tbuckley/cabot-search huggingface dataset:
Reducing infusion wait time: An initiative to increase early signing of medication orders by providers at a comprehensive cancer center.
Authors: Jing Jing Wang Yakowec, Michael S. Rabin, Ursula A. Matulonis, Shital Shukla, Michael D Kearney, Barbara Fine, Rachel A Wolfberg, Mark Pettengill, Nancy Hilton, Sylvia Bartel, Andrew J. Wagner, Hakim Lakhani
Journal: Journal of Clinical Oncology (2018)

123 Background: Many factors contribute to long wait times for oncology patients on the day of their infusion appointment. At Dana-Farber Cancer Institute (DFCI), one of the main causes of delay to infusion start is providers not signing medication orders in advance of patients checking in for their infusion appointment. We conducted a project to improve provider order signing behavior on the gynecology cancer patient infusion floor at DFCI. Methods: A data working group was formed which consisted of the infusion floor medical leads, nurse lead, pharmacy lead, and analytics and process improvement leads. Starting in February 2018, the working group shared baseline order signing data from September 2017 through January 2018 with the Gynecology Cancer Group. Descriptive and timestamp data from Epic were extracted and cleaned via Tableau to analyze the percentage of non-investigational medication orders, including chemotherapy, that were signed after a patient checked into infusion and the distributions of late order signing times. Results: Gynecology cancer patient providers had higher late order signing percentages at baseline (September 2017 through January 2018) than after sharing those data, which occurred from February through May 2018. The table below provides medication order counts and late order signing percentages by month. Although late signing percentages decreased after sharing the baseline data, the distribution of how late the late orders were signed did not show improvement, staying at an average of 20 minutes late. Conclusions: Sharing late order signing data with providers on a routine basis reduced late signing percentages. Initiating this process with all disease groups is crucial so that downstream workflows can start sooner and patient wait times reduced.[Table: see text]
Should we be talking about guidelines with patients? A qualitative analysis in metastatic breast cancer.
Authors: Gabrielle Betty Rocque, Audrey S. Wallace, Soumya J. Niranjan, Beverly R Williams, Yasemin E. Turkman, Stacey A. Ingram, Courtney Williams, Aysha Rasool, Andres Forero-Torres, Smita Bhatia, Sara J. Knight
Journal: Journal of Clinical Oncology (2018)

217 Background: Little data exist on patient perceptions of guideline-based care. This qualitative analysis describes patient and oncologist views on the value of discussing guidelines when making metastatic breast cancer (MBC) treatment decisions. Methods: In-person interviews completed by MBC patients and community medical oncologists and focus groups for academic medical oncologists were audio-recorded and transcribed. Two coders utilized a content analysis approach to analyze transcripts independently using NVivo. Major themes and exemplary quotes were extracted. Results: Participants included 20 MBC patients, 6 community oncologists, and 5 academic oncologists. The majority of patients (80%) were unfamiliar with the term “guidelines”. However, all patients desired to know if they were receiving guideline discordant treatment. As one patient commented “ I'm supposed to know the guidelines and it's not supposed to be a secret to me.” Among patients willing to receive care inconsistent with guidelines, several themes emerged including trusting the oncologist, relying on the oncologist’s prior experiences, being informed of rationale for deviation, personalized treatment, and openness to novel therapies. Physician discussions on the importance of guidelines revealed themes such as consistency with scientific evidence, insurance coverage, and limiting unusual practices. Oncologists identified limitations to guidelines including lack of expert consensus, inability to “ think outside the box” to personalize treatment, and lack of guideline timeliness. Although some oncologists discussed guidelines, a common sentiment was that sharing this information is not a priority. One physician commented that sharing the guidelines with patients is, “ getting too much into the how you practice medicine, and they may not want to know, kind of like eating at a restaurant. You don't need to know how the cook's preparing everything.” Conclusions: Both patients and physicians expressed reasons why guideline discordant treatments would be acceptable. Providers’ preference to limit discussions of guidelines is discordant with patients’ desire for this information and may limit shared decision-making.
Potential utility of the Genedrive point-of-care test for HCV RNA detection
Authors: Alba Llibre, Yusuke Shimakawa, Darragh Duffy
Journal: Gut (2018)

In an article in Gut ,1 Lemoine and Tillman reviewed our recent publication on the development and validation of a novel point-of-care (POC) HCV viral assay.2 They acknowledge that Genedrive is the only CE-In Vitro Diagnostic-qualified device for HCV detection, and that the limit of detection (LOD: 1406–3203 IU/mL) permits identification of the vast majority of HCV chronic cases.3 However, they emphasise some limitations of the study and Genedrive. One limitation highlighted is the need for plasma which is still required for 100% of HCV clinical tests. Nevertheless, recent studies demonstrated microfluidic plasma separation without centrifugation4 or with low-cost hand-powered paper centrifuges.5 It is feasible to foresee such devices overcoming the need for conventional centrifuges and facilitating Genedrive testing.

They also question whether 15 µL of plasma can be obtained by fingerprick. Published studies report 20–25 µL …
Mechanisms Preserving Insulin Action during High Dietary Fat Intake
Authors: Anne-Marie Lundsgaard, Jacob B. Holm, Kim A. Sjøberg, Kirstine N. Bojsen-Møller, Lene S. Myrmel, Even Fjære, Benjamin A.H. Jensen, Trine S. Nicolaisen, Janne R. Hingst, Sine L. Hansen, Sophia Doll, Philip E. Geyer, Atul S. Deshmukh, Jens J. Holst, Lise Madsen, Karsten Kristiansen, Jørgen F.P. Wojtaszewski, Erik A. Richter, Bente Kiens
Journal: Cell Metabolism (2018)
Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility
Authors: Towfique Raj, Yang I. Li, Garrett Wong, Jack Humphrey, Minghui Wang, Satesh Ramdhani, Ying-Chih Wang, Bernard Ng, Ishaan Gupta, Vahram Haroutunian, Eric E. Schadt, Tracy Young-Pearse, Sara Mostafavi, Bin Zhang, Pamela Sklar, David A. Bennett, Philip L. De Jager
Journal: Nature Genetics (2018)
Carfilzomib Combined with Thalidomide and Low-Dose Dexamethasone for Remission Induction and Consolidation in Newly Diagnosed, Transplant Eligible Patients with Multiple Myeloma: The Carthadex Trial
Authors: Ruth Wester, Bronno van der Holt, Emelie Asselbergs, Sonja Zweegman, Marie José Kersten, Edo Vellenga, Marinus van Marwijk Kooij, Okke de Weerdt, Monique C Minnema, Sarah Lonergan, Antonio Palumbo, Henk M Lokhorst, Annemiek Broyl, Karim Saad Iskander, Pieter Sonneveld
Journal: Blood (2017)
Abstract 16904: Are All Omega-3s Created Equal? Comparison of the Bioavailability and Efficacy of Four Omega-3 Preparations
Authors: Rodney W Butt, Carla A Cockerline, William J Rowe, Maggie Laidlaw
Journal: Circulation (2015)

There are many omega-3 products available in the prescription and non-prescription marketplace. Neither health care professionals nor consumers may be aware of the potential influence of the manufacturing processes and source(s) of the starting material. Manufacturers of the various omega-3 preparations imply that their product is superior to others, based on its structural characteristics, whether phospholipid, triglyceride or ethyl ester. The objective of this study was to compare the ability of four (4) different omega-3 preparations to raise whole blood fatty acid levels. This was a Prospective, Open-label, Blinded Endpoint (PROBE), four period, cross-over study. Thirty-five (35) healthy subjects were randomized to consume one of four test articles for four weeks, followed by a four-week washout, and this process was repeated until all products had been consumed by all subjects. The test article doses were based on their label specifications. The four products and daily doses were: Triglyceride fish oil: EPA of 650 mg, DHA of 450 mg Ethyl Ester fish oil: EPA of 756 mg, DHA of 228 mg Phospholipid krill oil: EPA of 150 mg, DHA of 90 mg Triglyceride salmon oil: EPA of 180 mg, DHA of 220 mg Blood samples before and after supplementation were quantified for whole blood fatty acids by gas chromatography flame ionization. Bioavailability was assessed for each product individually, based on its change from baseline. Percentage change from baseline was then compared across all four products. TG fish oil was statistically superior to all of its comparators in the bioavailability of EPA+DHA, and of DHA alone. Its EPA percentage increase was more than four times that of PL krill oil and TG salmon oil. Only the two TG products significantly increased whole blood DHA levels. For investigators and clinicians, the type and dose of omega-3s may be clinically important when assessing potential clinical impact.
Comorbidities in the first 2 years after arthroscopic hip surgery: substantial increases in mental health disorders, chronic pain, substance abuse and cardiometabolic conditions
Authors: Daniel I Rhon, Tina A Greenlee, Bryant G Marchant, Charles Dennis Sissel, Chad E Cook
Journal: British Journal of Sports Medicine (2018)

Objectives We aimed to identify the rate of seven comorbidities (mental health disorders, chronic pain, substance abuse disorders, cardiovascular disorders, metabolic syndrome, systemic arthropathy and sleep disorders) that occurred within 2 years after hip arthroscopy. Methods Data from individuals (ages 18–50 years) undergoing arthroscopic hip surgery between 2004 and 2013 were collected from the Military Health System (MHS) Data Repository (MDR). The MDR captures all healthcare encounters in all settings and locations for individuals within the MHS. Person-level data over 36 months were pulled and aggregated. Seven comorbidities related to poor outcomes from musculoskeletal disorders (mental health disorders, chronic pain, substance abuse disorders, cardiovascular disorders, metabolic syndrome, systemic arthropathy and sleep disorders) were examined 12 months prior and 24 months after surgery. Changes in frequencies were calculated as were differences in proportions between presurgery and postsurgery. Results 1870 subjects were identified (mean age 32.24 years; 55.5% men) and analysed. There were statistically significant increases (p&lt;0.001) proportionally for all comorbidities after surgery. Relative to baseline, cases of mental health disorders rose 84%, chronic pain diagnoses increased 166%, substance abuse disorders rose 57%, cardiovascular disorders rose by 71%, metabolic syndrome cases rose 85.9%, systemic arthropathy rose 132% and sleep disorders rose 111%. Conclusions Major (potentially ‘hidden’) clinical comorbidities increased substantially after elective arthroscopic hip surgery when compared with preoperative status. These comorbidities appear to have been overlooked in major studies evaluating the benefits and risks of arthroscopic hip surgery. Level of evidence Prognostic, level III.
GAAD: A Gene and Autoimmiune Disease Association Database
Authors: Guanting Lu, Xiaowen Hao, Wei-Hua Chen, Shijie Mu
Journal: Genomics Proteomics & Bioinformatics (2018)

Abstract Autoimmune diseases (ADs) arise from an abnormal immune response of the body against substances and tissues normally present in the body. More than a hundred of ADs have been described in the literature so far. Although their etiology remains largely unclear, various types of ADs tend to share more associated genes with other types of ADs than with non-AD types. Here we present GAAD, a gene and AD association database. In GAAD, we collected 44,762 associations between 49 ADs and 4249 genes from public databases and MEDLINE documents. We manually verified the associations to ensure the quality and credibility. We reconstructed and recapitulated the relationships among ADs using their shared genes, which further validated the quality of our data. We also provided a list of significantly co-occurring gene pairs among ADs; with embedded tools, users can query gene co-occurrences and construct customized co-occurrence network with genes of interest. To make GAAD more straightforward to experimental biologists and medical scientists, we extracted additional information describing the associations through text mining, including the putative diagnostic value of the associations, type and position of gene polymorphisms, expression changes of implicated genes, as well as the phenotypical consequences, and grouped the associations accordingly. GAAD is freely available at http://gaad.medgenius.info.
DNA repair defects and implications for immunotherapy
Authors: Katherine M. Bever, Dung T. Le
Journal: Journal of Clinical Investigation (2018)

A complex DNA repair machinery has evolved to protect genomic integrity in the face of a myriad of DNA damage sources. When DNA repair fails, this damage can lead to carcinogenesis and tumor genomic instability. Indeed, many heritable cancer predisposition syndromes are attributable to germline defects in DNA repair pathways. On the other hand, these defects may also portend particular vulnerabilities of the cancer and may be exploited therapeutically. Most recently this has been demonstrated in the case of mismatch repair-deficient cancers, in which the immune checkpoint inhibitors have been demonstrated to be highly active. This observation has paved the way for further research investigating other sources of genomic instability that may serve as biomarkers to select patients for immunotherapy.
Vascular and Neurogenic Rejuvenation in Aging Mice by Modulation of ASM
Authors: Min Hee Park, Ju Youn Lee, Kang Ho Park, In Kyung Jung, Kyoung-Tae Kim, Yong-Seok Lee, Hyun-Hee Ryu, Yong Jeong, Minseok Kang, Markus Schwaninger, Erich Gulbins, Martin Reichel, Johannes Kornhuber, Tomoyuki Yamaguchi, Hee-Jin Kim, Seung Hyun Kim, Edward H. Schuchman, Hee Kyung Jin, Jae-sung Bae
Journal: Neuron (2018)
Renal medulla in severe gout: typical findings on ultrasonography and dual-energy CT study in two patients
Authors: Thomas Bardin, Khoi Minh Tran, Quang Dinh Nguyen, Marine Sarfati, Pascal Richette, Nhan Thanh Vo, Valérie Bousson, Jean-Michel Correas
Journal: Annals of the Rheumatic Diseases (2018)

Monosodium urate (MSU) crystal deposition in renal medulla, described as early as the 1800s,1 was documented by autopsy studies in the 1950s to 1970s,2 3 and later by renal biopsies.4 Renal deposits have been reported mainly in patients with gout and rarely in non-gout patients with renal failure.4 Deposits appeared to be surrounded by inflammatory granulomas and medullary fibrosis. These observations led to the description of microcrystalline gouty nephropathy, a concept that was later challenged and even denied.5 

Here, we report on two patients with severe gout and the use of modern imaging modalities to reveal widespread crystal deposition in the renal medulla.

Patient 1 was a French 54-year-old man with Lesch–Nyhan syndrome; the gene defect was previously reported.6 The patient experienced several episodes of renal colic and had severe tophaceous gout, frequent flares, urate arthropathies and worsening dystonia. He was poorly adherent to urate-lowering drugs, and the uricaemia fluctuated over the years from rarely normal to frequently high (10–15 mg/dL). The patient took a beta-blocker for hypertension; the body mass …
Improving communication with referring oncologists (RO): Indiana University experience.
Authors: Neda Hashemi-Sadraei, Maitri Kalra, Olumide B. Gbolahan, Anthony Michel Betbadal, Sara Grethlein
Journal: Journal of Clinical Oncology (2018)

276 Background: Poor communication between referring physicians and consultants can lead to disruptions in continuity of care, unnecessary testing, and iatrogenic complications. We sought to identify the barriers to effective communication between Indiana University Simon Cancer Center (IUSCC) oncologists and ROs. Methods: We retrospectively analyzed communication surrounding the visits of consecutive new oncology patients (pt) to IUSCC during Dec 2017 and Jan 2018. Demographics, diagnoses, RO’s information, and IUSCC physician’s information were recorded from the electronic medical record (EMR). ROs were contacted and a questionnaire was administered about timeliness, methods, and satisfaction with the communication. Results: A total of 110 new pt consultations were undertaken during the study period. There were 9 self-referrals, 69 interfacility referrals from the IU Health system, and 32 referrals by community RO. We were able to reach 27 community ROs, and their comments were included in the final analysis. RO interviews revealed that 78% had received notes (21 of 27 visits). Median time from pts’ clinic visit at IUSCC to ROs receiving a note was 2.5 days (range, 0-38 days). Five (25%) notes were received on the same day of consultation, and 10 (50%) were received within 2-7 days from pt visit. Of 18 traditionally dictated notes, 16 (89%) were received by ROs. Of 9 EMR typed notes, 5 (55%) were received by ROs. Only 62% of ROs received notes when their information was missing in the EMR. Based on feedback from ROs, effective communication was defined as communication within 7 days from pt visit. Ineffective communication was seen mostly on Mondays, followed by Fridays (75% and 50%, respectively). Conclusions: Effective communication was achieved in 75% of consultations. Effective communication was impacted by the day of the week, accuracy of RO information in the EMR, and the method of note documentation. Correcting ineffective communication can be explored through improvement of both human factors (ex.reinforcement of timely communication goals with physicians) and system factors (ex. Improving the accuracy of RO data in the EMR). Checklists, audits and other process analytics may help overcome the barriers identified.
The Washington State Community Cancer Care Report: A multi-stakeholder effort to characterize quality of care and costs for Washington State oncology practices.
Authors: Scott David Ramsey, Karma L. Kreizenbeck, Laura Elizabeth Panattoni, Catherine R. Fedorenko, Li Li, Qin Sun, Sarah Barger, Gary H. Lyman
Journal: Journal of Clinical Oncology (2018)

31 Background: Although many quality measures exist in oncology, there have been few efforts to prioritize, measure, and report quality and costs for an entire region. Here, we report the results of a multi-year, multi-stakeholder effort aimed at public reporting of nationally recognized quality metrics for oncology practices in Washington State. Methods: Quality metrics were selected from nationally-recognized measures through a structured process involving oncology providers, health insurance leaders, patient advocates, and policy experts. Cancer registry records from 2014 to 2016 were linked with claims data from two commercial insurers and Medicare, representing approximately 70% of cancer patients in the state. Patients were assigned to oncology clinics using claims data; 27 clinics were large enough for inclusion in at least one measure in the report. Thirteen metrics were combined to produce one clinic-level quality score per measure. Each quality score was mapped to total episode cost per patient. Results were adjusted to account for clinic size, cancer characteristics (e.g. stage), demographics, and comorbidity where appropriate. Results: Conclusions: The Community Cancer Care in Washington State: Quality and Cost Report 2018 is the first publicly accessible report showing clinic-level quality measures linked to cost in oncology. Its ultimate goal is to improve care and lower costs by spurring collaboration, research and innovation.[Table: see text]
Pesticide Use and Incident Hypothyroidism in Pesticide Applicators in the Agricultural Health Study
Authors: Srishti Shrestha, Christine G. Parks, Whitney S. Goldner, Freya Kamel, David M. Umbach, Mary H. Ward, Catherine C. Lerro, Stella Koutros, Jonathan N. Hofmann, Laura E. Beane Freeman, Dale P. Sandler
Journal: Environmental Health Perspectives (2018)

Background: Though evidence suggests that some pesticides may have thyroid-disrupting properties, prospective studies of associations between specific pesticides and incident thyroid disease are limited. Objective: We evaluated associations between use of specific pesticides and incident hypothyroidism in private pesticide applicators in the Agricultural Health Study (AHS). Methods: Self-reported incident hypothyroidism (n=829 cases) was studied in relation to ever-use and intensity-weighted cumulative days of pesticide use at study enrollment. We estimated adjusted hazard ratios (HRs) and 95% confidence intervals (CI) using Cox proportional hazards models applied to 35,150 male and female applicators followed over 20 y. All models were stratified by state and education to meet proportional hazards assumptions (p≤0.10 for age x covariate interactions). Models of pesticides that did not meet proportional hazards assumptions were stratified by median attained age (62 y). Results: Hypothyroidism risk was significantly increased with ever- vs. never-use of four organochlorine insecticides (aldrin, heptachlor, and lindane among participants with attained age >62y; chlordane in all participants), four organophosphate insecticides (coumaphos in those >62y; diazinon, dichlorvos, and malathion in all participants) and three herbicides (dicamba, glyphosate, and 2,4-D in all participants). HRs ranged from 1.21; 95% CI: 1.04, 1.41 (chlordane) to 1.54; 95% CI: 1.23, 19.4 (lindane in those >62y). Hypothyroidism risk was greatest among those with higher intensity-weighted lifetime days of using chlordane, lindane, coumaphos (over age 62), diazinon, permethrin, and 2,4-D. Conclusions: Our findings support associations between exposure to several pesticides and increased hypothyroidism risk. These findings are generally consistent with prior analyses of prevalent hypothyroidism in the AHS. https://doi.org/10.1289/EHP3194
Urine-derived lymphocytes as a non-invasive measure of the bladder tumor immune microenvironment
Authors: Yien Ning Sophia Wong, Kroopa Joshi, Pramit Khetrapal, Mazlina Ismail, James L. Reading, Mariana Werner Sunderland, Andrew Georgiou, Andrew J.S. Furness, Assma Ben Aissa, Ehsan Ghorani, Theres Oakes, Imran Uddin, Wei Shen Tan, Andrew Feber, Ursula McGovern, Charles Swanton, Alex Freeman, Teresa Marafioti, Timothy P. Briggs, John D. Kelly, Thomas Powles, Karl S. Peggs, Benjamin M. Chain, Mark D. Linch, Sergio A. Quezada
Journal: The Journal of Experimental Medicine (2018)

Despite the advances in cancer immunotherapy, only a fraction of patients with bladder cancer exhibit responses to checkpoint blockade, highlighting a need to better understand drug resistance and identify rational immunotherapy combinations. However, accessibility to the tumor prior and during therapy is a major limitation in understanding the immune tumor microenvironment (TME). Herein, we identified urine-derived lymphocytes (UDLs) as a readily accessible source of T cells in 32 patients with muscle invasive bladder cancer (MIBC). We observed that effector CD8+ and CD4+ cells and regulatory T cells within the urine accurately map the immune checkpoint landscape and T cell receptor repertoire of the TME. Finally, an increased UDL count, specifically high expression of PD-1 (PD-1hi) on CD8+ at the time of cystectomy, was associated with a shorter recurrence-free survival. UDL analysis represents a dynamic liquid biopsy that is representative of the bladder immune TME that may be used to identify actionable immuno-oncology (IO) targets with potential prognostic value in MIBC.