tbuckley/cabot-search huggingface dataset:
Correction: <i>KIT</i> Exon 11 Codons 557–558 Deletion Mutation Promotes Liver Metastasis Through the CXCL12/CXCR4 Axis in Gastrointestinal Stromal Tumors
Authors: Hao-Chen Wang, Tzu-Ying Li, Ying-Jui Chao, Ya-Chin Hou, Yuan-Shuo Hsueh, Kai-Hsi Hsu, Yan-Shen Shan
Journal: Clinical Cancer Research (2019)

In the original version of this article (1), the figure legends did not clarify that controls were the same across figures because either the experiments were run at the same time (Figs. 4B and 5C; Figs. 2B, 4D, and 5D; and Figs. 6D and E) or the IHC stains represent the same patient (Figs. 5B and 6A). The error has been corrected in the latest online HTML and PDF versions of the article. The authors regret this error.
Factors Associated With Brain Heterogeneity in Schizophrenia—Reply
Authors: Dag Alnæs, Lars T. Westlye
Journal: JAMA Psychiatry (2019)

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 Psychiatry HomeNew OnlineCurrent IssueFor Authors Podcast 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) 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 Psychiatry journal
Comprehensive geriatric assessment (CGA)-adapted chemotherapy (CT) in 100 elderly patients (pts) (&gt;70 years) with diffuse large B-cell non-Hodgkin’s lymphoma (DLBCL)
Authors: U. Tirelli, M. Balzarotti, L. Uziel, A. Ferreri, L. Fratino, E. Vaccher, A. Santoro, M. Spina
Journal: Journal of Clinical Oncology (2007)

19515 Rituximab+CHOP (R-CHOP) is the standard CT regimen for elderly pts with CD20+ DLBCL. However, many pts ≥70 yrs are often unable to received R-CHOP and are excluded from clinical trials. Moreover, CGA has been demonstrated a useful instrument to predict the clinical outcome of elderly cancer pts even if it has never been tested prospectively. Within the GOL (Onco-hematological Lymphoma Group) from June 2000 to March 2006 we started a phase II prospective study to evaluate the feasibility and activity of a CGA-driven CT for elderly pts with DLBCL. Rituximab was used in all pts after February 2002. Pts with no comorbidity received CHOP or R-CHOP; in pts with mild cardiopathy epirubicin was used instead of doxorubicin (CEOP or R-CEOP); in pts with moderate or severe cardiopathy the use of antracyclines was omitted (CVP or R-CVP). CT dosage was decided according to CGA: pts with a good CGA score (ADL=6, IADL&gt;6) received full doses of CT; pts with an intermediate score (ADL=5, IADL&gt;4) received 75% of the planned dose; pts with a poor score (ADL&lt;5, IADL&lt;5) received 50% dose. All pts received prophylactic filgrastim; 100 pts (41 males and 59 females) have been treated and no pt was excluded from this approach. Median age was 75 yrs (range 70–89) and 51% were stages III-IV. Sixty-one per cent of pts received full doses of CT, 86% received antracycline (doxorubicin in 56% and epirubicin in 30%) and 54% received rituximab plus CT. The following regimens were used: R-CHOP 22%, CHOP 16%, 75%-R-CHOP 10%, 75%-CHOP 8%, CEOP 11%, R-CEOP 4%, 75%-R-CEOP 9%, 75%-CEOP 6%. The remaining pts received CVP in 5% of cases and reduced R-CVP in 9% of cases. The toxicity was quite acceptable, however 4 toxic deaths occurred (2 septic shock, 1 acute respiratory failure and 1 acute myocardial infarction). Overall, 76% achieved CR and with a median follow-up of 24 months (range 1–71 months) only 16% relapsed. Seventy-three pts are alive and 63% in CR. Our results demonstrated that a CGA-driven approach is feasible and highly active in elderly pts with DLBCL. Moreover this strategy allows a potentially curative approach to all pts with aggressive NHL avoiding both to under-treat elderly pts with a curable disease and to over-treat elderly pts with comorbidities. No significant financial relationships to disclose.
Outcomes of Allogeneic Hematopoietic Stem Cell Transplantation for Acute Myelogenous Leukemia (AML) with Complex Karyotypes (CK): A Retrospective Study from the Acute Leukemia Working Party (ALWP) of the European Society for Blood and Marrow Transplantation (EBMT) and MD Anderson Cancer Center (MDACC)
Authors: Stefan O. Ciurea, Myriam Labopin, Emmanuelle Polge, Piyanuch Kongtim, Gabriela Rondon, Gerard Socie, Liisa Volin, Jakob R Passweg, Patrice Chevallier, Dietrich W. Beelen, Stéphane Vigouroux, Didier Blaise, Jan J. Cornelissen, Nathalie Fegueux, Mohamad Mohty, Bipin N. Savani, Richard E. Champlin, Arnon Nagler
Journal: Blood (2016)
miR-448 targets IDO1 and regulates CD8+ T cell response in human colon cancer
Authors: Qiong Lou, Ruixian Liu, Xiangling Yang, Weiqian Li, Lanlan Huang, Lili Wei, Huiliu Tan, Nanlin Xiang, Kawo Chan, Junxiong Chen, Huanliang Liu
Journal: Journal for ImmunoTherapy of Cancer (2019)

Indoleamine 2,3-dioxygenase 1 (IDO1) is a critical regulator of T cell function, contributing to immune tolerance. Upregulation of IDO1 has been found in many cancer types; however, the regulatory mechanisms and clinical significance of IDO1 in colon cancer are still unclear. Here, we investigated the role of dysregulated microRNA (miRNA) targeting IDO1 in the colon cancer microenvironment.We elucidated IDO1 function by performing cell-based assays and establishing transplanted tumor models in BALB/c mice and BALB/c nude mice. We evaluated IDO1 protein expression by immunohistochemistry (IHC) in a tissue microarray (TMA) and analyzed IDO1 mRNA expression with The Cancer Genome Atlas (TCGA). We screened miRNAs targeting IDO1 by using a dual luciferase reporter assay. We tested the function of microRNA-448 (miR-448) by using western blotting (WB) and fluorescence-activated cell sorting (FACS).We demonstrated that stable IDO1 overexpression enhanced xenograft tumor growth in BALB/c mice but not in BALB/c nude mice. We also revealed the involvement of posttranscriptional regulation of IDO1 in colon cancer by observing IDO1 protein levels and mRNA levels. Furthermore, ectopic expression of miRNA mimics suggested that miR-448 could significantly downregulate IDO1 protein expression. Notably, we proved that miR-448 suppressed the apoptosis of CD8+ T cells by suppressing IDO1 enzyme function.Our findings indicated that IDO1 suppressed the CD8+ T cell response in colon cancer. miR-448, as a tumor-suppressive miRNA, enhanced the CD8+ T cell response by inhibiting IDO1 expression. The results provide a theoretical basis for the development of new immunotherapy for the treatment of colon cancer.
Impact of pathways on chemotherapy administration before death.
Authors: Marcus A. Neubauer, Jody S. Garey, Brian Turnwald, Robyn K. Harrell, Josh Howell, Jad Hayes, Debajyoti Bhowmik, J. Russell Hoverman, Barry Don Brooks, Roy Beveridge
Journal: Journal of Clinical Oncology (2013)

6580 Background: Continuing IV chemotherapy (chemo) in patients (pts) with advanced cancer near death neither extends survival nor improves quality, but does increase costs. Pathways (PW) programs have focused on comparing treatment (tx) costs but have not evaluated the impact on chemo given near death. The primary goal is to evaluate IV chemo administered in the last 14 days of life for pts treated On-PW vs. Off-PW. Methods: Eligible pts: in US Oncology’s (USO) iKnowMed (iKM) EHR; diagnosis (dx) of breast, colon, NSCLC, SCLC or pancreas cancer; &gt;/=3 visits to a USO clinic; assessed for Level I PW compliance in the last 12 mths of life; and a documented date of death. IV chemo received in the last year of life was assessed. Pts were defined On-PW if all tx was On-PW or if pts did not receive IV chemo 12 mths before death (best supportive care). Pts were defined Off-PW if any tx received was Off-PW. PW-status, age, sex, dx, and last line of therapy (LOT) received were assessed. Multivariate logistic regression analysis was used to assess if PW status predicted likelihood of chemo within 14-days of death. Results: From 7/1/09-6/30/12, 12,551 pts met inclusion criteria. PW status was independently associated with chemo 14 days before death. Pts treated Off-PW had a two-fold higher odds of receiving IV chemo within 14 days of death compared to pts treated On-PW (OR: 1.99; 95% CI: 1.77-2.26), see the Table. Findings were similar for each dx. Tx for pts On-PW vs Off-PW showed lower mean last LOT overall (1 vs. 2) and by dx. Conclusions: Pts On-PW were less likely to receive IV chemo within 14 days of death and had fewer LOT. This suggests adherence to Level I PWs is associated with improved quality metrics. [Table: see text]
Health checks and cardiovascular risk factor values over six years’ follow-up: Matched cohort study using electronic health records in England
Authors: Samah Alageel, Martin C. Gulliford
Journal: PLoS Medicine (2019)

Background The National Health Service (NHS) in England introduced a population-wide programme for cardiovascular disease (CVD) prevention in 2009, known as NHS Health Checks. This research aimed to measure the cardiovascular risk management and cardiovascular risk factor outcomes of the health check programme during six years' follow-up. Methods and findings A controlled interrupted time series study was conducted. Participants were registered with general practices in the Clinical Practice Research Datalink (CPRD) in England and received health checks between 1 April 2010 and 31 December 2013. Control participants, who did not receive a health check, were matched for age, sex, and general practice. Outcomes were blood pressure, body mass index (BMI), smoking, and total cholesterol (TC) and high-density lipoprotein cholesterol (HDL). Analyses estimated the net effect of health check by year, allowing for the underlying trend in risk factor values and baseline differences between cases and controls, adjusting for age, sex, deprivation, and clustering by general practice. There were 127,891 health check participants and 322,910 matched controls. Compared with controls, health check participants had lower BMI (cases mean 27.0, SD 4.8; controls 27.3, SD 5.6, Kg/m2), systolic blood pressure (SBP) (cases 129.0, SD 14.3; controls 129.3, SD 15.0, mm Hg), and smoking (21% in health check participants versus 27% in controls), but total and HDL cholesterol were similar. Health check participants were more likely to receive weight management advice (adjusted hazard ratio [HR] 5.03, 4.98 to 5.08, P < 0.001), smoking cessation interventions (HR 3.20, 3.13 to 3.27, P < 0.001), or statins (HR 1.24, 1.21 to 1.27, P < 0.001). There were net reductions in risk factor values up to six years after the check for BMI (−0.30, −0.39 to −0.20 Kg/m2, P < 0.001), SBP (−1.43, −1.70 to −1.16 mm Hg, P < 0.001), and smoking (17% in health check participants versus 25% in controls; odds ratio 0.90, 0.87 to 0.94, P < 0.001). The main study limitation was that residual confounding may be present because randomisation was not employed; health check–associated measurement introduced differential recording that might cause bias. Conclusions Our results suggest that people who take up a health check generally have lower risk factor values than controls and are more likely to receive risk factor interventions. Risk factor values show net reductions up to six years following a health check in BMI, blood pressure, and smoking, which may be of public health importance.
MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations
Authors: Zifan Zhu, Jie Ren, Sonia Michail, Fengzhu Sun
Journal: Genome biology (2019)

We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show that including reads from unknown organisms significantly increases the prediction accuracy of the disease status for three of the four datasets. We identify new microbial organisms associated with these diseases and show viruses play important prediction roles in colorectal cancer and liver cirrhosis, but not in type 2 diabetes. MicroPro is freely available at https://github.com/zifanzhu/MicroPro .
Clinical and cost impact of diagnostic slide review.
Authors: Justin Cuff, Daniel Yarlett, Daniel Arber
Journal: Journal of Clinical Oncology (2012)

6072 Background: Diagnostic error is postulated to represent a significant source of preventable mortality, morbidity, and cost. A primary pathologic diagnosis of cancer has a relatively high error rate necessitating cost effective solutions to mitigate diagnostic related harm. Methods: A review of 773 consecutive inbound transfers to Stanford, with review of prior pathology material, was performed to measure diagnostic discrepancy. Information was collected about the originating practice size and type, subspecialty area, additional testing, and a description of the disagreement. For a subset of cases, itemized payment data was collected to explore the financial impact of slide review. Results: We found that 9% of cases have diagnostic discrepancies when comparing the incoming working diagnosis with the result of the pathology slide review. Major diagnostic discrepancies, likely to alter treatment, were identified in 3% of cases. Discrepancy rates differed significantly between subspecialty areas (p&lt;0.01) although few areas were spared major error. Disagreements about classification were common as were over/under calling malignancy, grading errors, and incorrect ordering or interpretation of ancillary testing. The subset of cases (n=107) with billing information demonstrated ~42,800 unique charge events associated with these episodes of care. The mean charge for patients was $292,813 (median $130,467). Typical of charge data the dollar amounts exhibited strong right-skew. Average reimbursement was $76,017 (median $23,999) and the median charge:reimbursement ratio was 3.3. When analyzing cases by service line, only 1.4% of charges related to the diagnostic review of the prior pathology material, demonstrating a remarkably small impact on the overall cost. While additional testing was performed on 10% of cases, there was no evidence that cases with a discrepancy were associated with increased overall costs. Conclusions: Diagnostic slide review on prior material is relatively inexpensive in terms of the cost of overall care and permits the detection of significant errors that may affect treatment planning. Pathology slide review represents a clinically impactful and low cost way to prevent errors in diagnosis from becoming errors in management.
The impact of varying rectal contours on rectal dose in prostate cancer patients treated with hypofractionated radiation
Authors: B. B. Joshua, S. Faria, H. Patrocinio, F. DeBlois, M. Duclos, M. David, G. Shenouda, L. Souhami
Journal: Journal of Clinical Oncology (2007)

15598 Background: In curative radiation treatment of prostate cancer,the advent of 3DCRT has made a reduction in the incidence of normal tissue toxicities while optimizing tumor control. To optimize 3DCRT, the ICRU has published standard definitions of target volumes and organs at risk such that the tumor can receive the optimal dose with as little as possible dose to the organs at risk. However, the definition of the rectum as an organ at risk in radiation treatment of the prostate varies widely among institutions and so does the report of toxicities. We studied the effect of varying rectal contouring on rectal dose obtained from DVHs in a homogenous group of prostate cancer patients treated with hypo fractionationed radiation. Methods: 71 patients with favorable risk prostate cancer treated with a total of 66Gy in 3Gy/day fractionation.18 MV photons in a 5-field technique was used. None of the patients received hormonal therapy. Their treatment plans were archived and the rectum was re-contoured by a single investigator. 4 different contours were drawn to compare the rectal dose: i) the whole rectum from the anal verge to the recto sigmoid junction (WR); ii) the rectum from 1cm below the PTV to 1cm above (RPTV); iii) the rectal wall (i.e. the inner and outer rectal wall) from the anal verge to the recto sigmoid junction (RW); iv) the rectal wall from 1cm below the PTV to 1cm above (RWPTV) Results: There were significant differences in the median volume, minimum, mean rectal doses and dose to 50% of the volume, (p=0.0001). The whole rectum (WR) is having the lowest and the rectal wall with 1cm above and below the PTV (RWPTV) having the highest in all the parameters. The only parameter not significantly different among the 4 contours is the maximum rectal dose. Conclusion: the varied rectal contouring across different institutions is a possible reason for the broadly different reports of rectal toxicity after prostate irradiation. Our results suggest significant differences in rectal doses with varied contouring. Contouring the rectal wall only and limiting the volume to 1cm above and below the PTV confers the highest mean rectal dose. Comparison of rectal toxicity between institutions can only be meaningful if a consensual volume definition of the organ at risk is agreed upon. No significant financial relationships to disclose.
Comparison of early warning scores in patients with COPD exacerbation: DECAF and NEWS score
Authors: Carlos Echevarria, John Steer, Stephen C Bourke
Journal: Thorax (2019)

Background The National Early Warning Score 2 (NEWS2) includes two oxygen saturation scales; the second adjusts target saturations to 88%–92% for those with hypercapnic respiratory failure. Using this second scale in all patients with COPD exacerbation (‘NEWS2 All COPD ’) would simplify practice, but the impact on alert frequency and prognostic performance is unknown. Admission NEWS2 score has not been compared with DECAF (dyspnoea, eosinopenia, consolidation, acidaemia, atrial fibrillation) for inpatient mortality prediction. Methods NEWS, NEWS2 and NEWS2 All COPD and DECAF were calculated at admission in 2645 patients with COPD exacerbation attending consecutively to one of six UK hospitals, all of whom met spirometry criteria for COPD. Alert frequency and appropriateness were assessed for all NEWS iterations. Prognostic performance was compared using the area under the receiver operating characteristic (AUROC) curve. Missing data were imputed using multiple imputation. Findings Compared with NEWS, NEWS2 reclassified 3.1% patients as not requiring review by a senior clinician (score≥5). NEWS2 All COPD reduced alerts by 12.6%, or 16.1% if scoring for injudicious use of oxygen was exempted. Mortality was low in reclassified patients, with no patients dying the same day as being identified as low risk. NEWS2 All COPD was a better prognostic score than NEWS (AUROC 0.72 vs 0.65, p&lt;0.001), with similar performance to NEWS2 (AUROC 0.72 vs 0.70, p=0.090). DECAF was superior to all scores (validation cohort AUROC 0.82) and offered a more clinically useful range of risk stratification (DECAF=1.2%–25.5%; NEWS2=3.5%–15.4%). Conclusion NEWS2 All COPD safely reduces the alert frequency compared with NEWS2. DECAF offers superior prognostic performance to guide clinical decision-making on admission, but does not replace repeated measures of NEWS2 during hospitalisation to detect the deteriorating patient.
Abstract 20732: Identification of a Novel Mitochondrial Targeting Sequence in Tafazzin, the Mitochondrial Enzyme Associated With the Cardiomyopathic Disorder Barth Syndrome
Authors: Wei-Ming Chien, Ana Dinca, Michael T Chin
Journal: Circulation (2017)

Mutations in tafazzin (TAZ) result in Barth syndrome, a devastating X-linked inherited disorder in which young boys present with hypotonia, cyclic neutropenia and cardiomyopathy, which is the major...
SWOG S0635 and S0636: Phase II trials in advanced-stage NSCLC of erlotinib (OSI-774) and bevacizumab in bronchioloalveolar carcinoma (BAC) and adenocarcinoma with BAC features (adenoBAC), and in never-smokers with primary NSCLC adenocarcinoma (adenoCa).
Authors: Howard Jack West, James Moon, Fred R. Hirsch, Philip C Mack, Antoinette J. Wozniak, Derick Lau, Louis Fehrenbacher, Martin Joseph Bury, Mary Weber Redman, David R. Gandara
Journal: Journal of Clinical Oncology (2012)

7517 Background: Despite recent changes to lung adenoCa pathologic classification, adv stage BAC remains a definable and clinically applicable entity. Patients (pts) with BAC, as well as never-smoking (NS) pts with adv lung adenoCa, have emerged as relevant clinical subpopulations with a high probability of clinical benefit from epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), likely related to the high proportion of activating mutations in the EGFR gene in such pts. Based on these results and the potential for increased clinical activity conferred by addition of B to E, SWOG initiated a pair of phase II trials of this combination in pts with adv BAC (S0635) or NS pts with adv lung adenoCa (S0636). Methods: NS pts with BAC or adenoBAC were preferentially enrolled on S0636. A total of 78 and 85 eligible pts were enrolled and treated on the S0635 and S0636 trials, respectively. Patients received E 150 mg PO daily and B 15 mg/kg IV q21 days until progression or prohibitive toxicity. Tumor tissue submission for pathologic review and assessment of molecular markers was mandated. Results: Pt demographics of the two trials are as shown in the table below. RECIST response rate among 61 BAC pts on S0635 with measurable disease was 18%, and among 53 NS pts on S0636, it was 47%. Median progression-free survival is 5 and 8 months (mo) on S0635 and S0636, respectively; median overall survival (OS) is 17 and 26 mo on S0635 and S0636, respectively. Toxicity consisted primarily of rash, diarrhea, and hypertension; no treatment-related deaths were reported. Molecular marker studies will be presented separately. Conclusions: In populations selected by clinical parameters, E withB is associated with modest toxicity and encouraging clinical efficacy that exceeded the prespecified OS threshold of 16 mo in studies of both adv BAC and NS pts, exceeding two years in NS pts. [Table: see text]
Impact of Tyrosine Kinase Inhibitors Used in Chronic Myeloid Leukemia on Signaling and Epigenetics in Endothelial Cells
Authors: Srila Gopal, Qing Lu, Wendy Baur, Sitara Rao, Lev Litichevskiy, Malvina Papanastasiou, Amanda Creech, Adam Officer, Shawn Egri, Desiree Davison, Jacob D Jaffe, Iris Zamir Jaffe
Journal: Blood (2017)