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Harrison JM, Yala A, Mikhael P, Roldan J, Ciprani D, Michelakos T, Bolm L, Qadan M, Ferrone C, Fernandez-Del Castillo C, Lillemoe KD, Santus E, Hughes K. Successful Development of a Natural Language Processing Algorithm for Pancreatic Neoplasms and Associated Histologic Features. Pancreas 2023; 52:e219-e223. [PMID: 37716007 DOI: 10.1097/mpa.0000000000002242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
OBJECTIVES Natural language processing (NLP) algorithms can interpret unstructured text for commonly used terms and phrases. Pancreatic pathologies are diverse and include benign and malignant entities with associated histologic features. Creating a pancreas NLP algorithm can aid in electronic health record coding as well as large database creation and curation. METHODS Text-based pancreatic anatomic and cytopathologic reports for pancreatic cancer, pancreatic ductal adenocarcinoma, neuroendocrine tumor, intraductal papillary neoplasm, tumor dysplasia, and suspicious findings were collected. This dataset was split 80/20 for model training and development. A separate set was held out for testing purposes. We trained using convolutional neural network to predict each heading. RESULTS Over 14,000 reports were obtained from the Mass General Brigham Healthcare System electronic record. Of these, 1252 reports were used for algorithm development. Final accuracy and F1 scores relative to the test set ranged from 95% and 98% for each queried pathology. To understand the dependence of our results to training set size, we also generated learning curves. Scoring metrics improved as more reports were submitted for training; however, some queries had high index performance. CONCLUSIONS Natural language processing algorithms can be used for pancreatic pathologies. Increased training volume, nonoverlapping terminology, and conserved text structure improve NLP algorithm performance.
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Affiliation(s)
- Jon Michael Harrison
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | - Adam Yala
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Mass
| | - Peter Mikhael
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Mass
| | - Jorge Roldan
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | - Debora Ciprani
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | - Theodoros Michelakos
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | - Louisa Bolm
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | - Motaz Qadan
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | - Cristina Ferrone
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
| | | | | | - Enrico Santus
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Mass
| | - Kevin Hughes
- From the Department of GI and General Surgery, Massachusetts General Hospital, Boston
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Marino N, Putignano G, Cappilli S, Chersoni E, Santuccione A, Calabrese G, Bischof E, Vanhaelen Q, Zhavoronkov A, Scarano B, Mazzotta AD, Santus E. Towards AI-driven longevity research: An overview. Front Aging 2023; 4:1057204. [PMID: 36936271 PMCID: PMC10018490 DOI: 10.3389/fragi.2023.1057204] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023]
Abstract
While in the past technology has mostly been utilized to store information about the structural configuration of proteins and molecules for research and medical purposes, Artificial Intelligence is nowadays able to learn from the existing data how to predict and model properties and interactions, revealing important knowledge about complex biological processes, such as aging. Modern technologies, moreover, can rely on a broader set of information, including those derived from the next-generation sequencing (e.g., proteomics, lipidomics, and other omics), to understand the interactions between human body and the external environment. This is especially relevant as external factors have been shown to have a key role in aging. As the field of computational systems biology keeps improving and new biomarkers of aging are being developed, artificial intelligence promises to become a major ally of aging research.
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Affiliation(s)
- Nicola Marino
- Women’s Brain Project (WBP), Gunterhausen, Switzerland
- *Correspondence: Nicola Marino,
| | | | - Simone Cappilli
- Dermatology, Catholic University of the Sacred Heart, Rome, Italy
- UOC of Dermatology, Department of Abdominal and Endocrine Metabolic Medical and Surgical Sciences, A. Gemelli University Hospital Foundation-IRCCS, Rome, Italy
| | - Emmanuele Chersoni
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong, China
| | | | - Giuliana Calabrese
- Department of Translational Medicine and Surgery, CatholicUniversity of the Sacred Heart, Rome, Italy
| | - Evelyne Bischof
- Insilico Medicine Hong Kong Ltd., New Territories, Hong Kong SAR, China
| | - Quentin Vanhaelen
- Insilico Medicine Hong Kong Ltd., New Territories, Hong Kong SAR, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., New Territories, Hong Kong SAR, China
| | - Bryan Scarano
- Department of Translational Medicine and Surgery, CatholicUniversity of the Sacred Heart, Rome, Italy
| | - Alessandro D. Mazzotta
- Department of Digestive, Oncological and Metabolic Surgery, Institute Mutualiste Montsouris, Paris, France
- Biorobotics Institute, Scuola Superiore Sant’anna, Pisa, Italy
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Scaboro S, Portelli B, Chersoni E, Santus E, Serra G. Increasing adverse drug events extraction robustness on social media: Case study on negation and speculation. Exp Biol Med (Maywood) 2022; 247:2003-2014. [PMID: 36314865 PMCID: PMC9791307 DOI: 10.1177/15353702221128577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the last decade, an increasing number of users have started reporting adverse drug events (ADEs) on social media platforms, blogs, and health forums. Given the large volume of reports, pharmacovigilance has focused on ways to use natural language processing (NLP) techniques to rapidly examine these large collections of text, detecting mentions of drug-related adverse reactions to trigger medical investigations. However, despite the growing interest in the task and the advances in NLP, the robustness of these models in face of linguistic phenomena such as negations and speculations is an open research question. Negations and speculations are pervasive phenomena in natural language and can severely hamper the ability of an automated system to discriminate between factual and non-factual statements in text. In this article, we take into consideration four state-of-the-art systems for ADE detection on social media texts. We introduce SNAX, a benchmark to test their performance against samples containing negated and speculated ADEs, showing their fragility against these phenomena. We then introduce two possible strategies to increase the robustness of these models, showing that both of them bring significant increases in performance, lowering the number of spurious entities predicted by the models by 60% for negation and 80% for speculations.
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Affiliation(s)
- Simone Scaboro
- Department of Mathematics, Computer Science and Physics, University of Udine, Udine 33100, Italy
| | - Beatrice Portelli
- Department of Mathematics, Computer Science and Physics, University of Udine, Udine 33100, Italy,Università degli Studi di Napoli Federico II, Napoli 80138, Italy,Beatrice Portelli.
| | - Emmanuele Chersoni
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hung Hom 999077, Hong Kong
| | - Enrico Santus
- Decision Science and Advanced Analytics for MAPV & RA, Bayer, Bayer Pharmaceuticals, Whippany, NJ 07981-1544, USA
| | - Giuseppe Serra
- Department of Mathematics, Computer Science and Physics, University of Udine, Udine 33100, Italy
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4
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Harms RL, Ferrari A, Meier IB, Martinkova J, Santus E, Marino N, Cirillo D, Mellino S, Catuara Solarz S, Tarnanas I, Szoeke C, Hort J, Valencia A, Ferretti MT, Seixas A, Santuccione Chadha A. Digital biomarkers and sex impacts in Alzheimer’s disease management — potential utility for innovative 3P medicine approach. EPMA J 2022; 13:299-313. [PMID: 35719134 PMCID: PMC9203627 DOI: 10.1007/s13167-022-00284-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Abstract
Digital biomarkers are defined as objective, quantifiable physiological and behavioral data that are collected and measured by means of digital devices. Their use has revolutionized clinical research by enabling high-frequency, longitudinal, and sensitive measurements. In the field of neurodegenerative diseases, an example of a digital biomarker-based technology is instrumental activities of daily living (iADL) digital medical application, a predictive biomarker of conversion from mild cognitive impairment (MCI) due to Alzheimer’s disease (AD) to dementia due to AD in individuals aged 55 + . Digital biomarkers show promise to transform clinical practice. Nevertheless, their use may be affected by variables such as demographics, genetics, and phenotype. Among these factors, sex is particularly important in Alzheimer’s, where men and women present with different symptoms and progression patterns that impact diagnosis. In this study, we explore sex differences in Altoida’s digital medical application in a sample of 568 subjects consisting of a clinical dataset (MCI and dementia due to AD) and a healthy population. We found that a biological sex-classifier, built on digital biomarker features captured using Altoida’s application, achieved a 75% ROC-AUC (receiver operating characteristic — area under curve) performance in predicting biological sex in healthy individuals, indicating significant differences in neurocognitive performance signatures between males and females. The performance dropped when we applied this classifier to more advanced stages on the AD continuum, including MCI and dementia, suggesting that sex differences might be disease-stage dependent. Our results indicate that neurocognitive performance signatures built on data from digital biomarker features are different between men and women. These results stress the need to integrate traditional approaches to dementia research with digital biomarker technologies and personalized medicine perspectives to achieve more precise predictive diagnostics, targeted prevention, and customized treatment of cognitive decline.
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Affiliation(s)
| | | | | | - Julie Martinkova
- Women’s Brain Project, Guntershausen, Switzerland
- Memory Clinic, Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Enrico Santus
- Women’s Brain Project, Guntershausen, Switzerland
- Bayer, NJ USA
| | - Nicola Marino
- Women’s Brain Project, Guntershausen, Switzerland
- Dipartimento Di Scienze Mediche E Chirurgiche, Università Degli Studi Di Foggia, Foggia, Italy
| | - Davide Cirillo
- Women’s Brain Project, Guntershausen, Switzerland
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
| | | | | | - Ioannis Tarnanas
- Altoida Inc., Houston, TX USA
- Global Brain Health Institute, Dublin, Ireland
| | - Cassandra Szoeke
- Women’s Brain Project, Guntershausen, Switzerland
- Centre for Medical Research, Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Melbourne, Australia
| | - Jakub Hort
- Memory Clinic, Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Brno, Czech Republic
| | - Alfonso Valencia
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- ICREA - Institució Catalana de Recerca I Estudis Avançats, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | | | - Azizi Seixas
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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5
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Portelli B, Scaboro S, Tonino R, Chersoni E, Santus E, Serra G. Monitoring user opinions and side effects on COVID-19 vaccines in the Twittersphere: Infodemiology Study of Tweets. J Med Internet Res 2022; 24:e35115. [PMID: 35446781 PMCID: PMC9132143 DOI: 10.2196/35115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/29/2022] [Accepted: 03/09/2022] [Indexed: 11/18/2022] Open
Abstract
Background In the current phase of the COVID-19 pandemic, we are witnessing the most massive vaccine rollout in human history. Like any other drug, vaccines may cause unexpected side effects, which need to be investigated in a timely manner to minimize harm in the population. If not properly dealt with, side effects may also impact public trust in the vaccination campaigns carried out by national governments. Objective Monitoring social media for the early identification of side effects, and understanding the public opinion on the vaccines are of paramount importance to ensure a successful and harmless rollout. The objective of this study was to create a web portal to monitor the opinion of social media users on COVID-19 vaccines, which can offer a tool for journalists, scientists, and users alike to visualize how the general public is reacting to the vaccination campaign. Methods We developed a tool to analyze the public opinion on COVID-19 vaccines from Twitter, exploiting, among other techniques, a state-of-the-art system for the identification of adverse drug events on social media; natural language processing models for sentiment analysis; statistical tools; and open-source databases to visualize the trending hashtags, news articles, and their factuality. All modules of the system are displayed through an open web portal. Results A set of 650,000 tweets was collected and analyzed in an ongoing process that was initiated in December 2020. The results of the analysis are made public on a web portal (updated daily), together with the processing tools and data. The data provide insights on public opinion about the vaccines and its change over time. For example, users show a high tendency to only share news from reliable sources when discussing COVID-19 vaccines (98% of the shared URLs). The general sentiment of Twitter users toward the vaccines is negative/neutral; however, the system is able to record fluctuations in the attitude toward specific vaccines in correspondence with specific events (eg, news about new outbreaks). The data also show how news coverage had a high impact on the set of discussed topics. To further investigate this point, we performed a more in-depth analysis of the data regarding the AstraZeneca vaccine. We observed how media coverage of blood clot–related side effects suddenly shifted the topic of public discussions regarding both the AstraZeneca and other vaccines. This became particularly evident when visualizing the most frequently discussed symptoms for the vaccines and comparing them month by month. Conclusions We present a tool connected with a web portal to monitor and display some key aspects of the public’s reaction to COVID-19 vaccines. The system also provides an overview of the opinions of the Twittersphere through graphic representations, offering a tool for the extraction of suspected adverse events from tweets with a deep learning model.
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Affiliation(s)
- Beatrice Portelli
- Department of Mathematics, Computer Science and Physics, University of Udine, via delle Scienze 206, Udine, IT
| | - Simone Scaboro
- Department of Mathematics, Computer Science and Physics, University of Udine, via delle Scienze 206, Udine, IT
| | - Roberto Tonino
- Department of Mathematics, Computer Science and Physics, University of Udine, via delle Scienze 206, Udine, IT
| | | | - Enrico Santus
- Decision Science and Advanced Analytics for MAPV & RA, Bayer, Bayer Pharmaceuticals, Whippany, US
| | - Giuseppe Serra
- Department of Mathematics, Computer Science and Physics, University of Udine, via delle Scienze 206, Udine, IT
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6
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Maggiolino A, Landi V, Bartolomeo N, Bernabucci U, Santus E, Bragaglio A, De Palo P. Effect of Heat Waves on Some Italian Brown Swiss Dairy Cows' Production Patterns. Front Anim Sci 2022. [DOI: 10.3389/fanim.2021.800680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Climate change is impacting worldwide efficiency and welfare standards in livestock production systems. Considering the sensibility to heat stress reported for different milk production patterns in Italian Brown Swiss, this study aims to evaluate the effect of heat waves (HWs)of different lengths on some milk production traits (fat-corrected milk, energy-corrected milk, protein and fat yield, protein percentage, cheese production at 24 h, and cheese yield). A 10-year dataset (2009–2018), containing 202,776 test-day records from 23,296 Brown Swiss cows, was used. The dataset was merged both with the daily maximum temperature–humidity index (THI) recorded by weather stations and with the daily maximum THI threshold for each trait in Italian Brown Swiss cows. The study considered 4 different HWs according to their length: 2, 3, 4, and 5 consecutive days before the test-day over the weighted THI threshold. Milk production traits were determined as the difference in losses compared to those after only 1 day before the test-day over the weighted maximum THI. All traits showed to be affected by HWs. Particularly, protein percentage losses increased from −0.047% to −0.070% after 2 consecutive days over the daily THI threshold, reaching −0.10% to −0.14% after 5 days (p < 0.01), showing a worsening trend with the increasing length of HWs. First parity cows showed to be more sensitive to HWs than other parity classes, recording greater losses after shorter HWs, compared to multiparous cows, for protein yield and, consequently, for cheese production at 24 h. This suggests a less efficient metabolic response to heat stress and exposure time in primiparous, compared to multiparous cows, probably due to their incomplete growth process that overlaps milk production, making it more difficult for them to dissipate heat. Although actions to mitigate heat stress are always needed in livestock, this study points out that often time exposure to warm periods worsens milk production traits in Brown Swiss cows.
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7
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Santus E, Schuster T, Tahmasebi AM, Li C, Yala A, Lanahan CR, Prinsen P, Thompson SF, Coons S, Mynderse L, Barzilay R, Hughes K. Exploiting Rules to Enhance Machine Learning in Extracting Information From Multi-Institutional Prostate Pathology Reports. JCO Clin Cancer Inform 2021; 4:865-874. [PMID: 33006906 DOI: 10.1200/cci.20.00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Literature on clinical note mining has highlighted the superiority of machine learning (ML) over hand-crafted rules. Nevertheless, most studies assume the availability of large training sets, which is rarely the case. For this reason, in the clinical setting, rules are still common. We suggest 2 methods to leverage the knowledge encoded in pre-existing rules to inform ML decisions and obtain high performance, even with scarce annotations. METHODS We collected 501 prostate pathology reports from 6 American hospitals. Reports were split into 2,711 core segments, annotated with 20 attributes describing the histology, grade, extension, and location of tumors. The data set was split by institutions to generate a cross-institutional evaluation setting. We assessed 4 systems, namely a rule-based approach, an ML model, and 2 hybrid systems integrating the previous methods: a Rule as Feature model and a Classifier Confidence model. Several ML algorithms were tested, including logistic regression (LR), support vector machine (SVM), and eXtreme gradient boosting (XGB). RESULTS When training on data from a single institution, LR lags behind the rules by 3.5% (F1 score: 92.2% v 95.7%). Hybrid models, instead, obtain competitive results, with Classifier Confidence outperforming the rules by +0.5% (96.2%). When a larger amount of data from multiple institutions is used, LR improves by +1.5% over the rules (97.2%), whereas hybrid systems obtain +2.2% for Rule as Feature (97.7%) and +2.6% for Classifier Confidence (98.3%). Replacing LR with SVM or XGB yielded similar performance gains. CONCLUSION We developed methods to use pre-existing handcrafted rules to inform ML algorithms. These hybrid systems obtain better performance than either rules or ML models alone, even when training data are limited.
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Affiliation(s)
- Enrico Santus
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, MA
| | - Tal Schuster
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, MA
| | | | - Clara Li
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, MA
| | - Adam Yala
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, MA
| | - Conor R Lanahan
- Department of Oncology, Massachusetts General Hospital, Boston, MA
| | | | | | | | | | - Regina Barzilay
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, MA
| | - Kevin Hughes
- Department of Oncology, Massachusetts General Hospital, Boston, MA
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8
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Santus E, Marino N, Cirillo D, Chersoni E, Montagud A, Santuccione Chadha A, Valencia A, Hughes K, Lindvall C. Artificial Intelligence-Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development. J Med Internet Res 2021; 23:e22453. [PMID: 33560998 PMCID: PMC7958975 DOI: 10.2196/22453] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/07/2020] [Accepted: 01/31/2021] [Indexed: 01/07/2023] Open
Abstract
Artificial intelligence (AI) technologies can play a key role in preventing, detecting, and monitoring epidemics. In this paper, we provide an overview of the recently published literature on the COVID-19 pandemic in four strategic areas: (1) triage, diagnosis, and risk prediction; (2) drug repurposing and development; (3) pharmacogenomics and vaccines; and (4) mining of the medical literature. We highlight how AI-powered health care can enable public health systems to efficiently handle future outbreaks and improve patient outcomes.
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Affiliation(s)
- Enrico Santus
- Division of Decision Science and Advanced Analytics, Bayer Pharmaceuticals, Whippany, NJ, United States
- The Women's Brain Project, Zurich, Switzerland
| | - Nicola Marino
- The Women's Brain Project, Zurich, Switzerland
- Department of Medical and Surgical Sciences, Università degli Studi di Foggia, Foggia, Italy
| | - Davide Cirillo
- The Women's Brain Project, Zurich, Switzerland
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Emmanuele Chersoni
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong, China (Hong Kong)
| | | | | | - Alfonso Valencia
- Barcelona Supercomputing Center, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Kevin Hughes
- Massachusetts General Hospital, Boston, MA, United States
| | - Charlotta Lindvall
- Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
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9
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Ferrari A, Santus E, Cirillo D, Ponce-de-Leon M, Marino N, Ferretti MT, Santuccione Chadha A, Mavridis N, Valencia A. Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. NPJ Digit Med 2021; 4:9. [PMID: 33446891 PMCID: PMC7809354 DOI: 10.1038/s41746-020-00374-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/25/2020] [Indexed: 01/12/2023] Open
Abstract
Targeted contact-tracing through mobile phone apps has been proposed as an instrument to help contain the spread of COVID-19 and manage the lifting of nation-wide lock-downs currently in place in USA and Europe. However, there is an ongoing debate on its potential efficacy, especially in light of region-specific demographics. We built an expanded SIR model of COVID-19 epidemics that accounts for region-specific population densities, and we used it to test the impact of a contact-tracing app in a number of scenarios. Using demographic and mobility data from Italy and Spain, we used the model to simulate scenarios that vary in baseline contact rates, population densities, and fraction of app users in the population. Our results show that, in support of efficient isolation of symptomatic cases, app-mediated contact-tracing can successfully mitigate the epidemic even with a relatively small fraction of users, and even suppress altogether with a larger fraction of users. However, when regional differences in population density are taken into consideration, the epidemic can be significantly harder to contain in higher density areas, highlighting potential limitations of this intervention in specific contexts. This work corroborates previous results in favor of app-mediated contact-tracing as mitigation measure for COVID-19, and draws attention on the importance of region-specific demographic and mobility factors to achieve maximum efficacy in containment policies.
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Affiliation(s)
- Alberto Ferrari
- FROM Research Foundation, Papa Giovanni XXIII Hospital, Bergamo, Italy.
| | - Enrico Santus
- Bayer, Decision Science & Advanced Analytics for MA, PV & RA Division, Leverkusen, Germany
| | - Davide Cirillo
- Barcelona Supercomputing Center (BSC), C/Jordi Girona 29, 08034, Barcelona, Spain
- Women's Brain Project (WBP), Gunterhausen, Switzerland
| | - Miguel Ponce-de-Leon
- Barcelona Supercomputing Center (BSC), C/Jordi Girona 29, 08034, Barcelona, Spain
| | - Nicola Marino
- Women's Brain Project (WBP), Gunterhausen, Switzerland
- Dipartimento di Scienze Madiche e, Universitá di Foggia Chirurgiche, Foggia, Italy
| | | | | | - Nikolaos Mavridis
- Women's Brain Project (WBP), Gunterhausen, Switzerland
- Interactive Robots and Media Laboratory (IRLM), Abu Dhabi, United Arab Emirates
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/Jordi Girona 29, 08034, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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10
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Leiter RE, Santus E, Jin Z, Lee KC, Yusufov M, Chien I, Ramaswamy A, Moseley ET, Qian Y, Schrag D, Lindvall C. Deep Natural Language Processing to Identify Symptom Documentation in Clinical Notes for Patients With Heart Failure Undergoing Cardiac Resynchronization Therapy. J Pain Symptom Manage 2020; 60:948-958.e3. [PMID: 32585181 DOI: 10.1016/j.jpainsymman.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 11/26/2022]
Abstract
CONTEXT Clinicians lack reliable methods to predict which patients with congestive heart failure (CHF) will benefit from cardiac resynchronization therapy (CRT). Symptom burden may help to predict response, but this information is buried in free-text clinical notes. Natural language processing (NLP) may identify symptoms recorded in the electronic health record and thereby enable this information to inform clinical decisions about the appropriateness of CRT. OBJECTIVES To develop, train, and test a deep NLP model that identifies documented symptoms in patients with CHF receiving CRT. METHODS We identified a random sample of clinical notes from a cohort of patients with CHF who later received CRT. Investigators labeled documented symptoms as present, absent, and context dependent (pathologic depending on the clinical situation). The algorithm was trained on 80% and fine-tuned parameters on 10% of the notes. We tested the model on the remaining 10%. We compared the model's performance to investigators' annotations using accuracy, precision (positive predictive value), recall (sensitivity), and F1 score (a combined measure of precision and recall). RESULTS Investigators annotated 154 notes (352,157 words) and identified 1340 present, 1300 absent, and 221 context-dependent symptoms. In the test set of 15 notes (35,467 words), the model's accuracy was 99.4% and recall was 66.8%. Precision was 77.6%, and overall F1 score was 71.8. F1 scores for present (70.8) and absent (74.7) symptoms were higher than that for context-dependent symptoms (48.3). CONCLUSION A deep NLP algorithm can be trained to capture symptoms in patients with CHF who received CRT with promising precision and recall.
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Affiliation(s)
- Richard E Leiter
- Harvard Medical School, Boston, Massachusetts, USA; Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
| | - Enrico Santus
- Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Zhijing Jin
- Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Katherine C Lee
- Department of Surgery, University of California San Diego Health, San Diego, California, USA
| | - Miryam Yusufov
- Harvard Medical School, Boston, Massachusetts, USA; Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Isabel Chien
- Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Ashwin Ramaswamy
- Department of Surgery, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Edward T Moseley
- Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Yujie Qian
- Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Deborah Schrag
- Harvard Medical School, Boston, Massachusetts, USA; Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Charlotta Lindvall
- Harvard Medical School, Boston, Massachusetts, USA; Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
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11
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Cecchinato A, Toledo-Alvarado H, Pegolo S, Rossoni A, Santus E, Maltecca C, Bittante G, Tiezzi F. Integration of Wet-Lab Measures, Milk Infrared Spectra, and Genomics to Improve Difficult-to-Measure Traits in Dairy Cattle Populations. Front Genet 2020; 11:563393. [PMID: 33133149 PMCID: PMC7550782 DOI: 10.3389/fgene.2020.563393] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to evaluate the contribution of Fourier-transformed infrared spectroscopy (FTIR) data for dairy cattle breeding through two different approaches: (i) estimating the genetic parameters for 30 measured milk traits and their FTIR predictions and investigating the additive genetic correlation between them and (ii) evaluating the effectiveness of FTIR-derived phenotyping to replicate a candidate bull’s progeny testing or breeding value prediction at birth. Records were available from 1,123 cows phenotyped using gold standard laboratory methodologies (LAB data). This included phenotypes related to fine milk composition and milk technological characteristics, milk acidity, and milk protein fractions. The dataset used to generate FTIR predictions comprised 729,202 test-day records from 51,059 Brown Swiss cows (FIELD data). A first approach consisted of estimating genetic parameters for phenotypes available from LAB and FIELD datasets. To do so, a set of bivariate animal models were run, and genetic correlations between LAB and FIELD phenotypes were estimated using FIELD information obtained at the population level. Heritability estimates were generally higher for FIELD predictions than for the corresponding LAB measures. The additive genetic correlations (ra) between LAB and FIELD phenotypes had different magnitudes across traits but were generally strong. Overall, these results demonstrated the potential of using FIELD information as indicator traits for the indirect genetic improvement of LAB measures. In the second approach, we included genotype information for 1,011 cows from the LAB dataset, 1,493 cows from the FIELD dataset, 181 sires with daughters in both LAB and FIELD datasets, and 540 sires with daughters in the FIELD dataset only. Predictions were obtained using the single-step GBLUP method. A four fold cross-validation was used to assess the predictive ability of the different models, assessed as the ability to predict masked LAB records from daughters of progeny testing bulls. The correlation between observed and predicted LAB measures in validation was averaged over the four training-validation sets. Different sets of phenotypic information were used sequentially in cross-validation schemes: (i) LAB cows from the training set; (ii) FIELD cows from the training set; and (iii) FIELD cows from the validation set. Models that included FIELD records showed an improvement for the majority of traits. This study suggests that breeding programs for difficult-to-measure traits could be implemented using FTIR information. While these programs should use progeny testing, acceptable values of accuracy can be achieved also for bulls without phenotyped progeny. Robust calibration equations are, deemed as essential.
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Affiliation(s)
- Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | - Hugo Toledo-Alvarado
- Department of Genetics and Biostatistics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | | | - Enrico Santus
- Italian Brown Breeders Association, Bussolengo, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
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12
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Maggiolino A, Dahl GE, Bartolomeo N, Bernabucci U, Vitali A, Serio G, Cassandro M, Centoducati G, Santus E, De Palo P. Estimation of maximum thermo-hygrometric index thresholds affecting milk production in Italian Brown Swiss cattle. J Dairy Sci 2020; 103:8541-8553. [PMID: 32684476 DOI: 10.3168/jds.2020-18622] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/06/2020] [Indexed: 11/19/2022]
Abstract
It is known that heat stress affects dairy cow performance in multiple ways: physiological, behavioral, reproductive, and productive. The aim of the present study was to determine if a threshold of temperature-humidity index (THI) exists for multiple milk production traits (milk yield, fat-corrected milk, protein and fat yield and percentage, energy-corrected milk, cheese production, and cheese yield) in Italian Brown Swiss dairy cows from the period 15 d before the day of the Italian Breeders Association test-day sampling. A 10-yr data set (2009-2018) containing 202,776 test-day records of 23,296 Brown Swiss cows was matched with the maximum THI. In all parities considered, no THI thresholds were observed for milk yield in Brown Swiss. In contrast, a THI threshold of 75 was identified for fat-corrected milk. No THI threshold was found for fat percentage, but fat yield showed the highest THI thresholds in cows of first and second parity. Protein yield and cheese production were affected by heat stress with average THI threshold of 74. The THI thresholds identified indicate that the Brown Swiss breed has higher thermal tolerance versus literature values reported for Holstein cows. As THI rises, Brown Swiss cows tend to produce the same volume of milk, but with a decreasing quality with regard to components. Further study is necessary to estimate the genetic component of heat tolerance, in Brown Swiss cattle, considering that the correct estimation of THI thresholds represents the first step to identify components that could be included in selection procedures.
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Affiliation(s)
- A Maggiolino
- Department of Veterinary Medicine, University of Bari A. Moro, 70010 Valenzano, Italy.
| | - G E Dahl
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - N Bartolomeo
- Medical Statistics, Department of Biomedical Science and Human Oncology, University of Bari, 70124 Bari, Italy
| | - U Bernabucci
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo 01100, Italy
| | - A Vitali
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo 01100, Italy
| | - G Serio
- Medical Statistics, Department of Biomedical Science and Human Oncology, University of Bari, 70124 Bari, Italy
| | - M Cassandro
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis, Legnaro (Padova), 35020, Italy
| | - G Centoducati
- Department of Veterinary Medicine, University of Bari A. Moro, 70010 Valenzano, Italy
| | - E Santus
- Italian Brown Breeders Association, Loc. Ferlina 204, Bussolengo 37012, Italy
| | - P De Palo
- Department of Veterinary Medicine, University of Bari A. Moro, 70010 Valenzano, Italy
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13
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Santus E, Li C, Yala A, Peck D, Soomro R, Faridi N, Mamshad I, Tang R, Lanahan CR, Barzilay R, Hughes K. Do Neural Information Extraction Algorithms Generalize Across Institutions? JCO Clin Cancer Inform 2020; 3:1-8. [PMID: 31310566 DOI: 10.1200/cci.18.00160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Natural language processing (NLP) techniques have been adopted to reduce the curation costs of electronic health records. However, studies have questioned whether such techniques can be applied to data from previously unseen institutions. We investigated the performance of a common neural NLP algorithm on data from both known and heldout (ie, institutions whose data were withheld from the training set and only used for testing) hospitals. We also explored how diversity in the training data affects the system's generalization ability. METHODS We collected 24,881 breast pathology reports from seven hospitals and manually annotated them with nine key attributes that describe types of atypia and cancer. We trained a convolutional neural network (CNN) on annotations from either only one (CNN1), only two (CNN2), or only four (CNN4) hospitals. The trained systems were tested on data from five organizations, including both known and heldout ones. For every setting, we provide the accuracy scores as well as the learning curves that show how much data are necessary to achieve good performance and generalizability. RESULTS The system achieved a cross-institutional accuracy of 93.87% when trained on reports from only one hospital (CNN1). Performance improved to 95.7% and 96%, respectively, when the system was trained on reports from two (CNN2) and four (CNN4) hospitals. The introduction of diversity during training did not lead to improvements on the known institutions, but it boosted performance on the heldout institutions. When tested on reports from heldout hospitals, CNN4 outperformed CNN1 and CNN2 by 2.13% and 0.3%, respectively. CONCLUSION Real-world scenarios require that neural NLP approaches scale to data from previously unseen institutions. We show that a common neural NLP algorithm for information extraction can achieve this goal, especially when diverse data are used during training.
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Affiliation(s)
- Enrico Santus
- Massachusetts Institute of Technology, Cambridge, MA
| | - Clara Li
- Massachusetts Institute of Technology, Cambridge, MA
| | - Adam Yala
- Massachusetts Institute of Technology, Cambridge, MA
| | - Donald Peck
- Henry Ford Health System, Detroit, MI.,Michigan Technological University, Houghton, MI
| | - Rufina Soomro
- Liaquat National Hospital & Medical College, Karachi, Pakistan
| | - Naveen Faridi
- Liaquat National Hospital & Medical College, Karachi, Pakistan
| | - Isra Mamshad
- Liaquat National Hospital & Medical College, Karachi, Pakistan
| | - Rong Tang
- Rochester General Hospital, Rochester, NY
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Franceschi P, Malacarne M, Faccia M, Rossoni A, Santus E, Formaggioni P, Summer A. New Insights in Cheese Yield Capacity of the Milk of Italian Brown and Italian Friesian Cattle in the Production of High-Moisture Mozzarella. Food Technol Biotechnol 2020; 58:91-97. [PMID: 32684793 PMCID: PMC7365334 DOI: 10.17113/ftb.58.01.20.6386] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The aim of the present study is to investigate the effect of κ-casein B content in milk on the yield of high-moisture mozzarella cheese. The study was carried out by monitoring the production of eight mozzarella cheese batches at four cheese making factories. At each factory, two cheese making trials were performed in parallel: one using bulk milk from Italian Brown cattle and the other using bulk milk from Italian Friesian cattle. The average κ-casein B content was 0.04 g per 100 g in the Italian Friesian cows’ milk, whereas it was four time higher in the Italian Brown cows’ milk, reaching values of 0.16 g per 100 g. Both the κ-casein content and κ-casein B to casein ratio were positively correlated with actual cheese yield. Both parameters showed correlation coefficient values over 0.9, higher than for any other protein fraction. The influence of the level of κ-casein on the increase of the yield is probably due to smaller and more homogeneous micelles, with more efficient rennet coagulation. Consequently, milk with higher κ-casein B content produces a more elastic curd that withstands better the technological treatments and limits losses during curd mincing and stretching. In conclusion, the Italian Brown cows’ milk used, characterized by higher κ-casein content than the Italian Friesian’s one, allowed a yield increase of about 2.65%, which is a very relevant result for both farms and cheese making factories.
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Affiliation(s)
- Piero Franceschi
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Massimo Malacarne
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Michele Faccia
- Department of Soil, Plant and Food Sciences (Di.S.S.P.A.), University of Bari, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Attilio Rossoni
- ANARB - Italian Brown Cattle Breeders Association, Loc. Ferlina 204, 37012 Bussolengo (VR), Italy
| | - Enrico Santus
- ANARB - Italian Brown Cattle Breeders Association, Loc. Ferlina 204, 37012 Bussolengo (VR), Italy
| | - Paolo Formaggioni
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Andrea Summer
- Department of Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
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Hu SY, Santus E, Forsyth AW, Malhotra D, Haimson J, Chatterjee NA, Kramer DB, Barzilay R, Tulsky JA, Lindvall C. Can machine learning improve patient selection for cardiac resynchronization therapy? PLoS One 2019; 14:e0222397. [PMID: 31581234 PMCID: PMC6776390 DOI: 10.1371/journal.pone.0222397] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
RATIONALE Multiple clinical trials support the effectiveness of cardiac resynchronization therapy (CRT); however, optimal patient selection remains challenging due to substantial treatment heterogeneity among patients who meet the clinical practice guidelines. OBJECTIVE To apply machine learning to create an algorithm that predicts CRT outcome using electronic health record (EHR) data avaible before the procedure. METHODS AND RESULTS We applied machine learning and natural language processing to the EHR of 990 patients who received CRT at two academic hospitals between 2004-2015. The primary outcome was reduced CRT benefit, defined as <0% improvement in left ventricular ejection fraction (LVEF) 6-18 months post-procedure or death by 18 months. Data regarding demographics, laboratory values, medications, clinical characteristics, and past health services utilization were extracted from the EHR available before the CRT procedure. Bigrams (i.e., two-word sequences) were also extracted from the clinical notes using natural language processing. Patients accrued on average 75 clinical notes (SD, 29) before the procedure including data not captured anywhere else in the EHR. A machine learning model was built using 80% of the patient sample (training and validation dataset), and tested on a held-out 20% patient sample (test dataset). Among 990 patients receiving CRT the mean age was 71.6 (SD, 11.8), 78.1% were male, 87.2% non-Hispanic white, and the mean baseline LVEF was 24.8% (SD, 7.69). Out of 990 patients, 403 (40.7%) were identified as having a reduced benefit from the CRT device (<0% LVEF improvement in 25.2%, death by 18 months in 15.6%). The final model identified 26% of these patients at a positive predictive value of 79% (model performance: Fβ (β = 0.1): 77%; recall 0.26; precision 0.79; accuracy 0.65). CONCLUSIONS A machine learning model that leveraged readily available EHR data and clinical notes identified a subset of CRT patients who may not benefit from CRT before the procedure.
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Affiliation(s)
- Szu-Yeu Hu
- Department of Radiology, Masachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Enrico Santus
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, Massachusetts, United States of America
| | - Alexander W. Forsyth
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, Massachusetts, United States of America
| | - Devvrat Malhotra
- Department of Health Policy and Management, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Josh Haimson
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, Massachusetts, United States of America
| | - Neal A. Chatterjee
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel B. Kramer
- Richard A. and Susan F. Smith Center for Outcomes Research, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Regina Barzilay
- Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, Massachusetts, United States of America
| | - James A. Tulsky
- Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Division of Palliative Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Charlotta Lindvall
- Department of Psychosocial Oncology and Palliative Care, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Division of Palliative Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
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Acevedo F, Armengol VD, Deng Z, Tang R, Coopey S, Mazzola E, Lanahan C, Braun D, Yala A, Barzilay R, Li C, Santus E, Colwell A, Guidi A, Cetrulo C, Garber JE, Smith BL, King TA, Hughes KS. Incidental atypical hyperplasia/LCIS in mammoplasty specimens and subsequent risk of breast cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1561 Background: Proliferative breast lesions with atypia (atypical hyperplasia and lobular carcinoma in-situ (LCIS)) increase the risk of breast cancer (BC). Most cases are diagnosed in the context of an abnormal mammogram. Little is known about BC risk for patients with these lesions who are asymptomatic. Mammoplasty specimens allow us to study breast tissue in asymptomatic healthy women. We previously published the rate of atypia in the largest reported mammoplasty cohort. The aim of this study is to examine the risk of BC in the atypia cohort. Methods: Breast pathology reports were retrospectively reviewed for evidence of atypical ductal hyperplasia (ADH), atypical lobular hyperplasia (ALH) or LCIS in bilateral reduction mammoplasty specimens from five institutions within a single healthcare system between 1990 to 2017. Patients with prior or concurrent BC or prior atypia were excluded. Data was extracted from electronic medical records using natural language processing and manual review to assess subsequent risk of BC. Results: From our mammoplasty cohort of 4771 patients, 295 patients were found to have atypia (6.2%) at baseline. 40 of these patients were lost to follow-up and excluded from the study. For the remaining 255 patients, 13 had severe ADH bordering on ductal carcinoma in situ, 52 had LCIS, 119 had ALH, and 71 had ADH at baseline. The median age at baseline was 52.1 (range 17.9 – 74.3). With a median follow-up of 7.7 years, of the 255 patients 9 patients developed BC (8 invasive carcinomas, 1 ductal carcinoma in situ). 81.3% of the cohort did not receive chemoprevention. Only one patient out of the nine who developed BC received chemoprevention. The risk of developing BC among women with atypia at baseline was 0.5%, 2.9% and 4.1%, at 3, 5 and 10 years respectively. Conclusions: Patients with asymptomatic atypias found in reduction mammoplasty specimens appear to be at lower risk of developing BC than those diagnosed with atypia in the context of an abnormal mammogram. These results may provide guidance on how to manage this group of patients related to future screening and/or chemoprevention.
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Affiliation(s)
| | | | | | - Rong Tang
- Massachusetts General Hospital, Boston, MA
| | | | | | | | | | - Adam Yala
- Massachusetts Institute of Technology, Cambridge, MA
| | | | - Clara Li
- Massachusetts General Hospital, Boston, MA
| | | | | | | | | | - Judy Ellen Garber
- Center for Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA
| | | | - Tari A. King
- Breast Oncology Program, Dana-Farber/Brigham and Women’s Cancer Center, Boston, MA
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Dadousis C, Biffani S, Cipolat-Gotet C, Nicolazzi EL, Rosa GJM, Gianola D, Rossoni A, Santus E, Bittante G, Cecchinato A. Genome-wide association study for cheese yield and curd nutrient recovery in dairy cows. J Dairy Sci 2016; 100:1259-1271. [PMID: 27889122 DOI: 10.3168/jds.2016-11586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022]
Abstract
Cheese production and consumption are increasing in many countries worldwide. As a result, interest has increased in strategies for genetic selection of individuals for technological traits of milk related to cheese yield (CY) in dairy cattle breeding. However, little is known about the genetic background of a cow's ability to produce cheese. Recently, a relatively large panel (1,264 cows) of different measures of individual cow CY and milk nutrient and energy recoveries in the cheese (REC) became available. Genetic analyses showed considerable variation for CY and for aptitude to retain high proportions of fat, protein, and water in the coagulum. For the dairy industry, these characteristics are of major economic importance. Nevertheless, use of this knowledge in dairy breeding is hampered by high costs, intense labor requirement, and lack of appropriate technology. However, in the era of genomics, new possibilities are available for animal breeding and genetic improvement. For example, identification of genomic regions involved in cow CY might provide potential for marker-assisted selection. The objective of this study was to perform genome-wide association studies on different CY and REC measures. Milk and DNA samples from 1,152 Italian Brown Swiss cows were used. Three CY traits expressing the weight (wt) of fresh curd (%CYCURD), curd solids (%CYSOLIDS), and curd moisture (%CYWATER) as a percentage of weight of milk processed, and 4 REC (RECFAT, RECPROTEIN, RECSOLIDS, and RECENERGY, calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk) were analyzed. Animals were genotyped with the Illumina BovineSNP50 Bead Chip v.2. Single marker regressions were fitted using the GenABEL R package (genome-wide association using mixed model and regression-genomic control). In total, 103 significant associations (88 single nucleotide polymorphisms) were identified in 10 chromosomes (2, 6, 9, 11, 12, 14, 18, 19, 27, 28). For RECFAT and RECPROTEIN, high significance peaks were identified in Bos taurus autosome (BTA) 6 and BTA11, respectively. Marker ARS-BFGL-NGS-104610 (∼104.3 Mbp) was highly associated with RECPROTEIN and Hapmap52348-rs29024684 (∼87.4 Mbp), closely located to the casein genes on BTA6, with RECFAT. Genomic regions identified may enhance marker-assisted selection in bovine cheese breeding beyond the use of protein (casein) and fat contents, whereas new knowledge will help to unravel the genomic background of a cow's ability for cheese production.
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Affiliation(s)
- C Dadousis
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - S Biffani
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche (CNR), Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - C Cipolat-Gotet
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - E L Nicolazzi
- Bioinformatics Core, Parco Tecnologico Padano, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - G J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison 53706
| | - D Gianola
- Department of Animal Sciences, University of Wisconsin, Madison 53706; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison 53706
| | - A Rossoni
- Italian Brown Breeders Association, Loc. Ferlina 204, Bussolengo 37012, Italy
| | - E Santus
- Italian Brown Breeders Association, Loc. Ferlina 204, Bussolengo 37012, Italy
| | - G Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - A Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
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Dimauro C, Manca E, Rossoni A, Santus E, Cellesi M, Gaspa G. 0323 Use of multivariate statistical analyses to preselect SNP markers for GWAS on residual feed intake in dairy cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Prinsen R, Strillacci M, Schiavini F, Santus E, Rossoni A, Maurer V, Bieber A, Gredler B, Dolezal M, Bagnato A. A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dadousis C, Biffani S, Cipolat-Gotet C, Nicolazzi E, Rossoni A, Santus E, Bittante G, Cecchinato A. Genome-wide association of coagulation properties, curd firmness modeling, protein percentage, and acidity in milk from Brown Swiss cows. J Dairy Sci 2016; 99:3654-3666. [DOI: 10.3168/jds.2015-10078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022]
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Rossoni A, Nicoletti C, Bonetti O, Testa L, Santus E. Genetic evaluation for body condition score in Italian Brown Swiss cattle. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2007.1s.198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A. Rossoni
- Associazione Nazionale Allevatori di Razza Bruna., Verona, Italy
| | - C. Nicoletti
- Associazione Nazionale Allevatori di Razza Bruna., Verona, Italy
| | - O. Bonetti
- Associazione Nazionale Allevatori di Razza Bruna., Verona, Italy
| | - L. Testa
- Associazione Nazionale Allevatori di Razza Bruna., Verona, Italy
| | - E. Santus
- Associazione Nazionale Allevatori di Razza Bruna., Verona, Italy
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Crepaldi P, Nicoloso L, Milanesi E, Colli L, Santus E, Negrini R. Towards the understanding of bull fertility: phenotypic traits description and candidate gene approach. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2009.s2.60] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Paola Crepaldi
- Dipartimento di Scienze Animali, Università di Milano, Italy
| | | | | | - Licia Colli
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Enrico Santus
- 3Associazione Nazionale Allevatori di Razza Bruna (ANARB), Verona, Italy
| | - Riccardo Negrini
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Bagnato A, Schiavini F, Dolezal M, Dubini S, Rossoni A, Maltecca C, Santus E, Medugorac I, Sölkner J, Fontanesi L, Friedman A, Lipkin E, Soller M. The BovMAS Consortium: identification of QTL for milk yield and milk protein percent on chromosome 14 in the Brown Swiss breed. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2005.2s.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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McClure M, Kim E, Bickhart D, Null D, Cooper T, Cole J, Wiggans G, Ajmone-Marsan P, Colli L, Santus E, Liu GE, Schroeder S, Matukumalli L, Van Tassell C, Sonstegard T. Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2. PLoS One 2013; 8:e59251. [PMID: 23527149 PMCID: PMC3603989 DOI: 10.1371/journal.pone.0059251] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 02/13/2013] [Indexed: 12/12/2022] Open
Abstract
Bovine Progressive Degenerative Myeloencephalopathy (Weaver Syndrome) is a recessive neurological disease that has been observed in the Brown Swiss cattle breed since the 1970's in North America and Europe. Bilateral hind leg weakness and ataxia appear in afflicted animals at 6 to 18 months of age, and slowly progresses to total loss of hind limb control by 3 to 4 years of age. While Weaver has previously been mapped to Bos taurus autosome (BTA) 4∶46-56 Mb and a diagnostic test based on the 6 microsatellite (MS) markers is commercially available, neither the causative gene nor mutation has been identified; therefore misdiagnosis can occur due to recombination between the diagnostic MS markers and the causative mutation. Analysis of 34,980 BTA 4 SNPs genotypes derived from the Illumina BovineHD assay for 20 Brown Swiss Weaver carriers and 49 homozygous normal bulls refined the Weaver locus to 48-53 Mb. Genotyping of 153 SNPs, identified from whole genome sequencing of 10 normal and 10 carrier animals, across a validation set of 841 animals resulted in the identification of 41 diagnostic SNPs that were concordant with the disease. Except for one intergenic SNP all are associated with genes expressed in nervous tissues: 37 distal to NRCAM, one non-synonymous (serine to asparagine) in PNPLA8, one synonymous and one non-synonymous (lysine to glutamic acid) in CTTNBP2. Haplotype and imputation analyses of 7,458 Brown Swiss animals with Illumina BovineSNP50 data and the 41 diagnostic SNPs resulted in the identification of only one haplotype concordant with the Weaver phenotype. Use of this haplotype and the diagnostic SNPs more accurately identifies Weaver carriers in both Brown Swiss purebred and influenced herds.
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Affiliation(s)
- Matthew McClure
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Euisoo Kim
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Derek Bickhart
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Daniel Null
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - Tabatha Cooper
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - John Cole
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - George Wiggans
- USDA, ARS, ANRI, Animal Improvement Programs Laboratory, Beltsville, Maryland, United States of America
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico, Università Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Licia Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico, Università Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Enrico Santus
- Associazione Nazionale Allevatori bovini della Razza Bruna, Italian Brown Swiss Association, Bussolengo, Italy
| | - George E. Liu
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Steve Schroeder
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Lakshmi Matukumalli
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Curt Van Tassell
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Tad Sonstegard
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
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Summer A, Santus E, Casanova L, Joerg H, Rossoni A, Nicoletti C, Donofrio G, Mariani P, Malacarne M. Short communication: characterization of a monoclonal antibody for kappa-casein B of cow's milk. J Dairy Sci 2010; 93:796-800. [PMID: 20105552 DOI: 10.3168/jds.2009-2636] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/26/2009] [Indexed: 11/19/2022]
Abstract
A monoclonal antibody (antik-B) against an oligopeptide of 23 AA corresponding to the region 131-153 of bovine kappa-casein (kappa-CN) B was generated using the Human Combinatorial Antibody Library (HuCAL) technology. Both AA substitutions distinguishing kappa-CN A and B are located in that region (positions 136 and 148). In this study, the reactivity of antik-B to milk samples collected from cows previously genotyped as CSN3*AA, CSN3*AB, and CSN3*BB was tested. According to Western blot results, antik-B recognized kappa-CN B and it showed no cross-reactivity toward kappa-CN A and other milk proteins. Furthermore, a modified Western blot method, urea-PAGE Western blot, was set up to assess the reactivity of antik-B toward all isoforms of kappa-CN B. In conclusion, antik-B was specific to kappa-CN B in milk and it seemed to be reactive toward all its isoforms.
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Affiliation(s)
- A Summer
- Department of Animal Production, Veterinary Biotechnologies, Food Quality and Safety, University of Parma, via del Taglio 10, 43126 Parma, Italy
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Maltecca C, Rossoni A, Nicoletti C, Santus E, Weigel KA, Bagnato A. Estimation of Genetic Parameters for Perinatal Sucking Behavior of Italian Brown Swiss Calves. J Dairy Sci 2007; 90:4814-20. [PMID: 17881704 DOI: 10.3168/jds.2007-0183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Brown Swiss breeders sometimes experience difficulties in feeding calves because of the weak sucking ability of the calves in the early days of life. For the welfare of the calves, they should be suckled by their dams or should aggressively ingest colostrum immediately after birth. The composition of colostrum changes rapidly during the first few days of lactation, and the ability of calves to absorb the Ig decreases quickly as well. The aim of this study was to increase our knowledge of environmental and genetic components affecting the sucking response, to evaluate the possibility of selecting for this trait. Sucking ability was recorded in 3 categories (drank from the milk bucket nipple or bottle without help, drank with help, did not drink) at 5 post-natal meals (6, 12, 24, 48, and 72 h from birth). Records were analyzed with 2 different models: a single-trait threshold sire model, in which all observations were analyzed as a single trait with 5 levels, and a multiple-trait threshold liability sire model, in which meal-by-meal observations were analyzed as 5 different binary traits. Management procedures, the interval between birth and meals, parity, and season of birth were environmental factors affecting the variability in sucking ability. The heritability estimate for the single-trait analysis was 0.14, whereas heritabilities for the multiple-trait analysis were 0.26, 0.22, 0.21 0.12, and 0.13 for the first, second, third, fourth, and fifth meal, respectively. Estimated genetic correlations among traits were high (0.82 to 0.99). This study suggests the possibility of selection based on sucking ability. Future collection of larger data sets on the sucking response of calves in the first 2 meals after birth would increase the accuracy of genetic parameter estimates.
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Affiliation(s)
- C Maltecca
- Dairy Science Department, University of Wisconsin, Madison 53706, USA
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Abstract
The bovine oxidized LDL receptor 1 (OLR1) was chosen as a candidate gene for association tests with milk composition traits. Genotyping of 773 Italian Brown Swiss for a SNP at position 8232 in OLR1 (NW_215807:g.8232C>A) revealed a frequency of 0.95 for the g.8232C allele. The University of Wisconsin Holstein resource population was genotyped for the OLR1 NW_215807:g.[7160C>T; 7161A>G; 8232C>A] SNPs, and four haplotypes were inferred based on the genotypes of sires and their daughters. Oxidized LDL receptor 1 haplotypes were significantly associated with fat percentage (P = 0.0015). Haplotype [C; A; C] was associated with a significant increase in fat percentage when compared with the other haplotypes.
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Affiliation(s)
- H Khatib
- Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA.
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Bagnato A, Schiavini F, La Mattina V, Santus E, Soller M, Lipkin E. Mapping QTL affecting milk somatic Cell count in the Italian Brown Swiss dairy Cattle – the QuaLAT Project. Italian Journal of Animal Science 2007. [DOI: 10.4081/ijas.2007.1s.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A. Bagnato
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare. Università di Milano, Italy
| | - F. Schiavini
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare. Università di Milano, Italy
| | - V. La Mattina
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare. Università di Milano, Italy
| | - E. Santus
- Associazione Nazionale Allevatori Razza Bruna, Italy
| | - M. Soller
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - E. Lipkin
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
- 4Faculty of Medicine. The Technion - Israel Institute of Technology, Haifa, Israel
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