tbuckley/cabot-search huggingface dataset:
External validation of a convolutional neural network artificial intelligence tool to predict malignancy in pulmonary nodules
Authors: David R Baldwin, Jennifer Gustafson, Lyndsey Pickup, Carlos Arteta, Petr Novotny, Jerome Declerck, Timor Kadir, Catarina Figueiras, Albert Sterba, Alan Exell, Vaclav Potesil, Paul Holland, Hazel Spence, Alison Clubley, Emma O'Dowd, Matthew Clark, Victoria Ashford-Turner, Matthew EJ Callister, Fergus V Gleeson
Journal: Thorax (2020)

Background Estimation of the risk of malignancy in pulmonary nodules detected by CT is central in clinical management. The use of artificial intelligence (AI) offers an opportunity to improve risk prediction. Here we compare the performance of an AI algorithm, the lung cancer prediction convolutional neural network (LCP-CNN), with that of the Brock University model, recommended in UK guidelines. Methods A dataset of incidentally detected pulmonary nodules measuring 5–15 mm was collected retrospectively from three UK hospitals for use in a validation study. Ground truth diagnosis for each nodule was based on histology (required for any cancer), resolution, stability or (for pulmonary lymph nodes only) expert opinion. There were 1397 nodules in 1187 patients, of which 234 nodules in 229 (19.3%) patients were cancer. Model discrimination and performance statistics at predefined score thresholds were compared between the Brock model and the LCP-CNN. Results The area under the curve for LCP-CNN was 89.6% (95% CI 87.6 to 91.5), compared with 86.8% (95% CI 84.3 to 89.1) for the Brock model (p≤0.005). Using the LCP-CNN, we found that 24.5% of nodules scored below the lowest cancer nodule score, compared with 10.9% using the Brock score. Using the predefined thresholds, we found that the LCP-CNN gave one false negative (0.4% of cancers), whereas the Brock model gave six (2.5%), while specificity statistics were similar between the two models. Conclusion The LCP-CNN score has better discrimination and allows a larger proportion of benign nodules to be identified without missing cancers than the Brock model. This has the potential to substantially reduce the proportion of surveillance CT scans required and thus save significant resources.
Intervention To Stop Transmission of Imported Pneumonic Plague — Uganda, 2019
Authors: Titus Apangu, Sarah Acayo, Linda A. Atiku, Harriet Apio, Gordian Candini, Felix Okoth, John Kaggwa Basabose, Lawrence Ojosia, Sam Ajoga, Grace Mongiba, Milton Makoba Wetaka, Joshua Kayiwa, Stephen Balinandi, Amy Schwartz, Brook Yockey, Christopher Sexton, Elizabeth A. Dietrich, Ryan Pappert, Jeannine M. Petersen, Paul S. Mead, Julius J. Lutwama, Kiersten J. Kugeler
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

Plague, an acute zoonosis caused by Yersinia pestis, is endemic in the West Nile region of northwestern Uganda and neighboring northeastern Democratic Republic of the Congo (DRC) (1-4). The illness manifests in multiple clinical forms, including bubonic and pneumonic plague. Pneumonic plague is rare, rapidly fatal, and transmissible from person to person via respiratory droplets. On March 4, 2019, a patient with suspected pneumonic plague was hospitalized in West Nile, Uganda, 4 days after caring for her sister, who had come to Uganda from DRC and died shortly thereafter, and 2 days after area officials received a message from a clinic in DRC warning of possible plague. The West Nile-based Uganda Virus Research Institute (UVRI) plague program, together with local health officials, commenced a multipronged response to suspected person-to-person transmission of pneumonic plague, including contact tracing, prophylaxis, and education. Plague was laboratory-confirmed, and no additional transmission occurred in Uganda. This event transpired in the context of heightened awareness of cross-border disease spread caused by ongoing Ebola virus disease transmission in DRC, approximately 400 km to the south. Building expertise in areas of plague endemicity can provide the rapid detection and effective response needed to mitigate epidemic spread and minimize mortality. Cross-border agreements can improve ability to respond effectively.
RETRACTED ARTICLE: Exosome-mediated lncRNA AFAP1-AS1 promotes trastuzumab resistance through binding with AUF1 and activating ERBB2 translation
Authors: Mingli Han, Yuanting Gu, Pengwei Lu, Jingyi Li, Hui Cao, Xiangke Li, Xueke Qian, Chao Yu, Yunqing Yang, Xue Yang, Na Han, Dongwei Dou, Jianguo Hu, Huaying Dong
Journal: Molecular Cancer (2020)

Abstract Background Although trastuzumab provides significant clinical benefit for HER2-positive breast cancers, responses are limited by the emergence of resistance. Recent evidence suggests that long noncoding RNAs (lncRNAs) play important roles in tumorigenesis and chemoresistance. However, the regulatory mechanism of lncRNAs in trastuzumab resistance is not well established to date. In this research, we identified the differentially expressed lncRNA and investigated its regulatory role in trastuzumab resistance of breast cancer. Methods LncRNA microarray and qRT-PCR were performed to identify the dysregulated lncRNAs. Transmission electron microscopy, differential ultracentrifugation and qRT-PCR were used to verify the existence of exosomal AFAP1-AS1 (actin filament associated protein 1 antisense RNA 1). Bioinformatics prediction, RNA fluorescence in situ hybridization (RNA-FISH) and immunoprecipitation assays were performed to identify the direct interactions between AFAP1-AS1 and other associated targets, such as AU-binding factor 1 (AUF1) and ERBB2. Finally, a series gain- or loss-functional assays were done to prove the precise role of AFAP1-AS1 in trastuzumab resistance. Results AFAP1-AS1 was screened out due to its higher expression in trastuzumab-resistant cells compared to sensitive cells. Increased expression of AFAP1-AS1was associate with poorer response and shorter survival time of breast cancer patients. AFAP1-AS1 was upregulated by H3K27ac modification at promoter region, and knockdown of AFAP1-AS1 reversed trastuzumab resistance. Moreover, extracellular AFAP1-AS1 secreted from trastuzumab resistant cells was packaged into exosomes and then disseminated trastuzumab resistance of receipt cells. Mechanically, AFAP1-AS1 was associated with AUF1 protein, which further promoted the translation of ERBB2 without influencing the mRNA level. Conclusion Exosomal AFAP1-AS1 could induce trastuzumab resistance through associating with AUF1 and promoting ERBB2 translation. Therefore, AFAP1-AS1 level may be useful for prediction of trastuzumab resistance and breast cancer treatment.
Expression of tight junction associated proteins in human gastric cancer: Reduced expression of Claudin-4 correlates with tumor aggressiveness and survival
Authors: M. Terashima, S. Ohtani, Z. Saze, S. Kashimura, N. Soeta, Y. Odashima, R. Nishikata, F. Ohsuka, Y. Hoshino, M. Kogure, M. Gotoh
Journal: Journal of Clinical Oncology (2007)

15000 Background: A tight junction is one of components of intercellular junctional complexes and play an important role in maintaining barrier function and cellular porlarity. Claudin, occluding, and ZO-1 are known as trans-membrane proteins which compose tight junction. Roles of these tight junction-associated proteins of gastric cancer is not yet determined. In this study, we investigated expression levels of these proteins in gastric cancer immunohistochemically and compared the results with clinicopathological features of the tumors and patient prognosis. Methods: One hundred and twenty-four gastric cancer patients underwent gastrectomy between 2000 and 2004 were included in this study. Formalin fixed and parafine embedded tissues were sliced into 4-μm sections and immunohistchemistry was performed using anti-claudin-4, anti-occluding and anti-ZO-1 antibodies. Stained slides were investigated and the incidence of positive cells was graded as: 0, negative; 1, &lt; 20 %; 2, 20–80 %; 3, &gt;80 %. Results: The expression of claudin-4, occludin, and ZO-1 was observed at the membrane, and the positivity rates in cancer tissues were 87.1%, 95.2% and 100%, respectively. In concerning with correlation between protein expression and clinicopathologic features, claudin-4 expression was significantly decreased in tumors with undifferentiated type adenocarcinoma (p&lt;0.001), advanced T stage (p=0.0022), lymph node metastasis (p&lt;0.001), and peritoneal metastasis (p&lt;0.001). However, there was no significant correlation between the expression of occluding and ZO-1 and clinicopathological features. Survival time was significantly shorter in patients with reduced claudin-4 expression (p=0.0018). Cox’s multivariate analysis revealed that claudin-4 was selected as an independent prognostic factor as well as histological type and peritoneal metastasis. Conclusions: Tight junction associated proteins, especially claudin-4, appears to play an important role on tumor progression, invasion, and metastasis and correlate with poor prognosis in patients with gastric cancer. No significant financial relationships to disclose.
The USMLE Step 1 Decision
Authors: Humayun J. Chaudhry, Peter J. Katsufrakis, Alfred F. Tallia
Journal: JAMA (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient
Authors: Sean Wei Xiang Ong, Yian Kim Tan, Po Ying Chia, Tau Hong Lee, Oon Tek Ng, Michelle Su Yen Wong, Kalisvar Marimuthu
Journal: JAMA (2020)

This study documents results of SARS-CoV-2 polymerase chain reaction (PCR) testing of environmental surfaces and personal protective equipment surrounding 3 COVID-19 patients in isolation rooms in a Singapore hospital.
Identification of epigenetic aberrant promoter methylation of <i>RASSF1A</i> in serum DNA and its clinicopathological significance in lung cancer
Authors: L. Chen, Y. Wang, Z. Yu
Journal: Journal of Clinical Oncology (2007)

21014 Objective: To detect the hypermethylation status of RASSF1A promoter in serum DNA of lung cancer patients and to analyze its correlation with clinicopathological features. Methods: Serum DNA was extracted from peripheral blood from 80 primary lung cancer patients, 35 benign pulmonary disease patients and 15 healthy donors. The methylation status of RASSF1A promoter was determined using methylation-specific PCR technique, and the correlation between methylation profiles and clinicopathological parameters was statistically analyzed. Results: Aberrant methylation of RASSF1A was detected in 27 of the 80 (33.8%) patients with lung cancer but no benign pulmonary disease patients or healthy donors (p&lt;0.001). RASSF1A was preferentially observed in small cell lung cancer (p=0.042), while no statistical difference was found among methylation frequencies of different subtypes of non-small cell lung cancer. The methylation status was also found to be associated with relative poor differentiation (p=0.009) and late stage (p=0.013), but not with gender, age or treatment. Conclusion: RASSF1A promoter is frequently hypermethylated in serum DNA of primary lung cancer patients, and RASSF1A is a promising novel biomarker for lung cancer diagnosis. No significant financial relationships to disclose.
Stem Cell–Derived Cardiomyocytes and Beta-Adrenergic Receptor Blockade in Duchenne Muscular Dystrophy Cardiomyopathy
Authors: Forum Kamdar, Satyabrata Das, Wuming Gong, André Klaassen Kamdar, Tatyana A. Meyers, Pruthvi Shah, James M. Ervasti, DeWayne Townsend, Timothy J. Kamp, Joseph C. Wu, Mary G. Garry, Jianyi Zhang, Daniel J. Garry
Journal: Journal of the American College of Cardiology (2020)
Phase II study of oral fluoropyrimidine (UFT) plus vinorelbine in the elderly (age &gt; 70) with advanced non-small cell lung cancer
Authors: H. Suyama, Y. Shigeoka, T. Igishi, S. Matsumoto, K. Yasuda, A. Sugitani, S. Katayama, M. Yamamoto, Y. Hitsuda, E. Shimizu
Journal: Journal of Clinical Oncology (2007)

18075 Background: Many pts with non-small cell lung cancer (NSCLC) are in elderly population. There are few pts who can receive standard treatment with platinum-based chemotherapy because of their poor organ functions. Thus, the development of a low-toxic and highly- effective regimen is needed for these populations. We have reported schedule-dependent synergism of vinorelbine and 5-FU against NSCLC cell lines. Furthermore, we have already conducted phase I study using vinorelbine and UFT, and have decided the recommended dose of this regimen. Methods: The objective of this prospective phase II study was to assess the efficacy and toxicity of this regimen in the elderly. Chemonaive NSCLC stage IIIB or IV pts, aged 70 or more, with performance status 0/1 were enrolled in this study. The pts received a treatment consisting of 20mg/m 2 of vinorelbine on days 1 and 8, followed by 600mg of UFT orally on days 2–6 and 9–13 every 3 weeks for more than 4 cycles. Results: Until April 24, 2006, of 30 pts enrolled in this study, 29 pts were evaluable. Median age was 78 (range 71–86) and median cycles of chemotherapy were 4 (1–32). Objective response rate was 27% (95% CI; 10–44%), median time to progression was 150 days (15–470) and median over all survival time was 270 days (77–892). Treatment-related toxicity were neutropenia G3 33%, G4 7%; febrile neutropenia G3 4%; pneumonia G3 10%. Conclusions: This data points out vinorelbine and UFT as an active and tolerable regimen in the elderly with advanced NSCLC. No significant financial relationships to disclose.
FcRn overexpression in human cancer drives albumin recycling and cell growth; a mechanistic basis for exploitation in targeted albumin-drug designs
Authors: Maja Thim Larsen, Ole A. Mandrup, Karen Kræmmer Schelde, Yonglun Luo, Karina Dalsgaard Sørensen, Frederik Dagnæs-Hansen, Jason Cameron, Magnus Stougaard, Torben Steiniche, Kenneth A. Howard
Journal: Journal of Controlled Release (2020)
A phase II trial of rapid androgen cycling and docetaxel (Doc) in prostate cancer patients with a rising prostate-specific antigen (PSA) in the noncastrate state
Authors: D. E. Rathkopf, M. A. Carducci, S. Slovin, M. J. Morris, M. Kelsen, R. Pili, S. R. Denmeade, M. Eisenberger, H. I. Scher
Journal: Journal of Clinical Oncology (2007)

5004 Introduction: Prostate cancer patients in the noncastrate state with a rapidly rising PSA are at high-risk for cancer-specific mortality. Since hormonal therapy alone is not curative, we have explored the use of rapid androgen cycling with Doc to recruit proliferating cells into successive waves of apoptosis, thereby shifting the treatment outcome for these patients from palliation to cure. Methods: Patients with noncastrate levels of testosterone (T), a rising PSA ± metastases, and = 6 months of prior hormones were eligible. Cohort 1: Six 4- week cycles of monthly leuprolide and Doc (75 mg/m2), with 7 days of topical T repletion (AndroGel 1% 5G) prior to each treatment. Cohort 2: Nine 3-week cycles of Doc (70 mg/m2), with 3 days of T repletion per cycle and 3-month depot leuprolide on day 1 of cycles 1, 5, and 9. The primary endpoint was the proportion of patients with a treatment-specific undetectable PSA at 6 and 18 months defined as: = 0.05 after surgery, = 0.5 after radiation, or = 2.0ng/ml with untreated disease. This is based on the premise that an undetectable PSA is a prerequisite to, but no guarantee of cure. Results: There were no increases in sequential PSA peaks or troughs and 100 out of 102 patients completed the planned 6 months of chemohormonal treatment. Twenty three of 62 (37%) patients in cohort 1, and 25 of 38 (66%) patients in cohort 2 achieved the primary endpoint of a treatment-specific undetectable PSA at 6 months. At 12 months, no patient in cohort 1 had maintained an undetectable PSA in the setting of a noncastrate T level; whereas, 8 of 15 (53%) patients in cohort 2 have achieved the endpoint at 12 months. Toxicities were similar to those observed with Doc and hormonal therapy administered separately. Conclusions: Rapid androgen cycling with docetaxel is feasible, and can induce successive declines in PSA peaks and troughs. The more dose-dense cohort 2 schedule of 21-day Doc administration for 9 cycles, along with reduced exposure to androgen repletion from 7 to 3 days, has resulted in a higher proportion of undetectable PSA outcomes at both 6 (66% vs. 37%) and 12 (53% vs. 0%) months. Complete PSA outcomes for cohort 2 at 12 and 18 months are still pending. Supported by Sanofi-Aventis, CA-05816, and PepsiCo. No significant financial relationships to disclose.
Abstract 14126: Impact of Time off Anticoagulation in Patients With Continuous Flow Left Ventricular Assist Devices
Authors: Ashley Patel, Christian Inchaustegui, Harveen Lamba, Andrew Brown, Kevin Ting, Justin Arunthamakun, Joggy George, Andrew Civitello
Journal: Circulation (2019)

Objective: Determine the impact of time off therapeutic anticoagulation (AC) following continuous flow left ventricular assist device (CF-LVAD) implantation. Methods: Patients who underwent CF-LVAD...
Predictors for Cardiac Resynchronization Therapy: The Importance of QRS Duration and QRS Morphology
Authors: Okamura Hideo, Nakajima Ikutaro, Wada Mitsuru, Ishibashi Kohei, Miyamoto Koji, Noda Takashi, Aiba Takeshi, Yasuda Satoshi, Ogawa Hisao, Kamakura Shiro, Kusano Kengo
Journal: Circulation (2015)
Abstract P6-08-26: Clinical characteristics of breast cancer patients with ATM mutations
Authors: Loredana Militello, Angelica M Gutierrez Barrera, Constance Albarracin, Isabelle Bedrosian, Banu K Arun
Journal: Cancer Research (2020)

Abstract Background: Pathogenic ATM gene mutations are associated with increased risk of developing several cancers such as lymphoid, gastric, breast, central nervous system, skin, and other cancers. The relative risk of breast cancer is 2.3, with a higher risk seen for women under the age of 50 years. Only few and small studies have reported on the characteristics of breast cancers in women with ATM mutations. Here, we aimed to describe the clinical and pathological characteristics of a single institution largest cohort, to the best of our knowledge, of breast cancer patients with ATM mutations. Methods: Patients with breast cancer who presented to the University of Texas MD Anderson Cancer Center Clinical Cancer Genetics clinics and underwent genetic testing for hereditary breast cancer and were found to have an ATM mutation were included. A retrospective review of a prospectively maintained research database was performed for ATM mutation status as well as patient clinical and pathological characteristics. IRB approval was granted for this analysis. Results: Between 2012 and 2019, a total of 4093 breast cancer patients underwent genetic testing for hereditary breast cancer that included ATM gene testing. The median age of diagnosis of breast cancer was 49.3 (17-89), and median age at genetic testing was 52.1 (18-86). 72% of patients had stage 0-III and 3.2% stage 4 disease. Among patients with ATM pathogenic mutations, 37.7% (10) versus 21.7% (843) of ATM negative patients had a history of multiple primaries of any cancers. The table below shows characteristics of ATM pathogenic mutation carriers versus ATM negative patients. Conclusion: This is a single institution cohort of breast cancer patients with ATM mutations that show distinct clinical characteristics, such as multiple primary cancers. These findings could have therapeutic implications and should be confirmed in larger cohorts. Pathogenic Mutation of ATM ATM NegativesVariablesn%n%ERPositive4075.5221757.1Negative11.976019.6Unknown1222.690423.3PRPositive3667.9188448.5Negative59.4107027.6Pos/Neg00.010.03Unknown1222.692623.9Her2Positive1018.958611.3Negative2241.5206257.0Unknown2139.6123314.2Stage059.43178.2I1324.597825.2II1120.8106527.4III713.243611.2IV47.51243.2Unknown1324.596124.8Nuclear GradeI23.82596.7II1935.8111228.7III1120.8115629.8Unknown2139.6135434.9Triple Negative?Yes00.053913.9No3769.8222757.4Unknown1630.2111528.7 Citation Format: Loredana Militello, Angelica M Gutierrez Barrera, Constance Albarracin, Isabelle Bedrosian, Banu K Arun. Clinical characteristics of breast cancer patients with ATM mutations [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-26.
Rebates—The Little-Known Factor Behind Increasing Drug List Prices
Authors: Rita Rubin
Journal: JAMA (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal