tbuckley/cabot-search huggingface dataset:
EMBR-18. LASER INTERSTITIAL THERMAL THERAPY FOR RECURRENT MEDULLOBLASTOMA
Authors: Jordan Xu, Jodi Pathare, Clay Hoerig, Aaron Goldberg, Chenue Abongwa, Ashley Plant, Joffre Olaya
Journal: Neuro-Oncology (2021)

Abstract Background Medulloblastoma is one of the most common malignant childhood brain tumors and is managed by maximal surgical resection followed by cranio-spinal irradiation and adjuvant chemotherapy. The estimates for survival have not significantly improved over the last two decades, and survivors have an increased risk of poor quality of life. Disease relapse occurs in around 30% of children and survival is less than 20%. Laser interstitial thermal therapy (LITT) is a minimally invasive approach that has been increasingly used to treat brain lesions, particularly for high-risk surgeries. While LITT has been described in a variety of primary brain tumors, including glioblastoma multiforme and metastatic brain tumors, there have been few reports of LITT for recurrent medulloblastoma. Case Description We describe a case of an 11-year-old female with recurrent medulloblastoma first treated at age 5. She initially underwent gross total resection complicated by severe posterior fossa syndrome followed by chemotherapy and radiation (per ACNS0332). She was unfortunately found to have a new enhancing lesion on surveillance imaging 6 years later, and a biopsy confirmed recurrent tumor. Due to morbidity from initial surgery, the family did not wish to pursue further open resection but agreed to proceed with laser ablation as an alternative. She continues on Avastin/irinotecan/TMZ. Surveillance MRI nearly a year later shows a significant reduction in tumor size and enhancement. Conclusion Recurrent medulloblastoma is a highly aggressive tumor that conveys a poor prognosis. LITT offers a less invasive procedure that may serve as an adjunct in treating recurrent tumor or as palliation. Longer term follow-up and additional cases will help understand the efficacy of LITT in recurrent medulloblastoma.
Chemothery (pacitaxol or irinotecan), plus apatinib and sintilimab as second-/third-line treatment for advanced gastric cancer.
Authors: Ting Deng, Le Zhang, Jingjing Duan, Hongli Li, Shaohua Ge, Ming Bai, Tao Ning, Yuchong Yang, Zhi Ji, Rui Liu, Xia Wang, Haiyang Zhang, Yi Ba
Journal: Journal of Clinical Oncology (2021)

e16080 Background: Patients with advanced gastric or gastro-esophageal junction cancer have poor prognosis after progression on first-line chemotherapy. We investigated to combine second-line chemotherpy with third-line drugs, apatinib and anti-PD-1 antibody in these patients. Methods: This study is a single center, exploratory study in China. Eligible patients are adults with histologically confirmed advanced gastric or GEJ adenocancinoma, who were failure of first-line or second-line chemotherapy. Subjects receive chemotherapy, pacitaxol or iritecan (investigator choice), apatinib 250mg po qd, sintilimab 200mg ivd q3w. Response was assessed every 6 weeks. (RECIST version1.1) Primary endpoint was progression free survival (PFS). Results: Between May 30, 2019 and November 5, 2020, a total of 26 patients were enrolled in this study, and 4 (15.4%) patients were failure of second-line chemotherapy. There were 21 males and 5 females, and the median age was 61. The total number of treatment cycles was 140 and the median number was 5.5. Among 24 patients who were evaluated, partial response (PR) was obtained in 12 cases, stable disease (SD) in 8 cases and progressive disease (PD) in 4 cases. Objective response rate was 50.0%，and disease control rate was 83.3%. The median PFS was 7.06 months (95% CI 5.52-8.60), and the median overal survival has not yet been reached. The most common adverse events (AE) were leukopenia (61.5%), anemia (57.7%), neutropenia (53.8%), proteinuria (42.3%), alopecia (42.3%), hypothyroidism (38.5%), elevated alanine aminotransferase (34.6%), elevated aspartate aminotransferase (34.6%) and elevated alkaline phosphatase (34.6%), but most of them were grade 1 or 2, and the most common grade 3 or 4 treatment-related adverse events was neutropenia (11.5%). Conclusions: Chemotherapy, plus apatinib and sintilimab demonstrated promising activity and manageable safety profile as second- even third-line treatment in advanced gastric or GEJ cancer. Demographics and baseline characteristics.[Table: see text]
Breaching Confidentiality to Protect the Public: Evolving Standards of Medical Confidentiality for Military Detainees
Authors: Matthew K. Wynia∗
Journal: The American Journal of Bioethics (2007)

Confidentiality is a core value in medicine and public health yet, like other core values, it is not absolute. Medical ethics has typically allowed for breaches of confidentiality when there is a credible threat of significant harm to an identifiable third party. Medical ethics has been less explicit in spelling out criteria for allowing breaches of confidentiality to protect populations, instead tending to defer these decisions to the law. But recently, issues in military detention settings have raised the profile of decisions to breach medical confidentiality in efforts to protect the broader population. National and international ethics documents say little about the confidentiality of detainee medical records. But initial decisions to use detainee medical records to help craft coercive interrogations led to widespread condemnation, and might have contributed to detainee health problems, such as a large number of suicide attempts several of which have been successful. More recent military guidance seems to reflect lessons learned from these problems and does more to protect detainee records. For the public health system, this experience is a reminder of the importance of confidentiality in creating trustworthy, and effective, means to protect the public's health.
Predictors of early readmission to hospital and mortality in patients with malignant ascites: Analysis of the nationwide readmissions database.
Authors: Omid Yazdanpanah, Tanveer Mir, Sohaip Kabashneh, Ibrahim Azar, Misako Nagasaka, Mohammed Najeeb Al Hallak
Journal: Journal of Clinical Oncology (2021)

12057 Background: Malignant ascites accounts for 7 percent of ascites cases in the United States. It is a common manifestation of several solid tumors and is associated with poor prognosis with median survival of 3 months. Moreover, patients with malignant ascites are at risk of recurrent hospitalizations. Hospital readmissions are costly for health-care system and are regarded as a quality of care index. Nevertheless, predictive factors for hospital readmissions and mortality in patients with malignant ascites are limited. Understanding these factors can expedite development of strategies to reduce the readmission and health-care costs. Methods: Utilizing the Nationwide Readmissions Database (NRD), we conducted a retrospective cohort study on patients admitted with malignant ascites between 2016 and 2018 across the United States. We used multivariable logistic regression to determine the predictors of unplanned 30-days readmissions and mortality among patients with malignant ascites. Results: Out of 130,648 patients hospitalized with malignant ascites, 15,756 individuals (12.1%) were readmitted within next 30 days. Predictors of early readmission included pulmonary embolism (OR 2.40; 95% CI 1.55-3.74), complicated diabetes (OR 1.28; 95% CI 1.05-1.56) and having Medicaid insurance (OR 1.34; 95% CI 1.11-1.62). In-hospital mortality for patients with malignant ascites was 14.1%. The comorbidities associated with increased mortality were liver disease (OR 1.87; 95% CI 1.77-1.97), pulmonary embolism (OR 1.60; 95% CI 1.34-1.90), renal failure (OR 1.39; 95% CI 1.27-1.52), and congestive heart failure (OR 1.27; 95% CI 1.16-1.38). Patients with Medicaid insurance also had higher mortality (OR 1.21; 95% CI 1.12-1.32) among the payers. Conclusions: One in eight patients with malignant ascites was readmitted to the hospital within 30 days of discharge. By examining the risk factors leading to readmission, this study helped to identify the subpopulations of patients likely to become more ill. The strong association of pulmonary embolism with readmission and in hospital mortality suggests the benefit of prophylactic anticoagulation. Furthermore, higher readmission and mortality rate within Medicaid insurance population can open a new window in studying health care disparities.
Evaluation of the effectiveness of telephone consultations and the level of satisfaction of patients attending the Unidad Docente Asistencial de Mastología [Mastology Care Teaching Unit] using this method during the COVID health emergency.
Authors: Natalia Camejo, Cecilia Castillo, Nora Artagaveytia, Dahiana Amarillo, Florencia Vitureira, Florencia Rodriguez, Lucia Beatriz Delgado
Journal: Journal of Clinical Oncology (2021)

e13610 Background: In March 2020, a health emergency was decreed due to COVID-19 and this produced changes in the organization of health services. One of the objectives of the reorganization that took place was a reduction in face-to-face consultations (FTFC), and the promotion of telephone consultations (TC). Objective: Evaluate the effectiveness of TC and the level of satisfaction of patients attending the Mastology Unit using this method during the COVID health emergency. Methods: A prospective, cross-sectional study. A survey was used to assess the effectiveness of TC and the level of satisfaction with the method. Results: : Forty-two patients were surveyed, of which 69% were receiving adjuvant treatment and 14.2% palliative treatment. With regard to the effectiveness of TC, 76.1% of those surveyed had their appointment resolved by telephone; 78.6% of patients preferred to do the consultation by telephone; 97.6% believed that sufficient time was spent and that the timing of the appointment was appropriate. The responses showed a high degree of satisfaction with the care received. The medical care met the expectations of all patients, and 83.3% believed that once normalcy was restored, TC would be an option for their situation Conclusions: The TC method was evaluated with a high degree of satisfaction and allowed care to be maintained during the emergency. Although it is early to assess the healthcare impact of TC and the method's capacity to resolve issues, preliminary results show that it is a useful and valuable tool in clinical practice during periods of healthcare emergency.
Current Methodological Challenges of Single-Cell and Single-Nucleus RNA-Sequencing in Glomerular Diseases
Authors: Dries Deleersnijder, Jasper Callemeyn, Ingrid Arijs, Maarten Naesens, Amaryllis H. Van Craenenbroeck, Diether Lambrechts, Ben Sprangers
Journal: Journal of the American Society of Nephrology (2021)

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. This review provides an overview of the technical challenges that should be addressed when designing single-cell transcriptomics experiments that focus on glomerulopathies. The isolation of glomerular cells from core needle biopsy specimens for single-cell transcriptomics remains difficult and depends upon five major factors. First, core needle biopsies generate little tissue material, and several samples are required to identify glomerular cells. Second, both fresh and frozen tissue samples may yield glomerular cells, although every experimental pipeline has different (dis)advantages. Third, enrichment for glomerular cells in human tissue before single-cell analysis is challenging because no effective standardized pipelines are available. Fourth, the current warm cell-dissociation protocols may damage glomerular cells and induce transcriptional artifacts, which can be minimized by using cold dissociation techniques at the cost of less efficient cell dissociation. Finally, snRNA-seq methods may be superior to scRNA-seq in isolating glomerular cells; however, the efficacy of snRNA-seq on core needle biopsy specimens remains to be proven. The field of single-cell omics is rapidly evolving, and the integration of these techniques in multiomics assays will undoubtedly create new insights in the complex pathophysiology of glomerular diseases.
Integrin alpha6-Deletion Induces Apoptosis and Src Signaling Changes in Acute Lymphoblastic Leukemia Cells
Authors: Eun Ji Gang, Hye Na Kim, Johanna Scott, Matthew J Oberley, Etan Orgel, Steven D. Mittelman, Yao-Te Hsieh, Markus Muschen, Deepa Bhojwani, Daniel Braas, Thomas Graeber, Nora Heisterkamp, Yong-Mi Kim
Journal: Blood (2017)
OMIC-14. OPENPBTA: AN OPEN PEDIATRIC BRAIN TUMOR ATLAS
Authors: Joshua Shapiro, Candace Savonen, Chante Bethell, Krutika Gaonkar, Yuankun Zhu, Miguel Brown, Nhat Duong, Komal Rathi, Nighat Noureen, Bo Zhang, Brian Ennis, Stephanie Spielman, Bailey Farrow, Nicolas Van Kuren, Tejaswi Koganti, Shrivats Kannan, Pichai Raman, Daniel Miller, Payal Jain, Yiran Guo, Xiaoyan Huang, Adam Kraya, Allison Heath, Mateusz Koptyra, Jessica Wong, Jennifer Mason, Shannon Robbins, Mariarita Santi, Angela Viaene, Angela Waanders, Derek Hanson, Laura Scolaro, Hongbo Xie, Siyuan Zheng, Cassie Kline, Jena Lilly, Philip Storm, Adam Resnick, Jo Lynne Rokita, Casey Greene, Jaclyn Taroni
Journal: Neuro-Oncology (2021)

Abstract Pediatric brain tumors comprise a heterogeneous molecular and histological landscape that challenges most current precision-medicine approaches. While recent large-scale efforts to molecularly characterize distinct histological entities have dramatically advanced the field’s capacity to classify and further define molecular subtypes, developing therapeutic and less toxic molecularly-defined clinical approaches remains a challenge. To define new approaches to meet these challenges and advance scalable, shared biospecimen- and data-resources for pediatric brain tumors, the Children’s Brain Tumor Network and Pacific Pediatric Neuro-Oncology Consortium, in partnership with the Alex’s Lemonade Stand Foundation Childhood Cancer Data Lab, launched OpenPBTA, a global open science Pediatric Brain Tumor Atlas initiative to comprehensively define the molecular landscape of pediatric brain tumors. The initiative contains multi-modal analyses of research- and clinical-trial based DNA and RNA sequences from nearly 1,000 subjects (with 1,256 tumors) along with their longitudinal clinical data. The OpenPBTA’s open science framework for analysis tests the capacity of crowd-sourced collaborative architectures to advance more rapid, iterative and integrated discovery of the underlying mechanisms of disease across pediatric brain and spinal cord tumors. Since the launch of the project, OpenPBTA has collaboratively created reproducible workflows for integrated consensus SNV, CNV, and fusion calling, enabled RNA-Seq-based classification of medulloblastoma subtypes, and more than 25 additional DNA- and RNA-based analyses. The open-science platform and associated datasets and processed results provide a continuously updated, global view of the integrated cross-disease molecular landscape of pediatric brain tumors. Such biospecimen- and clinically-linked scalable data resources provide unprecedented collaborative opportunities for precision-based, personalized therapeutic discovery and drug development with the upcoming further integration of proteomic sample data (N &amp;gt;300) and drug response datasets, additionally diversifying the multimodal discovery potential of crowd-sourced approaches for accelerated impact for children with brain tumors.
Confounding by Socioeconomic Status in Epidemiological Studies of Air Pollution and Health: Challenges and Opportunities
Authors: Anjum Hajat, Richard F. MacLehose, Anna Rosofsky, Katherine D. Walker, Jane E. Clougherty
Journal: Environmental Health Perspectives (2021)

BACKGROUND: Despite a vast air pollution epidemiology literature to date and the recognition that lower-socioeconomic status (SES) populations are often disproportionately exposed to pollution, there is little research identifying optimal means of adjusting for confounding by SES in air pollution epidemiology, nor is there a strong understanding of biases that may result from improper adjustment.OBJECTIVE: We aim to provide a conceptualization of SES and a review of approaches to its measurement in the U.S. context and discuss pathways by which SES may influence health and confound effects of air pollution.We explore bias related to measurement and operationalization and identify statistical approaches to reduce bias and confounding.DISCUSSION: Drawing on the social epidemiology, health geography, and economic literatures, we describe how SES, a multifaceted construct operating through myriad pathways, may be conceptualized and operationalized in air pollution epidemiology studies.SES varies across individuals within the contexts of place, time, and culture.Although no single variable or index can fully capture SES, many studies rely on only a single measure.We recommend examining multiple facets of SES appropriate to the study design.Furthermore, investigators should carefully consider the multiple mechanisms by which SES might be operating to identify those SES indicators that may be most appropriate for a given context or study design and assess the impact of improper adjustment on air pollution effect estimates.Last, exploring model contraction and expansion methods may enrich adjustment, whereas statistical approaches, such as quantitative bias analysis, may be used to evaluate residual confounding.
Long-term oncologic outcomes of robotic gastrectomy for gastric cancer compared with laparoscopic gastrectomy.
Authors: Woo Jin Hyung, Kazutaka Obama, Yu Min Kim, Yanghee Woo, Kyung Ho Pak, Hyoung-Il Kim, Sung Hoon Noh
Journal: Journal of Clinical Oncology (2013)

8 Background: Although robotic gastrectomy (RG) showed satisfactory early postoperative outcomes, the oncologic safety of RG for gastric cancer remains a concern. We aimed to evaluate the oncologic safety of RG by comparing its long term outcomes with that of laparoscopic gastrectomy (LG). Methods: From July 2005 to December 2009, we performed 313 RGs and 524 LGs to the patients with gastric cancer. We retrospectively analyzed the patients’ characteristics, operative outcomes, overall survival (OS) and relapse-free survival (RFS), then compared between RG and LG groups using a prospectively maintained database. Results: With a median follow-up of 46 (1-80) months, there was no difference in the OS (log-rank p=0.625) nor in the RFS (p=0.761) between the two groups. When we compared the two groups stage by stage, the OS and RFS also did not differ significantly. Postoperative recurrence was observed in 17 patients (5.4%) in RG and 18 (3.4%) in LG, which showed no significant difference (p=0.745). The pattern of recurrence in RG showed 5 peritoneal, 5 loco-regional, 3 hematogenous,3 distant lymph node, and 1 mixed one. The recurence pattern of the two groups did not differ significantly. Conclusions: These data suggest that robotic assistance in gastrectomy for gastric cancer is acceptable because the oncologic outcome of RG was comparable to conventional LG in our experience.
Biomarker testing in non-small cell lung cancer (NSCLC): An assessment of current practices in precision oncology in the community setting—A trial of the ECOG-ACRIN cancer research group (EAQ161CD).
Authors: Julia Rachel Trosman, Jorean Sicks, Christine B. Weldon, Gregory J. Tsongalis, Bruce Rapkin, Kathryn E. Weaver, Gary Irvin Cohen, Thomas E. Lad, Emily Van Meter Dressler, Bill Stanfield, Judith O. Hopkins, Judy Hancock, Heather Kehn, Preston D. Steen, Lynne I. Wagner, Ruth Carlos
Journal: Journal of Clinical Oncology (2021)

e18649 Background: Molecular biomarker testing is integral to NSCLC cancer care, but adoption and testing practices in the community are varied and often suboptimal. Testing practices, such as standard testing protocols and results turnaround time (TAT), impact timely treatment decisions. We examined adoption and testing practices for guideline recommended NSCLC biomarkers among National Cancer Institute Community Research Program (NCORP) sites. The study was conducted in collaboration with Wake Forest NCORP Research Base. Methods: An online survey was administered to onsite labs affiliated with NCORP sites April 2019 – June 2020. We assessed testing practices for 7 NCCN recommended biomarkers, including 3 with category 1 recommendation (EGFR, ALK, PD-L1) and 4 with category 2 recommendations (BRAF, ROS1, MET, RET). Guideline concordant result TAT was defined as return of EGFR and ALK results in ≤ 10 days (Lindeman 2018) (see Table for other outcomes). We used proportions, including two-sided Fischer exact tests, to compare outcomes by site characteristics (safety net, practice size). Results: The survey response rate was 69% (58/85). All responding labs offered testing for category 1 biomarkers (EGFR, ALK and PD-L1); only 10% conducted these tests in-house (Table). The majority of labs also tested for category 2 biomarkers (67%). TAT varied, with most labs returning results in ≤ 10 days for EGFR and ALK (69%, but only a minority meet this TAT for all biomarkers. Larger practice size (&gt; 1400 new cancer cases a year) was associated with in-house testing of EGFR, ALK, PD-L1 (p=0.03) and having standard testing protocols (p&lt;0.001). Safety net affiliation did not significantly impact practices. Conclusions: We found universal adoption of NCCN category 1 biomarkers among the labs affiliated with NCORP sites, with the majority meeting guideline concordant results TAT. There is opportunity for improvement in adoption of category 2 biomarkers and result TAT, for example, by using standard testing protocols. Reassuringly, no difference in testing practices was detected by safety net affiliation.[Table: see text]