tbuckley/cabot-search huggingface dataset:
AI-based Quantification of Lung Emphysema and its Correlation with Lung Function Test Results (Literature Review)
Authors: N. A. Griva, P. V. Gavrilov, E. G. Sokolovich
Journal: Radiology - Practice (2021)

Quantification of emphysema has been a topic of research for many years due to the time-consuming process that it requires and the subjectivity of the visual quantification of emphysema. In recent years there are a lot of studies dedicated to the comparison of automatic analysis data with the results of functional pulmonary tests. The previously used Tiffno index-based system for assessing the severity of chronic obstructive pulmonary disease (COPD) has lost its independent value, so today it is recommended to establish the diagnosis and stage of the disease taking into account the frequency and severity of exacerbations. Thus, there is a need to search for more objective diagnostic criteria, which can become an AI-based emphysema quantification.
Therapeutic implications of ongoing alveolar viral replication in COVID-19
Authors: Dennis McGonagle, Mary F Kearney, Anthony O'Regan, James S O'Donnell, Luca Quartuccio, Abdulla Watad, Charles Bridgewood
Journal: The Lancet Rheumatology (2021)

In patients with moderate-to-severe COVID-19 pneumonia, an aberrant post-viral alveolitis with excessive inflammatory responses and immunothrombosis underpins use of immunomodulatory therapy (eg, corticosteroids and interleukin-6 receptor antagonism). By contrast, immunosuppression in individuals with mild COVID-19 who do not require oxygen therapy or in those with critical disease undergoing prolonged ventilation is of no proven benefit. Furthermore, a window of opportunity is thought to exist for timely immunosuppression in patients with moderate-to-severe COVID-19 pneumonia shortly after clinical presentation. In this Viewpoint, we explore the shortcomings of a universal immunosuppression approach in patients with moderate-to-severe COVID-19 due to disease heterogeneity related to ongoing SARS-CoV-2 replication, which can manifest as RNAaemia in some patients treated with immunotherapy. By contrast, immunomodulatory therapy has overall benefits in patients with rapid SARS-CoV-2 clearance, via blunting of multifaceted, excessive innate immune responses in the lungs, potentially uncontrolled T-cell responses, possible autoimmune responses, and immunothrombosis. We highlight this therapeutic dichotomy to better understand the immunopathology of moderate-to-severe COVID-19, particularly the role of RNAaemia, and to refine therapy choices.
Abstract 13249: Temporal Trends in Out-of-Hospital Cardiac Arrest Bystander CPR and Defibrillation Following Implementation of Citizen Responder Programs
Authors: Louise Kollander Jakobsen, Sidsel Gamborg Moeller, Kristian Bundgaard Ringgren, Amalie Lykkemark Moeller, Linn Andelius, Carolina Malta Hansen, Mads Christian Tofte Gregers, Nanna B Christensen, Julie Kjoelbye, Christian Torp-Pedersen, Fredrik Folke
Journal: Circulation (2021)

Introduction: In Denmark, survival after out-of-hospital cardiac arrest (OHCA) has increased markedly in the past years, from 3.9% in 2001 to 15.8% in 2019. Still, bystander defibrillation remains low, especially for OHCAs in residential areas. To improve bystander defibrillation, smartphone activated Citizen Responder (CR) Programs have expanded to nationwide coverage in Denmark during September 2017 to May 2020. Hypothesis: Implementation of CR programs in Denmark was associated with increased bystander CPR and defibrillation. Methods: We conducted an observational study of 15,308 OHCAs from the Danish Cardiac Arrest Registry from 2016-2019. App-based CR programs were implemented in four out of five Danish regions during the study period. All OHCAs were divided into two groups according to the date of CR implementation (“before” and “after CR” implementation). The groups were compared focusing on bystander defibrillation, bystander CPR and 30-day survival. Results: “Before CR” included 8,819 OHCAs and the “after CR” 6,489 OHCAs. The proportion of bystander CPR was 77.9% and 78.0% (p-value 0.91) for the before -and after CR implementation groups, respectively. The corresponding numbers for bystander defibrillation were 7.4% and 9.5% (p-value &lt; 0.001), respectively. In residential OHCA, bystander defibrillation went from 4.0% to 6.3% (p-value&lt;0.001) in the before -and after group respectively. In public, bystander defibrillation was 19.3% and 22.2% (p-value 0.05) in the groups respectively. 30-day survival was 12.7% before and 13.1% after CR implementation (p-value 0.49). Conclusion: We found no changes in bystander CPR or 30-day survival following implementation of CR programs in Denmark, but a significant increase in bystander defibrillation for all OHCAs. Importantly bystander defibrillation also increased significantly in residential locations, where the majority of OHCAs occur and where bystander defibrillation has remained low for decades.
Enterovirus D68-Associated Acute Respiratory Illness ─ New Vaccine Surveillance Network, United States, July–November 2018–2020
Authors: Melisa M. Shah, Ariana Perez, Joana Y. Lively, Vasanthi Avadhanula, Julie A. Boom, James Chappell, Janet A. Englund, Wende Fregoe, Natasha B. Halasa, Christopher J. Harrison, Robert W. Hickey, Eileen J. Klein, Monica M. McNeal, Marian G. Michaels, Mary E. Moffatt, Catherine Otten, Leila C. Sahni, Elizabeth Schlaudecker, Jennifer E. Schuster, Rangaraj Selvarangan, Mary A. Staat, Laura S. Stewart, Geoffrey A. Weinberg, John V. Williams, Terry Fan Fei Ng, Janell A. Routh, Susan I. Gerber, Meredith L. McMorrow, Brian Rha, Claire M. Midgley
Journal: MMWR Morbidity and Mortality Weekly Report (2021)

Enterovirus D68 (EV-D68) is associated with a broad spectrum of illnesses, including mild to severe acute respiratory illness (ARI) and acute flaccid myelitis (AFM). Enteroviruses, including EV-D68, are typically detected in the United States during late summer through fall, with year-to-year fluctuations. Before 2014, EV-D68 was infrequently reported to CDC (1). However, numbers of EV-D68 detection have increased in recent years, with a biennial pattern observed during 2014-2018 in the United States, after the expansion of surveillance and wider availability of molecular testing. In 2014, a national outbreak of EV-D68 was detected (2). EV-D68 was also reported in 2016 via local (3) and passive national (4) surveillance. EV-D68 detections were limited in 2017, but substantial circulation was observed in 2018 (5). To assess recent levels of circulation, EV-D68 detections in respiratory specimens collected from patients aged <18 years* with ARI evaluated in emergency departments (EDs) or admitted to one of seven U.S. medical centers† within the New Vaccine Surveillance Network (NVSN) were summarized. This report provides a provisional description of EV-D68 detections during July-November in 2018, 2019 and 2020, and describes the demographic and clinical characteristics of these patients. In 2018, a total of 382 EV-D68 detections in respiratory specimens obtained from patients aged <18 years with ARI were reported by NVSN; the number decreased to six detections in 2019 and 30 in 2020. Among patients aged <18 years with EV-D68 in 2020, 22 (73%) were non-Hispanic Black (Black) persons. EV-D68 detections in 2020 were lower than anticipated based on the biennial circulation pattern observed since 2014. The circulation of EV-D68 in 2020 might have been limited by widespread COVID-19 mitigation measures; how these changes in behavior might influence the timing and levels of circulation in future years is unknown. Ongoing monitoring of EV-D68 detections is warranted for preparedness for EV-D68-associated ARI and AFM.
Long-term Follow-up of Psychiatric Disorders in Children and Adolescents Conceived by Assisted Reproductive Techniques in Sweden
Authors: Chen Wang, Anna L. V. Johansson, Kenny A. Rodriguez-Wallberg, Mikael Landén, Catarina Almqvist, Sonia Hernández-Díaz, Anna S. Oberg
Journal: JAMA Psychiatry (2021)

Individuals conceived with assisted reproductive techniques (ARTs) could be at elevated risk of psychiatric disorders owing to potential adverse effects of the procedures themselves, or because such traits or their risk factors may be more common in couples with infertility.
Reduced neutralisation of SARS-CoV-2 omicron B.1.1.529 variant by post-immunisation serum
Authors: Wanwisa Dejnirattisai, Robert H Shaw, Piyada Supasa, Chang Liu, Arabella SV Stuart, Andrew J Pollard, Xinxue Liu, Teresa Lambe, Derrick Crook, Dave I Stuart, Juthathip Mongkolsapaya, Jonathan S Nguyen-Van-Tam, Matthew D Snape, Gavin R Screaton
Journal: The Lancet (2021)
Peace of Mind: A Role in Unnecessary Care?
Authors: Michelle M. Chen, Tasha M. Hughes, Lesly A. Dossett, Susan C. Pitt
Journal: Journal of Clinical Oncology (2021)

Consider this excerpt from a real patient-surgeon conversation about treatment for a small, early-stage thyroid cancer and deliberating three equivalent treatment options: active surveillance, hemithyroidectomy, and total thyroidectomy.
Characteristics and Outcomes of Hospitalized Pregnant Women With Influenza, 2010 to 2019
Authors: Rachel Holstein, Fatimah S. Dawood, Alissa O’Halloran, Charisse Cummings, Dawud Ujamaa, Pam Daily Kirley, Kimberly Yousey-Hindes, Emily Fawcett, Maya L. Monroe, Sue Kim, Ruth Lynfield, Chelsea McMullen, Alison Muse, Nancy M. Bennett, Laurie M. Billing, Melissa Sutton, Ann Thomas, H. Keipp Talbot, William Schaffner, Ilene Risk, Carrie Reed, Shikha Garg
Journal: Annals of Internal Medicine (2021)

Pregnant women may be at increased risk for severe influenza-associated outcomes.To describe characteristics and outcomes of hospitalized pregnant women with influenza.Repeated cross-sectional study.The population-based U.S. Influenza Hospitalization Surveillance Network during the 2010-2011 through 2018-2019 influenza seasons.Pregnant women (aged 15 to 44 years) hospitalized with laboratory-confirmed influenza identified through provider-initiated or facility-based testing practices.Clinical characteristics, interventions, and in-hospital maternal and fetal outcomes were obtained through medical chart abstraction. Multivariable logistic regression was used to evaluate the association between influenza A subtype and severe maternal influenza-associated outcomes, including intensive care unit (ICU) admission, mechanical ventilation, extracorporeal membrane oxygenation, or in-hospital death.Of 9652 women aged 15 to 44 years and hospitalized with influenza, 2690 (27.9%) were pregnant. Among the 2690 pregnant women, the median age was 28 years, 62% were in their third trimester, and 42% had at least 1 underlying condition. Overall, 32% were vaccinated against influenza and 88% received antiviral treatment. Five percent required ICU admission, 2% required mechanical ventilation, and 0.3% (n = 8) died. Pregnant women with influenza A H1N1 were more likely to have severe outcomes than those with influenza A H3N2 (adjusted risk ratio, 1.9 [95% CI, 1.3 to 2.8]). Most women (71%) were still pregnant at hospital discharge. Among 754 women who were no longer pregnant at discharge, 96% had a pregnancy resulting in live birth, and 3% experienced fetal loss.Maternal and fetal outcomes that occurred after hospital discharge were not captured.Over 9 influenza seasons, one third of reproductive-aged women hospitalized with influenza were pregnant. Influenza A H1N1 was associated with more severe maternal outcomes. Pregnant women remain a high-priority target group for vaccination.Centers for Disease Control and Prevention.
Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster — Nebraska, November–December 2021
Authors: Lauren Jansen, Bryan Tegomoh, Kate Lange, Kimberly Showalter, Jon Figliomeni, Baha Abdalhamid, Peter C. Iwen, Joseph Fauver, Bryan Buss, Matthew Donahue
Journal: MMWR Morbidity and Mortality Weekly Report (2021)

The B.1.1.529 (Omicron) variant of SARS-CoV-2 (the virus that causes COVID-19) was first detected in specimens collected on November 11, 2021, in Botswana and on November 14 in South Africa;* the first confirmed case of Omicron in the United States was identified in California on December 1, 2021 (1). On November 29, the Nebraska Department of Health and Human Services was notified of six probable cases† of COVID-19 in one household, including one case in a man aged 48 years (the index patient) who had recently returned from Nigeria. Given the patient's travel history, Omicron infection was suspected. Specimens from all six persons in the household tested positive for SARS-CoV-2 by reverse transcription-polymerase chain reaction (RT-PCR) testing on December 1, and the following day genomic sequencing by the Nebraska Public Health Laboratory identified an identical Omicron genotype from each specimen (Figure). Phylogenetic analysis was conducted to determine if this cluster represented an independent introduction of Omicron into the United States, and a detailed epidemiologic investigation was conducted. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.§.
Risk for Recurrent Venous Thromboembolism and Bleeding With Apixaban Compared With Rivaroxaban: An Analysis of Real-World Data
Authors: Ghadeer K. Dawwas, Charles E. Leonard, James D. Lewis, Adam Cuker
Journal: Annals of Internal Medicine (2021)

Apixaban and rivaroxaban are replacing vitamin K antagonists for the treatment of venous thromboembolism (VTE) in adults; however, head-to-head comparisons remain limited.To assess the effectiveness and safety of apixaban compared with rivaroxaban in patients with VTE.Retrospective new-user cohort study.U.S.-based commercial health care insurance database from 1 January 2015 to 30 June 2020.Adults with VTE who were newly prescribed apixaban or rivaroxaban.The primary effectiveness outcome was recurrent VTE, a composite of deep venous thrombosis and pulmonary embolism. The primary safety outcome was a composite of gastrointestinal and intracranial bleeding.Of 49 900 eligible patients with VTE, 18 618 were new users of apixaban and 18 618 were new users of rivaroxaban. Median follow-up was 102 days (25th, 75th percentiles: 30, 128 days) among apixaban and 105 days (25th, 75th percentiles: 30, 140 days) among rivaroxaban users. After propensity score matching, apixaban (vs. rivaroxaban) was associated with a lower rate for recurrent VTE (hazard ratio, 0.77 [95% CI, 0.69 to 0.87]) and bleeding (hazard ratio, 0.60 [CI, 0.53 to 0.69]). The absolute reduction in the probability of recurrent VTE with apixaban versus rivaroxaban was 0.006 (CI, 0.005 to 0.011) within 2 months and 0.011 (CI, 0.011 to 0.013) within 6 months of initiation. The absolute reduction in the probability of gastrointestinal and intracranial bleeding with apixaban versus rivaroxaban was 0.011 (CI, 0.010 to 0.011) within 2 months and 0.015 (CI, 0.013 to 0.015) within 6 months of initiation.Short follow-up.In this population-based cohort study, patients with VTE who were new users of apixaban had lower rates for recurrent VTE and bleeding than new users of rivaroxaban.None.
Morphologic and Genomic Characteristics of Breast Cancers Occurring in Individuals with Lynch Syndrome
Authors: Christopher J. Schwartz, Edaise M. da Silva, Antonio Marra, Andrea M. Gazzo, Pier Selenica, Vikas K. Rai, Diana Mandelker, Fresia Pareja, Maksym Misyura, Timothy M. D'Alfonso, Edi Brogi, Pamela Drullinsky, Pedram Razavi, Mark E. Robson, Joshua Z. Drago, Hannah Y. Wen, Liying Zhang, Britta Weigelt, Jinru Shia, Jorge S. Reis-Filho, Hong Zhang
Journal: Clinical Cancer Research (2021)

Lynch syndrome is defined by germline pathogenic mutations involving DNA mismatch repair (MMR) genes and linked with the development of MMR-deficient colon and endometrial cancers. Whether breast cancers developing in the context of Lynch syndrome are causally related to MMR deficiency (MMRd), remains controversial. Thus, we explored the morphologic and genomic characteristics of breast cancers occurring in Lynch syndrome individuals.A retrospective analysis of 20,110 patients with cancer who underwent multigene panel genetic testing was performed to identify individuals with a likely pathogenic/pathogenic germline variant in MLH1, MSH2, MSH6, or PMS2 who developed breast cancers. The histologic characteristics and IHC assessment of breast cancers for MMR proteins and programmed death-ligand 1 (PD-L1) expression were assessed on cases with available materials. DNA samples from paired tumors and blood were sequenced with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (≥468 key cancer genes). Microsatellite instability (MSI) status was assessed utilizing MSISensor. Mutational signatures were defined using SigMA.A total of 272 individuals with Lynch syndrome were identified, 13 (5%) of whom had primary breast cancers. The majority of breast cancers (92%) were hormone receptor-positive tumors. Five (42%) of 12 breast cancers displayed loss of MMR proteins by IHC. Four (36%) of 11 breast cancers subjected to tumor-normal sequencing showed dominant MSI mutational signatures, high tumor mutational burden, and indeterminate (27%) or high MSISensor scores (9%). One patient with metastatic MMRd breast cancer received anti-PD1 therapy and achieved a robust and durable response.A subset of breast cancers developing in individuals with Lynch syndrome are etiologically linked to MMRd and may benefit from anti-PD1/PD-L1 immunotherapy.
Prophylaxis with rFIXFc Reduces the Frequency and Delays Time to First Spontaneous Bleed Event in Previously Untreated Patients with Hemophilia B: A Post Hoc Analysis of the PUPs B-LONG Trial
Authors: Beatrice Nolan, Michael Recht, Pablo Rendo, Aletta Falk, Meredith Foster, Sandra Casiano, Antoine Rauch, Amy D. Shapiro
Journal: Blood (2021)
Transgenic Epidermal Cultures for Junctional Epidermolysis Bullosa — 5-Year Outcomes
Authors: Maximilian Kueckelhaus, Tobias Rothoeft, Laura De Rosa, Burcu Yeni, Tobias Ohmann, Christoph Maier, Lynn Eitner, Dieter Metze, Lorena Losi, Alessia Secone Seconetti, Michele De Luca, Tobias Hirsch
Journal: New England Journal of Medicine (2021)

Inherited junctional epidermolysis bullosa is a severe genetic skin disease that leads to epidermal loss caused by structural and mechanical fragility of the integuments. There is no established cure for junctional epidermolysis bullosa. We previously reported that genetically corrected autologous epidermal cultures regenerated almost an entire, fully functional epidermis on a child who had a devastating form of junctional epidermolysis bullosa. We now report long-term clinical outcomes in this patient. (Funded by POR FESR 2014-2020 - Regione Emilia-Romagna and others.).
Abstract 12583: Low-Dose, High-Frequency Psychomotor CPR Skills Training Results in Improved and Sustained Performance of Optimal Adult/Child Ventilations in Fire-Based EMS Personnel
Authors: DAVID E SLATTERY, Chase Hamilton, Khanhha Tran, Aaron Singer
Journal: Circulation (2021)

Background: Hyper/over-ventilation (HOV) negatively effects cerebral blood and coronary artery flow during cardiac arrest. The resuscitation quality improvement (RQI) model of low-dose, high-frequency (LDHF) CPR training has been shown to improve CPR skills. Due to the deleterious impact of HOV on survival, our study seeks to determine if the RQI model improves ventilation skills for EMS personnel. We test the hypothesis that the RQI training results in improved and sustained ventilation performance. Methods: In 2014, our department transitioned from traditional BLS/ACLS training to the RQI model. Performance metrics are captured automatically for each rescuer on a quarterly basis using high-fidelity mannequins. Inclusion: All data from adult RQI attempts by EMS personnel from 2015-2019. Exclusion: attempts by non-EMS personnel. The 1 outcome measure is the overall mean (95% CI) ventilation score (composite measure, range 0-100, derived from average volume/rate and % with correct volume). The 2nd outcome measure is the proportion (95%CI) of rescuers with ventilation scores &gt;90%. Data were extracted from RQI and analyzed with Prism statistical software. Comparisons for the 1 outcome was performed using one-way ANOVA and we report mean and 95% CI and proportions and 95% CI as appropriate. Results: During the study period, 740 personnel completed 1,490 ventilation activities in the baseline period and 5,077 in the subsequent years. The mean (95% CI) composite ventilation scores for the baseline was 84.10 (83.09,85.10) vs 2016 = 83.13 (82.17,84.09), 2017=88.79 (87.91,89.66), 2018=90.36 (89.45, 91.27), 2019= 88.59 (87.37, 89.81) for years 2016-2019; F= 41.36, R2=0.024, p value &lt;0.0001. 10outcome: In the baseline RQI year, there were 55.3 % (95%CI= 52.8,57.8) participants with composite ventilation scores &gt;/=90% vs. 2016= 53.5% (51.2,55.8), 2017=65.2%(62.6,68.6), 2018= 71.7%(69.1,74.3) and 2019=69.3%(66.1,72.2) in subsequent years. Limitations: Individual performance not reported, single agency. Conclusions: LDHF CPR training improves proper, and exceptional, ventilation performance in fire-based EMS personnel. Our results may be useful for other EMS agencies who are considering transitioning to LDHF training such as the RQI system.
Applying Syndemic Theory to Acute Illness
Authors: Kristina E. Rudd, Christina F. Mair, Derek C. Angus
Journal: JAMA (2021)

This Viewpoint describes how syndemic theory, a way of analyzing harmful social conditions that contribute to chronic disease, could be applied to acute conditions of sepsis and COVID-19 that could guide the development of more precise strategies to clinical care, research, and health policies.
Time and the decider
Authors: David Spurrett
Journal: Behavioral and Brain Sciences (2021)

Abstract Shadmehr and Ahmed's book is a welcome extension of optimal foraging theory and neuroeconomics, achieved by integrating both with parameters relating to effort and rate of movement. Their most persuasive and prolific data come from saccades, where times before and after decision are reasonably determinate. Skeletal movements are less likely to exhibit such tidy temporal organization.
The Quest to Define and Target Cellular Senescence in Cancer
Authors: Boshi Wang, Marco Demaria
Journal: Cancer Research (2021)

Cellular senescence represents a double-edged sword in cancer and its therapy. On one side, senescence-associated growth arrest and immunomodulatory properties exert potent antimalignant functions. On the other side, senescence bypass and secretory phenotype are associated with tumor progression and relapse. Recent studies have demonstrated the enormous potential to combine pro- to antisenescence interventions as a new anticancer approach. However, the heterogeneity of senescence-associated features makes definition and targeting of therapy-induced senescent cells a challenging task. Here, we describe these challenges and discuss how to exploit senescence-associated features to improve treatment efficacy and tolerability.
Efficacy of Oral Decitabine/Cedazuridine (ASTX727) in the CMML Subgroup from the Ascertain Phase 3 Study
Authors: Michael R. Savona, James K McCloskey, Elizabeth A. Griffiths, Karen Yee, Amer M. Zeidan, Aref Al-Kali, H. Joachim Deeg, Prapti Patel, Mitchell Sabloff, Mary-Margaret Keating, Kim-Hien Dao, Nancy Zhu, Nashat Gabrail, Salman Fazal, Joseph Maly, Olatoyosi Odenike, Hagop Kantarjian, Amy E. DeZern, Casey L. O'Connell, Gail J. Roboz, Lambert Busque, Richard A. Wells, Harshad Amin, Jasleen K. Randhawa, Brian Leber, Yong Hao, Harold N. Keer, Mohammad Azab, Guillermo Garcia-Manero
Journal: Blood (2021)