tbuckley/cabot-search huggingface dataset:
Estimating Nonfatal Gunshot Injury Locations With Natural Language Processing and Machine Learning Models
Authors: Susan T. Parker
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Nonfatal gunshot injuries are the most common firearm injury, but where they frequently occur remains unclear owing to data limitations. Natural language processing can be applied to medical text narratives of gunshot injury records to classify injury location and inform prevention efforts. <h3>Objective</h3> To examine the performance of natural language processing (NLP) and machine learning models to predict nonfatal gunshot injury locations and generate new national estimates of the locations in which these injuries occur. <h3>Design, Setting, and Participants</h3> Cross-sectional study of data from the National Electronic Injury Surveillance System Firearm Injury Surveillance Study on nonfatal gunshot injuries that occurred in the US between January 1, 1993, and December 31, 2015. The unweighted sample included 59 025 gunshot injuries that were initially treated at emergency departments. Data were analyzed from June 1, 2019 to July 24, 2020. <h3>Main Outcomes and Measures</h3> The primary outcomes were classification of injury location and subsequent estimation of nonfatal gunshot injury location. The NLP was used to generate 6 sets of predictors, and 4 machine learning models were trained to classify the missing locations: multinomial support vector machines, lasso regression, XgBoost gradient descent, and feed-forward neural networks. For each of the 6 sets of NLP predictors, 70% of records with locations were randomly sampled to form the training set and the remaining 30% of records composed the test set. The best-performing model was validated by comparing the predicted locations were with those from existing national estimates of nonfatal gunshot injuries stratified by location and intent. <h3>Results</h3> The unweighted sample included 59 025 nonfatal gunshot injuries; patients with these injuries were predominantly male (n = 52 630, [89.2%]), of Black race/ethnicity (n = 29 304 [49.6%]), and young (15-24 years; n = 27 037 [45.8%]). In total, 54 089 nonfatal gunshot injuries that were weighted to approximate national estimates were included in the analysis. Existing national estimates suggest that the most prevalent nonfatal gunshot injury location is the home (n = 14 764 [23.4%]), followed by the street or highway (n = 14 402 [22.9%]), and other public places (n = 7276 [11.6%]). After implementation of NLP classification, the most frequent gunshot injury location was the street or highway (n = 27 200 [46.1%]), followed by the home (n = 23 738 [37.7%]), and other public places (n = 10 439 [15.1%]). <h3>Conclusions and Relevance</h3> The findings of this study suggest that NLP and machine learning models may be useful for classifying gunshot injury location and that most nonfatal gunshot injuries occur in the street or highway rather than in the home; these findings can inform future firearm injury prevention efforts.
Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory
Authors: Megan S. F. Soon, Hyun Jae Lee, Jessica A. Engel, Jasmin Straube, Bryce S. Thomas, Clara P. S. Pernold, Lachlan S. Clarke, Pawat Laohamonthonkul, Rohit N. Haldar, Cameron G. Williams, Lianne I. M. Lansink, Marcela L. Moreira, Michael Bramhall, Lambros T. Koufariotis, Scott Wood, Xi Chen, Kylie R. James, Tapio Lönnberg, Steven W. Lane, Gabrielle T. Belz, Christian R. Engwerda, David S. Khoury, Miles P. Davenport, Valentine Svensson, Sarah A. Teichmann, Ashraful Haque
Journal: Nature Immunology (2020)
Using an integrated social-behavioral text message approach to improve screening mammography in African American women.
Authors: Amina Dhahri, Paapa Nyanin, Shana Ntiri
Journal: Journal of Clinical Oncology (2020)

240 Background: The rate of breast cancer among Black and White women is nearly equivalent but the death rate is 40% higher for Blacks. This disparity is often attributed to lower screening mammography rates in Black women. The effectiveness of text messages on increasing screening mammography among Black women is not well known. Importantly, the themes that are most effective at promoting behavioral changes in Black women’s breast cancer screening practices through text message interventions have not been explored. An integrated social-behavioral approach was used to identify themes associated with Black women’s response to two types of text messaging: reminder and educational texts. Methods: A qualitative study was conducted in Metropolitan Baltimore with two focus groups among Black breast cancer survivors. Participants completed a demographic survey and indicated text messaging practices and preferences for future breast screening texts via survey. Participants provided feedback on a series of 17 educational and reminder text messages. Focus groups were digitally recorded and transcribed for analysis. Text message preferences were analyzed using a content analysis approach. Multiple themes were identified, discussed and recorded. Results: 17 participants had an average age of 60. All participants reported cell phone ownership and 82% of participants reported texting. 46% reported an interest in reminder text messages and 54% reported an interest in educational text messages. Four main themes were derived from participants’ responses the text message series: 1) access to cancer care surveillance, 2) social network support, 3) patient-centered approach, and 4) self-advocacy. Text messages that included themes of self-advocacy, social network support, and patient-centered approach generated positive responses and the text messages that included access to cancer care surveillance were perceived as demotivating. Educational text messages were perceived to be more motivating than reminder text messages. Conclusions: Breast cancer screening behaviors are affected by various demographic, social-behavioral, and socioeconomic factors. The findings from this study suggest that developing an educational text message content that incorporates social and behavioral themes focusing on the patient may be more beneficial to improve breast cancer screening rates in this population.
Perception of patients regarding telemedicine at times of COVID-19: Did they miss the personal touch?
Authors: Shira Peleg Hasson, Barliz Waissengrin, Marah Hodruj, Eliya Shachar, Sharon Pelles, Ido Wolf
Journal: Journal of Clinical Oncology (2020)

260 Background: The patient-oncologist relationship is cultivated from the first clinic visit, trust and assurance established throughout the follow up period until the end of life. In March 2020, with the break of the COVID-19 pandemic, social distancing restrictions were implement throughout Israel. The adoptions of telemedicine services were incorporate as a response at our institution. Almost all ambulatory activity in the oncology division in Tel Aviv Medical Center was converted to telemedicine services. Several studies report favorable results regarding patient preference and cost effectiveness of telemedicine. Methods: We conducted a telephone interview questionnaire assessing patient satisfaction. Inclusion criteria included solid tumor patients over 18 years who utilized the telemedicine platform at Tel Aviv Sourasky Medical Center between March 2020 - May 2020. We aimed to evaluate patient's perspectives and preferences regarding telemedicine and assess whether this virtual communication affects the patient-doctor relationship. Results: Following the COVID-19 outbreak, 400 telephone calls were made to patients, 100 patients agreed to participate and surveyed. Fifty-two percent were female. The majority of patients independently downloaded the telemedicine application and did not encounter technical constraints (67%). Family members and friend attended 45% of telemedicine visits. Patients cancer diagnosis included colorectal cancer (47%), breast cancer (18%), genitourinary cancer (18%), sarcoma (9%) lung malignancies (6%), gynecological cancer (1%) and CNS tumors (2%). Visit intent included post-treatment follow up (40%), active treatment follow (53%), and first visit intake (7%). The majority of patients felt their emotional needs were met (88%) and felt that their treatment was not harmed due to absence of a physical visit (84%). Almost all patients (99%) felt their privacy was maintained. Ninety-five percent of patients affirmed that the virtual visit relieved their worries regarding treatment interruption. Importantly, 75% of patients affirmed their interest to continue telemedicine regardless of COVID-19 pandemic. Conclusions: Telemedicine is an acceptable platform that may replace follow up visits without comprising patients’ experience. Our data call for research and development of tools enabling long-term implementation of remote telemedicine and assess the patient-physician relationship and quality of care among oncology patients.
Caregiver-oncologist concordance in patient prognosis, caregiver depression, and caregiver mastery.
Authors: Kah Poh Loh, Eva Culakova, Huiwen Xu, Sindhuja M Kadambi, Allison Magnuson, Marie Anne Flannery, Paul Duberstein, Ronald M. Epstein, Colin McHugh, Ryan David Nipp, Kelly Marie Trevino, Chandrika Sanapala, Beverly Canin, Arlene Angela Gayle, Alison Katherine Conlin, James Bearden, Supriya Gupta Mohile
Journal: Journal of Clinical Oncology (2020)

143 Background: Caregivers of older adults with advanced cancer often have a different understanding of the patient’s prognosis compared with their oncologist. Among patients, accurate prognostic awareness is associated with greater depressive symptoms, except when patients utilize more adaptive coping skills. We examined the relationship between caregiver-oncologist prognostic concordance and caregiver depressive symptoms and explored whether this relationship differed by caregiver mastery, the capacity to cope, adjust, and adapt to problems. Methods: We utilized data from a national geriatric assessment cluster-randomized trial (URCC 13070: PI Mohile) that recruited patients aged ≥70 with incurable cancer considering any line of cancer treatment at community oncology practices, their caregivers, and oncologists. At enrollment, caregivers and oncologists estimated the patient’s prognosis (0-6 months, 7-12 months, 1-2 years, 2-5 years, &gt; 5 years); same response was considered concordant. Caregivers completed Ryff’s mastery subscale (range 7-35, higher is better) at enrollment and depression screen (the Patient Health Questionnaire (PHQ)-2 (range 0-6) 4-6 weeks later. To assess the association of prognostic concordance with caregiver depressive symptoms, we used generalized estimating equations in models adjusted for cancer type, study arm, practice sites, and caregiver demographics. We then assessed moderation effect of caregiver mastery on this association. Results: Among 410 caregiver-oncologist dyads, mean caregiver age was 66.5, 75% were female, and 26% were caregivers of patients with lung cancer. Mean mastery score at enrollment was 27.6 (SD 4.7) and 19% screened positive on PHQ-2 at week 4-6. Among dyads who provided response (N = 370), 28% were concordant. Prognostic concordance was associated with higher caregiver depressive symptoms (β = 0.30; p = 0.04). Significant moderation effect was found between concordance and mastery for caregiver depressive symptoms (p = 0.02). Among caregivers with low mastery ( &lt; median), prognostic concordance was associated with higher depressive symptoms (β = 0.68; p = 0.003). Among caregivers with high mastery (≥median), concordance was not associated with depressive symptoms (β = -0.06; p = 0.67). Conclusions: There is a need to study how prognostic understanding might lead to depression in at-risk caregivers. Interventions targeting caregiver prognostic understanding need to consider its relationship with depressive symptoms, while seeking to increase caregiver mastery.
Long-term Oncologic Outcomes of Immediate Breast Reconstruction vs Conventional Mastectomy Alone for Breast Cancer in the Setting of Neoadjuvant Chemotherapy
Authors: Zhen-Yu Wu, Hee-Jeong Kim, Jong-Won Lee, Il-Yong Chung, Ji-Sun Kim, Sae-Byul Lee, Byung-Ho Son, Jin-Sup Eom, Sung-Bae Kim, Kyung Hae Jung, Gyungyub Gong, Hak Hee Kim, Sei-Hyun Ahn, BeomSeok Ko
Journal: JAMA Surgery (2020)

An increasing number of patients with breast cancer receiving neoadjuvant chemotherapy (NACT) undergo immediate breast reconstruction (IBR) with nipple-sparing mastectomy (NSM) or skin-sparing mastectomy (SSM) as surgical treatment. However, the oncologic efficacy and safety of this treatment sequencing strategy is unclear.To compare the long-term oncologic outcomes of IBR with NSM/SSM and conventional mastectomy (CM) alone for breast cancer in the NACT setting.A retrospective, propensity score-matched case-control study was conducted at Asan Medical Center, Seoul, Korea. A total of 1266 patients with breast cancer who underwent NACT followed by mastectomy with or without breast reconstruction between January 1, 2010, and November 30, 2016, were included. Data analysis was performed from July 1, 2019, to January 24, 2020. After propensity score matching, 323 patients who underwent IBR with NSM/SSM and 323 who underwent CM alone were selected for comparison of long-term oncologic outcomes.The 5-year local recurrence-free survival, disease-free survival, distant metastasis-free survival, and overall survival rates were calculated using the Kaplan-Meier method and compared using log-rank tests. Hazard ratios (HRs) and 95% CIs were estimated using the Cox proportional hazards regression model.After matching, the median follow-up periods were 67 (range, 17-125) months for the IBR group and 68 (range, 17-126) months for the CM-alone group. Median age of the women in the IBR group was 42 (range, 23-72) years; median age of those in the CM-alone group was 46 (range, 30-75) years. No significant differences were observed between the IBR and CM-alone groups in local recurrence (3.7% vs 3.4%; P = .83), regional recurrence (7.1% vs 5.3%; P = .33), or distant metastasis (17.3% vs 18.6%; P = .68) rates. There was also no significant difference between the IBR and CM-alone groups in 5-year local recurrence-free survival (95.6% vs 96.7%; HR, 1.124; 95% CI, 0.495-2.549; P = .78), disease-free survival (76.5% vs 79.9%; HR, 1.089; 95% CI, 0.790-1.500; P = .60), distant metastasis-free survival (82.5% vs 82.5%; HR, 0.941; 95% CI, 0.654-1.355; P = .74), or overall survival (92.0% vs 89.3%; HR, 0.847; 95% CI, 0.530-1.353; P = .49) rates.The long-term oncologic outcomes of IBR with NSM/SSM for breast cancer in this study appeared to be comparable to those of CM alone after NACT, suggesting the feasibility of IBR with NSM/SSM in the NACT setting.
Evaluating compliance of NCCN cancer and chemotherapy-induced anemia guidelines in a community healthcare setting.
Authors: Jamie Haber, Brian J. Byrne
Journal: Journal of Clinical Oncology (2020)

16 Background: The National Comprehensive Cancer Network has released guidelines for management of cancer- and chemotherapy-induced anemia which are defined as Hb less than 11g/dL or a greater than 2g/dL decrease from baseline. The myelosuppressive effects of cancer, chemotherapy and associated treatments, can accumulate with each cycle leading to severe and worsening anemia. It is important to properly identify and treat anemia in cancer patients in a timely manner. This project evaluates the degree to which NCCN guidelines are followed within a multi-site community healthcare setting. Methods: Obtained patient medical records within Hartford Healthcare system in a 4 month period (Nov. 2019-Feb. 2020), who were started on new cancer chemotherapy treatment plans. Patients on single agent immunotherapy or hormone therapy only plans were excluded. Reviewed patient’s medical records to identify who met criteria for cancer- and chemotherapy-induced anemia and who received recommended work up and treatment based on NCCN guidelines. Age, sex, disease, renal function, and goals of treatment were also recorded. Results: A total of 869 patient records were obtained. 598 patients met the inclusion criteria. 452 patients (75.6%) met criteria for cancer- and chemotherapy-induced anemia. 235 patients (52%) had anemia appropriately documented in the physician medical record. 111 patients with anemia (24.6%) had an iron panel performed and 29 patients (6.4%) had a reticulocyte count resulted. For those eligible by NCCN criteria for anemia specific interventions 27 patients (40%) received appropriate iron supplementation, 95 patients (85.6%) received appropriate blood transfusions and 10 patients (7.7%) received appropriate EPO. Conclusions: It is apparent that based on NCCN guidelines, monitoring, evaluation, and treatment of anemia is not being appropriately performed in this healthcare setting. Based on this data a quality improvement project for proper documentation, workup, and treatment of anemia is being developed. [Table: see text]
A Novel Role for Histone Deacetylase 10 (HDAC10) in the Regulation of PD-L1 Expression and Immune Tolerance Mediated By Antigen Presenting Cells (APCs)
Authors: Michael Wang, Fengdong Cheng, Jie Chen, Yixuan Li, Alejandro Villagra, Mitchell R. Smith, Edward Seto, Eduardo Martin Sotomayor
Journal: Blood (2017)
Subtype-Discordant Pancreatic Ductal Adenocarcinoma Tumors Show Intermediate Clinical and Molecular Characteristics
Authors: James T. Topham, Joanna M. Karasinska, Michael K.C. Lee, Veronika Csizmok, Laura M. Williamson, Gun Ho Jang, Robert E. Denroche, Erica S. Tsang, Steve E. Kalloger, Hui-li Wong, Grainne M. O'Kane, Richard A. Moore, Andrew J. Mungall, Faiyaz Notta, Jonathan M. Loree, Julie M. Wilson, Oliver Bathe, Patricia A. Tang, Rachel Goodwin, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer
Journal: Clinical Cancer Research (2020)

Abstract Purpose: RNA-sequencing–based subtyping of pancreatic ductal adenocarcinoma (PDAC) has been reported by multiple research groups, each using different methodologies and patient cohorts. “Classical” and “basal-like” PDAC subtypes are associated with survival differences, with basal-like tumors associated with worse prognosis. We amalgamated various PDAC subtyping tools to evaluate the potential of such tools to be reliable in clinical practice. Experimental Design: Sequencing data for 574 PDAC tumors was obtained from prospective trials and retrospective public databases. Six published PDAC subtyping strategies (Moffitt regression tools, clustering-based Moffitt, Collisson, Bailey, and Karasinska subtypes) were used on each sample, and results were tested for subtype call consistency and association with survival. Results: Basal-like and classical subtype calls were concordant in 88% of patient samples, and survival outcomes were significantly different (P &amp;lt; 0.05) between prognostic subtypes. Twelve percent of tumors had subtype-discordant calls across the different methods, showing intermediate survival in univariate and multivariate survival analyses. Transcriptional profiles compatible with that of a hybrid subtype signature were observed for subtype-discordant tumors, in which classical and basal-like genes were concomitantly expressed. Subtype-discordant tumors showed intermediate molecular characteristics, including subtyping gene expression (P &amp;lt; 0.0001) and mutant KRAS allelic imbalance (P &amp;lt; 0.001). Conclusions: Nearly 1 in 6 patients with PDAC have tumors that fail to reliably fall into the classical or basal-like PDAC subtype categories, based on two regression tools aimed toward clinical practice. Rather, these patient tumors show intermediate prognostic and molecular traits. We propose close consideration of the non-binary nature of PDAC subtypes for future incorporation of subtyping into clinical practice.
Influenza in hospitalized cancer patients: A propensity score matching analysis.
Authors: Jiarui Li, Dingding Zhang, Lin Zhao, Zhao Sun, Chunmei Bai
Journal: Journal of Clinical Oncology (2020)

170 Background: Cancer patients are vulnerable to influenza viruses and are at great risk of developing related complications. However, few studies have assessed the impact of influenza infection among hospitalized cancer patients in the United States. Methods: We identified cancer-related hospitalizations from National Inpatient Sample between 2012 and 2014. A 1:1 propensity score matching analysis was conducted to compare the clinical outcomes between hospitalized cancer patients with and without influenza. Results: We identified 13,186,849 cancer-related hospitalizations, and 47,850 of them (0.36%) had a concomitant diagnosis of influenza. After propensity score matching, cancer patients with influenza had a higher mortality (5.4% vs. 4.2%; odds ratio [OR]: 1.3; 95% confidence interval [CI], 1.13 to 1.49; P &lt; 0.001), longer length of stay (6.3 vs. 5.6 days; P &lt; 0.001) but lower costs (14605.9 vs. 14625.5 dollars; P &lt; 0.001) in hospital than those without influenza. In addition, patients with influenza had a higher incidence of pneumonia (18.4% vs. 13.2%; OR, 1.49; 95% CI, 1.37 to 1.62; P &lt; 0.001), neutropenia (7.1% vs. 3.4%; OR, 2.18; 95% CI, 1.91 to 2.50; P &lt; 0.001), sepsis (19.5% vs. 9.3%; OR, 2.36; 95% CI, 2.16 to 2.58; P &lt; 0.001), dehydration (14.8% vs. 8.8%; OR, 1.80; 95% CI, 1.65 to 1.97; P &lt; 0.001), and acute kidney injury (19.9% vs. 17.6%; OR, 1.16; 95% CI, 1.08 to 1.25; P &lt; 0.001) than those without influenza. Conclusions: Influenza is associated with worse clinical outcomes among hospitalized cancer patients. Influenza vaccination is recommended in this population.
Patient-reported outcomes (PRO) in patients (pts) with advanced or recurrent dMMR/MSI-H endometrial cancer (EC) treated with dostarlimab in the GARNET trial.
Authors: Rebecca Sophie Kristeleit, Cara Amanda Mathews, Andrés Redondo, Joice Huang, Laurie Eliason, Ellie Im, Jubilee Brown
Journal: Journal of Clinical Oncology (2020)

275 Background: PRO enable direct measurement of the experiences of patients with cancer. Anti-programmed death 1 (PD-1) therapies have shown favorable PRO in lung cancer but a data gap remains in EC. Dostarlimab is an investigational anti-PD-1 monoclonal antibody which has shown promising activity in GARNET in advanced mismatch repair deficient (dMMR) EC pts and a low incidence of symptomatic grade ≥3 treatment-related adverse events. Here, we report on PRO measures collected from pts with dMMR/microsatellite instability high (MSI-H) EC in the single-arm GARNET trial. Methods: Pts with dMMR/MSI-H EC confirmed by local tests, with recurrent or advanced disease that progressed on a platinum regimen were enrolled. Pts received 500 mg Q3W of dostarlimab for 4 cycles, then 1000 mg Q6W until disease progression or discontinuation. PRO assessment was an exploratory endpoint and was measured by the EORTC Quality of Life Questionnaire (QLQ-C30), a validated instrument used evaluate quality of life (QOL), functioning, disease symptoms, and treatment-related side effects. PRO were collected at each dose administration, end of treatment, and follow-up. A mixed-model for repeated measures was used to assess change from baseline, accounting for time and baseline ECOG scores. The threshold to determine clinically meaningful group-level change was ±10 points. Results: PRO data were available for 43 pts. Compliance rates were 98%. Relative to baseline, pts reported meaningful improvements in pain, insomnia, and social and emotional functioning over the trial duration. Appetite, nausea, vomiting, constipation, diarrhea, and physical and role functioning were stable over the trial duration. QOL and global health status were also maintained. Conclusions: PRO from 43 pts enrolled in the GARNET trial show that disease- and treatment-related symptoms and QOL are improved or maintained while receiving treatment. These data, along with the efficacy and safety profile of dostarlimab, strongly support the use of dostarlimab in dMMR/MSI-H advanced EC. Funding: GlaxoSmithKline, Waltham, MA, USA. Clinical trial information: NCT02715284 .