tbuckley/cabot-search huggingface dataset:
Artificial intelligence to predict West Nile virus outbreaks with eco-climatic drivers
Authors: Zia Farooq, Joacim Rocklöv, Jonas Wallin, Najmeh Abiri, Maquines Odhiambo Sewe, Henrik Sjödin, Jan C. Semenza
Journal: The Lancet Regional Health - Europe (2022)

In Europe, the frequency, intensity, and geographic range of West Nile virus (WNV)-outbreaks have increased over the past decade, with a 7.2-fold increase in 2018 compared to 2017, and a markedly expanded geographic area compared to 2010. The reasons for this increase and range expansion remain largely unknown due to the complexity of the transmission pathways and underlying disease drivers. In a first, we use advanced artificial intelligence to disentangle the contribution of eco-climatic drivers to WNV-outbreaks across Europe using decade-long (2010-2019) data at high spatial resolution.We use a high-performance machine learning classifier, XGBoost (eXtreme gradient boosting) combined with state-of-the-art XAI (eXplainable artificial intelligence) methodology to describe the predictive ability and contribution of different drivers of the emergence and transmission of WNV-outbreaks in Europe, respectively.Our model, trained on 2010-2017 data achieved an AUC (area under the receiver operating characteristic curve) score of 0.97 and 0.93 when tested with 2018 and 2019 data, respectively, showing a high discriminatory power to classify a WNV-endemic area. Overall, positive summer/spring temperatures anomalies, lower water availability index (NDWI), and drier winter conditions were found to be the main determinants of WNV-outbreaks across Europe. The climate trends of the preceding year in combination with eco-climatic predictors of the first half of the year provided a robust predictive ability of the entire transmission season ahead of time. For the extraordinary 2018 outbreak year, relatively higher spring temperatures and the abundance of Culex mosquitoes were the strongest predictors, in addition to past climatic trends.Our AI-based framework can be deployed to trigger rapid and timely alerts for active surveillance and vector control measures in order to intercept an imminent WNV-outbreak in Europe.The work was partially funded by the Swedish Research Council FORMAS for the project ARBOPREVENT (grant agreement 2018-05973).
EJECTION FRACTION, BIOMARKERS, AND OUTCOMES IN HEART FAILURE WITH REDUCED EJECTION FRACTION AND THE IMPACT OF VERICIGUAT ON OUTCOMES IN THE VICTORIA TRIAL
Authors: Javed Butler, Yinggan Zheng, Diana Bonderman, Lars Lund, Christopher R. DeFilippi, Robert Blaustein, Justin A. Ezekowitz, Cecilia Freitas, Adrian F. Hernandez, Christopher M. O’Connor, Adriaan Voors, Cynthia M. Westerhout, Carolyn S.P. Lam, Paul Wayne Armstrong
Journal: Journal of the American College of Cardiology (2022)
TRENDS IN THE INCIDENCE, MORTALITY AND CLINICAL OUTCOMES IN PATIENTS WITH VENTRICULAR SEPTAL RUPTURE FOLLOWING AN ST ELEVATION MYOCARDIAL INFARCTION
Authors: Emily Hiltner, Meghan Nahass, Shiochee Liang, Mark Russo, Ashish Awasthi, Abdul Hakeem, John Kassotis, Ankur Sethi
Journal: Journal of the American College of Cardiology (2022)
CLO22-047: Outcomes of SARS-COV-2 mRNA-1273 Vaccine in Cancer Patients: Seroconversion and Adverse Events
Authors: Javier David Benitez Fuentes, Alicia de Luna Aguilar, Alejandro Francisco Jimenez Ortega, Alberto Delgado-Iribarren Garcia-Campero, Elvira Baos Muñoz, Sara Gil Useros, Pedro Perez Segura
Journal: Journal of the National Comprehensive Cancer Network (2022)
Trends in Debt Valuations of Private Equity–Backed Dermatology Groups Before and During the COVID-19 Pandemic
Authors: Rohail Memon, Abdullah Memon, Joseph Francis, Sailesh Konda
Journal: JAMA Dermatology (2022)

Private equity (PE) firms have invested in and consolidated dermatology practices. Private equity firms typically operate by conducting leveraged buyouts, which occur when target companies are acquired with capital from PE firms and a combination of debt, which may include debt instruments held in business development corporations (BDCs).To investigate the valuations of dermatology PE-backed group (DPEG) debt instruments in BDCs' portfolios both before and during the COVID-19 pandemic.This cross-sectional study, conducted from August 1, 2016, to August 31, 2021, examined public financial statements filed by BDCs lending to DPEGs. The public filings of BDCs were searched from inception of the DPEG's debt instrument in a BDC's portfolio, and the amortized cost and fair value of each debt instrument were tabulated.The premium or discount at which each debt instrument was valued at a given time was calculated by dividing the difference between the fair value and the amortized cost by the amortized cost. Different testing methods were conducted for normal or nonnormal data to test differences in debt valuations across all DPEGs between 2 consecutive or nonconsecutive quarters.The search of the public filings found 10 BDCs containing data on 9 unique DPEGs. Overall, there were 15 trackable DPEG debt instruments because multiple BDCs can hold debt instruments for a given DPEG. Data were available from August 2016 through August 2021. During the study time frame, the amortized cost of the loans for an individual DPEG ranged from a low of $1.7 million to a high of $100 million. The valuation of debt instruments was stable for many DPEGs until some were discounted starting in May 2018, with a significant decrease from May 2019 to August 2019 (-1.4%; 95% CI, not applicable; P = .04), prior to the COVID-19 pandemic. Another significant decrease occurred during the pandemic from February to June 2020 (-9.0%; 95% CI, -13.6% to -4.4%; P = .002). US Dermatology Partners decreased to the lowest valuation (Golub BDC, -39.7%; TCG BDC Inc, -48.8%; TCG BDC II, -48.8%) of the DPEGs examined in November 2020 even after receiving a $10 million forgivable Small Business Administration Paycheck Protection Program loan in May 2020. After pharmaceutical companies announced effective COVID-19 vaccine candidates in November 2020, there was a modest and significant improvement in debt valuations (2.3%; 95% CI, 0.2%-0.4%; P = .03); however, they remained discounted. Only PhyNet Dermatology's debt instruments improved to a premium valuation by August 2021.Debt valuations of some DPEGs found in this cross-sectional study suggest a lower probability that their loans will be repaid in full. This could be a signal that some DPEGs are not performing well financially.
Derivation and validation of the UCAP-Q case-finding questionnaire to detect undiagnosed asthma and COPD
Authors: Chau Huynh, G.A. Whitmore, Katherine L. Vandemheen, J. Mark FitzGerald, Celine Bergeron, Louis-Philippe Boulet, Andreanne Cote, Stephen K. Field, Erika Penz, R. Andrew McIvor, Catherine Lemière, Samir Gupta, Irvin Mayers, Mohit Bhutani, Paul Hernandez, M. Diane Lougheed, Christopher J. Licskai, Tanweer Azher, Martha Ainslie, Ian Fraser, Masoud Mahdavian, Gonzalo G. Alvarez, Tetyana Kendzerska, Shawn D. Aaron
Journal: European Respiratory Journal (2022)

Background Many people with asthma and COPD remain undiagnosed. We developed and validated a new case-finding questionnaire to identify symptomatic adults with undiagnosed obstructive lung disease. Methods Adults in the community with no prior history of physician-diagnosed lung disease who self-reported respiratory symptoms were contacted via random-digit dialling. Pre- and post-bronchodilator spirometry was used to confirm asthma or COPD. Predictive questions were selected using multinomial logistic regression with backward elimination. Questionnaire performance was assessed using sensitivity, predictive values and area under the receiver operating characteristic curve (AUC). The questionnaire was assessed for test–retest reliability, acceptability and readability. External validation was prospectively conducted in an independent sample and predictive performance re-evaluated. Results A 13-item Undiagnosed COPD and Asthma Population Questionnaire (UCAP-Q) case-finding questionnaire to predict undiagnosed asthma or COPD was developed. The most appropriate risk cut-off was determined to be 6% for either disease. Applied to the derivation sample (n=1615), the questionnaire yielded a sensitivity of 92% for asthma and 97% for COPD; specificity of 17%; and an AUC of 0.69 (95% CI 0.64–0.74) for asthma and 0.82 (95% CI 0.78–0.86) for COPD. Prospective validation using an independent sample (n=471) showed sensitivities of 93% and 92% for asthma and COPD, respectively; specificity of 19%; with AUCs of 0.70 (95% CI 0.62–0.79) for asthma and 0.81 (95% CI 0.74–0.87) for COPD. AUCs for UCAP-Q were higher compared to AUCs for currently recommended case-finding questionnaires for asthma or COPD. Conclusions The UCAP-Q demonstrated high sensitivities and AUCs for identifying undiagnosed asthma or COPD. A web-based calculator allows for easy calculation of risk probabilities for each disease.
ASSOCIATION OF LEFT ATRIAL FUNCTION WITH COGNITIVE FUNCTION IN PARTICIPANTS FREE OF STROKE, TIA, ATRIAL FIBRILLATION, AND FLUTTER IN THE MULTI-ETHNIC STUDY OF ATHEROSCLEROSIS (MESA)
Authors: Yitzhak Rosen, Henrique Doria De Vasconcellos, Boaz D. Rosen, Thor Edvardsen, Ela Chamera, Susan R. Heckbert, Timothy M. Hughes, Jingzhong Ding, Lisa B. VanWagner, David A. Bluemke, Bharath Ambale Venkatesh, Joao A.C. Lima
Journal: Journal of the American College of Cardiology (2022)
Abstract P1-09-06: Insulinemic potential of diet and risk of total and subtypes of breast cancer among US women
Authors: Andrea Romanos-Nanclares, Walter C. Willett, Bernard A. Rosner, Rulla M. Tamimi, Fred K. Tabung, Michelle D. Holmes, Wendy Y Chen, A. Heather Eliassen
Journal: Cancer Research (2022)

Abstract Background: Insulin resistance and hyperinsulinemia play important roles in the progression of multiple chronic disease and conditions. Diet modulates insulin response; however, evidence is limited regarding whether diet with higher insulinemic potential is associated with invasive breast cancer risk.Objectives: We prospectively evaluated the association between adherence to a food-based empirical dietary index for hyperinsulinemia (EDIH) and the incidence of invasive breast cancer.Methods: We prospectively followed 76,595 women from the Nurses’ Health Study (NHS, 1984-2016) and 93,295 women from the Nurses’ Health Study II (NHSII, 1991-2017). Diet was assessed by food frequency questionnaires every 4 years. The insulinemic potential of diet was evaluated using the EDIH that was pre-defined based on circulating C-peptide concentrations. Higher scores indicate higher insulinemic potential, while lower scores indicate lower insulinemic potential.Results: During 4,215,162 person-years of follow-up, we documented 10,595 breast cancer cases (6,639 NHS; 3,914 NHSII). Being in the highest, compared with the lowest, EDIH quintile was associated with higher breast cancer risk (HRQ5vsQ1 1.18; 95% CI 1.10, 1.27; P-trend&amp;lt;0.01). The association was suggestively strongest among women with current BMI&amp;lt;25 kg/m2 (HRQ5vsQ1 1.20; 95% CI 1.08, 1.34; P-trend&amp;lt;0.01; P-interaction=0.06) compared to overweight/obese women. Although heterogeneity by estrogen receptor (ER) status was non-significant (P=0.17), the strongest association between EDIH and breast cancer was observed with ER-negative tumors (HRQ5vsQ1 1.26; 95% CI 1.04, 1.51; P-trend&amp;lt;0.01). Among tumor molecular subtypes, the strongest associations were observed with HER2-enriched tumors (HRQ5vsQ1 1.75; 95% CI 1.08, 2.82; P-trend=0.01).Conclusions: A dietary pattern contributing to hyperinsulinemia was associated with greater breast cancer risk in women from the NHS/NHSII. In particular, a more hyperinsulinemic diet was associated with higher risk of breast cancer among lean women when compared to overweight or obese women. Moreover, the hyperinsulinemic diet showed a stronger positive association with ER-negative breast tumors, independent of adiposity. Our findings suggest that dietary interventions to reduce insulinemic potential may have a role in breast cancer prevention. Citation Format: Andrea Romanos-Nanclares, Walter C. Willett, Bernard A. Rosner, Rulla M. Tamimi, Fred K. Tabung, Michelle D. Holmes, Wendy Y Chen, A. Heather Eliassen. Insulinemic potential of diet and risk of total and subtypes of breast cancer among US women [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-09-06.
THE EFFECT OF SGLT2 INHIBITORS ON HEART FAILURE OUTCOMES ACROSS DIFFERENT DISEASE STATES: A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Muhammad Shariq Usman, Tariq Jamal Siddiqi, Andrew Coats, Giuseppe Rosano, Gerasimos Filippatos, Stefan D. Anker, Javed Butler
Journal: Journal of the American College of Cardiology (2022)
THE JAILED SINOATRIAL NODE: SINUS ARREST-INDUCED CARDIOGENIC SHOCK FOLLOWING PERCUTANEOUS INTERVENTION
Authors: Ebubechukwu Ezeh, Esiemoghie J. Akhigbe, Mohammad Amro, Ebad Ur Rahman, Salem Omar, Kanaan Mansoor, Mehiar El-Hamdani
Journal: Journal of the American College of Cardiology (2022)
Preliminary evidence of safety and tolerability of atezolizumab plus bevacizumab in patients with hepatocellular carcinoma and Child‐Pugh A and B cirrhosis: A real‐world study
Authors: Antonio D’Alessio, Claudia Angela Maria Fulgenzi, Naoshi Nishida, Martin Schönlein, Johann von Felden, Kornelius Schulze, Henning Wege, Vincent E. Gaillard, Anwaar Saeed, Brooke Wietharn, Hannah Hildebrand, Linda Wu, Celina Ang, Thomas U. Marron, Arndt Weinmann, Peter R. Galle, Dominik Bettinger, Bertram Bengsch, Arndt Vogel, Lorenz Balcar, Bernhard Scheiner, Pei‐Chang Lee, Yi‐Hsiang Huang, Suneetha Amara, Mahvish Muzaffar, Abdul Rafeh Naqash, Antonella Cammarota, Nicola Personeni, Tiziana Pressiani, Rohini Sharma, Matthias Pinter, Alessio Cortellini, Masatoshi Kudo, Lorenza Rimassa, David J. Pinato
Journal: Hepatology (2022)

Atezolizumab plus bevacizumab (AtezoBev) is the standard of care for first-line treatment of unresectable HCC. No evidence exists as to its use in routine clinical practice in patients with impaired liver function.
De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
Authors: Ming Li, Congjiao Sun, Naiyi Xu, Peipei Bian, Xiaomeng Tian, Xihong Wang, Yuzhe Wang, Xinzheng Jia, Rasmus Heller, Mingshan Wang, Fei Wang, Xuelei Dai, Rongsong Luo, Yingwei Guo, Xiangnan Wang, Peng Yang, Dexiang Hu, Zhenyu Liu, Weiwei Fu, Shunjin Zhang, Xiaochang Li, Chaoliang Wen, Fangren Lan, Amam Zonaed Siddiki, Chatmongkon Suwannapoom, Xin Zhao, Qinghua Nie, Xiaoxiang Hu, Yu Jiang, Ning Yang
Journal: Molecular Biology and Evolution (2022)

The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.
Reductive TCA cycle catalyzed by wild-type IDH2 promotes acute myeloid leukemia and is a metabolic vulnerability for potential targeted therapy
Authors: Peiting Zeng, Wenhua Lu, Jingyu Tian, Shuang Qiao, Jiangjiang Li, Christophe Glorieux, Shijun Wen, Hui Zhang, Yiqing Li, Peng Huang
Journal: Journal of Hematology & Oncology (2022)

Abstract Background Isocitrate dehydrogenase-2 (IDH2) is a mitochondrial enzyme that catalyzes the metabolic conversion between isocitrate and alpha-ketoglutarate (α-KG) in the TCA cycle. IDH2 mutation is an oncogenic event in acute myeloid leukemia (AML) due to the generation of 2-hydroxyglutarate. However, the role of wild-type IDH2 in AML remains unknown, despite patients with it suffer worse clinical outcome than those harboring mutant type. Methods IDH2 expression in AML cell lines and patient samples was evaluated by RT-qPCR, western blotting and database analyses. The role of wild-type IDH2 in AML cell survival and proliferation was tested using genetic knockdown and pharmacological inhibition in AML cells and animal models. LC–MS, GC–MS, isotope metabolic tracing, and molecular analyses were performed to reveal the underlying mechanisms. Results We found that wild-type IDH2 was overexpressed in AML and played a major role in promoting leukemia cell survival and proliferation in vitro and in vivo. Metabolomic analyses revealed an active IDH2-mediated reductive TCA cycle that promoted the conversion of α-KG to isocitrate/citrate to facilitate glutamine utilization for lipid synthesis in AML cells. Suppression of wild-type IDH2 by shRNA resulted in elevated α-KG and decreased isocitrate/citrate, leading to reduced lipid synthesis, a significant decrease in c-Myc downregulated by α-KG, and an inhibition of AML viability and proliferation. Importantly, pharmacological inhibition of IDH2 showed significant therapeutic effect in mice inoculated with AML cells with wt-IDH2 and induced a downregulation of C-MYC in vivo. Conclusions Wt-IDH2 is an essential molecule for AML cell survival and proliferation by promoting conversion of α-KG to isocitrate for lipid synthesis and by upregulating c-Myc expression and could be a potential therapeutic target in AML.
Correction to: Effect of therapeutic drug monitoring-based dose optimization of piperacillin/tazobactam on sepsis-related organ dysfunction in patients with sepsis: a randomized controlled trial
Authors: Stefan Hagel, Friedhelm Bach, Thorsten Brenner, Hendrik Bracht, Alexander Brinkmann, Thorsten Annecke, Andreas Hohn, Markus Alexander Weigand, Guido Michels, Stefan Kluge, Axel Nierhaus, Dominik Jarczak, Christina König, Dirk Weismann, Otto Frey, Dominic Witzke, Carsten Müller, Michael Bauer, Michael Kiehntopf, Sophie Neugebauer, Thomas Lehmann, Jason A. Roberts, Mathias W. Pletz, Anke Braune, Karsten Schmidt, Johann Motsch, Nadine Pinder, Daniel Richter, Peter Schlattmann, Andreas Ameln-Mayerhofer von, Markus Schappacher, Thomas Fuchs, Anka Röhr, Max Kurlbaum, Oliver Schreiner, Lars Hüter, Matthias Gründling, Stefan Angermair, Maria Deja, Frank Bloos, Sandra Fiedler, Hicham Chkirni
Journal: Intensive Care Medicine (2022)
Chronic rhinosinusitis endotypes associate with distinct local cytokine milieus that shape the distribution of innate lymphoid cells
Authors: Young Gyun Ko, Min Ho Kim, Joo Yong Park, Chan Hee Gil, Tae Soo Kim, Ji‐Yeob Choi, Doo Hyun Chung, Hyun Jik Kim, Dong Young Kim, Hye Young Kim
Journal: Allergy (2022)

The authors declare that they have no competing interests. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
EVALUATION OF GUIDELINE DIRECTED MEDICAL THERAPY IN A PHARMACIST-LED HEART FAILURE CLINIC
Authors: Katelyn Dulgar, Jona Lekura, Jacqueline Pyle, James Kalus, Marissa Agnello, Lorne Loveland, Jovan Lozo, Nadeen Abdallah, Thomas Senneff, Henry E. Kim, Gillian Grafton, Celeste T. Williams, Long To
Journal: Journal of the American College of Cardiology (2022)
A CASE OF FATAL SINGLE CORONARY ARTERY ANOMALY MIMICKING AN AORTOCORONARY DISSECTION
Authors: Harris Khan, Adithya Thomas Mathews, Tracey Topacio, Enrique Rodriguez-Paz, Kapil Hemant Painter, Bharadwaj Satyavolu, Jean-Pierre S. Awaida
Journal: Journal of the American College of Cardiology (2022)
Lack of Prognostic Value of <i>CTNNB1</i> Mutation Profile in Desmoid-Type Fibromatosis
Authors: Nicolas Penel, Sylvie Bonvalot, André-Michel Bimbai, Alexandra Meurgey, François Le Loarer, Sébastien Salas, Sophie Piperno-Neumann, Christine Chevreau, Pascaline Boudou-Rouquette, Pascale Dubray-Longeras, Jean-Emmanuel Kurtz, Cécile Guillemet, Emmanuelle Bompas, Antoine Italiano, Axel Le Cesne, Daniel Orbach, Julien Thery, Marie-Cécile Le Deley, Jean-Yves Blay, Olivier Mir
Journal: Clinical Cancer Research (2022)

Abstract Purpose: This prospective nationwide cohort study aimed to investigate desmoid-type fibromatosis (DF) outcomes, focusing on the prognostic value of CTNNB1 mutations. Experimental Design: ALTITUDES (NCT02867033) was a nationwide prospective cohort study of DF diagnosed between January 2016 and December 2020. At diagnosis, CTNNB1 molecular alterations were identified using next-generation sequencing or Sanger sequencing. The primary endpoint was event-free survival (EFS; progression, relapse, or death). We enrolled 628 patients managed by active surveillance, surgical resection, or systemic treatment as first-line therapy. Results: Overall, 516 (82.2%) patients [368 females (71.3%), median age 40.3 years (range, 1–89)] were eligible for analysis. In 435 (84.3%) cases, there was one CTNNB1 molecular alteration: p.T41A, p.S45F, or p.S45P. The first-line management was active surveillance in 352 (68.2%), surgical resection in 120 (23.3%), and systemic treatments in 44 (8.5%) patients. CTNNB1 mutation distribution was similar across the three therapeutic groups. The median follow-up period was 24.7 (range, 0.4–59.7) months. The estimated 3-year EFS rate was 66.2% [95% confidence interval (CI), 60.5%–71.2%]. DF harboring p.S45F was significantly associated with male sex (P = 0.03), non-abdominal wall sites (P = 0.05), pain (P = 0.007), and large tumor size (P = 0.025). CTNNB1 p.S45F mutation was not significantly associated with EFS, either in univariate (HR, 1.06; 95% CI, 0.65–1.73; P = 0.81) or in multivariate analysis (HR, 0.91; 95% CI, 0.55–1.49; P = 0.71). Conclusions: We found that CTNNB1 mutation profile was associated with unfavorable prognostic factors but was not a prognostic factor for EFS. See related commentary by Greene and Van Tine, p. 3911