tbuckley/cabot-search huggingface dataset:
FRONTiER: A feasibility trial of nivolumab with neoadjuvant CF or DCF therapy for locally advanced esophageal carcinoma (JCOG1804E)—The short-term results of cohort A and B.
Authors: Shun Yamamoto, Ken Kato, Hiroyuki Daiko, Takashi Kojima, Hiroki Hara, Tetsuya Abe, Yasuhiro Tsubosa, Hirofumi Kawakubo, Takeo Fujita, Takashi Fukuda, Shigenori Kadowaki, Takahiro Tsushima, Yasuo Hamamoto, Kengo Nagashima, Kazunori Aoki, Yukihiro Mizoguchi, Shigehisa Kitano, Shinichi Yachida, Satoshi Shiba, Yuko Kitagawa
Journal: Journal of Clinical Oncology (2021)

202 Background: The standard neoadjuvant chemotherapy (NAC) in Japan for locally advanced esophageal squamous cell cancer (ESCC) is CDDP + 5-FU (CF). Immune checkpoint inhibitors (ICI) such as nivolumab provide a survival benefit in ESCC, and have potential as NAC agents in lung, skin, and breast cancers, amongst others. However, whether ICI are efficacious in combination with cytotoxic agents, and whether ICI impact the safety of subsequent surgery after they are used as NAC for ESCC patients (pts) is currently unclear. Methods: FRONTiER is a multi-cohort phase I study designed to evaluate the safety and efficacy of ICI combined with NAC in ESCC. Histologically proven ESCC pts with cT1N1-3M0 or cT2-3N0-3M0 (8th-UICC TNM classification), 20–75 years old, PS ≤ 1, no prior therapies against any cancer were eligible. The primary endpoint was the incidence of dose-limiting toxicities (DLT) from the initial dose to the 30th postoperative day. This study contained 4 experimental cohorts, the NAC regimen of cohort A consisted of 2 courses of CDDP at 80 mg/m 2 , nivolumab at 360 mg/body on day 1 and 5-FU at 800 mg/m 2 on days 1–5, q3wks. The regimen of cohort B consisted of one administration of nivolumab at 240 mg/body 2 weeks before chemotherapy, followed by the same treatments as cohort A. Results: Thirteen pts were enrolled to cohort A (n = 6) and B (n = 7). Characteristics were follows; median age: 62 (range: 34–75), PS 0/1: 9/4 pts, clinical stage I/II/III: 2/1/10 pts. One pt in cohort B was excluded from safety evaluation due to R2 resection, no DLTs were observed in 12 pts. The most frequent adverse events (≥ grade 3) were neutropenia in 6 pts during NAC, lung infection in 1, hyperglycemia in 1, pleural effusion in 1, infection (right neck) in 1, anemia in 1, abdominal pain in 1, and anatomic leakage in 1 during the postoperative period. Within 30 days post-operation, grade 2 adrenal insufficiency was observed in 1 pt of cohort B. No grade 4 adverse events or treatment-related deaths were seen. All pts received two courses of NAC + nivolumab and R0 resection was achieved in 12 pts (92.3%) without interruption of treatment. A pathological complete response was achieved in 2 pts (33.3%) in cohort A. Conclusions: Neoadjuvant CF + nivolumab with/without prior administration of nivolumab followed by surgery for locally advanced ESCC was well tolerated and showed promising efficacy. Clinical trial information: NCT03914443.
Impact of COVID-19 on in vivo work and patient sample availability for cancer research
Authors: Eoghan J. Mulholland
Journal: Nature reviews. Cancer (2021)

The COVID-19 pandemic has destabilized the traditional bench to bedside workflow of cancer research. Particularly, in vivo experimentation plus the collection and distribution of patient samples has been significantly affected. Strategies are needed now to revolutionize current cancer research practices in order to avoid history repeating itself in future pandemics. In light of the COVID-19 pandemic, this World View highlights the need to revolutionize current cancer research practices in terms of animal models and the collection and distribution of patient samples, in order to avoid history repeating itself in future pandemics.
Endoscopic ultrasound (EUS)-guided fine needle biopsy alone vs. EUS-guided fine needle aspiration with rapid onsite evaluation in pancreatic lesions: a multicenter randomized trial
Authors: Yen-I Chen, Avijit Chatterjee, Robert Berger, Yonca Kanber, Jonathan Wyse, Eric Lam, Ian Gan, Manon Auger, Sana Kenshil, Jennifer Telford, Fergal Donnellan, James Quinlan, Gregory Lutzak, Fatma Alshamsi, Josee Parent, Kevin Waschke, Adel Alghamdi, Jeffrey Barkun, Peter Metrakos, Prosanto Chaudhury, Myriam Martel, Alastair Dorreen, Kristen Candido, Corey Miller, Viviane Adam, Alan Barkun, George Zogopoulos, Clarence Wong
Journal: Endoscopy (2021)

Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is the standard in the diagnosis of solid pancreatic lesions, in particular when combined with rapid onsite evaluation of cytopathology (ROSE). More recently, a fork-tip needle for core biopsy (FNB) has been shown to be associated with excellent diagnostic yield. EUS-FNB alone has however not been compared with EUS-FNA + ROSE in a large clinical trial. Our aim was to compare EUS-FNB alone to EUS-FNA + ROSE in solid pancreatic lesions.A multicenter, non-inferiority, randomized controlled trial involving seven centers was performed. Solid pancreatic lesions referred for EUS were considered for inclusion. The primary end point was diagnostic accuracy. Secondary end points included sensitivity/specificity, mean number of needle passes, and cost.235 patients were randomized: 115 EUS-FNB alone and 120 EUS-FNA + ROSE. Overall, 217 patients had malignant histology. The diagnostic accuracy for malignancy of EUS-FNB alone was non-inferior to EUS-FNA + ROSE at 92.2 % (95 %CI 86.6 %-96.9 %) and 93.3 % (95 %CI 88.8 %-97.9 %), respectively (P = 0.72). Diagnostic sensitivity for malignancy was 92.5 % (95 %CI 85.7 %-96.7 %) for EUS-FNB alone vs. 96.5 % (93.0 %-98.6 %) for EUS-FNA + ROSE (P = 0.46), while specificity was 100 % in both. Adequate histological yield was obtained in 87.5 % of the EUS-FNB samples. The mean (SD) number of needle passes and procedure time favored EUS-FNB alone (2.3 [0.6] passes vs. 3.0 [1.1] passes [P < 0.001]; and 19.3 [8.0] vs. 22.7 [10.8] minutes [P = 0.008]). EUS-FNB alone cost on average 45 US dollars more than EUS-FNA + ROSE.EUS-FNB alone is non-inferior to EUS-FNA + ROSE and is associated with fewer needle passes, shorter procedure time, and excellent histological yield at comparable cost.
THU0075 Mycoplasma pneumoniae infection and rheumatoid arthritis
Authors: AS Ramirez-Corbera, JA Hernández-Beriain, A Rosas, E Girona
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> An infective aetiology for rheumatoid arthritis (RA) has often been postulated. Thirteen species of mycoplasmas has been implicated in the origin of arthritis in experimental models and animals. Fragments of mycoplasma (PCR) has been detected in RA although the results are conflictive. <h3>Objectives</h3> The main of our work is to evaluate previous mycoplasma pneumoniae (MP) infection in a cohort of RA outpatients and further evaluation of MP infection and RA outcome. <h3>Methods</h3> In 80 RA patients IgG antiMP was evaluated with ELISA. RA was evaluated according to disease duration, RF status and radiological stage. In control group were included 150 healthy people. Statistical analysis included Kruskal-Wallis test for IgG levels and determination of relative risk (odds ratio). <h3>Results</h3> Mean age of RA patients was 53.17 (22–81 years); 83% were females. MP serology was positive in 54% of RA patients and 31% of controls (p &lt; 0.05). Medium level of IgG was 1.431 in RA patients and 0.87 in controls (p &lt; 0.0001). Previous MP infection conditioned a relative risk (odds ratio) for RA of 3.22 (95 CI; 1.76–5.91). <h3>Conclusion</h3> Previous MP infection was more frequent in RA patients than controls. MP infection could play a role in RA genesis.
Risks of AKI and Major Adverse Clinical Outcomes in Patients with Severe Acute Respiratory Syndrome or Coronavirus Disease 2019
Authors: Jeremy Yuen-Chun Teoh, Terry Cheuk-Fung Yip, Grace Chung-Yan Lui, Vincent Wai-Sun Wong, Viola Chi-Ying Chow, Tracy Hang-Yee Ho, Timothy Chun-Man Li, Yee-Kit Tse, Peter Ka-Fung Chiu, Chi-Fai Ng, David Shu-Cheong Hui, Henry Lik-Yuen Chan, Cheuk-Chun Szeto, Grace Lai-Hung Wong
Journal: Journal of the American Society of Nephrology (2021)

Severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19) are closely related. The effect of AKI on the clinical outcomes of these two conditions is unclear.This retrospective, territory-wide cohort study used an electronic public healthcare database in Hong Kong to identify patients with SARS or COVID-19 by diagnosis codes, virologic results, or both. The primary endpoint was a composite of intensive care unit admission, use of invasive mechanical ventilation, and/or death.We identified 1670 patients with SARS and 1040 patients with COVID-19 (median ages, 41 versus 35 years, respectively). Among patients with SARS, 26% met the primary endpoint versus 5.3% of those with COVID-19. Diabetes mellitus, abnormal liver function, and AKI were factors significantly associated with the primary endpoint among patients with either SARS or COVID-19. Among patients with SARS, 7.9%, 2.1%, and 3.7% developed stage 1, stage 2, and stage 3 AKI, respectively; among those with COVID-19, 6.6%, 0.4%, and 1.1% developed stage 1, stage 2, and stage 3 AKI, respectively. In both groups, factors significantly associated with AKI included diabetes mellitus and hypertension. Among patients with AKI, those with COVID-19 had a lower rate of major adverse clinical outcomes versus patients with SARS. Renal function recovery usually occurred within 30 days after an initial AKI event.AKI rates were higher among patients with SARS than those with COVID-19. AKI was associated with major adverse clinical outcomes for both diseases. Patients with diabetes mellitus and abnormal liver function were also at risk of developing severe consequences after SARS and COVID-19 infection.
Beyond fine-tuning: Classifying high resolution mammograms using function-preserving transformations
Authors: Tao Wei, Angelica I. Aviles-Rivero, Shuo Wang, Yuan Huang, Fiona J. Gilbert, Carola-Bibiane Schönlieb, Chang Wen Chen
Journal: Medical Image Analysis (2022)

The task of classifying mammograms is very challenging because the lesion is usually small in the high resolution image. The current state-of-the-art approaches for medical image classification rely on using the de-facto method for convolutional neural networks-fine-tuning. However, there are fundamental differences between natural images and medical images, which based on existing evidence from the literature, limits the overall performance gain when designed with algorithmic approaches. In this paper, we propose to go beyond fine-tuning by introducing a novel framework called MorphHR, in which we highlight a new transfer learning scheme. The idea behind the proposed framework is to integrate function-preserving transformations, for any continuous non-linear activation neurons, to internally regularise the network for improving mammograms classification. The proposed solution offers two major advantages over the existing techniques. Firstly and unlike fine-tuning, the proposed approach allows for modifying not only the last few layers but also several of the first ones on a deep ConvNet. By doing this, we can design the network front to be suitable for learning domain specific features. Secondly, the proposed scheme is scalable to hardware. Therefore, one can fit high resolution images on standard GPU memory. We show that by using high resolution images, one prevents losing relevant information. We demonstrate, through numerical and visual experiments, that the proposed approach yields to a significant improvement in the classification performance over state-of-the-art techniques, and is indeed on a par with radiology experts. Moreover and for generalisation purposes, we show the effectiveness of the proposed learning scheme on another large dataset, the ChestX-ray14, surpassing current state-of-the-art techniques.
ST-Segment– Elevation Myocardial Infarction for Pharmacoinvasive Strategy or Primary Percutaneous Coronary Intervention in Gaza (STEPP- PCI)
Authors: Mohammed Hasirah, Mohammed Habib
Journal: Clinical Cardiology and Cardiovascular Interventions (2019)

Background A primary percutaneous coronary intervention (PCI) Primary PCI continues to be the optimal reperfusion therapy in patients with ST elevation myocardial infarction however, in areas where PCI centers are not readily available, a pharmacoinvasive strategy has been proposed. This study investigated the safety and efficacy of a pharmacoinvasive strategy compared with primary (PCI) strategy for ST-segment elevation myocardial infarction (STEMI) in Gaza. Methods: We randomized 145 patients presenting within 2 hours of symptom onset of acute ST elevation myocardial infarction to primary CPI (PCI) or for pharmaco-invasive PCI 2-24 hours after streptokinase, except in the event of failed reperfusion, in which case, emergency angiography was recommended. The primary endpoint a composite of death, shock and congestive heart failure at 30 days. Results: Total 145 patients with mean age 56.5+10.48 years. (The mean age of patients is) The primary endpoint in primary PCI (17%) and in pharmaco-invasive PCI (16.1%) p = 0.24.???? There was no difference in 30-day mortality (4.7 % in primary PCI and 4.9% in pharmacoinvasive strategy (P=0.94). Secondary endpoints:Emergency angiography was required in 39.5% of the patients in the pharmaco-invasive strategy and the median time for underwent angiography was 6 hours after randomization. TIMI major bleeding occurred among 4 patients ( 4.9 % ) in the pharmacoinvasive group and in 2 patients (3.1%) of the primary PCI group (P = 0.59).The pharmacoinvasive group had 1.9 times the odds of having TIMI major bleed compared with the primary PCI group Conclusions In this randomized trial, early-presenting STEMI patients unable to undergo primary PCI within 1 hour (median, 75±20 minutes) were randomized to primary PCI or a pharmaco-invasive strategy with streptokinase followed by PCI. At 1 month follow-up, there was no statistical difference in all-cause mortality, heart failure or shock. This study suggests that, if primary PCI cannot be performed within 1 hour of presentation, a pharmaco-invasive strategy may be as good as primary PCI.
Association between hospital‐diagnosed atopic dermatitis and psychiatric disorders and medication use in childhood*
Authors: I. Vittrup, Y. M. F. Andersen, C. Droitcourt, L. Skov, A. Egeberg, M. C. Fenton, P. Mina‐Osorio, S. Boklage, J. P. Thyssen
Journal: British Journal of Dermatology (2021)

While adult atopic dermatitis (AD) is associated with anxiety and depression, and paediatric AD is linked to attention deficit hyperactivity disorder (ADHD), the relationship between AD in childhood and other psychiatric disorders is largely unknown.To determine the relationship between AD and diagnosis and treatment of psychiatric disorders in children.All Danish children born between 1 January 1995 and 31 December 2012 with a hospital diagnosis of AD (n = 14 283) were matched 1 : 10 with children without a hospital diagnosis of AD. Endpoints were psychotropic medication use, hospital diagnoses of depression, anxiety, ADHD, or self-harming behaviour, accidental/suicidal death, and consultation with a psychiatrist or psychologist.Significant associations were observed between hospital-diagnosed AD and antidepressant [adjusted hazard ratio (aHR) 1·19, 95% confidence interval (CI) 1·04-1·36], anxiolytic (aHR 1·72, 95% CI 1·57-1·90), and centrally acting sympathomimetic (aHR 1·29, 95% CI 1·18-1·42) medication use. Consultation with a psychiatrist (aHR 1·33, 95% CI 1·16-1·52) or psychologist (aHR 1·25, 95% CI 1·11-1·41) was also associated with AD. No association with a hospital diagnosis of depression (aHR 0·58, 95% CI 0·21-1·56), anxiety (aHR 1·47, 95% CI 0·98-2·22) or self-harming behaviour (aHR 0·88, 95% CI 0·27-2·88) was observed, but a diagnosis of ADHD (aHR 1·91, 95% CI 1·56-2·32) was significantly associated with AD. The absolute risks were generally low.The increased risk of treatment, but not of a hospital diagnosis of psychiatric disorders in children with hospital-diagnosed AD, suggests that psychiatric issues in children with AD could be of a transient, reversible or mild-moderate nature.
Comparison of clinical characteristics and survival outcomes in patients with malignant peritoneal and pleural mesothelioma.
Authors: Vatsala Katiyar, Rohit Kumar, Ishaan Vohra, Adam Rojan
Journal: Journal of Clinical Oncology (2021)

460 Background: Malignant peritoneal mesothelioma (MPeM) is an aggressive tumor strongly associated with asbestos exposure. We analyzed a large nationwide database to better understand the differences in the demographic and clinical patterns of MPeM and pleural mesothelioma (MPlM). Methods: The National Cancer Database (NCDB) 2010-15 was queried to identify all patients diagnosed with MpeM and MPlM. The demographic and clinical characteristics were compared using Pearson’s chi-square test. Kaplan-Meier method and associated log-rank test were used to compare the unadjusted overall survival of the two malignant mesothelioma (MM) sites. A multivariate Cox regression analysis was done to determine survival difference between the 2 groups. Results: Of the 8,668 patients included in the study, 1,081 (12.5%) had MPeM and 7,587 (87.5%) had MPlM. The MPeM cohort was younger (median age at diagnosis 61 vs 73 years), predominantly females (45.7% vs 23.5%), had a lower Charlson Deyo Comorbidity Score ( &gt; = 1: 24.5% vs 32.1%), had higher percentage of uninsured patients (4% vs 2.2%), was less likely to be treated at a community or comprehensive community center (36.1% vs 47.3%) and had lower proportion of sarcomatous or biphasic histology (9.3% vs 22.4%) compared to MPlM cohort. The MPeM cohort was more likely to receive surgery (56.5% vs 28%) and chemotherapy (68.4% vs 54.5%) but less likely to receive radiation (0.8% vs 11%). The p-value was &lt; 0.001 for all comparisons. The median OS was 19.7 and 9.7 months for patients with MPeM and MPlM, respectively (log-rank p value &lt; 0.001). On multivariate Cox proportional hazards analysis, OS was significantly worse for MPlP compared to MPeP [HR adj: 1.19, 95% confidence interval (CI): 1.09-1.30 (p &lt; 0.001)]. Conclusions: There is paucity of data about clinical characteristics and outcomes of MPeM. Much of our current knowledge about MPeM is extrapolated from MPlM. Our study suggests significant differences in prognostic factors and survival outcomes between the two sites.
Development of Electronic Health Record–Based Prediction Models for 30-Day Readmission Risk Among Patients Hospitalized for Acute Myocardial Infarction
Authors: Michael E. Matheny, Iben Ricket, Christine A. Goodrich, Rashmee U. Shah, Meagan E. Stabler, Amy M. Perkins, Chad Dorn, Jason Denton, Bruce E. Bray, Ram Gouripeddi, John Higgins, Wendy W. Chapman, Todd A. MacKenzie, Jeremiah R. Brown
Journal: JAMA Network Open (2021)

<h3>Importance</h3> In the US, more than 600 000 adults will experience an acute myocardial infarction (AMI) each year, and up to 20% of the patients will be rehospitalized within 30 days. This study highlights the need for consideration of calibration in these risk models. <h3>Objective</h3> To compare multiple machine learning risk prediction models using an electronic health record (EHR)–derived data set standardized to a common data model. <h3>Design, Setting, and Participants</h3> This was a retrospective cohort study that developed risk prediction models for 30-day readmission among all inpatients discharged from Vanderbilt University Medical Center between January 1, 2007, and December 31, 2016, with a primary diagnosis of AMI who were not transferred from another facility. The model was externally validated at Dartmouth-Hitchcock Medical Center from April 2, 2011, to December 31, 2016. Data analysis occurred between January 4, 2019, and November 15, 2020. <h3>Exposures</h3> Acute myocardial infarction that required hospital admission. <h3>Main Outcomes and Measures</h3> The main outcome was thirty-day hospital readmission. A total of 141 candidate variables were considered from administrative codes, medication orders, and laboratory tests. Multiple risk prediction models were developed using parametric models (elastic net, least absolute shrinkage and selection operator, and ridge regression) and nonparametric models (random forest and gradient boosting). The models were assessed using holdout data with area under the receiver operating characteristic curve (AUROC), percentage of calibration, and calibration curve belts. <h3>Results</h3> The final Vanderbilt University Medical Center cohort included 6163 unique patients, among whom the mean (SD) age was 67 (13) years, 4137 were male (67.1%), 1019 (16.5%) were Black or other race, and 933 (15.1%) were rehospitalized within 30 days. The final Dartmouth-Hitchcock Medical Center cohort included 4024 unique patients, with mean (SD) age of 68 (12) years; 2584 (64.2%) were male, 412 (10.2%) were rehospitalized within 30 days, and most of the cohort were non-Hispanic and White. The final test set AUROC performance was between 0.686 to 0.695 for the parametric models and 0.686 to 0.704 for the nonparametric models. In the validation cohort, AUROC performance was between 0.558 to 0.655 for parametric models and 0.606 to 0.608 for nonparametric models. <h3>Conclusions and Relevance</h3> In this study, 5 machine learning models were developed and externally validated to predict 30-day readmission AMI hospitalization. These models can be deployed within an EHR using routinely collected data.
Persistent cellular immunity to SARS-CoV-2 infection
Authors: Gaëlle Breton, Pilar Mendoza, Thomas Hägglöf, Thiago Y. Oliveira, Dennis Schaefer-Babajew, Christian Gaebler, Martina Turroja, Arlene Hurley, Marina Caskey, Michel C. Nussenzweig
Journal: The Journal of Experimental Medicine (2021)

SARS-CoV-2 is responsible for an ongoing pandemic that has affected millions of individuals around the globe. To gain further understanding of the immune response in recovered individuals, we measured T cell responses in paired samples obtained an average of 1.3 and 6.1 mo after infection from 41 individuals. The data indicate that recovered individuals show persistent polyfunctional SARS-CoV-2 antigen–specific memory that could contribute to rapid recall responses. Recovered individuals also show enduring alterations in relative overall numbers of CD4+ and CD8+ memory T cells, including expression of activation/exhaustion markers, and cell division.