, respectively, for the two compounds. Median survival was 8.5 months for VP-16-treated patients versus 11.3 months for VM-26-treated patients (P = .58). It is concluded that both VP-16 and VM-26 are highly active single agents in SCLC.
P0511 : Direct comparison of 3 elastrometry devices (fibroscan, acoustic radiation force impulse, supersonic shearwave imaging) for the non-invasive diagnosis of liver fibrosis in chronic liver diseases
Authors: J. Boursier, V. Cartier, J. Lebigot, F. Oberti, I. Fouchard-Hubert, S. Bertrais, P. Cales, C. Aube
Journal: Journal of Hepatology (2015)
Abstract 14930: Contribution of Remote Magnetic Navigation to Supraventricular Tachycardia Ablation in Complex Congenital Heart Diseases
Authors: Akiko Ueda, Irina Horduna, Lilian Mantziari, Procolo Marchese, Marko Gujic, Beatrice Bonello, Sonya V Babu-Narayan, Siew Y Ho, Sabine Ernst
Journal: Circulation (2012)

Aim To assess the contribution of remote magnetic navigation (RMN) and three-dimensional (3D) mapping and image integration in adult congenital heart disease (ACHD) patients through reviewing our e...
Abstract P4-01-03: Digital measurement of mammographic density and the risk of overlooking cancer in Japanese women
Authors: T Sawada, M Ikeda, T Kuwayama, ST Akashi, S Nakamura
Journal: Cancer Research (2016)

Abstract Introduction: mammographic density is a strong risk factor for breast cancer and an essential determinant of screening sensitivity, but the breast density of Japanese women has yet to be objectively examined. Single mammographic examination fails to detect approximately half of breast cancers in women with dense breasts. We objectively evaluated mammographic density to clarify the relation between breast density and incidence of breast cancer in Japanese women. Method: We enrolled 269 patients diagnosed with breast cancer and 397 healthy controls, who participated in screening mammography at Showa University Hospital. Breast density was measured using Volpara (a software application which analyses breast composition volumetrically). Results: The average age of both control and breast cancer groups was 55. Of the control group, 308 (78%) were characterized as having dense breasts, being defined as volumetric density grade (VDG) 3 or 4. More than 50% of the total population (all ages) had dense breasts (VDG 3 or 4) and more than 20% were extremely dense (VDG:4). Of the breast cancer patients, 232 (87%) were VDG 3 or 4. 52 (23%) of those with dense breasts showed negative results in single mammography examination. In primary breast cancer patients with dense breasts, 30% of those under age 70, but only 13% of those over age 70, showed no abnormal findings from mammographic examination. Conclusion and Discussion: In comparison of our present results and other papers, In the Japanese control group, 72% of patients had dense breasts (VDG 3 or 4) at age 50 or greater, but in Holland, for example, only 36% of women had breasts classed as dense. 87% of Japanese women with breast cancer had dense breasts, approximately the same ratio (88%) as found in Korea. For Japanese and other Asians, women under 70 years old with dense breasts may warrant additional screening. Citation Format: Sawada T, Ikeda M, Kuwayama T, Akashi ST, Nakamura S. Digital measurement of mammographic density and the risk of overlooking cancer in Japanese women. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-01-03.
Prospective Observational Study on Chemotherapy-Induced Nausea and Vomiting for Patients with Colorectal Cancer in Japan
Authors: Yumi Shibata, Hideo Baba, Yasushi Tsuji, Michiya Kobayashi, Yoshihiko Maehara, Masahiro Goto, Kazuhiro Yoshida, Norihiro Kokudo, Yoshihiro Kakeji, Keisuke Aiba
Journal: Annals of Oncology (2014)
Abstract B16: Combination of docetaxel with histone deacetylase inhibitor inhibits AR signaling synergistically in hormone-independent 22Rv1 prostate cancer cells
Authors: Ha-Gyeong Kim, Jung Jin Hwang, Choung-Soo Kim
Journal: Clinical Cancer Research (2015)

Abstract Globally prostate cancer is the sixth leading cause of cancer-related death in men, and it is now the first in the United Kingdom and second in the United States. At the early stage, prostate cancer growth and progression depend on androgen receptor (AR) signaling. Therefore, androgen-deprivation therapy (ADT) is effective to patient with prostate cancer by inhibition of androgen synthesis. With time, however, most patients with prostate cancer eventually lose sensitivity to androgen withdrawal and progress to the development of castration-resistant prostate cancer (CRPC). Though docetaxel is a standard of care therapy in CRPC, most of patients develop resistance to this therapy. Therefore, the novel therapeutic strategies and combination therapy are needed to overcome this resistance. In this study, we examined whether histone deacetylase inhibitor (HDACI), suberoylanilide hydroxamic acid (SAHA) might enhance the effect of docetaxel in CRPC. Hormone-independent 22Rv1 cells harboring AR were treated with docetaxel and/or SAHA. Co-treatment of docetaxel and SAHA inhibited the growth of 22Rv1 cells synergistically. Combination treatment decreased the levels of AR, prostate specific antigen (PSA), and anti-apoptotic Bcl-2 proteins (Mcl-1, Bcl-xl) more efficiently compared with docetaxel or SAHA alone, when it analyzed by Western blot. And combination treatment increased activation of caspase-3 remarkably, while docetaxel or SAHA alone increased it slightly. Moreover, immunocytochemistry and analysis of nuclear fractionated proteins showed that combination treatment induced acetylation and bundling of tubulin, inhibiting nuclear accumulation of AR significantly. These results suggested that docetaxel in combination with SAHA inhibited cell growth efficiently and induced apoptosis by repressing expression and translocation to nucleus of AR in 22Rv1 cells, and this combination can be a useful therapeutics for the treatment of CRPC patients. Citation Format: Ha-Gyeong Kim, Jung Jin Hwang, Choung-Soo Kim. Combination of docetaxel with histone deacetylase inhibitor inhibits AR signaling synergistically in hormone-independent 22Rv1 prostate cancer cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B16.
Peri‐transplant clostridium difficile infections in patients undergoing allogeneic hematopoietic progenitor cell transplant
Authors: Aya Agha, Alison Sehgal, Matthew J. Lim, David Weber, Jing‐Zhou Hou, Rafic Farah, Anastasios Raptis, Annie Im, Kathleen Dorritie, Stanley Marks, Mounzer Agha, Seah H. Lim
Journal: American Journal of Hematology (2015)

Clostridium difficile infections (CDI) remain the leading cause of infectious diarrhea among hospitalized patients in this country. Patients with hematologic malignancies, especially those who undergo hematopoietic progenitor cell transplants are particularly at risk for developing CDI. One hundred and forty seven consecutive allogeneic hematopoietic progenitor cell transplants were analyzed for peri-transplant Clostridium difficile infections (PT-CDI). Sixteen patients (11%) developed PT-CDI (Median time = 7 days after transplant). The probability for developing PT-CDI during the peri-transplant period was 12.3%. History of CDI was strongly associated with the development of PT-CDI (P = 0.008) (OR = 5.48) (P = 0.017). These patients also developed PT-CDI much earlier than in those without a history (median 1 day vs. 8 days, P = 0.03). The probability for developing PT-CDI for those with a history was 39%. There was a trend toward significance (P = 0.065) between matched related donor grafts and the development of PT-CDI (OR = 0.245) (P = 0.08). Age, sex, diagnosis, transplant preparative regimens, Graft-versus-host disease (GVHD) prophylaxis, grade 3/4 acute GVHD, or use of antimicrobials within 8 weeks of transplant were not associated with PT-CDI. Non-CDI-related deaths occurred in one patient in the PT-CDI group and nine in the group without PT-CDI. In the remaining 139 patients, the length of hospital stay for those with PT-CDI was significantly longer than those without (mean 27 days vs. 22 days; P = 0.02).
Prospective, randomized trial of 5-fluorouracil, leucovorin, doxorubicin, and cyclophosphamide chemotherapy in combination with the interleukin-3/granulocyte-macrophage colony-stimulating factor (GM-CSF) fusion protein (PIXY321) versus GM-CSF in patients with advanced breast cancer
Authors: JA O'Shaughnessy, A Tolcher, D Riseberg, D Venzon, J Zujewski, M Noone, M Gossard, D Danforth, J Jacobson, V Chang, B Goldspiel, P Keegan, R Giusti, KH Cowan
Journal: Blood (1996)
Focal type of peliosis hepatis
Authors: Gil-Sun Hong, Kyoung Won Kim, Jihyun An, Ju Hyun Shim, Jihun Kim, Eun Sil Yu
Journal: Clinical and Molecular Hepatology (2015)

Although peliosis hepatis is a rare entity, it is increasingly found as a focal liver lesion in the routine practice with the popular use of modern cross-sectional imaging studies. As peliosis hepatis may present with a broad spectrum of potentially misleading findings on imaging studies, a high level of suspicion is a prerequisite for the diagnosis. Peliosis hepatis should be suspected when the imaging findings of an incidental focal liver lesion do not favor the diagnosis of the common hepatic tumors and tumor-like lesions. Non-tumefactive margin, the lack of mass effect, and late iso-attenuating enhancement on dynamic post-contrast study may further raise the suspicion.
Abstract 16673: Meta-Analysis of Three Randomized Controlled Trials Comparing Coronary Artery Bypass Grafting With Percutaneous Coronary Intervention Using Drug-Eluting Stenting in Patients With Diabetes
Authors: Zaher Fanari, Sandra A Weiss, Wei Zhang, Mazen Hadid, William S Weintraub
Journal: Circulation (2013)

OBJECTIVES: Coronary artery bypass grafting (CABG) was found to be the preferred strategy of revascularization in patients with diabetes in the bare-metal stent (BMS) era. The introduction of drug-eluting stents (DESs) led to a significant reduction in the rates of repeat revascularization (RRV) when compared with BMSs. We did a collaborative analysis of data from randomized controlled trials in the contemporary era to compare CABG versus percutaneous coronary intervention using DESs in diabetic patients. METHODS: We performed a systematic review and meta-analysis from randomized trials in the contemporary era comparing PCI with DESs with CABG in diabetic patients with multivessel disease. A comprehensive literature search (1 January 2003 to 18 May 2013) identified randomized controlled trials that reported long-term outcomes comparing PCI using DESs with CABG in 2974 diabetic patients. RESULTS: At 1 year, PCI was associated with a significant increase in the incidence of RRV [2.48 (1.56–3.94); P ≤0.0001], lower incidence of stroke [relative risk (RR) = 0.43 (0.19–0.81); P= 0.017], and no difference in death or myocardial infarction (MI). At 5 years, PCI was still associated with a lower incidence of stroke, but was associated with a significant increase in the incidence of death [RR = 1.36 (1.11–1.66); P= 0.0033] and MI [RR = 2.01 (1.54–2.62); P ≤0.0001]. CONCLUSIONS: In patients with diabetes, PCI was associated with no difference in death and MI at 1 year. However, at 5 years, PCI was associated with a higher incidence of death and MI. PCI was associated with a higher incidence of RRV but a lower incidence of stroke.
National Institute for Clinical Excellence: NICE works
Authors: Michael D Rawlins
Journal: Journal of the Royal Society of Medicine (2015)

The National Institute for Clinical Excellence was established in 1999. Its original remit was to undertake technology appraisals of (mainly) new interventions and to develop clinical guidelines. In providing both forms of guidance, it was required to take into account both clinical and cost effectiveness. After a difficult first few months, it gained the confidence and trust of the professions. It subsequently gained additional responsibilities with a commensurate increase in its staffing and budget. It is, moreover, the only one of the National Health Service organisations established in the late 1990s and early 2000s to have not only survived but grown. This paper describes not only the National Institute for Clinical Excellence's early years but also, in the author's view, the features of its guidance programmes that led to its success and (in retrospect) some things it could have done differently.
Abstract 10733: Tissue Doppler Derived Mitral Annular Velocity and Acceleration During Isovolumic Contraction Predict Pulmonary Capillary Wedge Pressure in Patients With Significant Mitral Regurgitation
Authors: Alaa M Omar, Hidekazu Tanaka, Kensuke Matsumoto, Kazuhiro Tatsumi, Mohammed A Abdel-Rahman, Hala M Raslan, Osama Rifaie, Hiroya Kawai, Ken-ichi Hirata
Journal: Circulation (2013)

Background: We previously reported that tissue Doppler derived mitral annular isovolumic contraction velocity (IVV) and acceleration (IVA) predict pulmonary capillary wedge pressure (PCWP) in patie...
Modulation of the Terminal Differentiation of Human Squamous Carcinoma Cells In Vitro by &lt;italic&gt;all-trans&lt;/italic&gt;-Retinoic Acid&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: M Reiss, S W Pitman, A C Sartorelli
Journal: JNCI Journal of the National Cancer Institute (1985)

A malignant human cell line (SqCC/Y1) derived from a squamous carcinoma of the buccal mucosa is described. It formed a stratified cellular structure with ultrastructural characteristics of a fully differentiated stratified squamous epithelium when cultured in equal parts of Dulbecco's modified Eagle medium and Ham's medium F12, supplemented only with insulin, transferrin, and selenium. After 14 days in culture in this defined medium, 30% of the cells became keratinized (insoluble in detergent), and 75% of the cells were capable of being induced to form cornified cell envelopes. Involucrin, the precursor protein of the cornified cell envelope, could be detected by immunofluorescence only in suprabasal cells. Treatment of SqCC/Y1 cultures with 5 X 10(-8) M all-trans-retinoic acid (RA) completely inhibited stratification and markedly increased cell desquamation. In the presence of RA, less than 10% of the cells became keratinized, and only 15-20% of the cells acquired envelope-forming competence. The fraction of colony-forming cells in RA-treated cultures was tenfold higher than in fully mature cultures. Thus RA appears to be an effective inhibitor of terminal differentiation of SqCC/Y1 cells.
Acute and Chronic Graft-Versus-Host Disease: Clinical Manifestations, Prophylaxis, and Treatment&lt;xref ref-type="fn" rid="FN1"&gt;1&lt;/xref&gt;&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;&lt;xref ref-type="fn" rid="FN3"&gt;3&lt;/xref&gt;
Authors: H J Deeg, R Storb
Journal: JNCI Journal of the National Cancer Institute (1986)

Graft-versus-host disease (GvHD) is a clinical syndrome observed in recipients of allogeneic marrow grafts, presumably due to an attack of donor T-lymphocytes against host (patient) tissue. Acute GvHD develops within the first 2–3 months of transplantation and occurs in 25–60% of recipients of HLA genotypically identical transplants. The major target organs are skin, liver, intestinal tract, and conjunctivae. About one-half of the patients with moderately severe to severe GvHD die, generally from associated infections. Attempts at prevention of acute GvHD, such as selection of HLA-identical donors, postgrafting immunosuppression, decontamination of the patient and placement in a sterile environment, or T-cell depletion of the donor marrow, have met with only partial success. Treatment of established GvHD inVOlves the use of immunosuppressants, such as steroids, antithymocyte globulin, cyclosporine, and monoclonal antibodies. Chronic GvHD generally develops 3 months to 1 year after grafting and affects 40–45% of surviving patients. Target organs, in addition to those of acute GvHD, include exocrine glands and mucous and serous membranes. The clinical picture strongly resembles collagen vascular diseases. Chronic GvHD occurs more frequently in older patients and patients with preceding acute GvHD. These patients are susceptible to bacterial or fungal infections that may be fatal. Treatment of chronic GvHD involves the use of immunosuppressive and cytotoxic drugs and prophylactic antibodies.
Radiological features combined with<i>IDH1</i>status for predicting the survival outcome of glioblastoma patients
Authors: Kai Wang, Yinyan Wang, Xing Fan, Jiangfei Wang, Guilin Li, Jieling Ma, Jun Ma, Tao Jiang, Jianping Dai
Journal: Neuro-Oncology (2015)

Radiological characteristics may reflect the biological features of brain tumors and may be associated with genetic alterations that occur in tumorigenesis. This study aimed to investigate the relationship between radiological features and IDH1 status as well as their predictive value for survival of glioblastoma patients. The clinical information and MR images of 280 patients with histologically confirmed glioblastoma were retrospectively reviewed. The radiological characteristics of tumors were examined on MR images, and the IDH1 status was determined using DNA sequencing for all cases. The Kaplan-Meier method and Cox regression model were used to identify prognostic factors for progression-free and overall survival. The IDH1 mutation was associated with longer progression-free survival (P = .022; hazard ratio, 0.602) and overall survival (P = .018; hazard ratio, 0.554). In patients with the IDH1 mutation, tumor contrast enhancement and peritumoral edema indicated worse progression-free survival (P = .015 and P = .024, respectively) and worse overall survival (P = .024 and P = .032, respectively). For tumors with contrast enhancement, multifocal contrast enhancement of the tumor lesion was associated with poor progression-free survival (P = .002) and poor overall survival (P = .010) in patients with wild-type IDH1 tumors. Combining the radiological features and IDH1 status of a tumor allows more accurate prediction of survival outcomes in glioblastoma patients. The complementary roles of genetic changes and radiological features of tumors should be considered in future studies.
Chimpanzee fetal G gamma and A gamma globin gene nucleotide sequences provide further evidence of gene conversions in hominine evolution.
Authors: J L Slightom, L Y Chang, B F Koop, M Goodman
Journal: Molecular Biology and Evolution (1985)

The fetal globin genes G gamma and A gamma from one chromosome of a chimpanzee (Pan troglodytes) were sequenced and found to be closely similar to the corresponding genes of man and the gorilla. These genes contain identical promoter and termination signals and have exons 1 and 2 separated by the conserved short intron 1 (122 bp) and exons 2 and 3 separated by the more rapidly evolving, larger intron 2 (893 bp and 887 bp in chimpanzee G gamma and A gamma, respectively). Each intron 2 has a stretch of simple sequence DNA (TG)n serving possibly as a "hot spot" for recombination. The two chimpanzee genes encode polypeptide chains that differ only at position 136 (glycine in G gamma and alanine in A gamma) and that are identical to the corresponding human chains, which have aspartic acid at position 73 and lysine at 104 in contrast to glycine and arginine at these respective positions of the gorilla A gamma chain. Phylogenetic analysis by the parsimony method revealed four silent (synonymous) base substitutions in evolutionary descent of the chimpanzee G gamma and A gamma codons and none in the human and gorilla codons. These Homininae (Pan, Homo, Gorilla) coding sequences evolved at one-tenth the average mammalian rate for nonsynonymous and one-fourth that for synonymous substitutions. Three sequence regions that were affected by gene conversions between chimpanzee G gamma and A gamma loci were identified: one extended 3' of the hot spot with G gamma replaced by the A gamma sequence, another extended 5' of the hot spot with A gamma replaced by G gamma, and the third conversion extended from the 5' flanking to the 5' end of intron 2, with G gamma replaced here by the A gamma sequence. A conversion similar to this third one has occurred independently in the descent of the gorilla genes. The four previously identified conversions, labeled C1-C4 (Scott et al. 1984), were substantiated with the addition of the chimpanzee genes to our analysis (C1 being shared by all three hominines and C2, C3, and C4 being found only in humans). Thus, the fetal genes from all three of these hominine species have been active in gene conversions during the descent of each species.