tbuckley/cabot-search huggingface dataset:
The impact of social determinants on receipt of colonoscopy in an under-resourced hospital service area: A retrospective cohort study.
Authors: Amina Dhahri, Sam Azargoon, Darshan Gandhi, Dhruvi Barot, Himan Goli, Homayoon Mahjoob, Teshome Tegene, Shana Ntiri
Journal: Journal of Clinical Oncology (2020)

216 Background: Although colorectal cancer (CRC) screening with colonoscopy reduces the risk of CRC mortality, screening rates remain low among African Americans and low social economic status (SES) patients. However, few studies have assessed CRC screening rates in under-resourced hospital service areas. Using a granular measure of socioeconomic deprivation (SED), we examined the association between social determinants and CRC screening. Methods: We conducted a retrospective cohort study from 2014-2019 to identify primary care patients referred for CRC screening with colonoscopy at an academic hospital system. Patients were assessed at annual visits for completion of colonoscopy. SED was assessed using the area deprivation index (ADI), a composite measure of 17 SED indicators including income, housing, education, and employment at the census block group level. Other social determinants analyzed were race and insurance status. Frequency and multivariable logistic regression were used for statistical analysis. Results: 1040 patients met CRC screening guidelines and were referred for colonoscopy. 136 (13.1%) underwent colonoscopy in the follow-up period. High and low SED made up 655 (63%) and 77 (7.4%) of patients, respectively. SED, race, age, and sex were not associated with higher screening rates. Uninsured patients had a lower rate of screening. After controlling for other social determinants, uninsured patients had the lowest odds of colonoscopy (OR 0.28; 95% CI, 0.08-0.92). Conclusions: In this under-resourced hospital service area, receipt of colonoscopy for CRC screening is significantly lower than previously reported. Furthermore, screening rates were persistently low across strata of SED, race and insurance status, with uninsured patients having the lowest odds of screening. These data suggest that in an under-resourced hospital service area with extensive SED, further research is needed to understand the role of social determinants and behavioral factors to address disparities in CRC screening with colonoscopy. [Table: see text]
Statistical deformation reconstruction using multi-organ shape features for pancreatic cancer localization
Authors: Megumi Nakao, Mitsuhiro Nakamura, Takashi Mizowaki, Tetsuya Matsuda
Journal: Medical Image Analysis (2020)

Respiratory motion and the associated deformations of abdominal organs and tumors are essential information in clinical applications. However, inter- and intra-patient multi-organ deformations are complex and have not been statistically formulated, whereas single organ deformations have been widely studied. In this paper, we introduce a multi-organ deformation library and its application to deformation reconstruction based on the shape features of multiple abdominal organs. Statistical multi-organ motion/deformation models of the stomach, liver, left and right kidneys, and duodenum were generated by shape matching their region labels defined on four-dimensional computed tomography images. A total of 250 volumes were measured from 25 pancreatic cancer patients. This paper also proposes a per-region-based deformation learning using the reproducing kernel to predict the displacement of pancreatic cancer for adaptive radiotherapy. The experimental results show that the proposed concept estimates deformations better than general per-patient-based learning models and achieves a clinically acceptable estimation error with a mean distance of 1.2 $\pm$ 0.7 mm and a Hausdorff distance of 4.2 $\pm$ 2.3 mm throughout the respiratory motion.
Re-opening universities might be high risk, but it is essential for medical students
Journal: BMJ (2020)

Yamey and Walensky discuss some considerations for UK universities re-opening this academic year.1 This is important because rising covid-19 cases in the UK seem to be concentrated in younger people—many of whom are likely to begin or return to university this autumn.2

Healthcare students face unique challenges because of the added risk of exposure to covid-19 in the clinical environment and the necessity for some aspects of medical training to be …
Eligibility of real-world patients with metastatic lung cancer for clinical trial participation: A population-based analysis.
Authors: Atul Batra, Shiying Kong, Rodrigo Rigo, Winson Y. Cheung
Journal: Journal of Clinical Oncology (2020)

93 Background: Due to highly selective enrollment in clinical trials, the generalizability of results may be limited. This study aimed to identify the proportion of real-world patients with metastatic lung cancer (MLC) eligible to participate in a clinical trial. Methods: We identified patients diagnosed with MLC in a large Canadian province from 2004 to 2017. Ineligibility to participate in a clinical trial was defined by common exclusion criteria: age &gt; 75 years, anemia, comorbid conditions (heart disease, uncontrolled diabetes, kidney disease, or liver disease) and history of a prior malignancy or immunosuppression. Logistic regression models were used to describe the likelihood of receiving systemic therapy and Cox regression models were constructed to determine the association of trial ineligibility with overall survival (OS). Results: A total of 13,996 patients were included; the median age was 70 years and 46.9% were women. Of these, 8,615 (61.6%) were trial-ineligible. The common reasons for ineligibility were age &gt; 75 years (11.5%), abnormal renal function (8.3%) and prior immunosuppression (3.2%). Further, 32.3% of patients were ineligible by multiple exclusion criteria. In the real-world, 40.6% and 21.8% of trial-eligible and ineligible patients received systemic therapy (P &lt; .001), respectively. After adjusting for age and sex, trial-ineligible patients had lower odds of receiving systemic therapy (odds ratio, .84; 95% confidence interval [CI], .76-.92; P &lt; .001). At a median follow-up of 66.2 months, the median OS of trial-eligible patients was 5.1 months as compared to 2.9 months in those deemed ineligible (P &lt; .001). Receipt of systemic therapy was associated with longer OS in both trial-eligible (10.5 vs 2.7 months, P &lt; .001) and ineligible (9.3 vs 2.1 months, P &lt; .001) patients. In a Cox regression model that adjusted for age, sex and systemic therapy, ineligibility was predictive of worse OS. Conclusions: More than half of patients with MLC are ineligible to participate in clinical trials. Real-world use of systemic therapy was generally low, but its use was associated with improvement in OS even among individuals considered trial-ineligible. Clinical trials should broaden their eligibility criteria to better represent the phenotype of real-world patients so that findings are more generalizable. [Table: see text]
A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae
Authors: Wenlu Yang, Deyan Wang, Yiling Li, Zhiyang Zhang, Shaofei Tong, Mengmeng Li, Xu Zhang, Lei Zhang, Liwen Ren, Xinzhi Ma, Ran Zhou, Brian J Sanderson, Ken Keefover-Ring, Tongming Yin, Lawrence B Smart, Jianquan Liu, Stephen P DiFazio, Matthew Olson, Tao Ma
Journal: Molecular Biology and Evolution (2020)

Abstract Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.
Targeting epithelial-mesenchymal transition pathway in hepatocellular carcinoma
Authors: Jaewhan Song
Journal: Clinical and Molecular Hepatology (2020)

See the Original "Inhibition of PI3K/Akt signaling suppresses epithelial-to-mesenchymal transition in hepatocellular carcinoma through the Snail/GSK-3/beta-catenin pathway" on page 529.
Molecular Imaging of Apoptosis in Atherosclerosis by Targeting Cell Membrane Phospholipid Asymmetry
Authors: Farhan Chaudhry, Hideki Kawai, Kipp W Johnson, Navneet Narula, Aditya Shekhar, Fayzan Chaudhry, Takehiro Nakahara, Takashi Tanimoto, Dongbin Kim, Matthew K M Y Adapoe, Francis G Blankenberg, Jeffrey A Mattis, Koon Y Pak, Phillip D Levy, Yukio Ozaki, Eloisa Arbustini, H William Strauss, Artiom Petrov, Valentin Fuster, Jagat Narula
Journal: Journal of the American College of Cardiology (2020)
Increased risk of <scp>COVID</scp>‐19 infection and mortality in people with mental disorders: analysis from electronic health records in the United States
Authors: QuanQiu Wang, Rong Xu, Nora D. Volkow
Journal: World Psychiatry (2020)

Concerns have been expressed that persons with a pre‐existing mental disorder may represent a population at increased risk for COVID‐19 infec­tion and with a higher likelihood of adverse outcomes of the infection, but there is no systematic research evidence in this respect. This study assessed the impact of a recent (within past year) diagnosis of a mental disorder – including attention‐deficit/hyperactivity disorder (ADHD), bipolar disorder, depression and schizophrenia – on the risk for COVID‐19 infection and related mortality and hospitalization rates. We analyzed a nation‐wide database of electronic health records of 61 million adult patients from 360 hospitals and 317,000 providers, across 50 states in the US, up to July 29, 2020. Patients with a recent diagnosis of a mental disorder had a significantly increased risk for COVID‐19 infection, an effect strongest for depression (adjusted odds ratio, AOR=7.64, 95% CI: 7.45‐7.83, p&lt;0.001) and schizophrenia (AOR=7.34, 95% CI: 6.65‐8.10, p&lt;0.001). Among patients with a recent diagnosis of a mental disorder, African Americans had higher odds of COVID‐19 infection than Caucasians, with the strongest ethnic disparity for depression (AOR=3.78, 95% CI: 3.58‐3.98, p&lt;0.001). Women with mental disorders had higher odds of COVID‐19 infection than males, with the strongest gender disparity for ADHD (AOR=2.03, 95% CI: 1.73‐2.39, p&lt;0.001). Patients with both a recent diagnosis of a mental disorder and COVID‐19 infection had a death rate of 8.5% (vs. 4.7% among COVID‐19 patients with no mental disorder, p&lt;0.001) and a hospitalization rate of 27.4% (vs. 18.6% among COVID‐19 patients with no mental disorder, p&lt;0.001). These findings identify individuals with a recent diagnosis of a mental disorder as being at increased risk for COVID‐19 infection, which is further exacerbated among African Americans and women, and as having a higher frequency of some adverse outcomes of the infection. This evidence highlights the need to identify and address modifiable vulnerability factors for COVID‐19 infection and to prevent delays in health care provision in this population.
Temporal changes in rural-urban treatment patterns for early-stage non-small cell lung cancer in North Carolina, 2006 to 2015.
Authors: Joshua Herb, Tzy-Mey Kuo, Vaibhav Kumar, Benjamin Wu, Mark Holmes, Jennifer Leigh Lund, Katherine Elizabeth Reeder-Hayes, Christopher Baggett, Karyn Beth Stitzenberg
Journal: Journal of Clinical Oncology (2020)

112 Background: Rural-urban disparities in the receipt of surgery for early-stage non-small cell lung cancer (NSCLC) have been noted, but few studies have considered access to other available treatments (i.e. radiation) or examined changes over time. Rural hospital closures, regionalization and workforce changes could lead to temporal changes in treatment access. Therefore, the primary objective was to evaluate geographic disparities in lung cancer treatment modalities in North Carolina and to characterize how practice patterns are changing over time. We hypothesized that rural patients would be less likely to undergo treatment compared to urban patients with widening disparities over time. Methods: North Carolina cancer registry data linked with Medicaid, Medicare, and private insurance claims were used to identify patients with Stage I or II NSCLC from 2006-2015. The primary outcome was first course treatment modality: surgery, radiation, or no treatment. Rural-urban status was defined based on Rural-Urban Commuting Codes. Calendar years were split into early (2006-10) and late (2011-15) periods. Multivariable logistic regression was used to assess the association of rural/urban status and time period with surgery and any treatment (surgery or radiation) while controlling for clinical, demographic, and area-level factors. Results: Among 7532 patients, 4144 (56%) patients underwent surgery, 1991 (27%) received radiation, and 1397 (19%) had no therapy. Rural patients were as likely to undergo treatment in either time period as urban patients. Among rural patients, the odds of surgery decreased over time (2011-15 vs. 2006-10 OR 0.79, 95%CI 0.66,0.94) and the odds of radiation increased (2011-15 vs. 2006-10 OR 1.46, 95%CI 1.40,1.78). Meanwhile urban patients had no significant change in surgery over time, but also had an increase in likelihood of undergoing radiation (2011-15 vs. 2006-10 OR 1.34 95%CI 1.18,1.52). Conclusions: Between 2006-2015, nearly 1 in 5 insured patients in North Carolina did not receive any treatment for potentially curable lung cancer. Over time, rural patients are less likely to undergo surgery, the standard of care, while radiation use is increasing everywhere. As rural patients are less likely to undergo surgery over time, this may have downstream effects on rural-urban disparities in survival. Further work aims to understand the patient and system level drivers behind these trends.
32 Does faecal calprotectin measurement have an impact on patient management
Authors: B Callaghan, P Lynch, S Jacob, K Caneborg, K Love
Journal: Gut (2017)

Background  Faecal calprotectin (FC) is recommended to support the differential diagnosis of IBD or IBS in adults with recent onset lower gastrointestinal symptoms. FC can assess IBD activity in those with known disease, as a rising level is an early marker of potential relapse. There is presently no formal funding for FC within Northern Ireland.  Aim  To assess if FC measurement directs an immediate modification in patient management within two out-patient groups: 1) new patients with differential diagnosis of IBS or IBD; 2) review patients with known IBD.  Method  A random selection of FC results from secondary care patients over 12 months were analysed. Patient outcomes following the FC result stratified patients into one of four groups: Discharged, colonoscopy performed, clinic review or escalation of medical therapy.  Results  Group 1 (n=28): 8 positive FC, all proceeding to endoscopy. In the 14 negative FC, 12 patients were discharged, 2 had clinic review. For indeterminate result: one patient with 2 indeterminate results underwent colonoscopy; 4 had clinic review; 1 was discharged. Group 2 (n=28): of the 20 positive results, 11/20 (55%) had medical management escalated, 5/20 (25%) underwent colonoscopy and 20% had clinic review. In the negative and indeterminate results: 7/8 had clinic review.  Conclusions  For patients with suspected IBS, a negative FC avoided unnecessary colonoscopy. In patients with known IBD, a raised FC led to an escalation in therapy in the majority of patients to minimise the risk of relapse and potential hospital admission. This study supports the need for a Northern Ireland FC service.
Association of State-Level Medicaid Expansion With Treatment of Patients With Higher-Risk Prostate Cancer
Authors: Wen Liu, Michael Goodman, Christopher P. Filson
Journal: JAMA Network Open (2020)

<h3>Importance</h3> The Patient Protection and Affordable Care Act broadened insurance coverage, partially through voluntary state-based Medicaid expansion. <h3>Objective</h3> To determine whether patients with higher-risk prostate cancer residing in Medicaid expansion states were more likely to receive treatment after expansion compared with patients in states electing not to pursue Medicaid expansion. <h3>Design, Setting, and Participants</h3> This population-based cohort study included 15 332 patients diagnosed with higher-risk prostate cancer (ie, grade group &gt;2; grade group 2 with prostate-specific antigen levels &gt;10 ng/mL; or grade group 1 with prostate-specific antigen levels &gt;20 ng/mL) from January 2010 to December 2016 aged 50 to 64 years who were candidates for definitive treatment. Patients residing in states that partially expanded Medicaid coverage before 2010 (ie, California and Connecticut) and those with diagnosis not confirmed by histology were excluded. Data were collected from the Surveillance, Epidemiology, and End Results Program. Data were analyzed between August and December 2019. <h3>Exposure</h3> State-level Medicaid expansion status. <h3>Main Outcomes and Measures</h3> Insurance status before and after expansion, treatment with prostatectomy or radiation therapy (including brachytherapy), treatment trends over time. <h3>Results</h3> Of 15 332 patients, 7811 (50.9%) lived in expansion states (mean [SD] age, 59.1 [3.8] years; 5532 [71.9%] non-Hispanic White), and 7521 (49.1%) lived in nonexpansion states (mean [SD] age, 59.0 [3.9] years; 3912 [52.1%] non-Hispanic White). Residence in an expansion state was associated with higher pre-expansion levels of Medicaid coverage (292 [8.1%] vs 161 [3.8%]; odds ratio [OR], 2.12; 95% CI, 1.78 to 2.53) and lower likelihood of being uninsured (136 [3.2%] vs 38 [1.1%]; OR, 0.28; 95% CI, 0.15 to 0.54). After expansion, there was no difference in trends in treatment receipt between expansion and nonexpansion states (change, −0.39%; 95% CI, −0.11% to 0.28%;<i>P</i> = .25). Patients with private or Medicare coverage were more likely to receive treatment vs those with Medicaid or no coverage across racial/ethnic groups (eg, Black patients with coverage: OR, 2.30; 95% CI, 1.68 to 3.10; Black patients with no coverage: OR, 1.48; 95% CI, 1.09 to 2.00;<i>P</i> &lt; .001). Medicaid patients were not more likely to be treated compared with those without insurance (737 [78.8%] vs 435 [79.5%]; OR, 0.97; 95% CI, 0.76 to 1.25). <h3>Conclusions and Relevance</h3> In this cohort study, state-level expansion of Medicaid was associated with increased Medicaid coverage for men with higher-risk prostate tumors but did not appear to affect treatment patterns at a population level. This may be related to the finding that Medicaid coverage was not associated with increased treatment rates compared with those without insurance.
Increasing lung cancer screening rates in HIV clinics.
Authors: Shawn Jindal, Maria Serrano, Sarah Baron, Matthew Stuart, Mariam Alexander, Meryl Kravitz, Stevyn Fernandes, Vikas Mehta, Robert M. Grossberg, Hilda Ortiz-Morales, Jose Nahun Galeas, Stuart H. Packer, Balazs Halmos
Journal: Journal of Clinical Oncology (2020)

189 Background: Data at our institution shows lung cancer is more prevalent and aggressive in HIV patients. A study of lung cancer patients revealed a mean age of 55.8 years in those with HIV vs. 68.0 in those without. Additionally, 67% of HIV patients had metastasis at time of diagnosis, compared to 49% in the overall population. One study found an 18.9% reduction in lung cancer mortality among HIV patients who receive NLST-recommended screening. Despite this, data from 2018 estimated only 13% of eligible HIV patients had completed screening at our institution. We pursued a quality improvement initiative to increase lung cancer screening in our HIV clinics. Methods: Our multi-disciplinary team studied charts of the 628 HIV clinic patients seen in a four-month span to identify those who had not received lung cancer screening and potential reasons why referrals were not made. We also spoke with clinic providers to identify improvement areas. Our intervention encompassed HIV patients that met CMS screening criteria (i.e. age 55-77, 30 pack-year smoking). Our process measure was new referrals to our dedicated screening coordinator, who contacts patients to arrange for CT scans. We plotted trends in appointment referrals on a run chart. Results: Areas for improvement included EMR documentation to assess screening eligibility and an occasional lack of awareness regarding criteria. Providers also cited time constraints may limit referrals. Our team identified patients that met screening criteria and generated EMR reminders for providers to refer patients to radiology. We also held sessions with providers and nursing staff to increase awareness of our screening program. Of 628 patients, 128 (20.4%) had sufficient documented smoking history to assess for screening eligibility. 81 patients (63.3%) met our criteria. Of these patients, 58 (71.6%) had not been screened or referred for screening. Through our most recent interventions, 16 (31.3%) patients have been referred to our screening coordinator, and 7 (12.1%) have received screening CT scans. Our interventions ultimately led to an increase from 23 of 81 (28.4%) patients with completed screening to a projected 46 of 81 (56.8%). Conclusions: Providing education and EMR alerts to raise awareness regarding eligibility, we substantially increased the screening rate in our clinics. Our interventions will be broadened as we return from COVID stoppages. Future interventions include increasing smoking history documentation in the EMR to allow for automated identification of screening eligibility. PDSA and interventions are ongoing with continued follow-up of efficacy.