tbuckley/cabot-search huggingface dataset:
Abstract PS9-35: Volumetric assessment of lymphedema with 3D sensor
Authors: Alejandro Maciel-Miranda, Miriam I Otero-Hernández, Darinka Martínez-Silva, Jesus F Escrivá-Machado
Journal: Cancer Research (2021)

Abstract Volumetric assessment of lymphedema with 3D sensor: A new practical method Secondary lymphedema of the upper extremities is an important quality-of-life issue for around 40% of patients who were treated for breast cancer and required axillary nodal dissection and radiotherapy. Volume measurement is an important aspect of diagnosis, follow up, and evaluation after conservative or surgical treatment for lymphedema. Until now, there have been complex techniques to assess volume of affected limbs: bioimpedance, liquid-displacement volumetry, CT, MRI. There is a need for a practical method of volumen assessment in lymphedema patients. The objective of the present study is to confirm whether or not 3D scanning for volumetric assessment is useful and correlates with direct perimeter measurement and indirect volume calculation. Methods: A 3D sensor (Structure Sensor, Occipital Inc) mounted on an Ipad (Apple, Inc.) was used to make a 3D model file of the affected limb, that was later analyzed by 3DsizeME software (TechMed 3D, Inc.) in a desktop computer. 3D model analysis allows to measure perimeters and volumes. Fifteen patients were measured, lymphedema and normal limbs (30 extremities) by this technique and were also measured with tape, as traditional method; results were compared to assess correlation. Results: There were not statistical difference between the two techniques (p 0.05). Table attached. Discussion: volumetric assessment by 3D sensor allows consistent and reproducible measurements. It is practical as we only need the space of an ipad, it can be performed in the clinic visit, by any doctor, nurse or physical therapist. It is not expensive, as the software charges US$10 by each analysis. It do not expose the patient to any harmful radiation, as is obtained by and infrared camera. Allows electronic records of all measurements. Average time to capture 3D model is 5 minutes. We think this new method is a valuable tool for any lymphedema clinic as volume measurement is important for disease evaluation and now, more important, with a growing field of surgical treatment for this disease. Citation Format: Alejandro Maciel-Miranda, Miriam I Otero-Hernández, Darinka Martínez-Silva, Jesus F Escrivá-Machado. Volumetric assessment of lymphedema with 3D sensor [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS9-35.
Abstract PS1-51: A nomogram for predicting three or more axillary lymph node involvement before breast cancer surgery
Authors: Young-Joon Kang
Journal: Cancer Research (2021)

Abstract Introduction Focus has moved to de-escalate of axillary surgery in the management of early breast cancer. Based on the American College of Surgeons Oncology Group-Z0011, our team created the nomogram to be useful for identifying patients who do not require intraoperative analysis of the sentinel lymph node. The nomogram could identify as patients likely to three or more positive axillary lymph nodes by preoperative imaging. But the nomogram had several limitations. This study investigated a developed nomogram by excluding the chest computed tomography (CT) and adding 18F-Fluorodeoxyglucose (FDG) positron emission tomography (PET)/CT as a modality. Material and Methods Patients underwent preoperative ultrasonography (US) and PET/CT. The training set consisted of 1030 patients with clinical T1-2 and node-negative invasive breast cancer. Factors associated with ≥ 3 involved axillary lymph nodes (ALNs) were evaluated by logistic regression analysis. The validation set consisted of 781 independent patients. The nomogram was applied to 1,067 patients who met the selection criteria of the ACOSOG-Z0011. Results Of the 1,030 patients, 89 (8.6%) had ≥ 3 positive nodes. Multivariate analysis according to be used for making a new nomogram to predict the probability of involvement ≥ 3 nodes, there was significantly associated with larger tumor size, higher grade ultrasonographic ALN classification, and findings suspicious of positive ALN on PET/CT. The areas under the receiver operating characteristic curve of the nomogram were 0.856 (95% confidence interval [CI], 0.815 to 0.897) for the training set and 0.866 (95% CI, 0.799 to 0.934) for the validation set. Application of the nomogram to the patients who met the ACOSOG-Z0011 showed that 90/1067 (8.4%) had scores above the cut-off and the false-negative rate was 37/977 (3.8%). And the specificity was 93.8%, and the negative predictive value was 96.4%. Conclusion The upgraded nomogram improved predictive accuracy, and that was possible using only US and PET/CT. It reduced operation time and cost, with a very low re-operation rate. This nomogram is useful for identifying patients who do not require intraoperative analysis of sentinel lymph nodes. Citation Format: Young-Joon Kang. A nomogram for predicting three or more axillary lymph node involvement before breast cancer surgery [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS1-51.
Re: Internal Jugular Vein and Cerebral Venous Sinus Infective Thrombophlebitis Detected With 99mTc-HMPAO White Blood Cell Scintigraphy
Authors: Luca Valerio, William Pleming, Stefano Barco
Journal: Clinical Nuclear Medicine (2021)

Valerio, Luca MD; Pleming, William MBBS, FRCR; Barco, Stefano MD, PhD Author Information
Demographic and Clinical Characteristics Associated with Minimally Invasive Glaucoma Surgery Use
Authors: Mildred M.G. Olivier, Oluwatosin U. Smith, Clarisse C. Croteau-Chonka, Brian L. VanderBeek, Maureen G. Maguire, Flora Lum, Danielle Fujino, Scott P. Kelly, William L. Rich, Eydie G. Miller-Ellis
Journal: Ophthalmology (2021)
Utility of a Deep-Learning Algorithm to Guide Novices to Acquire Echocardiograms for Limited Diagnostic Use
Authors: Akhil Narang, Richard Bae, Ha Hong, Yngvil Thomas, Samuel Surette, Charles Cadieu, Ali Chaudhry, Randolph P. Martin, Patrick M. McCarthy, David S. Rubenson, Steven Goldstein, Stephen H. Little, Roberto M. Lang, Neil J. Weissman, James D. Thomas
Journal: JAMA Cardiology (2021)

Artificial intelligence (AI) has been applied to analysis of medical imaging in recent years, but AI to guide the acquisition of ultrasonography images is a novel area of investigation. A novel deep-learning (DL) algorithm, trained on more than 5 million examples of the outcome of ultrasonographic probe movement on image quality, can provide real-time prescriptive guidance for novice operators to obtain limited diagnostic transthoracic echocardiographic images.
A Bibliometric Analysis of <i>Advanced Healthcare Materials</i>: Research Trends of Biomaterials in Healthcare Application
Authors: Shuang Zhu, Yaping Liu, Zhanjun Gu, Yuliang Zhao
Journal: Advanced Healthcare Materials (2021)

In the field of biomaterials for healthcare applications, Advanced Healthcare Materials (AHM) has become one of the leading journals. Since 2011, AHM keeps bringing the latest research results in biomaterial science aimed at promoting human health. Nowadays, bibliometrics, of which methodological approaches can quantitively and qualitatively analyze the research performance of journals or subject fields, has attracted considerable attention among the scientific community. A general bibliometric overview of the research performance of AHM is presented. With the aid of Web of Science Core Collection database and VOSviewer software, the annual publication, the most prolific and influential authors/countries from AHM is identified. In addition, the most cited documents and keyword cooccurrence network analysis allow to recognize the major research topics in AHM. At last, the summary of current research trends based on AHM bibliometric analysis, several considerations for the clinical translation of biomaterials, and prospects to advance the field are also proposed. This editorial presents major research trends in the field of engineered materials for healthcare applications.
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data
Authors: Andre E. Minoche, Ben Lundie, Greg B. Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schonrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger, Mark J. Cowley
Journal: Genome Medicine (2021)

Abstract Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV , a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs &gt; 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5–4.5%) and reproducibility high (95–99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35–63% were not detectable by current clinical microarray designs. ClinSV is available at https://github.com/KCCG/ClinSV .
iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
Authors: Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu, Zemin Zhang
Journal: Genome biology (2021)

Abstract The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and interactions in complex biological systems. We present a novel unsupervised batch effect removal framework, called iMAP, based on both deep autoencoders and generative adversarial networks. Compared with current methods, iMAP shows superior, robust, and scalable performance in terms of both reliably detecting the batch-specific cells and effectively mixing distributions of the batch-shared cell types. Applying iMAP to tumor microenvironment datasets from two platforms, Smart-seq2 and 10x Genomics, we find that iMAP can leverage the powers of both platforms to discover novel cell-cell interactions.
Flexible working and teamwork are needed to protect doctors’ wellbeing, say leaders
Authors: Elisabeth Mahase
Journal: BMJ (2021)

Organisational interventions such as flexible working arrangements are urgently needed to improve the wellbeing of doctors and healthcare workers, the Royal College of Physicians (RCP) has said.1

Writing in the Lancet , RCP president Andrew Goddard and global vice president Mumtaz Patel said that the covid-19 pandemic has further exacerbated existing “tensions between medical professionalism …
Abstract PS10-14: Efficacy and safety of palbociclib (PAL) in patients (pts) with estrogen receptor-positive (ER+)/human epidermal growth factor receptor 2-negative (HER2-) advanced breast cancer (ABC) with preexisting conditions: A post hoc analysis of PALOMA-2
Authors: Karen Gelmon, Janice M Walshe, Reshma Mahtani, Anil A Joy, Meghan Karuturi, Patrick Neven, Dongrui Ray Lu, Sindy Kim, Patrick Schnell, Eustratios Bananis, Lee Schwartzberg
Journal: Cancer Research (2021)

Abstract Background: In the PALOMA-2 trial, PAL + letrozole (LET) significantly prolonged progression-free survival (PFS) vs placebo (PBO) + LET in pts with ER+/HER2– ABC. This post hoc analysis assessed efficacy and safety of PAL + LET in pts from PALOMA-2 with baseline preexisting conditions grouped by Medical Dictionary for Regulatory Activities (MedDRA) System Organ Class (SOC). Methods: Postmenopausal pts with ER+/HER2– ABC received PAL (125 mg/d, 3/1 schedule) + LET (2.5 mg/d, continuous) or PBO + LET. Pts were grouped by the following MedDRA SOC preexisting conditions: Gastrointestinal, Musculoskeletal, Metabolism, and Vascular/Cardiac. Baseline characteristics, PFS, and safety were assessed. Results: At baseline, 41.4% of pts had preexisting gastrointestinal disorders, 58.6% musculoskeletal disorders, 38.9% metabolism disorders, and 57.4% vascular/cardiac disorders. Baseline characteristics were similar between treatment arms within each subgroup and also between subgroups. Within each subgroup, ≥40% of pts also had ≥1 of the other coexisting conditions. Median PFS (mPFS) was significantly longer with PAL + LET vs PBO + LET regardless of preexisting condition (Table). In general, adverse events (AEs) were more frequent with PAL + LET in all subgroups; neutropenia was most common. Within each treatment arm, AEs and dose modifications due to AEs were similar regardless of preexisting condition. Conclusion: PAL + LET showed prolonged PFS and a consistent safety profile regardless of baseline preexisting condition in pts with ER+/HER2– ABC. Clinical trial identification: Pfizer Inc (NCT01740427) TablePreexisting ConditionPAL + LETPBO + LETPAL + LET vs PBO + LETnmPFS (95% CI)nmPFS (95% CI)HR (95% CI)P ValueGastrointestinal17627.6 (17.5–33.1)10013.6 (11.0–18.5)0.57 (0.42–0.78)&amp;lt;0.001Musculoskeletal25227.6 (21.4–33.1)13816.3 (11.2–19.1)0.53 (0.41–0.69)&amp;lt;0.001Metabolism18627.6 (19.3–30.6)7313.8 (8.3–27.4)0.62 (0.44–0.87)0.003Vascular/Cardiac25430.4 (25.1–36.2)12814.5 (11.0–18.5)0.51 (0.39–0.66)&amp;lt;0.001 Citation Format: Karen Gelmon, Janice M Walshe, Reshma Mahtani, Anil A Joy, Meghan Karuturi, Patrick Neven, Dongrui Ray Lu, Sindy Kim, Patrick Schnell, Eustratios Bananis, Lee Schwartzberg. Efficacy and safety of palbociclib (PAL) in patients (pts) with estrogen receptor-positive (ER+)/human epidermal growth factor receptor 2-negative (HER2-) advanced breast cancer (ABC) with preexisting conditions: A post hoc analysis of PALOMA-2 [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS10-14.
Integrative transcriptome analysis of malignant pleural mesothelioma reveals a clinically relevant immune-based classification
Authors: Ania Alay, David Cordero, Sara Hijazo-Pechero, Elisabet Aliagas, Adriana Lopez-Doriga, Raúl Marín, Ramón Palmero, Roger Llatjós, Ignacio Escobar, Ricard Ramos, Susana Padrones, Víctor Moreno, Ernest Nadal, Xavier Solé
Journal: Journal for ImmunoTherapy of Cancer (2021)

Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasia affecting the lung mesothelium. Immune checkpoint inhibitors (ICI) in MPM have not been extremely successful, likely due to poor identification of suitable candidate patients for the therapy. We aimed to identify cellular immune fractions associated with clinical outcome and classify patients with MPM based on their immune contexture. For each defined group, we sought for molecular specificities that could help further define our MPM classification at the genomic and transcriptomic level, as well as identify differential therapeutic strategies based on transcriptional signatures predictive of drug response. The abundance of 20 immune cell fractions in 516 MPM samples from 7 gene expression datasets was inferred using gene set variation analysis. Identification of clinically relevant fractions was performed with Cox proportional-hazards models adjusted for age, stage, sex, and tumor histology. Immune-based groups were defined based on the identified fractions. T-helper 2 (TH2) and cytotoxic T (TC) cells were found to be consistently associated with overall survival. Three immune clusters (IG) were subsequently defined based on TH2 and TC immune infiltration levels: IG1 (54.5%) was characterized by high TH2 and low TC levels, IG2 (37%) had either low or high levels of both fractions, and IG3 (8.5%) was defined by low TH2 and high TC levels. IG1 and IG3 groups were associated with worse and better overall survival, respectively. While no differential genomic alterations were identified among immune groups, at the transcriptional level, IG1 samples showed upregulation of proliferation signatures, while IG3 samples presented upregulation of immune and inflammation-related pathways. Finally, the integration of gene expression with functional signatures of drug response showed that IG3 patients might be more likely to respond to ICI. This study identifies a novel immune-based signature with potential clinical relevance based on TH2 and TC levels, unveiling a fraction of patients with MPM with better prognosis and who might benefit from immune-based therapies. Molecular specificities of the different groups might be used to tailor specific potential therapies in the future.
SARS-CoV-2 Variants of Concern in the United States—Challenges and Opportunities
Authors: Rochelle P. Walensky, Henry T. Walke, Anthony S. Fauci
Journal: JAMA (2021)

Wenjuan Zhang, PhD; Brian D. Davis, BSc; Stephanie S. Chen, BSc; Jorge M. Sincuir Martinez, BS; Jasmine T. Plummer, PhD; Eric Vail, MD
Abstract PS6-51: Identification of a low-risk luminal breast cancer cohort that may not benefit from multi-gene testing
Authors: Lei Lei, Han-Ching Chan, Tzu-Pin Lu, Xian-Yuan Miao, Zi-Yan Yang, Jia-Huan Huang, Xiao-Jia Wang, Hung-Chun Skye Cheng
Journal: Cancer Research (2021)

Abstract Purpose: Dutch clinical risk criteria (low-risk definition: age &amp;gt; 35 years and (grade 1 with tumor ≤3cm, grade 2 with tumor ≤2cm, or grade 3 with tumor ≤1cm) have been used to stratify the benefit of MammaPrint and Oncotype DX for the decision-making regarding adjuvant chemotherapy for early-stage luminal breast cancer. We propose that the criteria could help to identify low-risk patients who could barely benefit from multi-gene testing. Materials and methods: Breast cancer patients from Taiwan Cancer Database initially treated with primary surgeries between 2008 and 2012 who met the following criteria: (1) pathologic node-negative, (2) hormone receptor-positive, (3) HER2-negative, (4) undergone hormonal therapy, and (5) a minimum follow-up time of 5-year if free from any event, were enrolled in this study. Out of the total 2679 eligible patients, 1074 (40.1%) patients received adjuvant chemotherapy in addition to endocrine therapy. The study endpoints included breast cancer-specific survival (BCSS) and overall survival (OS). Kaplan-Meier statistics estimated the difference between clinical outcomes in low- and high-risk groups. Results: The median follow-up time of BSCC and OS was 5.9 years (range, 0-7 years) and 5.8 years (range, 0-7 years), respectively. There were statistical significances of 5-year BCSS (n=2679) and 5-year OS (n=2636) between low-risk and high-risk groups (in both endpoints, P &amp;lt; 0.0001). According to the Dutch criteria, low-risk patients with and without adjuvant chemotherapy had a 5-year BCSS of 99.0% vs. 99.2% and a 5-year OS of 98.4% vs. 97.4%, respectively. High-risk patients with and without adjuvant chemotherapy had a 5-year BCSS of 97.7% vs. 98.1% and a 5-year OS of 96.4% vs. 95.3%, respectively. Conclusion: The benefit of chemotherapy in low-risk patients classified by Dutch criteria might be very small since the breast cancer mortality was less than 1% with a minimum of 5-year follow-up. Dutch criteria cannot identify high-risk patients who would benefit from chemotherapy. We assumed that multi-gene testing in low-risk patients would not be cost-effective. Citation Format: Lei Lei, Han-Ching Chan, Tzu-Pin Lu, Xian-Yuan Miao, Zi-Yan Yang, Jia-Huan Huang, Xiao-Jia Wang, Hung-Chun Skye Cheng. Identification of a low-risk luminal breast cancer cohort that may not benefit from multi-gene testing [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS6-51.
Vitamin D<sub>3</sub> to Treat COVID-19
Authors: David E. Leaf, Adit A. Ginde
Journal: JAMA (2021)

Igor H. Murai, PhD; Alan L. Fernandes, PhD; Lucas P. Sales, MSc; Ana J. Pinto, BSc; Karla F. Goessler, PhD; Camila S. C. Duran, MD; Carla B. R. Silva, MD; André S. Franco, MD; Marina B. Macedo, MD, MSc; Henrique H. H. Dalmolin, MD; Janaina Baggio, MD; Guilherme G. M. Balbi, MD; Bruna Z. Reis, PhD; Leila Antonangelo, MD, PhD; Valeria F. Caparbo, PhD; Bruno Gualano, PhD; Rosa M. R. Pereira, MD, PhD
ERBB2 in anti-EGFR-resistant colorectal cancer: cancer stem cells come into play
Authors: Sophie Mouillet-Richard
Journal: Gut (2021)

With over 900 000 deaths per year worldwide in 2020 according to Globocan, colorectal cancer (CRC) represents the third deadliest cancer. Over the past 20 years, the median overall survival for CRC has substantially increased, especially in patients with metastatic disease, which has doubled to reach 30 months, as a result of the advent of targeted therapies. Despite this progress, the 5-year survival rate for patients with metastatic CRC remains below 15%, calling for an improved management of these patients, which account for roughly 20%–30% of new diagnosed cases.

A consensus view is that CRC arises from uncontrolled expansion of intestinal stem cells (ISCs).1 By analogy with ISCs, CRC stem cells (CSCs) are endowed with self-renewal potential and display significant plasticity. They are believed to fuel CRC growth as well as metastasis, and display resistance to therapy, making their targeting one of the most critical challenges in the field of oncology.1 The study by Mangiapane et al 2 tackles this issue by leveraging a collection of colorectal CSCs growing as spheroids and expressing the CSC marker CD44v6, which they previously showed to define a population of CSCs with enhanced metastatic potential.3 Among those, some bear RAS or BRAF mutations and were thoroughly resistant to the anti-epidermal growth factor receptor (EGFR) antibody cetuximab, as anticipated. Unexpectedly, a significant proportion of RAS and BRAF wild-type CSCs also displayed resistance to …
Response assessment during chemoradiation using a hypercellular/hyperperfused imaging phenotype predicts survival in patients with newly diagnosed glioblastoma
Authors: Michelle M Kim, Madhava P Aryal, Yilun Sun, Hemant A Parmar, Pin Li, Matthew Schipper, Daniel R Wahl, Theodore S Lawrence, Yue Cao
Journal: Neuro-Oncology (2021)

Abstract Background Adversely prognostic hypercellular and hyperperfused regions of glioblastoma (GBM) predict progression-free survival, and are a novel target for dose-intensified chemoradiation (chemoRT) recently implemented in a phase II clinical trial. As a secondary aim, we hypothesized that dose-intensified chemoRT would induce greater mid-treatment response of hypercellular/hyperperfused tumor regions vs standard chemoradiation, and that early response would improve overall survival (OS). Methods Forty-nine patients with newly diagnosed GBM underwent prospective, multiparametric high b value diffusion-weighted MRI (DW-MRI) and perfusion dynamic contrast-enhanced MRI (DCE-MRI) pre-RT and 3-4 weeks into RT. The hypercellular tumor volume (TVHCV, mean contralateral normal brain + 2SD) and hyperperfused tumor volume (TVCBV, contralateral normal frontal gray matter + 1SD) were generated using automated thresholding. Twenty-six patients were enrolled on a dose-escalation trial targeting TVHCV/TVCBV with 75 Gy in 30 fractions, and 23 non-trial patients comprised the control group. OS was estimated using the Kaplan-Meier method and compared using the log-rank test. The effect of TVHCV/TVCBV and Gd-enhanced tumor volume on OS was assessed using multivariable Cox proportional-hazard regression. Results Most patients had gross total (47%) or subtotal resection (37%), 25% were MGMT-methylated. Patients treated on the dose-escalation trial had significantly greater reduction in TVHCV/TVCBV (41% reduction, IQR 17%-75%) vs non-trial patients (6% reduction, IQR 6%-22%, P = .002). An increase in TVHCV/TVCBV during chemoRT was associated with worse OS (adjusted hazard ratio [aHR] 1.2, 95%CI 1.0-1.4, P = .02), while pre-treatment tumor volumes (P &amp;gt; .5) and changes in Gd-enhanced volume (P = .9) were not. Conclusions Multiparametric MRI permits identification of therapeutic resistance during chemoRT and supports adaptive strategies in future trials.