tbuckley/cabot-search huggingface dataset:
<i>CHFR</i> methylation as an epigenetic marker for recurrence of colon cancer
Authors: M. Tanaka, S. Sethi, D. Li, G. Bland, S. R. Hamilton, J. L. Abbruzzese, C. Eng
Journal: Journal of Clinical Oncology (2009)

4043 Background: Currently, no definitive epigenetic markers exist to predict recurrence and overall survival (OS) of colorectal cancer patients after surgical resection. Promoter hypermethylation of the ID4 (inhibitor of DNA binding), RECK (reversion-inducing cysteine rich protein with Kazal motifs), and CHFR (checkpoint with forkhead-associated and RING finger domains) genes have been associated with reduced mRNA and protein expression in colorectal cancer. The purpose of this study was to determine the association of methylation of these genes and also MINT1 (methylated in tumor loci) with recurrence-free survival (RFS) and OS in colon cancer patients. Methods: DNA methylation was quantitatively evaluated using pyrosequencing in tissue samples from 64 patients with AJCC stage II and III colon cancer without HNPCC seen at M.D. Anderson during 1999–2007. Survival outcomes were determined by retrospective chart review and evaluated by Kaplan-Meier plot and log-rank test for univariate analysis and Cox's proportional hazard model for multivariate analysis. Mean methylation rate of multiple CpG sites in the promoter region was used. For this analysis, we defined &lt;15%, 15%-30%, and &gt;30% as methylation-negative, -low, and -high, respectively. Results: There were 19 stage II (30%) and 45 stage III (70%) patients. The median age was 62.1 years (range: 31–86). Adjuvant chemotherapy was completed in 49 patients (77%). After a median follow-up of 54.9 months, 12 (19%) patients developed recurrence and 7 (11%) have died. Methylation of MINT1, ID4, and RECK did not correlate with RFS and OS. The CHFR methylation-high (42%) group had low RFS (P=.04) and OS (P=.03) when compared with the CHFR methylation- negative (38%) and -low (20%) group. CHFR methylation-high was associated with N 2 disease (P=.04) and right-sided tumors (P=.002). Multivariate analysis indicated T 4 disease [P=.004, HR=8.42 (95% CI: 1.98–35.8)] and CHFR methylation-high [P=.04, HR = 3.79 (95% CI: 1.04–13.8)], were poor prognostic factors for recurrence. Conclusions: The presence of high CHFR promoter methylation correlates with advanced lymph node metastasis and shortened RFS and OS. Methylation of the CHFR promoter is a potential epigenetic marker for colon cancer recurrence and overall survival. No significant financial relationships to disclose.
The efficacy of chemotherapy in the advanced NSCLC patients who failed with the treatment of EGFR-TKI
Authors: S. Zhou, S. Ren, L. Zhang, H. Sun, C. Zhou
Journal: Journal of Clinical Oncology (2009)

e19078 Background: EGFR-TKI such as gefitinib and erlotinib were used as standard 2 nd /3 rd line therapy in previously treated NSCLC. However, those who benefit from EGFR-TKI will inevitably progress from the disease. We reported the efficacy of chemotherapy(CT) in the advanced NSCLC pts failed with the previously 2 nd /3 rd line treatment of EGFR-TKIs. Methods: Eligibility criteria included advanced NSCLC pts who got disease control(included CR, PR or SD) initially from TKI therapy and then progressed, PS = 0–2, and normal fatal organ function. Pts received systemic CT (docetaxal, pemetrexed, gemicitabine, novelbine or combined with platinum agent) until disease progression or unacceptable toxicity. Results: 32 pts were enrolled from Oct 15 2007 to Nov 30 2008. Demographics: M 56.3%/F 43.7%; median age 56 y [range 34–72]; stage IV 100%; PS 0/1/2: 3 (9.4%)/22(68.8%)/7(21.8%); adenocarcinoma/non-adenocarcinoma 29(90.6%)/3(9.4%); EGFR-TKI treatment duration &gt;6 m 20(62.5%) /&lt; 6 m 12(37.5%); monotherapy 16 (50%)/ doublets 16 (50%). All pts were evaluable for efficacy; partial response in 5 cases (15.6%), stable disease in 21 cases(37.5%), progressive disease in 15 (46.9%) ( Table ). The response of CT was not related with gender, age, regimens, but these with TKI treatment &gt; 6 m achieved a significantly better response than those &lt; 6 m(p=0.01) and these with PS 0–1 got a marginally significantly better response than PS 2(p=0.095). The toxicity was acceptable. Median progression free survival was 3.4 months and it was not correlated with the gender, age and regimens, but PFS were significant longer in the pts received &gt; 6 m of TKI (median 4.8 vs 1.9, p=0.009) and with PS 0–1 (median 4.7 vs 1.9, p=0.002). Conclusions: Pts benefited from TKI therapy and developed progressive disease could also benefit from CT. The response duration of EGFR-TKI and performance status could be predictive for the better efficacy of CT. [Table: see text] No significant financial relationships to disclose.
Abstract 12827: Impact of Concomitant Deep Vein Thrombosis on Clinical Outcomes in Patients With Acute Pulmonary Embolism
Authors: Shushi Nishiwaki, Yugo Yamashita, Yusuke Morita, Moriaki Inoko, Takeshi Morimoto, Hidewo Amano, toru takase, Seiichi Hiramori, Kitae Kim, Maki Oi, Takao Kato, Takeshi Kimura
Journal: Circulation (2019)

Introduction: For patients with acute pulmonary embolism (PE), risk stratification is important for decision-making regarding PE therapy. An increased thrombus burden such as concomitant deep venou...
Inferior Fragmented QRS as a New Predictor of Ventricular Arrhythmias in Patients With Nonischemic Cardiomyopathy
Authors: Hyoung-won Cho, Haeju Lee, Hyun Jin Lee, Dong Geum Shin, Jin-Kyu Park, Jeong Myung Lee, Jaewon Oh, Seok-Min Kang, Sung Shine Shim, Yookyung Kim, Hye-Jeong Lee, Young Jin Kim, Boyoung Joung, Junbeom Park
Journal: JACC. Cardiovascular imaging (2020)
CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations
Authors: Shuang Li, K. Joeri van der Velde, Dick de Ridder, Aalt D. J. van Dijk, Dimitrios Soudis, Leslie R. Zwerwer, Patrick Deelen, Dennis Hendriksen, Bart Charbon, Marielle E. van Gijn, Kristin Abbott, Birgit Sikkema-Raddatz, Cleo C. van Diemen, Wilhelmina S. Kerstjens-Frederikse, Richard J. Sinke, Morris A. Swertz
Journal: Genome Medicine (2020)

Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational prediction methods requires manual classification by experts. Here we introduce CAPICE, a new machine-learning-based method for prioritizing pathogenic variants, including SNVs and short InDels. CAPICE outperforms the best general (CADD, GAVIN) and consequence-type-specific (REVEL, ClinPred) computational prediction methods, for both rare and ultra-rare variants. CAPICE is easily added to diagnostic pipelines as pre-computed score file or command-line software, or using online MOLGENIS web service with API. Download CAPICE for free and open-source (LGPLv3) at https://github.com/molgenis/capice .
Association of Endocrine Therapy With Overall Survival in Women With Small, Hormone Receptor–Positive, <i>ERBB2</i>-Negative Breast Cancer
Authors: Sung Jun Ma, Oluwadamilola T. Oladeru, Anurag K. Singh
Journal: JAMA Network Open (2020)

This cohort study examines the association of overall survival with endocrine therapy to treat hormone receptor–positive, ERBB2-negative breast cancer.
A phase II study of the halichondrin B analog, E7389, in patients (pts) with advanced non-small cell lung cancer (NSCLC) previously treated with a taxane. A California Consortium/University of Pittsburgh/University of Chicago NCI/CTEP sponsored trial
Authors: B. J. Gitlitz, A. M. Davies, C. P. Belani, A. Argiris, S. S. Ramalingam, P. C. Hoffman, M. Koczwas, S. G. Groshen, D. R. Gandara
Journal: Journal of Clinical Oncology (2009)

8056 Background: E7389 is a structurally simplified synthetic macrocyclic ketone analog of halichondrin B and has a unique mechanism of microtubule binding and interaction, distinct from other agents in this class. Thus, it was our hypothesis that pts with prior taxane based therapy would respond to this agent. We conducted a phase II trial of E7389 in prior taxane-treated NSCLC pts. Methods: Eligible pts included: histologically confirmed advanced NSCLC, previous treatment with platinum-based therapy and a taxane, no more than 2 prior regimens, measurable disease, Zubrod performance status ≤ 2. Pts were classified by taxane-sensitivity status: taxane sensitive (TS) (progression &gt;90 days after taxane) or taxane resistant (TR) (progression during or ≤90 days after taxane). Treatment: E7389 1.4 mg/m 2 intravenously over 1–2 minutes on day 1 and 8 of a 21 day schedule until disease progression or unacceptable toxicity. Results: 41 pts were entered. There were 3 (15%) objective responses (7.2+, 8.5+, 10.6 mo) of 20 TS pts; and no response of 21 TR pts. Stable disease rate was 60% and 24% in TS and TR pts. respectively. Median progression free survival (PFS) is 6.3 mos TS pts. 95%CI (2.5–8.6 mos) and 1.2 mos TR pts. 95%CI (1.1–4.1 mos). Median number of cycles (range): TS 4 (1–14); TR 2 (1–7). Major toxicity included: 19 pts (46%) with grade 3 or 4 hematologic toxicity including only 1 episode of febrile neutropenia and 8 pts (20%) with grade 3 or 4 non-hematologic toxicity attributable to drug including: fatigue (1), dehydration (2), nausea (2), constipation (2). Only 1 pt developed grade 3 neuropathy (course 9). Conclusions: E7389 was well tolerated with encouraging objective response, PFS and disease control rate in the TS cohort. This cohort will be expanded, using a 2-stage design, to accrue up to another 25 pts. No significant financial relationships to disclose.
A survey of dermatologic health-related quality of life and resource access in patients experiencing homelessness
Authors: Amanda Truong, Aaron M. Secrest, Minyuan Zhang, Brayden R. Forbes, Caroline W. Laggis, Molly McFadden, Laura J. Gardner, Douglas L. Powell, Bethany K.H. Lewis
Journal: Journal of the American Academy of Dermatology (2020)
Abstract 2776: Real-time measurement of temperature and tissue damage during laser photothermal ablation
Authors: Faraneh Fathi, Dilip R. Maddirela, Venkateswara Rao Gogineni, Sarah B. White, Bing Yu
Journal: Cancer Research (2020)

Abstract Hepatocellular carcinoma (HCC) is the sixth most common cancer and tumor resection is feasible in only 25±30% of these patients. Thermal ablation therapies using lasers, radiofrequency waves and microwaves are considered as an alternative treatment for unresectable tumors. Our goal was to develop optical fiber-based laser ablation while monitoring the changes in temperature and tissue properties in real-time. A portable diffuse reflectance spectroscopy (DRS) system consisting of a DRS probe with self-calibration and fiber optic temperature sensor was made. Tissue mimicking phantoms using human hemoglobin powders and polystyrene particles with fixed total number of scatterers were used to calibrate the system. In vivo studies were performed in 8 rats orthotopically implanted with HCC. Temperature sensor was inserted in the center of the tumor via hypodermic needle and DRS fiber was overlaid on the temperature sensor. Ablation was performed by a fiber optic diffuser connected to an 808nm laser using different power settings in pulse mode. The tissue temperature and optical properties were continuously monitored until both plateaued using a custom LabVIEW program. Rats were immediately euthanized, and the ablated liver tissues were collected for histological analysis. The DRS showed average errors of 6.31% and 4.74% in measuring the absorption (μa) and reduced scattering coefficients (μs) of the phantoms respectively. Tumor bearing liver tissues showed a decreasing trend in both μa and μs irrespective of the laser power (1W-2.5W) and the temperatures recorded (50°C to 88°C) in different animals. Histological analysis showed discrete zones of tissue damage from treated regions with hemorrhage in the outer most zone. Changes in optical properties of the ablated tumors with temperatures and histological changes needs further correlation by performing more in vivo studies. Citation Format: Faraneh Fathi, Dilip R. Maddirela, Venkateswara Rao Gogineni, Sarah B. White, Bing Yu. Real-time measurement of temperature and tissue damage during laser photothermal ablation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2776.
Exposure of Infants Who Are Breastfed to Antiepileptic Drugs
Authors: Monique Hayes, Helen Puusepp-Benazzouz
Journal: JAMA Neurology (2020)

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Sericin microparticles enveloped with metal-organic networks as a pulmonary targeting delivery system for intra-tracheally treating metastatic lung cancer
Authors: Jia Liu, Yan Deng, Daan Fu, Ye Yuan, Qilin Li, Lin Shi, Guobin Wang, Zheng Wang, Lin Wang
Journal: Bioactive Materials (2020)

Chemotherapy is one of the major approaches for the treatment of metastatic lung cancer. However, systemic chemotherapy is limited by poor therapeutic efficiency and severe toxic side effects, due to the extremely low delivery efficacy and non-specificity of anticancer drugs. Herein, we report a sericin microparticles enveloped with metal-organic networks as a pulmonary delivery system for treating lung metastasis of breast cancer in an animal model. The sericin microparticles (SMPs) were prepared using water in oil (w/o) emulsification method. After doxorubicin (DOX) loading, tannic acid (TA)/ferric irons (Fe3+) based metal organic networks (MON) were coated on the particles to obtain DOX-loaded microparticles (DOX@SMPs-MON). The SMPs-MON with good biocompatibility could effectively encapsulate DOX and sustainably unload cargos in a pH-dependent manner. The DOX-loaded microparticles could be uptaken by 4T1 cells, and effectively kill the cancer cells. In vivo, DOX@SMPs-MON was deposited in the lungs and remained for over 5 days after pulmonary administration. In contrast to conventional DOX treatment that did not show significantly inhibitory effects on lung metastatic tumor, DOX@SMPs-MON markedly decreased the number and size of metastatic nodules in lungs, and the lung weight and appearance were similar to those of healthy mice. In summary, the sericin microparticles with MON wrapping might be a promising pulmonary delivery system for treating lung metastatic cancer.
SP0012 Malignancies in rheumatic diseases
Authors: A Ekbom
Journal: Annals of the Rheumatic Diseases (2001)

<h3></h3> Patients with rheumatic diseases have an increased risk overall for cancer compared to the normal population. This is most pronounced for patients with SLE, but patients with rheumatoid arthritis have also a significantly increased risk. Unpublished data from Sweden also indicate that such an association exist for patients with Morbus Bechterew as well as patients with psoriatic arthritis. However, the increased cancer risks are not general phenomenon for cancer as such. There are distinct differences in the patterns of cancer occurrence compared to the general population. Smoking related cancers, especially lung cancer, occur in excess for both rheumatoid arthritis and SLE patients as opposed to cancers of the gastrointestinal tract (especially colorectal cancer) which are inversely associated with all four disease entities mentioned above, possibly due to the pharmacotherapy these patients are exposed to. Hematopoetic cancers (lymphomas and leukemias) also occur more than that expected in patients with rheumatic diseases. In the case of SLE and rheumatoid arthritis these excess risks are especially prominent for lymphomas, but there is also a somewhat less pronounced increased risk for leukemias. This increased risk can probably, to some extent, be explained by immunosuppressive therapy. However, the increased risk for lymphomas in a Swedish setting was already present in these patient groups before the introduction of such therapies during the 1970’s. Moreover, the risk estimates for lymphomas have not been altered after the introduction of such therapies. The absence of an impact of immunosuppressives can, perhaps, to some extent be due to a substantially increased absolute risk of lymphomas in the general population, which means that the cumulative incidence of lymphomas among patients with rheumatic disease is presently higher than it was 20 years ago. High disease activity in patients with rheumatic arthritis seems to be associated with an even more pronounced risk for lymphomas. There are indications that anti-inflammatory therapy have a protective effect, although better data is needed before such an association can be firmly established. In conclusion, rheumatic diseases are associated with increased risk for cancer. Hematopoetic cancers are, however, the only malignancy where a causal association has been established.
Current status of antivirals and druggable targets of SARS CoV-2 and other human pathogenic coronaviruses
Authors: Anna Artese, Valentina Svicher, Giosuè Costa, Romina Salpini, Velia Chiara Di Maio, Mohammad Alkhatib, Francesca Alessandra Ambrosio, Maria Mercedes Santoro, Yehuda G. Assaraf, Stefano Alcaro, Francesca Ceccherini-Silberstein
Journal: Drug Resistance Updates (2020)
Experiment of inhibitive effect of Artemether on colorectal cancer growth and angiogenesis in BALB/c mice
Authors: Qi-shui Zhu, Zhi-ping Wu, Cheng-wei Gao, Yong-gui Wu, Xi-cai Wang
Journal: Cancer Research (2007)

4002  Purpose: To explore the inhibitive effect of Artemether on colorectal cancer growth and angiogenesis in tumor bearing BALB/c mice. Methods:Forty-eight (24 male and 24 female) BALB/c mice that were subcutaneously implanted with CT-26 colorectal cell (2×106) were divided into 6 groups; each group contained 8 mice. They were low dose group (33.3 mg/kg; oral); middle dose group (50 mg/kg; oral); high dose group (66.6 mg/kg; oral); middle dose plus ferralia (50 mg/kg+1.5 mg/kg; oral); positive control group DDP (5 mg/kg; ip) and blank control normal saline (oral). Microvascular density (MVD) was observed and countered under the microscopy by immunohistochemistry. Results: Inhibitive rates of Artemether by oral administration at low, middle, and high dosages were 42.3%, 51.4%, and 52.0%, respectively, and had significant difference inhibitive effects on colorectal cancer growth (P =0.007, P =0.006, P =0.024 respectively). Combination ferralia and Artemether synergenic the inhibitive effect on tumor bearing mice. MVD in different therapy groups was significantly lower than that in normal saline control group (P
Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA
Authors: Maturada Patchsung, Krittapas Jantarug, Archiraya Pattama, Kanokpol Aphicho, Surased Suraritdechachai, Piyachat Meesawat, Khomkrit Sappakhaw, Nattawat Leelahakorn, Theerawat Ruenkam, Thanakrit Wongsatit, Niracha Athipanyasilp, Bhumrapee Eiamthong, Benya Lakkanasirorat, Thitima Phoodokmai, Nootaree Niljianskul, Danaya Pakotiprapha, Sittinan Chanarat, Aimorn Homchan, Ruchanok Tinikul, Philaiwarong Kamutira, Kochakorn Phiwkaow, Sahachat Soithongcharoen, Chadaporn Kantiwiriyawanitch, Vinutsada Pongsupasa, Duangthip Trisrivirat, Juthamas Jaroensuk, Thanyaporn Wongnate, Somchart Maenpuen, Pimchai Chaiyen, Sirichai Kamnerdnakta, Jirawat Swangsri, Suebwong Chuthapisith, Yongyut Sirivatanauksorn, Chutikarn Chaimayo, Ruengpung Sutthent, Wannee Kantakamalakul, Julia Joung, Alim Ladha, Xin Jin, Jonathan S. Gootenberg, Omar O. Abudayyeh, Feng Zhang, Navin Horthongkham, Chayasith Uttamapinant
Journal: Nature Biomedical Engineering (2020)
AGE challenge: Angle Closure Glaucoma Evaluation in Anterior Segment Optical Coherence Tomography
Authors: Huazhu Fu, Fei Li, Xu Sun, Xingxing Cao, Jingan Liao, José Ignacio Orlando, Xing Tao, Yuexiang Li, Shihao Zhang, Mingkui Tan, Chenglang Yuan, Cheng Bian, Ruitao Xie, Jiongcheng Li, Xiaomeng Li, Jing Wang, Le Geng, Panming Li, Huaying Hao, Jiang Liu, Yan Kong, Yongyong Ren, Hrvoje Bogunović, Xiulan Zhang, Yanwu Xu
Journal: Medical Image Analysis (2020)
A very tall order for single-operator cholangioscopy
Authors: Theodor Voiosu, Cristian Băicuș, Andrei Voiosu
Journal: Endoscopy (2020)

See also: Limited diagnostic accuracy and clinical impact of single-operator peroral cholangioscopy for indeterminate biliary stricturesEndoscopy 2020; 52(02): 107-114DOI: 10.1055/a-1061-7067
Immediate impact of stay-at-home orders to control COVID-19 transmission on socioeconomic conditions, food insecurity, mental health, and intimate partner violence in Bangladeshi women and their families: an interrupted time series
Authors: Jena Derakhshani Hamadani, Mohammed Imrul Hasan, Andrew J Baldi, Sheikh Jamal Hossain, Shamima Shiraji, Mohammad Saiful Alam Bhuiyan, Syeda Fardina Mehrin, Jane Fisher, Fahmida Tofail, S M Mulk Uddin Tipu, Sally Grantham-McGregor, Beverley-Ann Biggs, Sabine Braat, Sant-Rayn Pasricha
Journal: The Lancet Global Health (2020)

Stay-at-home orders (lockdowns) have been deployed globally to control COVID-19 transmission, and might impair economic conditions and mental health, and exacerbate risk of food insecurity and intimate partner violence. The effect of lockdowns in low-income and middle-income countries must be understood to ensure safe deployment of these interventions in less affluent settings. We aimed to determine the immediate impact of COVID-19 lockdown orders on women and their families in rural Bangladesh.